chapter16 (broclk).docx

**Phylogenetic Diversity of *Bacteria*** 16 **Bacterial Diversity and Human Health** **Gut Microbes and Nutrient Conversion in Animals** - Animals, particularly herbivores (plant-eaters), have gut microbes that: - Convert ingested food into nutrients beneficial to the host an...

**Phylogenetic Diversity of *Bacteria*** 16 **Bacterial Diversity and Human Health** **Gut Microbes and Nutrient Conversion in Animals** - Animals, particularly herbivores (plant-eaters), have gut microbes that: - Convert ingested food into nutrients beneficial to the host animal. - Assist in breaking down complex plant components like lignin and cellulose, which are major components of plant cell walls. - Herbivorous animals: - Lack enzymes required to digest lignin and cellulose. - Have evolved specialized organs housing these microbes that perform these crucial digestive tasks. **The Human Colon and Its Microbial Population** - In humans: - The organ responsible for housing these gut microbes is the colon (large intestine). - The average human colon: - Contains hundreds of microbial species. - Hosts up to a hundred trillion microbial cells. - Many of these microbes belong to the order **Clostridiales** within the phylum **Firmicutes**. **Clostridiales: Key Microbial Players** - The Clostridiales group: - Consists of a highly diverse collection of gram-positive, anaerobic bacteria. - Employ a fermentative metabolism to break down nutrients. - Importance in gut function: - Changes in the abundance and diversity of Clostridiales can have significant consequences for human health. **Christensenella minuta: A Notable Clostridiales Member** - **Christensenella minuta**: - First identified in human feces. - Characteristics: - Strictly anaerobic. - Nonsporulating (does not form spores). - Nonmotile (does not move on its own). - Utilizes a fermentative metabolism: - Ferments sugars to produce short-chain fatty acids, hydrogen gas (H₂), and carbon dioxide (CO₂). - Interaction with Archaea: - Often found co-existing with methane-producing Archaea. - May engage in syntrophic relationships (mutually beneficial interactions) with H₂-consuming organisms. **The Role of Christensenellaceae in Gut Health** - Microbiome research indicates: - **C. minuta** and other members of the family **Christensenellaceae** are indicators of a healthy gut microbiome. - Health Implications: - **Christensenellaceae** are depleted in individuals suffering from: - Obesity. - Metabolic syndrome. - Inflammatory bowel disease (IBD). - Crohn's disease. - Ulcerative colitis. - Experimental Findings: - Introducing live **C. minuta** cells into mice leads to reduced body fat levels compared to control mice given heat-killed cells. - Genetic Influence: - The relative abundance of **Christensenellaceae** in the human gut is genetically influenced. - Up to 40% of the variation in their abundance is attributable to host genetics. **Key Insights into Gut Microbial Relationships** - The research highlights: - Our genes play a role in shaping our microbial relationships. - Gut microbes, in turn, have a significant influence on our health. - Understanding gut bacterial diversity is essential for a comprehensive understanding of gut health and overall well-being. **Shift in Focus: Phylogenetic Diversity of Microorganisms** **Previous Focus: Metabolic and Ecological Diversity of Microorganisms** - Earlier chapters concentrated on: - **Metabolic Diversity:** The different biochemical processes microorganisms use to obtain energy and carbon. - **Ecological Diversity:** The various ecosystems and interactions involving microorganisms. **Current and Upcoming Chapters: Phylogenetic Diversity** - In this chapter and the next two: - The focus shifts to **phylogenetic diversity**, emphasizing evolutionary lineages. - Section 15.1: - Discussed the distinctions between metabolic, ecological, and phylogenetic diversity. - The current chapter: - Examines the major lineages of **Bacteria**. - Figure 16.1a illustrates these bacterial lineages. - Upcoming chapters: - **Chapter 17:** Focuses on the **Archaea**. - **Chapter 18:** Focuses on **microbial Eukarya**. **Bacterial Phyla and 16S rRNA Gene Sequences** - **16S ribosomal RNA (rRNA) gene sequences**: - Retrieved from environmental samples, these sequences help identify bacterial phyla. - Sections 19.6 and 19.8 cover these sequences in more detail. - **Over 80 bacterial phyla** have been distinguished using these sequences. - However: - Only about 30 of these phyla contain species that have been characterized in laboratory cultures (Figure 16.1b). **Dominance of Cultivated Bacterial Genera and Species** - Among cultivated bacterial species: - More than **90%** belong to just four phyla: - **Proteobacteria** - **Actinobacteria** - **Firmicutes** - **Bacteroidetes** - Figure 16.1b highlights the overwhelming dominance of these four phyla. **The Vast Number of Bacterial Species Described** - More than **12,000 species of bacteria** have been described. - Due to this vast number, it is impossible to cover all species in this chapter. **Approach: Using Phylogenetic Trees to Explore Bacterial Diversity** - **Phylogenetic trees**: - Serve as tools to guide the discussion of bacterial diversity. - The chapter focuses on exploring well-known species from a broad range of phyla. **Selection of Bacterial Phyla for Exploration** - This chapter focuses on species from **20 bacterial phyla**. - Emphasis is placed on: - Phyla with the largest numbers of characterized species. - Species that represent the diversity within these phyla. **Beginning the Exploration: The Phylum Proteobacteria** - The chapter begins with: - **Proteobacteria**: - Described as a \"hotbed\" of cultured species within the domain Bacteria. - Proteobacteria is the first phylum explored due to its significant diversity and number of characterized species. - **I *Proteobacteria*** - T**he *Proteobacteria* are divided into six classes, the *Alpha*-,** - ***Beta*-, *Gamma*-, *Delta-*, *Epsilon-*, and *Zetaproteobacteria*.** - ***Proteobacteria* is the largest and most metabolically diverse** - **phylum of *Bacteria* and leads in numbers of cultivated and wellcharacterized** - **species.** **Proteobacteria: The Largest and Most Metabolically Diverse Phylum of Bacteria** **Overview and Significance** - **Proteobacteria**: - The largest and most metabolically diverse phylum of Bacteria (Figure 16.2). - Account for more than a third of all characterized bacterial species (Figure 16.1b). - Represent the majority of known bacteria with significant roles in: - Medicine. - Industry. - Agriculture. **Gram-Negative Nature** - All Proteobacteria are gram-negative bacteria. **Metabolic Diversity** - **Proteobacteria exhibit a vast range of energy-generating mechanisms**: - **Chemolithotrophic species**: Obtain energy by oxidizing inorganic compounds. - **Chemoorganotrophic species**: Obtain energy by oxidizing organic compounds. - **Phototrophic species**: Use light as an energy source (Figure 16.2). - Chapters 14 and 15: - Discussed the extensive metabolic and ecological diversity of Proteobacteria. - **Notable metabolic processes absent in Proteobacteria**: - **Methanogenesis**: Exclusive to Archaea (Section 17.2). - **Oxygenic phototrophy**: Exclusive to Cyanobacteria (Section 15.3). - **Anammox** (anaerobic ammonium oxidation): Found only in Planctomyces (Section 14.10). - **Complete ammonia oxidation (comammox)**: Found only in Nitrospirae (Section 16.21). - **Anaerobic methanotrophy**: Discussed in Section 14.16. **Oxygen Relationships** - Proteobacteria show wide variation in their relationship with oxygen: - **Anaerobic species**: Do not require oxygen for growