2526_MMB_-_cursus.pdf

# The origin of life and early evolution The origin of life and early evolution explores the scientific hypotheses and experimental evidence concerning how life arose on Earth and the subsequent major evolutionary transformations. ## 1. The origin of life The origin of life on Earth was a complex process requiring specific environmental conditions and the formation of organic molecules from inorganic precursors. ### 1.1 Hypotheses for the origin of organic molecules Early Earth's atmosphere, characterized by high levels of water vapor, nitrogen, carbon dioxide, methane, and ammonia, and a very low percentage of oxygen, provided the backdrop for the synthesis of organic molecules [9](#page=9). #### 1.1.1 The primordial soup theory Proposed independently by Oparin and Haldane in the 1920s, this theory posits that the early Earth's atmosphere was a reducing environment where simple organic molecules could form from inorganic ones, energized by UV radiation and lightning. Haldane envisioned the early ocean as a "primitive soup" of these organic molecules [10](#page=10) [9](#page=9). The Miller-Urey experiment in 1953 tested this hypothesis by simulating early Earth conditions in a closed system. They passed water vapor through a mixture of hydrogen, ammonia, and methane, subjected to electrical discharges to mimic lightning. After a week, the experiment yielded simple organic compounds like formaldehyde and hydrogen cyanide, as well as more complex ones such as amino acids and long hydrocarbon chains. This demonstrated the abiotic synthesis of organic molecules, though the primordial soup lacked nucleic acids, suggesting alternative pathways for their formation, possibly through the polymerization of hydrogen cyanide [10](#page=10) [11](#page=11). **Critique of the Primordial Soup Theory:** More recent insights suggest that the early Earth's atmosphere might not have been as reducing as initially thought. Experiments with atmospheres lacking significant methane and ammonia (primarily water vapor, CO2, and N2) produced simple organic molecules but not amino acids. This indicates that the primordial soup theory, as tested by Miller and Urey, may not be a complete explanation. The hypothesis also doesn't fully account for the lack of an ozone layer, which would have offered protection from high UV radiation that could degrade organic molecules [11](#page=11) [15](#page=15). #### 1.1.2 Hydrothermal and alkaline vents as sources of life An alternative hypothesis proposes that life originated around hydrothermal or alkaline vents on the ocean floor [12](#page=12). * **Hydrothermal vents (black smokers):** These are underwater volcanoes formed at tectonic spreading zones where ocean water seeps into the Earth's crust, heats up, and is ejected back into the ocean, forming chimney-like structures. They are characterized by high temperatures (300-400 °C) and release minerals that give them a dark appearance [12](#page=12). * **Alkaline vents:** These vents, discovered around 2000, operate at lower temperatures (40-90 °C) and have a high pH (9-11). They form through a reaction between olivine and water, producing serpentine and hydrogen gas. The structures resemble sponges with porous walls through which alkaline fluids flow [13](#page=13). These vents are considered promising sites for the origin of life due to their reducing nature and the presence of minerals and simple organic molecules. The pH gradient between the alkaline vent fluid and the more acidic ocean water (pH 5-7 on early Earth) could have provided an energy source for chemical reactions between hydrogen and carbon dioxide, leading to the formation of organic compounds like ribose, a component of nucleic acids. Hydrothermal vents, with their high temperatures, also drive the formation of new molecules from minerals. However, the high temperatures of black smokers raise questions about the stability of complex organic molecules and the survival of early life in such conditions. Alkaline vents offer more favorable temperatures, but concerns exist about the washout of building blocks and the availability of phosphorus for nucleic acid synthesis [13](#page=13) [15](#page=15). #### 1.1.3 The RNA world hypothesis This hypothesis, proposed in the 1960s, suggests that early life was based on RNA, with DNA evolving later. It posits that early life was heterotrophic, utilizing prebiotically synthesized organic compounds. Recent discoveries of new RNA enzymes and building blocks, along with evidence for the spontaneous abiotic synthesis of RNA building blocks like adenine, guanine, cytosine, and uracil, support this theory. However, the abiotic synthesis of complete ribonucleotides remains challenging, and RNA's inherent instability and the complexity of replication without accompanying molecules and compartmentalization pose counterarguments [14](#page=14) [15](#page=15). #### 1.1.4 Combination of hypotheses Currently, no single hypothesis fully explains the origin of life. Scientists often consider hybrid or sequential hypotheses. A prevalent view suggests that organic building blocks from atmospheric reactions and meteorites were concentrated and processed in various geological niches (e.g., volcanic rock pores, alkaline vent structures), utilizing energy from redox gradients or pH gradients. This could have led to the emergence of RNA (or RNA-like systems) which co-evolved with simple membranes and peptides [15](#page=15). ### 1.2 Polymerization of organic molecules The formation of macromolecules, such as proteins and nucleic acids, from simpler organic molecules is a crucial step. * **Amino acids:** These are the building blocks of proteins. Under the loss of water, amino acids can link together [16](#page=16). * **Clay as a catalyst:** The abundance of clay on early Earth, with its crystalline electrical charges, could have facilitated the weak binding of small molecules. This allowed them to form bonds with each other and then break their bond with the clay, making room for more molecules. Research shows that dripping mixtures of amino acids or RNA nucleotides onto warm sand, clay, or rock can lead to the spontaneous formation of polymers of these components, acting as weak catalysts [16](#page=16) [17](#page=17). ### 1.3 The first cells: protobionts The transition to life involved the formation of self-replicating molecules enclosed within membrane-like structures, known as protobionts [17](#page=17). * **Properties of protobionts:** These are collections of abiotically produced molecules surrounded by a membrane that exhibit some characteristics of life, such as simple multiplication, basic metabolism, and maintaining an internal chemical environment distinct from the surroundings [17](#page=17). * **Liposomes:** Small fat globules enclosed by a membrane, spontaneously formed when fat droplets are placed in water, are an example of such structures. When enzymes are added to liposomes, they can perform simple metabolic reactions [17](#page=17) [18](#page=18). * **Phospholipid bilayer:** Liposomes are formed by phospholipids, which have hydrophilic heads and hydrophobic tails. In an aqueous environment, they arrange into a bilayer, a structure also found in cell membranes [18](#page=18). * **Self-replicating RNA:** Protobionts likely contained self-replicating RNA molecules (ribozymes) capable of copying themselves with sufficient nucleotides. Protobionts with more stable and rapidly replicating RNA sequences would have had a selective advantage, leading to growth and division, a form of natural selection [18](#page=18) [19](#page=19). ### 1.4 What is 'life'? Defining life is a subject of ongoing debate, with no universally accepted definition. NASA defines life as "a self-sustaining chemical system capable of Darwinian evolution," but the "self-sustaining" aspect is problematic due to the inherent transience of life. The scientific community generally agrees on several characteristics common to all living cells [19](#page=19): 1. **Homeostasis:** The ability to maintain a stable internal environment [20](#page=20). 2. **Organization and structure:** The relationship between form and function, with the cell as the basic unit [20](#page=20). 3. **Growth:** An increase in size and complexity over a lifetime [20](#page=20). 4. **Metabolism:** The uptake and conversion of energy via biochemical processes [20](#page=20). 5. **Adaptation:** Structural or behavioral changes that enhance survival and reproduction, fundamental to evolution [20](#page=20). 6. **Responsiveness:** The ability to react to internal and external stimuli [20](#page=20). 7. **Reproduction:** The process of producing offspring, requiring self-replicating carriers of genetic material like RNA or DNA [20](#page=20). The earliest life on Earth is estimated to have emerged 3.5 to 4 billion years ago [20](#page=20). ## 2. Early evolution Early evolution saw the emergence of unicellular organisms, the "oxygen revolution," and the development of complex eukaryotic cells. ### 2.1 Important events in the history of life The history of life on Earth, spanning approximately 4.6 billion years, is marked by significant evolutionary milestones [22](#page=22). #### 2.1.1 The emergence of unicellular organisms The first microbial cells, prokaryotic unicellular organisms belonging to Archaea or Bacteria, appeared around 3.5 billion years ago on the ocean floor. For the first 2 billion years of Earth's existence, the atmosphere was anoxic (oxygen-free), with only nitrogen, carbon dioxide, and other gases present. Life during this period was limited to microorganisms capable of anaerobic metabolism. Early cells were likely chemolithotrophic, utilizing hydrogen and hydrogen sulfide from hydrothermal vents as electron donors and CO2 and N2 as sources for biosynthesis [22](#page=22) [23](#page=23). #### 2.1.2 Photosynthesis and the oxygen revolution The evolution of phototrophic microorganisms, which derive energy from sunlight, occurred within the first billion years of life. Initially, these were anoxygenic, meaning they did not produce oxygen. Cyanobacteria, oxygen-producing (oxygenic) phototrophs, evolved around 2.5 billion years ago. Through photosynthesis, they converted CO2 and H2O into glucose and O2, a process described by the equation [23](#page=23) [24](#page=24): $$ 6 \text{CO}_2 + 6 \text{H}_2\text{O} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6 \text{O}_2 $$ [24](#page=24). The oxygen released initially dissolved in the water, reacting with dissolved iron to form iron oxides that precipitated and accumulated as banded iron formations. Once all dissolved iron was precipitated, oxygen began to escape into the atmosphere. This "oxygen revolution," occurring between 2.7 and 2.4 billion years ago, led to an atmosphere containing about twenty percent oxygen [24](#page=24). The increased oxygen levels were detrimental to many anaerobic organisms, leading to extinctions or forcing them into anaerobic niches. However, aerobic organisms gained an energetic advantage, leading to faster reproduction and further evolutionary advancements [24](#page=24). #### 2.1.3 Endosymbiosis and the origin of eukaryotes For approximately two billion years, life was primarily prokaryotic and oxygen-poor. The emergence of the eukaryotic cell and multicellularity broadly coincided with the rise in atmospheric oxygen. The oldest microfossils with recognizable nuclei are about 2 billion years old [25](#page=25). Eukaryotic cells are more complex than prokaryotic cells, possessing membrane-bound nuclei, mitochondria, endoplasmic reticulum, and other organelles absent in prokaryotes. The modern eukaryotic cell is thought to be a genetic chimera, formed from contributions from both bacteria and archaea [25](#page=25). The endosymbiotic theory proposes that mitochondria and plastids (like chloroplasts) originated from smaller prokaryotes that took up residence within larger host cells. These endosymbionts, potentially an engulfed prey or an internal parasite, formed mutually beneficial relationships with the host cell. For example, an anaerobic host cell could benefit from an endosymbiont that consumed oxygen, while the endosymbiont benefited from the host's nutrients. Over time, these cells became integrated into a single organism [25](#page=25) [26](#page=26). **Evidence for the endosymbiotic theory:** * Mitochondrial and plastid membranes contain enzymes similar to those in bacterial plasma membranes [27](#page=27). * Mitochondria and plastids replicate through binary fission, akin to bacterial cell division [27](#page=27). * They possess their own circular DNA, which, like bacterial chromosomes, lacks histones or other major proteins [27](#page=27). * Mitochondria and plastids can perform transcription and translation to synthesize proteins, a process seen in bacteria [27](#page=27). * Their ribosomes are similar to prokaryotic ribosomes in size, nucleotide sequence, and sensitivity to antibiotics [27](#page=27). The engulfment of an aerobic bacterial cell by a prokaryotic cell (likely archaea) is believed to have given rise to mitochondria. A subsequent round of endosymbiosis, involving a photosynthetic microorganism, may have led to the formation of plastids. Additionally, the plasma membrane invaginated to form the nuclear envelope and endoplasmic reticulum, characteristic of eukaryotes [27](#page=27). #### 2.1.4 Multicellular organisms and the colonization of land The presence of oxygen facilitated the evolution of organisms that consume oxygen, leading to more efficient energy production and the development of multicellular life forms, including plants and animals. However, multicellular organisms, plants, and animals have only existed for about half a billion years. For the vast majority of Earth's history (80%), life was exclusively microbial, leading to the Earth being considered a microbial planet. Multicellular eukaryotic microfossils, such as algae, are found from 1.9 to 1.4 billion years ago [27](#page=27). --- # Diversity of life and classification This section explores the vast diversity of life on Earth, focusing on taxonomic classification systems, the three domains of life (Bacteria, Archaea, Eukarya), and phylogenetic analysis using cladograms. ### 3.1 Taxonomy Taxonomy is the scientific discipline concerned with classifying and naming organisms based on shared characteristics. This hierarchical system organizes the immense diversity of life, arranging species into progressively broader categories: domains, kingdoms, phyla, classes, orders, families, genera, and species. A taxonomic unit at any level is called a taxon [52](#page=52) [54](#page=54). #### 3.1.1 The grouping of species: the basic idea Estimating the total number of species on Earth is challenging, with figures ranging from 8.7 million to over 1 billion. Currently, about 2.16 million species have been formally described, with insects making up a significant portion. However, bacteria and archaea are believed to constitute 70-90% of all life [52](#page=52). The human tendency to group similar items is mirrored in taxonomy. Organisms are classified based on resemblances, leading to the identification of groups like "insects" or "rodents". This classification allows for effective communication about organisms, including their behavior, ecology, physiology, and evolutionary relationships [52](#page=52). Taxonomic nomenclature historically uses Latin for global clarity. Each species is given a two-part scientific name, the genus name followed by the species name, similar to a surname and first name. Strict rules govern the writing of these names: the genus is capitalized, the species is not, and the entire name is italicized. Carolus Linnaeus established these naming conventions in the 18th century [53](#page=53). #### 3.1.2 The three (?) domains of life Early attempts to understand evolutionary history relied on paleontology and comparative biology, which were less effective for microorganisms due to the lack of fossils and limited morphological features. The advent of DNA analysis, particularly using ribosomal RNA (rRNA), revolutionized this field. Carl Woese's research on methanogens led to the discovery of Archaea as a distinct domain, alongside Bacteria and Eukarya, establishing the three-domain system. This system replaced the older five-kingdom system (plants, animals, fungi, protists, prokaryotes). In the current system, Eukarya encompasses protists, fungi, plants, and animals [55](#page=55). More recent genomic studies indicate that eukaryotic cells possess a mix of archaeal, bacterial, and eukaryotic-specific characteristics. The endosymbiotic theory, which posits that eukaryotes arose from archaea and bacteria, is widely accepted, though the precise evolutionary relationship between eukaryotes and archaea remains a subject of discussion. Discoveries of previously unknown archaea, such as those in the Asgard group, suggest they are more closely related to eukaryotes than to other archaea, potentially leading to a shift towards a two-domain system where eukaryotes are nested within Archaea [56](#page=56) [57](#page=57). ### 3.2 Phylogeny Phylogeny is the study of the evolutionary history and relationships among organisms or groups of organisms. It aims to determine which species are closely related and share common ancestors [57](#page=57). #### 3.2.1 The link between phylogeny and classification Phylogenetic trees are diagrams that illustrate evolutionary history and relationships, akin to family trees. Organisms with recent common ancestors are likely to share similar characteristics, allowing for predictions about their traits. The hierarchical classification of Linnaeus is reflected in the branching patterns of phylogenetic trees. However, Linnaean classifications alone may not always accurately represent evolutionary relationships, as convergent evolution or loss of shared traits can lead to misclassification. DNA and other molecular evidence are crucial for refining classifications to reflect evolutionary history accurately [57](#page=57) [58](#page=58). #### 3.2.2 Convergent evolution Convergent evolution, also known as homoplasy, occurs when organisms independently evolve similar traits that are not inherited from a common ancestor. This often arises due to similar environmental pressures and natural selection, leading to analogous adaptations in unrelated lineages. For example, wings in insects and birds evolved independently. Organisms that appear similar externally due to convergent evolution may have significant differences in their internal anatomy, physiology, and reproductive systems [59](#page=59). #### 3.2.3 How to 'read' phylogenetic trees Phylogenetic trees are graphical representations of hypotheses about evolutionary relationships, consisting of nodes and branches. Branch tips represent existing species, while evolutionary lineages trace ancestral organisms. Nodes, or branching points, signify the divergence of evolutionary lines from a common ancestor. Sister taxa are groups that share a common ancestor not shared by any other group, indicating the closest evolutionary relatives [59](#page=59) [60](#page=60). The orientation of phylogenetic trees (horizontal, vertical, or diagonal) does not alter the relationships depicted; only the position of the nodes is informative. Rotation around nodes does not change the tree's topology. The branching pattern indicates the order in which descendants diverged from common ancestors, read from left to right over time. Branch length can sometimes represent the number of evolutionary changes along that lineage [60](#page=60). Rooted trees include a branch representing the most recent common ancestor of all taxa in the tree. A basal taxon is an early diverging lineage from the most recent common ancestor of the entire group. It's crucial to remember that phylogenetic trees illustrate descent patterns, not necessarily phenotypic similarity. For instance, crocodiles are more closely related to birds than to lizards due to their shared ancestry, despite superficial resemblances to lizards. Phylogenetic trees do not indicate the exact timing of species' evolution or the extent of change within a lineage; they only show shared ancestry [61](#page=61). #### 3.2.4 How to make phylogenetic trees Phylogenetic trees are constructed using molecular data, primarily DNA or protein sequences, comparing similarities and differences. Highly related organisms share very similar genetic sequences. Inferring the most accurate phylogenetic tree from sequence data can be complex, as the number of possible trees increases exponentially with the number of sequences [62](#page=62). Fylogenetic analysis employs molecular sequence data to identify the single correct tree representing evolutionary history. Trees can be constructed using algorithms or optimization criteria [62](#page=62). Cladistics is a method for constructing phylogenetic trees, resulting in a cladogram. A cladogram depicts evolutionary relationships between groups of organisms (clades), where a clade includes an ancestor and all its descendants. By identifying the point at which shared derived characteristics first appeared, evolutionary relationships can be inferred [62](#page=62). To construct a cladogram using morphological data, an outgroup (a closely related species not in the group being studied) is selected for comparison. Traits present in both the ingroup and outgroup are assumed to be ancestral. Traits found only within a subset of the ingroup are considered derived and indicate evolutionary branching points [62](#page=62) [63](#page=63). Alternatively, cladograms can be constructed from genetic data by aligning DNA or protein sequences and creating a dissimilarity matrix, which quantifies the differences between sequences. Hierarchical clustering, such as the UPGMA (unweighted pair group method with arithmetic mean) method, is then applied to group sequences based on their relatedness [64](#page=64). ### 3.3 Archaea The domain Archaea is named after the Archaean eon, the period when life first emerged on Earth. Initially thought to be relics of this ancient era due to their presence in extreme environments like volcanic systems and salt lakes, archaea are now known to inhabit a wide range of habitats and play crucial biogeochemical roles. Despite both being prokaryotic, Archaea and Bacteria are genetically and physiologically very distinct, with Archaea sharing more characteristics with Eukarya. It is probable that archaea contributed significantly to the origin of the Eukarya domain [66](#page=66). Most archaea are difficult to culture, suggesting much remains to be discovered about their properties. The most characterized archaea belong to the phyla Euryarchaeota and Crenarchaeota [66](#page=66). Common characteristics of all archaea include ether-linked lipids, absence of peptidoglycan in cell walls, and structurally complex RNA polymerases resembling those of eukaryotes. Common cell morphologies include cocci, rods, and spirals [67](#page=67). Early archaea are hypothesized to have lived at high temperatures, used H2 as an energy source, and fixed CO2. Current archaea exhibit significant metabolic diversity, functioning as chemoorganotrophs or chemolithotrophs, with either respiratory or fermentative metabolism, and can be aerobic or anaerobic [67](#page=67). Unique archaeal features include methanogenesis, the production of methane (CH4) from H2 and CO2 in anaerobic conditions, a process vital for natural gas production and climate regulation. Archaea also include many extremophiles, organisms thriving in extreme conditions like hyperthermosts (>80°C), halophiles, acidophiles, and psychrophiles [67](#page=67). ### 3.4 Bacteria #### 3.4.1 Bacteria are prokaryotes Cyanobacteria have profoundly influenced Earth over the last two billion years by causing oxygenation of the atmosphere and continue to produce a significant portion of the oxygen we breathe. The domain Bacteria encompasses numerous species with a prokaryotic cell structure, lacking a nucleus. Like archaea, bacteria can adapt readily to changing environmental conditions [67](#page=67). #### 3.4.2 Cell morphology in Bacteria Cell morphology is defined by size and shape, with a diverse range of forms found in the microbial world. Cell shape can aid in distinguishing microbes and often has ecological significance. Common bacterial shapes include cocci (spherical or oval), rods (cylindrical), spirilla (curved or spiral), and spirochetes (flexible spiral). Some bacteria exhibit irregular shapes or possess appendages like stalks and hyphae for attachment or increased surface area [68](#page=68). Cell division significantly impacts morphology, as cells that remain attached after division can form distinctive arrangements. Cocci can be found in pairs (diplococci), long chains (streptococci), three-dimensional clusters (tetrads, sarcinae), or grape-like clusters (staphylococci). Filamentous bacteria are long, thin rods that form long chains. Rods can be further classified into monobacilli (individual), streptobacilli (chains of 3+), and diplobacilli (chains of 2) [68](#page=68) [69](#page=69). #### 3.4.3 Cell multiplication in bacteria Bacterial cell multiplication involves complex biochemical reactions, including polymerization processes to form macromolecules. These macromolecules assemble into new cellular structures, leading to cell division. Many bacteria reproduce rapidly in favorable conditions through binary fission, where one cell divides into two identical daughter cells. For example, *Escherichia coli* can double its population in just 20 minutes [70](#page=70). #### 3.4.4 Bacteria, a diverse group with diverse properties Bacteria are known for causing diseases like strep throat and tuberculosis, as well as for their use in producing cheese and yogurt. Their wide nutritional requirements and diverse metabolisms lead to extensive applications [71](#page=71). ##### 3.4.4.1 The main phylogenetic groups within bacteria * **Proteobacteria:** A large, diverse clade of Gram-negative bacteria, including photoautotrophs, chemoautotrophs, and heterotrophs. Examples include pathogens like *Neisseria gonorrhoeae*, *Vibrio cholerae*, and *Helicobacter pylori* [71](#page=71). * **Chlamydias:** Bacteria that can only survive and parasitize animal cells, lacking peptidoglycan in their cell walls. *Chlamydia trachomatis* causes blindness and a common sexually transmitted infection [72](#page=72). * **Spirochetes:** Spiral-shaped, Gram-negative heterotrophs that move by rotating internal filaments. Pathogens include *Treponema pallidum* (syphilis) and *Borrelia burgdorferi* (Lyme disease) [72](#page=72). * **Cyanobacteria:** Gram-negative photoautotrophs and the only prokaryotes capable of photosynthesis. Plant chloroplasts are believed to have evolved from cyanobacteria via endosymbiosis [72](#page=72). * **Gram-positive bacteria:** A very diverse group, including actinomycetes (e.g., *Streptomyces* producing antibiotics) and pathogens like *Staphylococcus aureus*, *Bacillus anthracis*, and *Clostridium botulinum* [72](#page=72). ##### 3.4.4.2 Bacteria play an essential role in the biosphere Prokaryotes, including bacteria, are vital for recycling chemical elements in ecosystems, acting as decomposers that break down dead organic matter. They convert molecules into forms usable by other organisms. Cyanobacteria produce oxygen and fix atmospheric nitrogen (N2) into forms essential for protein and genetic material synthesis. Bacteria are also central to ecological interactions, often forming symbiotic relationships with larger organisms [72](#page=72) [73](#page=73). ##### 3.4.4.3 Bacteria have both beneficial and harmful consequences for humans The human gut hosts trillions of mutualistic bacteria that provide benefits to both host and microbe. *Bacteroides thetaiotaomicron*, for example, synthesizes essential nutrients and activates human genes involved in nutrient absorption [73](#page=73). All known pathogenic prokaryotes are bacteria, causing about half of all human diseases, such as tuberculosis. Bacterial toxins can also be harmful [73](#page=73). Bacteria are indispensable in science and technology, with *E. coli* serving as a model organism for biotechnology, used in producing insulin and sustainable plastics. They are also employed in bioremediation to remove pollutants from the environment [73](#page=73). ### 3.5 Fungi #### 3.5.1 Importance of fungi Fungi are a large, diverse, and widespread group of primarily sessile organisms, including molds, mushrooms, and yeasts. Most are microscopic terrestrial organisms that play a crucial role in decomposing organic matter, thereby recycling nutrients like carbon, nitrogen, and phosphorus. Some fungi are plant pathogens, and a few cause diseases in animals, including humans. Symbiotic relationships with plants can enhance mineral uptake. Fungi are also beneficial to humans through fermentation for producing organic acids and synthesizing antibiotics [73](#page=73). #### 3.5.2 Physiology and feeding mechanism of fungi Fungi are chemoorganotrophs with generally simple nutritional requirements, and most are aerobic. They feed by secreting extracellular enzymes that digest polymeric materials into monomers for absorption. As decomposers, they break down dead organisms; as parasites, they absorb nutrients from living cells [74](#page=74). Certain basidiomycetes are highly efficient at decomposing wood, paper, and textiles, breaking down the complex polymer lignin [74](#page=74). #### 3.5.3 Morphology Most fungi are multicellular, forming a network of thread-like structures called hyphae. Hyphae are tubular cell walls surrounding the cytoplasmic membrane. Vegetative hyphae are involved in nutrient uptake, while reproductive hyphae form reproductive structures. Hyphae often possess septa, cross-walls dividing them into cells (apocytic). In some cases, hyphae can be multinucleate without septa (coenocytic). Hyphal filaments grow primarily at their tips [74](#page=74). Hyphae aggregate to form a macroscopic visible tissue called a mycelium. Aerial hyphae from the mycelium produce spores called conidia at their tips, giving the mycelium a dusty appearance and aiding in dispersal. Some fungi form macroscopic fruiting bodies (e.g., mushrooms) that produce millions of spores. Yeasts, in contrast, grow as single cells [75](#page=75). Fungal cell walls are typically composed of chitin, a polymer of N-acetylglucosamine, arranged in microfibrils for structural integrity. Other polysaccharides like mannans and β-glucans, or even cellulose, can be present [75](#page=75). #### 3.5.4 Reproduction and phylogeny Fungi reproduce asexually and sexually [75](#page=75). ##### 3.5.4.1 Asexual reproduction in fungi Asexual reproduction in fungi involves mitosis and results in genetically identical offspring. Methods include [76](#page=76): * Production of haploid spores in a sporangium (sporangiospores) [76](#page=76). * Production of haploid spores via conidiospores (exogenous spore formation) [76](#page=76). * Fragmentation of hyphae forming arthrospores [76](#page=76). * Chlamydospores: resistant spores formed within hyphae [76](#page=76). * Cell division (cytokinesis) via mitosis, including budding in yeasts (blastospores) [77](#page=77). ##### 3.5.4.2 Sexual reproduction in fungi Sexual reproduction in fungi involves the fusion of hyphae of different mating types. Plasmogamy, the fusion of cytoplasm, leads to dikaryotic cells containing two haploid nuclei. Karyogamy, the fusion of these nuclei, forms a diploid zygote. Meiosis then produces genetically diverse haploid spores, which are often resistant to harsh conditions and aid in evolution. Fungal sexual spores are generally more resistant than asexual spores but less so than bacterial endospores [77](#page=77) [78](#page=78). ##### 3.5.4.3 Phylogeny of fungi Fungi share a common ancestor with animals and are more closely related to animals than any other eukaryotic group. Chytridiomycota is considered one of the earliest fungal lineages, characterized by motile zoospores. The loss of flagella in most fungi indicates it's a trait lost at different times in different lineages [78](#page=78). The major fungal groups include Mucoromycota, Ascomycota, and Basidiomycota, with Ascomycota and Basidiomycota housing the vast majority of described species. Ascomycota includes yeasts and molds, while Basidiomycota encompasses mushrooms and plant pathogens. Molecular analyses suggest that over 90% of fungal species remain undiscovered in environmental samples [79](#page=79). ##### 3.5.4.4 Reproduction in Mucoromycetes Mucoromycetes include fungi responsible for food spoilage. Asexual reproduction involves sporangiospores formed within a sporangium on a sporangiophore. Sexual reproduction involves plasmogamy followed by karyogamy to form a zygosporangium, which eventually produces haploid spores after meiosis [79](#page=79) [80](#page=80). ##### 3.5.4.5 Reproduction in Ascomycetes Ascomycetes are a diverse group found in various environments, including yeasts and complex organisms. Asexual reproduction occurs via conidiospores formed at the tips of conidiophores. Sexual reproduction involves plasmogamy, leading to dikaryotic asci where karyogamy and meiosis occur, resulting in 8 ascospore per ascus within an ascocarp. Yeasts, like *Saccharomyces cerevisiae*, reproduce asexually by budding or fission and sexually by forming ascospores [81](#page=81) [82](#page=82) [83](#page=83). ##### 3.5.4.6 Reproduction in Basidiomycetes Basidiomycetes, including mushrooms, form basidiospores on a basidium. Asexual reproduction involves hyphal fragmentation into arthrospores. Mushrooms can emerge rapidly from the underground mycelium through water absorption and cytoplasmic flow [85](#page=85). ### 3.6 Plantae There are over 325,000 described plant species, with most terrestrial plants playing a crucial role in enabling other life forms to survive on land by providing oxygen and food. This section focuses on the structure and organization of vascular plants, particularly angiosperms (flowering plants) [85](#page=85). #### 3.6.1 The plant body has a hierarchy of organs, tissues, and cells Plants, like animals, have organs composed of tissues, which are made up of specialized cells. A tissue is a group of cells with a common function or structure, while an organ comprises different tissue types performing specific functions [86](#page=86). The basic morphology of vascular plants reflects their terrestrial origin, with distinct aerial (shoot system: stems and leaves) and subterranean (root system) components. The root system anchors the plant and absorbs water and minerals, while the shoot system captures CO2 and light for photosynthesis. Stems support and orient leaves for maximal photosynthesis, and leaves are the primary photosynthetic organs [86](#page=86) [87](#page=87). #### 3.6.2 Dermal, vascular, and ground tissues Each plant organ consists of three fundamental tissue types: dermal, vascular, and ground tissue, forming interconnected tissue systems [87](#page=87). * **Dermal tissue:** The outer protective covering, forming the epidermis in non-woody plants and periderm in woody plants. It protects against damage, pathogens, and water loss. Specialized epidermal cells include root hairs for absorption and stomata for gas exchange [88](#page=88). * **Vascular tissue:** Responsible for long-distance transport of materials. Xylem transports water and minerals upwards, while phloem transports sugars from where they are produced to where they are needed [89](#page=89). * **Ground tissue:** Tissues not part of the dermal or vascular systems. Ground tissue within the vascular system is pith, and outside is cortex. It is involved in metabolic functions like storage, photosynthesis, and support [89](#page=89). #### 3.6.3 General plant cell types Plants exhibit cell differentiation, specializing cells for specific structures and functions [90](#page=90). ##### 3.6.3.1 The plant cell wall The plant cell wall is a chemically complex extracellular layer providing mechanical support, regulating growth, protecting the cell, and controlling water and ion transport. It is primarily composed of cellulose, hemicelluloses, and pectins, with structural proteins and sometimes lignin or cutin [90](#page=90). * **Primary cell wall:** Formed during cell division and growth. It is thin, rich in pectin and hemicellulose, and flexible [91](#page=91). * **Secondary cell wall:** Deposited inside the primary wall when growth stops. It is thicker, layered, and rich in cellulose, hemicellulose, and lignin, providing rigidity and strength [91](#page=91). The cell wall is dynamic, with composition and structure varying between species, organs, cell types, and developmental stages [91](#page=91). ##### 3.6.3.2 Parenchyma cells Parenchyma cells have thin, flexible primary cell walls and typically a large central vacuole. They are the least specialized and perform most metabolic functions, including photosynthesis and storage. Many can divide and differentiate into other plant tissues [91](#page=91) [92](#page=92). ##### 3.6.3.3 Collenchyma cells Collenchyma cells, often found in strands beneath the epidermis, provide flexible support to young, growing parts of the shoot. They have thicker primary cell walls but lack secondary walls and lignin, allowing them to elongate with the supported structures [92](#page=92). ##### 3.6.3.4 Sclerenchyma cells Sclerenchyma cells provide rigid support due to their thick, lignified secondary cell walls. Mature sclerenchyma cells are often dead but leave behind a supportive skeletal structure. They contribute to the hardness of nut shells and the fibers in hemp and flax [92](#page=92) [93](#page=93). ##### 3.6.3.5 Water-transporting cells of the xylem Tracheids and vessel elements are dead, tubular cells forming xylem for water transport. Tracheids are long and narrow with tapered ends, with water moving laterally through pits. Vessel elements are wider, shorter, and form long tubes with perforated end plates for unimpeded water flow. Their lignified secondary walls prevent collapse under pressure and provide structural support [93](#page=93) [94](#page=94). ##### 3.6.3.6 Sugar-transporting cells of the phloem Phloem cells, such as sieve cells and sieve-tube elements, are living when mature but lack nuclei and other organelles to facilitate nutrient flow. They are flanked by companion cells, which provide metabolic support [95](#page=95). ### 3.7 Protists Protists are a diverse collection of eukaryotic microorganisms that are not plants, animals, or fungi. This group exhibits a wide range of morphologies and phylogenetic diversity. Protist cells have a nucleus and other membrane-bound organelles [98](#page=98). #### 3.7.1 Protists, a collection of many different species The term "protist" encompasses all microbial eukaryotes that do not fit into the categories of plants, animals, or fungi. This group is highly diverse, with some protists being more closely related to plants, fungi, or animals than to other protists. They can be photo- or chemo-trophic, unicellular or multicellular, and are found worldwide [98](#page=98). #### 3.7.2 Phylogeny in protists The understanding of evolutionary relationships among protist groups and other eukaryotes is rapidly evolving [99](#page=99). #### 3.7.3 Excavata Excavata is a diverse group of protists that includes chemoorganotrophs and phototrophs, some of which are anaerobic. Members like Diplomonads and Parabasalids lack mitochondria and chloroplasts and live in anoxic habitats. Euglenoids are motile, chemo- and phototrophic eukaryotes [100](#page=100) [99](#page=99). #### 3.7.4 SAR The SAR supergroup, identified through DNA sequencing, comprises Stramenopiles, Alveolata, and Rhizarians [100](#page=100). * **Alveolata:** Characterized by alveoli (cytoplasmic sacs beneath the plasma membrane). This group includes ciliates, dinoflagellates, and apicomplexans [100](#page=100). * **Dinoflagellates:** Abundant in marine and freshwater phytoplankton, they possess two flagella and can cause "red tides" . * **Apicomplexans:** Nearly all are parasites of humans and other animals, with *Plasmodium* causing malaria . * **Stramenopiles:** Include diatoms, oomycetes, golden algae, and brown algae. Diatoms are single-celled algae with silica cell walls, forming a significant part of phytoplankton. Brown algae are large, multicellular seaweeds lacking true tissues. Oomycetes, like *Phytophthora*, were once mistaken for fungi but have cellulose cell walls . * **Rhizaria:** Diverse protists distinguished by their thread-like pseudopodia . #### 3.7.5 Amoebozoa Amoebozoa are a large group of terrestrial and aquatic protists using lobose pseudopodia for movement and feeding. They diverged from a lineage that eventually led to fungi and animals . ### 3.8 Algae Algae belong to the Archaeplastida and include red and green algae, which perform oxygenic photosynthesis . #### 3.8.1 General characteristics Algae are eukaryotic organisms containing chlorophyll and performing oxygenic photosynthesis. They can be microscopic or macroscopic and are found primarily in aquatic habitats . #### 3.8.2 Red algae Red algae (rhodophytes) are predominantly marine, containing chlorophyll a and phycobiliproteins. The red color is due to phycoerythrin, which allows them to absorb light at deeper water depths. Many red algae are multicellular "seaweeds" and are sources of agar and carrageen. Some, like *Porphyra*, are harvested for food (nori). Coral-like red algae play a role in reef development . #### 3.8.3 Green algae Green algae (chlorophytes and charophytes) have chloroplasts containing chlorophyll a and b, making them structurally and chemically similar to plants. They are phylogenetically closely related to plants. Most live in freshwater, though some are terrestrial or form symbiotic relationships in lichens. Their morphology ranges from unicellular to filamentous, colonial, and multicellular . ##### 3.8.3.1 General characteristics Green algae have chloroplasts containing chlorophyll a and b. They are phylogenetically closely related to plants . ##### 3.8.3.2 Morphology: from very small green algae to colonial green algae The green alga *Ostreococcus tauri* is one of the smallest known eukaryotes and serves as a model organism for studying genome reduction. *Volvox* forms colonies of hundreds of flagellated cells where some are specialized for photosynthesis and others for reproduction, connected by cytoplasmic strands. Colonial green algae like *Botryococcus braunii* produce hydrocarbons that can be used for biofuels . ##### 3.8.3.3 Endolithic phototrophic green algae Some green algae grow within porous rocks in dry or cold environments, utilizing sunlight and retained moisture. These endolithic communities contribute to rock weathering and habitat formation . ##### 3.8.3.4 Microalgae and diesel Microalgae are unicellular phototrophic eukaryotes that produce lipids, fatty acids, and carotenoids. Certain species, like *Chlorella* and *Chlamydomonas*, produce triacylglycerides (TAGs) that can be converted into biodiesel. The primary challenge for large-scale production is cost competitiveness with petroleum . ##### 3.8.3.5 Algae and the environment Algae play a significant role in wastewater treatment by absorbing excess nutrients like nitrogen and phosphorus, preventing eutrophication. Their photosynthetic activity produces oxygen, aiding aerobic bacteria in organic matter breakdown. Algae can also contribute to bioremediation by removing heavy metals and pollutants . ### 3.9 Cell culture and model organisms Researchers use model organisms and cell cultures to study biological mechanisms efficiently and safely . #### 3.9.1 Cell and tissue cultures * **Animal cell culture:** Animal cells are grown in vitro in nutrient-rich media, often supplemented with serum. Many cells require attachment to a surface. Cancer cells, unlike normal cells, can grow indefinitely in culture. HeLa cells are a famous example of immortalized human cervical cancer cells . * **Plant tissue culture:** Plant cells, tissues, or organs can be cultured in vitro for regeneration into whole plants, micropropagation, or metabolite production. Plant cells are often totipotent, meaning a single cell can develop into an entire plant. Plant hormones like auxins and cytokinins control cell differentiation . * **Limitations of in vitro cell cultures:** While offering controlled environments and rapid reproduction, cell cultures lack the anatomical architecture and systemic interactions of whole organisms. Therefore, in vitro results may not always be directly translatable to whole organisms . #### 3.9.2 Commonly used model organisms Model organisms are chosen for practical reasons (short life cycle, high fertility, ease of growth), evolutionary conservation of core processes, and availability of genetic tools. Genetic manipulation allows for the study of gene functions in their biological context. Ethical considerations and regulations govern the use of animal models, adhering to the 3R principles (replace, reduce, refine) . * ***Escherichia coli*:** A model for bacteria, widely used in molecular biology for studying gene function, biochemistry, and biotechnology. It is easy to grow, has a short generation time, and is amenable to genetic modification . * ***Arabidopsis thaliana*:** A model for plants, known for its rapid growth cycle (4-6 weeks), small size, small genome, and ease of transformation . * ***Caenorhabditis elegans*:** A nematode worm used in developmental biology and aging research. Its transparent cuticle allows for easy observation of cells, and its cell lineage is predictable . * ***Drosophila melanogaster*:** The fruit fly, a classic genetic model since the early 20th century due to its ease of cultivation, short life cycle, and abundant offspring . * ***Mus musculus* (laboratory mouse):** The primary mammalian model organism for biomedical research due to its physiological similarities to humans . * ***Danio rerio* (zebrafish):** An alternative to the lab mouse, offering rapid reproduction, transparent embryos for direct observation, and genetic similarity to humans in various systems . --- # Microbial growth and environmental factors This section delves into the principles of microbial growth, examining population dynamics and the crucial influence of environmental factors on microbial survival and proliferation. ### 4.3.1 Population growth dynamics Microbial populations, like all living organisms, have the capacity for significant expansion when provided with abundant resources. Ecologists study population growth in ideal, unlimited environments to understand the maximum potential growth rate and the conditions under which rapid growth can occur . #### 4.3.1.1 Exponential growth When a population experiences ideal conditions, with plentiful resources and no limiting factors, it exhibits exponential growth. This occurs when the population size increases by a constant factor at any given time. The rate of population increase ($dN/dt$) is proportional to the current population size ($N$) multiplied by a constant intrinsic growth rate ($r$) : $$ \frac{dN}{dt} = rN $$ In this equation: * $dN/dt$ represents the rate of population increase over time. * $N$ is the current population size. * $r$ is the intrinsic growth rate per capita. When population size is plotted against time, exponential growth results in a J-shaped curve. Although $r$ is constant, the number of new individuals added per unit of time increases as the population grows larger . #### 4.3.1.2 Logistic growth In reality, unlimited growth is rare because resources become limited as populations increase. The logistic growth model provides a more realistic description of population growth by incorporating the concept of carrying capacity ($K$), which is the maximum population size a given environment can sustain . The logistic growth equation modifies the exponential model to account for resource limitation: $$ \frac{dN}{dt} = rN \left( \frac{K - N}{K} \right) $$ In this model: * $K$ is the carrying capacity. * $(K - N)/K$ represents the fraction of the carrying capacity still available for population growth. When the population size ($N$) is small compared to $K$, the term $(K - N)/K$ is close to one, and growth approximates exponential growth. As $N$ approaches $K$, the term approaches zero, significantly slowing population growth. The logistic growth model produces a sigmoid (S-shaped) curve when population size is plotted against time. The fastest population growth typically occurs when the population size is at half the carrying capacity ($N = K/2$) . > **Tip:** The logistic model assumes immediate adaptation to growth and a smooth approach to carrying capacity. In natural populations, there can be a delay before the effects of increasing population size manifest, leading to temporary overshoots of the carrying capacity . #### 4.3.1.3 Microbial growth curve Microorganisms grown in a batch culture (a closed system with a finite volume of liquid medium) typically follow a growth cycle known as the microbial growth curve, which consists of four distinct phases : 1. **Lag phase:** The initial period where cells do not grow or grow very slowly after being inoculated into a new growth medium. This is due to the need for metabolic adaptation to the new environment. The duration depends on the cells' prior history, the medium, and growth conditions . 2. **Exponential (log) phase:** The period of rapid growth where the cell population doubles at regular intervals. Cells in this phase are metabolically uniform, and this is the preferred phase for experimental studies. Growth rates vary widely depending on media, conditions, and the organism . 3. **Stationary phase:** Growth stops when conditions can no longer support it, typically due to nutrient depletion or accumulation of toxic waste products. In this phase, the rate of cell death equals the rate of new cell formation, resulting in a constant number of living cells. The cellular metabolism shifts from growth to maintenance and survival . 4. **Death (or decline) phase:** The total number of cells decreases due to cell death exceeding cell division. Some sub-populations may adapt to cannibalize dying cells . ##### 4.3.1.4 Microbial growth parameters * **Generation time (g):** The time it takes for one cell to divide into two daughter cells. If starting with $N_0$ cells, the population size ($N_t$) after $n$ generations is given by: $$ N_t = N_0 \cdot 2^n $$ The number of generations ($n$) can be calculated as: $$ n = \frac{\log N_t - \log N_0}{\log } $$ [2](#page=2). And the generation time ($g$) is: $$ g = \frac{t}{n} $$ * **Specific growth rate (k):** Expresses the rate at which the population grows at any given moment, measured in reciprocal hours (h⁻¹) . Microbial growth is often visualized on a semilogarithmic graph, plotting the logarithm of the cell number against time, which shows a linear relationship during the exponential phase . > **Example:** Under optimal conditions, *E. coli* has a generation time of approximately 20 minutes. In 4 hours (240 minutes), this would result in 12 generations ($240/20 = 12$). Starting with 10 cells, the population would reach $10 \times 2^{12} = 40,960$ cells (#page=136, page=139) . ### 4.3.2 Nutritional requirements for microbial growth Microorganisms exhibit diverse metabolic strategies, leading to varied nutritional needs. However, all require a basic set of nutrients, categorized as macronutrients (needed in large quantities) and micronutrients (needed in trace amounts) . #### 4.3.2.1 Chemical composition of a bacterial cell The dry mass of a typical bacterial cell, such as *E. coli*, is predominantly composed of: * **Macronutrients:** Carbon, oxygen, nitrogen, hydrogen, phosphorus, and sulfur constitute approximately 96% of the dry weight . * **Other essential elements:** Potassium, sodium, calcium, magnesium, chlorine, and iron make up about 3.7% . * **Micronutrients:** At least 20 other elements are present in smaller amounts . Major cellular macromolecules include proteins, lipids, polysaccharides, lipopolysaccharides, and nucleic acids, which account for over 96% of the dry weight. Proteins and RNA are the most abundant . #### 4.3.2.2 Carbon, nitrogen, and other macronutrients * **Carbon:** Essential for biosynthesis. Heterotrophs obtain carbon from organic compounds, while autotrophs use carbon dioxide ($CO_2$) . * **Nitrogen:** Found in proteins and nucleic acids. Most microorganisms can utilize ammonia ($NH_3$), many can use nitrate ($NO_3^-$), and some can fix atmospheric nitrogen ($N_2$) . * **Phosphorus:** Crucial for nucleic acids and phospholipids, usually absorbed as inorganic phosphate ($PO_4^{3-}$) . * **Sulfur:** Found in amino acids (cysteine, methionine) and vitamins. Absorbed as sulfates ($SO_4^{2-}$), sulfides ($H_2S$), or organic sulfur compounds . * **Potassium:** Required for enzyme activity. * **Magnesium:** Stabilizes ribosomes, membranes, and nucleic acids; also needed for many enzymes. * **Calcium and Sodium:** Essential for only a few organisms, with marine microorganisms often requiring sodium chloride ($NaCl$) . #### 4.3.2.3 Micronutrients: trace elements and growth factors * **Trace elements:** Metal ions required as cofactors for enzyme activity. Iron is particularly important for respiration . * **Growth factors:** Organic micronutrients, most commonly vitamins, which often act as coenzymes. Some microorganisms can synthesize their own growth factors, while others must obtain them from the environment. Amino acids, purines, and pyrimidines are also common growth factors . > **Example:** Cyanobacteria are autotrophs that can synthesize all their growth factors, requiring minimal external additions. In contrast, lactic acid bacteria, living in nutrient-rich environments, often depend on external growth factors . ### 4.3.3 Environmental factors influencing microbial growth Even with optimal nutrients, microbial growth is dependent on suitable chemical and physical environmental conditions. Key factors include temperature, pH, water activity, and oxygen availability . #### 4.3.3.1 Temperature Temperature profoundly affects microbial growth and survival. Each microorganism has a minimum, optimum, and maximum temperature for growth . * **Minimum temperature:** Below this, metabolic reactions are too slow, and membranes may solidify. * **Optimum temperature:** The temperature at which the fastest growth occurs, with all cellular components functioning maximally. * **Maximum temperature:** Above this, essential cellular components (e.g., enzymes) denature, leading to cell death. Microorganisms are classified based on their optimal growth temperatures: * **Psychrophiles:** Optimum growth at 15°C or lower, with maximum growth below 20°C. Found in cold environments like oceans and glaciers . * **Mesophiles:** Optimum growth between approximately 20°C and 45°C. Common in moderate environments, including the human body (e.g., *E. coli* optima around 39°C) . * **Thermophiles:** Optimum growth between 45°C and 80°C. Found in warm environments like compost heaps . * **Hyperthermophiles:** Optimum growth above 80°C, with some thriving above 100°C. Found in extreme environments like hot springs and deep-sea hydrothermal vents . > **Tip:** Organisms adapted to extreme temperatures are called extremophiles. Psychrophilic enzymes are flexible at cold temperatures due to specific protein structures and amino acid compositions, while their membranes have higher unsaturated fatty acid content to maintain fluidity. Thermophiles and hyperthermophiles have heat-stable enzymes and lipids to withstand high temperatures . #### 4.3.3.2 pH (acidity) The pH of an environment influences microbial growth, with most organisms having a specific pH range for survival and an optimal pH for growth . * **Neutrophiles:** Grow optimally between pH 5.5 and 7.9 (e.g., *E. coli*) . * **Acidophiles:** Grow best at low pH values (below 5.5), with some thriving at pH 2 or even lower . * **Alkalophiles (or basophiles):** Grow optimally at high pH values (above 8), often in alkaline lakes and soils . Intracellular pH is generally maintained closer to neutrality (pH 5-9) to ensure the stability of macromolecules . #### 4.3.3.3 Water activity ($a_w$) Water availability, expressed as water activity ($a_w$), is crucial for growth. $a_w$ is the ratio of the vapor pressure of air in equilibrium with a substance to the vapor pressure of pure water, ranging from 0 (no free water) to 1 (pure water) . * **Osmosis:** Water moves from areas of high water concentration (low solute) to low water concentration (high solute). * **Halophiles:** Require salt for growth, with optimal growth at the $a_w$ of seawater (around 0.98) . * **Extreme halophiles:** Require very high salt concentrations (15-30%) for optimal growth. * **Halotolerant:** Can tolerate some salt but grow best without it. * **Osmophiles:** Thrive in environments with high solute concentrations, such as sugars. * **Xerophiles:** Grow in very dry environments . The minimum water activity for life is approximately 0.61. Organisms adapt to low water activity by increasing their internal solute concentration using compatible solutes (e.g., glycerol, sugars, amino acid derivatives) . #### 4.3.3.4 Oxygen ($O_2$) Oxygen requirements vary significantly among microorganisms: * **Obligate aerobes:** Require oxygen for growth and will die without it; rely solely on aerobic respiration . * **Microaerophiles:** Require oxygen but at lower concentrations than found in air (less than 21%) . * **Anaerobes:** Do not use oxygen. * **Aerotolerant anaerobes:** Can tolerate oxygen but do not use it for metabolism; rely on fermentation . * **Obligate (strict) anaerobes:** Killed or inhibited by oxygen. Found in oxygen-free environments like sediments and animal intestines . * **Facultative anaerobes:** Can grow in the presence or absence of oxygen, but grow better with oxygen (e.g., *E. coli*) . > **Tip:** Oxygen itself is not directly toxic to anaerobes, but its reduction by cellular processes can produce toxic reactive oxygen species (ROS) like superoxide anions ($O_2^{\cdot-}$), hydrogen peroxide ($H_2O_2$), and hydroxyl radicals ($HO^{\cdot}$). Aerobic organisms possess enzymes (e.g., superoxide dismutase, catalase) to neutralize these toxic byproducts . --- # Nutrient cycles and microbial processes This topic examines essential nutrient cycles, specifically the water, carbon, and nitrogen cycles, highlighting the crucial role of microorganisms in these biogeochemical processes and detailing key microbial metabolic functions involved. ### 4.1 Importance of nutrient cycles and their link to ecosystems Ecosystems are characterized by energy flow and chemical cycles. While energy, typically from sunlight, flows through trophic levels and is ultimately lost as heat, chemical elements like carbon and nitrogen are cycled between biotic and abiotic components. Autotrophic organisms fix inorganic elements from the environment into organic compounds, which are then consumed by heterotrophs. Decomposition and metabolic processes return these elements to inorganic forms, completing the cycle. Microbial activities are dominant in driving these nutrient cycles . Human activities, such as the burning of fossil fuels, release excess carbon dioxide (CO2) into the atmosphere, leading to global warming and ocean acidification, which severely impact sensitive ecosystems like coral reefs. A decrease in pH, even a small one, significantly reduces biogenic calcification, threatening marine biodiversity and food sources . ### 4.2 The water cycle Water is fundamental for all life, and its availability dictates ecosystem processes, particularly primary production and decomposition in terrestrial environments. The Earth's water is primarily stored in oceans (97%), with smaller amounts in glaciers, ice caps, lakes, rivers, and groundwater . The natural water cycle involves solar energy driving evaporation from oceans, water vapor rising and condensing into clouds, and precipitation returning water to Earth as rain and snow. Snowmelt and surface runoff replenish rivers, lakes, and oceans, while infiltration leads to groundwater storage. Plants can also contribute to water cycling through transpiration . Human activities have led to the development of the "urban water cycle," which includes water extraction, treatment, distribution, wastewater collection, and treatment before discharge . ### 4.3 The carbon cycle Carbon is the fundamental element for organic compounds, primarily sourced as CO2 from the atmosphere for photosynthetic organisms. The largest carbon reservoir is in the Earth's crust (sediments and rocks), but its release is very slow. Significant amounts of carbon are stored in terrestrial biomass (plants) and, even more so, in dead organic matter (humus) . CO2 is removed from the atmosphere by photosynthesis and returned through respiration and the microbial decomposition of organic matter. Since the Industrial Revolution, human activities have increased atmospheric CO2 by nearly 40%, leading to global warming. Microbial activities are expected to change in response to rising temperatures . #### 4.3.1 Photosynthesis and decomposition New organic compounds are biologically synthesized through CO2 fixation by autotrophs (phototrophs and chemolithotrophs). Phototrophs are the primary producers in the carbon cycle, using light energy to fix CO2 into organic matter, represented as (CH2O). The general equation for oxygenic photosynthesis is : $$ \text{CO}_2 + \text{H}_2\text{O} \xrightarrow{\text{light energy}} (\text{CH}_2\text{O}) + \text{O}_2 $$ Autotrophs also respire, both in light and dark. The general equation for respiration is the reverse of oxygenic photosynthesis : $$ (\text{CH}_2\text{O}) + \text{O}_2 \rightarrow \text{CO}_2 + \text{H}_2\text{O} $$ For organic matter to accumulate, the rate of photosynthesis must exceed the rate of respiration. Organic compounds are broken down into methane (CH4) and CO2 through aerobic and anaerobic respiration, primarily driven by microbial activity . #### 4.3.2 Coupling with the nitrogen cycle The carbon cycle is closely linked with other nutrient cycles, particularly the nitrogen cycle. CO2 fixation is influenced by factors such as photosynthetic biomass and nitrogen availability, which can be a limiting nutrient. Large-scale biomass loss reduces CO2 fixation. High levels of organic carbon stimulate microbial nitrogen fixation (N2 to NH3), while low levels have the opposite effect. High ammonia levels stimulate CO2 fixation and nitrification but inhibit nitrogen fixation. High nitrate levels stimulate CO2 fixation and increase denitrification rates, which removes fixed nitrogen and negatively impacts CO2 fixation . #### 4.3.3 Methanogenesis In anoxic environments, methanogenesis, the biological production of methane, is a significant process carried out by archaea called methanogens. Most methanogens use CO2 as an electron acceptor in anaerobic respiration, reducing it to CH4 with H2 as the electron donor. Some methanogens can directly convert acetate into CH4 and CO2. For most organic compounds to be converted to CH4, methanogens must cooperate with other organisms that provide precursors . This multi-step process begins with the hydrolysis of complex organic molecules (polysaccharides, proteins, lipids, nucleic acids) into monomers by hydrolytic bacteria. For instance, cellulose is hydrolyzed to glucose by cellulolytic bacteria, then fermented into short-chain fatty acids (acetate, propionate, butyrate), alcohols (ethanol, butanol), H2, and CO2 by fermentative organisms. Hydrogen and acetate are directly used by methanogens, while other fatty acids and alcohols require further bacterial breakdown before methanogens can utilize them . ### 4.4 The nitrogen cycle Nitrogen is essential for life, forming amino acids, proteins, and nucleic acids. Plants can absorb inorganic nitrogen as ammonium (NH4+) and nitrate (NO3-), and organic nitrogen (amino acids). Animals rely solely on organic nitrogen sources, while bacteria can utilize all forms, including nitrite (NO2-). The atmosphere is the largest nitrogen reservoir, composed of about 80% nitrogen gas (N2). Other reservoirs include soil, sediments, water bodies, and biomass . Key processes in the nitrogen cycle include nitrification, denitrification, anammox, and nitrogen fixation . #### 4.4.1 Nitrogen fixation and denitrification Nitrogen gas (N2) is the most stable form of nitrogen and is fixed into usable forms by a limited number of bacteria and Archaea through nitrogen fixation. The reaction for nitrogen fixation is : $$ \text{N}_2 + 8 \text{H}^+ \rightarrow 2 \text{NH}_3 + \text{H}_2 $$ Fixed nitrogen, such as ammonia (NH3) or nitrate (NO3-), is crucial for organisms, and nitrogen-fixing bacteria make it available where it's scarce . Denitrification, or nitrate respiration, is the conversion of nitrate to nitrogen gas under anoxic conditions by denitrifying bacteria. The simplified reaction is : $$ \text{NO}_3^- \rightarrow \text{N}_2 $$ Denitrification can be beneficial, as seen in wastewater treatment where it reduces nutrient load, preventing algal blooms. However, it can also be detrimental in agricultural soils, leading to nitrogen loss from fertilized land under waterlogged conditions . The production of nitrous oxide (N2O) and nitric oxide (NO) during denitrification has significant environmental consequences. N2O is a potent greenhouse gas, contributing substantially to global warming. N2O can also be oxidized to NO in the atmosphere, leading to ozone depletion and acid rain, which alters soil pH and impacts microbial communities, soil fertility, plant diversity, and crop yields . #### 4.4.2 Ammonification and nitrification Ammonification is the release of ammonia from the breakdown of organic nitrogen compounds like amino acids and nucleotides. At neutral pH, ammonia exists as ammonium (NH4+). Much of this released NH4+ is rapidly recycled by plants and microorganisms . Nitrification is the oxidation of ammonia to nitrate (NO3-) and is crucial in well-drained, oxygenated soils at neutral pH, carried out by nitrifying bacteria and archaea. Nitrification consumes NH4+ and produces NO3-, a key plant nutrient. This process was historically considered to occur in two steps: ammonia oxidation to nitrite (NO2-) by bacteria like *Nitrosomonas*, and nitrite oxidation to nitrate by bacteria like *Nitrobacter*. However, some bacteria, such as *Nitrospira*, can oxidize ammonia directly to nitrate . #### 4.4.3 Anammox Anammox (anaerobic ammonium oxidation) is a process where ammonium can be oxidized under anoxic conditions. In this reaction, ammonia is anaerobically oxidized using NO2- as the electron acceptor, producing N2 as the final product. This metabolic shortcut is particularly valuable for wastewater treatment plants and is performed by specific types of bacteria . ### 4.5 Microbial processes Microbial processes are central to nutrient cycles and overall ecosystem function. Key processes include: * **Photosynthesis:** The process by which phototrophic organisms convert light energy into chemical energy, fixing CO2 into organic compounds . * **Respiration:** The metabolic process by which organisms break down organic compounds to release energy, often involving the consumption of oxygen (aerobic respiration) or other electron acceptors (anaerobic respiration), returning CO2 to the atmosphere . * **Methanogenesis:** The biological production of methane (CH4) from CO2 and H2 or acetate in anoxic environments, carried out by methanogenic archaea . * **Nitrification:** The aerobic oxidation of ammonia (NH3) to nitrite (NO2-) and then to nitrate (NO3-) by nitrifying bacteria and archaea . * **Denitrification:** The conversion of nitrate (NO3-) to nitrogen gas (N2) under anoxic conditions by denitrifying bacteria, often as an alternative to oxygen respiration . * **Ammonification:** The release of ammonia (NH3) from the decomposition of organic nitrogen compounds . * **Anammox:** The anaerobic oxidation of ammonia (NH3) to nitrogen gas (N2) using nitrite (NO2-) as an electron acceptor . --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |------|------------| | Primordial soup theory | A hypothesis suggesting that the early Earth's ocean was a solution of organic molecules from which life could arise, proposed independently by Oparin and Haldane. | | Miller experiment | An experiment conducted by Stanley Miller and Harold Urey in 1953 that simulated the early Earth's atmosphere and produced simple organic compounds, including amino acids, from inorganic molecules. | | Hydrothermal vents | Underwater volcanic openings, also known as black smokers, found in volcanically active areas and tectonic spreading zones, where minerals precipitate from heated water. | | Alkaline vents | Underwater sources with lower temperatures than hydrothermal vents and a high pH, formed by a chemical reaction between olivine and water, producing hydrogen gas. | | RNA world hypothesis | A theory proposing that the earliest form of life was based on RNA molecules, with DNA and proteins developing later. | | Protobionts | Abiotically produced molecules enclosed by a membrane-like structure, exhibiting some properties of life such as simple reproduction and maintaining a distinct internal chemical environment. | | Homeostasis | The ability of an organism to maintain a constant internal environment. | | Metabolism | The sum of biochemical processes involved in energy production and consumption within a cell, essential for activity, growth, and reproduction. | | Prokaryote | A single-celled organism that lacks a membrane-bound nucleus and other membrane-bound organelles, found in bacteria and archaea. | | Eukaryote | An organism whose cells contain a nucleus and other organelles enclosed within membranes, such as plants, animals, fungi, and protists. | | Endosymbiosis | A symbiotic relationship in which one organism lives inside another, with the theory suggesting that mitochondria and plastids originated from prokaryotes that were engulfed by larger cells. | | Peptidoglycan | A polymer composed of N-acetylglucosamine and N-acetylmuramic acid that forms the cell wall of most bacteria, providing structural rigidity. | | Gram-positive bacteria | Bacteria that have a thick peptidoglycan layer in their cell wall and retain the crystal violet stain during Gram staining, appearing purple. | | Gram-negative bacteria | Bacteria that have a thin peptidoglycan layer, an outer membrane, and a periplasmic space, appearing pink after Gram staining. | | Lipopolysaccharide (LPS) | A complex molecule found in the outer membrane of Gram-negative bacteria, consisting of a lipid component and a polysaccharide chain, contributing to the cell wall's strength and acting as an endotoxin. | | S-layer | A protein or glycoprotein layer that surrounds the cell wall of many bacteria and archaea, providing structural support and protection. | | Pili | Filamentous appendages on the surface of bacteria, involved in adhesion and genetic material transfer (conjugation). | | Fimbriae | Short, hair-like appendages on the surface of bacteria, primarily involved in adhesion to surfaces and other cells. | | Endospores | Highly differentiated, dormant structures produced by some bacteria (e.g., Bacillus, Clostridium) that are resistant to extreme environmental conditions and can germinate into vegetative cells when conditions are favorable. | | Flagella | Long, whip-like structures used by many bacteria and archaea for locomotion, enabling them to move through liquid environments. | | Archaella | Motility structures found in Archaea that are structurally and functionally similar to bacterial flagella but have different protein compositions and energy sources. | | Taxonomie | The science of classification and naming of organisms, organizing biodiversity into hierarchical groups based on shared characteristics. | | Phylogeny | The study of the evolutionary history and relationships among individuals or groups of organisms, often visualized through phylogenetic trees. | | Convergent evolution (Homoplasy) | The independent evolution of similar features in different lineages, typically as an adaptation to similar environmental pressures, not due to shared ancestry. | | Phylogenetic tree | A diagram that represents the evolutionary history and relationships among species or groups of organisms, illustrating hypothesized branching patterns from common ancestors. | | Cladistics | A method of classification of animals and plants according to the proportion of measurable characteristics that they have in common, used to determine their evolutionary relationships. | | Cladogram | A branching diagram showing the evolutionary relationships among a group of organisms, based on shared derived characteristics. | | Archaea | A domain of single-celled microorganisms that are prokaryotic in cell structure but differ biochemically and genetically from Bacteria and Eukarya, often found in extreme environments. | | Bacteria | A domain of single-celled microorganisms that are prokaryotic and widespread in various environments, encompassing a wide range of metabolic and functional capabilities. | | Proteobacteria | A large phylum of Gram-negative bacteria that includes many important groups, such as photoautotrophs, chemoautotrophs, and heterotrophs, including pathogens. | | Cyanobacteria | Photosynthetic bacteria that produce oxygen as a byproduct of photosynthesis and are believed to have played a key role in the oxygenation of Earth's atmosphere. | | Fungi | A kingdom of eukaryotic organisms that include yeasts, molds, and mushrooms, characterized by their cell walls made of chitin and their heterotrophic mode of nutrition, often acting as decomposers. | | Hyphae | The long, branching filamentous structures of a fungus, used to absorb nutrients and form mycelia. | | Mycelium | A network of hyphae forming the vegetative part of a fungus, often found in soil or on decaying organic matter. | | Conidia | Asexual spores produced by fungi, typically formed at the tips of hyphae and dispersed to colonize new environments. | | Ascospores | Spores produced within a sac-like structure called an ascus, a characteristic of Ascomycetes fungi, formed during sexual reproduction. | | Basidiospores | Spores produced on a club-shaped structure called a basidium, characteristic of Basidiomycetes fungi, formed during sexual reproduction. | | Plantae | A kingdom of eukaryotic organisms that include plants, characterized by their cell walls made of cellulose and their autotrophic mode of nutrition through photosynthesis. | | Tissues | Groups of specialized cells that perform specific functions, such as dermal, vascular, and ground tissues in plants. | | Xylem | Vascular tissue in plants that transports water and dissolved minerals from the roots to the rest of the plant and also provides physical support. | | Phloem | Vascular tissue in plants that transports sugars produced during photosynthesis from the leaves to other parts of the plant where they are needed for growth or storage. | | Parenchyma cells | Versatile plant cells involved in metabolic functions like photosynthesis and storage, capable of differentiating into other cell types. | | Collenchyma cells | Plant cells with thickened primary cell walls that provide flexible mechanical support to growing parts of the plant, such as young stems and petioles. | | Sclerenchyma cells | Plant cells with rigid secondary cell walls, often lignified, that provide strong structural support; these cells are typically dead at maturity. | | Protists | A diverse group of eukaryotic microorganisms that are not plants, animals, or fungi. They are typically unicellular but can be colonial or multicellular and exhibit a wide range of metabolic strategies. | | Excavata | A diverse group of protists, including diplomonads, parabasalids, and euglenoids, often found in anaerobic environments or aquatic habitats. | | SAR (Stramenopiles, Alveolata, Rhizaria) | A supergroup of protists characterized by specific genetic and morphological features, encompassing a vast diversity of unicellular and multicellular organisms. | | Algae | Photosynthetic eukaryotic organisms that range from unicellular to large multicellular forms, typically found in aquatic environments. | | Rhodophytes (Red algae) | A group of algae that contain chlorophyll a and phycobiliproteins, giving them a red or purplish hue, and are primarily marine. | | Chlorophytes (Green algae) | A group of algae that contain chlorophyll a and b, similar to plants, and are found in freshwater, marine, and terrestrial environments. | | Ecology | The scientific study of interactions among organisms and their environment, including biotic and abiotic factors. | | Microbiome | A community of microorganisms that inhabit a particular environment, such as the human gut or soil. | | Population | A group of individuals of the same species that live in the same area and interbreed. | | Community | An interacting group of various species in a common location. | | Ecosystem | A community of living organisms (biotic) interacting with their non-living physical environment (abiotic). | | Water activity (a_w) | A measure of the availability of water for microbial growth, defined as the ratio of the vapor pressure of air in equilibrium with a substance to the vapor pressure of pure water. | | Psychrophiles | Microorganisms that thrive at low temperatures, with optimal growth temperatures at or below 15°C. | | Mesophiles | Microorganisms that grow best at moderate temperatures, with optimal growth temperatures typically between 20°C and 45°C. | | Thermophiles | Microorganisms that thrive at high temperatures, with optimal growth temperatures between 45°C and 80°C. | | Hyperthermophiles | Microorganisms that thrive at extremely high temperatures, with optimal growth temperatures above 80°C. | | Acidophiles | Organisms that thrive in acidic environments, with optimal pH values typically below 5.5. | | Alkaliphiles | Organisms that thrive in alkaline environments, with optimal pH values typically above 8.0. | | Halophiles | Organisms that require high salt concentrations for growth, often found in saline environments like salt lakes or the ocean. | | Batch culture | A closed system where microorganisms are grown in a fixed volume of culture medium with limited nutrients and no replenishment. | | Growth curve | A graphical representation of the changes in population size of microorganisms over time in a culture, typically showing lag, exponential, stationary, and death phases. | | Lag phase | The initial phase of a microbial growth curve where microorganisms adapt to a new environment and show little to no growth. | | Exponential phase (Log phase) | The phase of microbial growth where the population increases exponentially at a constant rate due to rapid cell division. | | Stationary phase | The phase of microbial growth where the rate of cell division equals the rate of cell death, resulting in a stable population size. | | Death phase | The final phase of microbial growth where the rate of cell death exceeds the rate of cell division, leading to a decline in population size. | | Generation time | The time it takes for a microbial population to double in number through cell division. | | Turbidimetry | A method used to estimate the number of cells in a suspension by measuring the turbidity (cloudiness) caused by light scattering. | | Colony-forming units (CFU) | Units used to quantify the number of viable microorganisms in a sample, representing the number of colonies that grow on a solid medium. | | Aseptic technique | Practices performed under sterile conditions to prevent contamination by unwanted microorganisms. | | Nutrient cycling | The movement and transformation of essential elements (e.g., carbon, nitrogen, phosphorus) through ecosystems, involving both biotic and abiotic components. | | Photosynthesis | The process by which green plants and some bacteria use sunlight, water, and carbon dioxide to create their own food (glucose) and release oxygen. | | Respiration | The process by which organisms release energy from organic molecules, typically involving the consumption of oxygen and the production of carbon dioxide and water. | | Methanogenesis | The biological production of methane (CH$_4$), primarily carried out by methanogenic archaea in anaerobic environments. | | Nitrification | The biological oxidation of ammonia or ammonium to nitrite followed by the oxidation of the nitrites to nitrate, carried out by nitrifying bacteria and archaea. | | Denitrification | The process by which nitrate is reduced to gaseous nitrogen compounds, such as N$_2$O or N$_2$, typically under anaerobic conditions. |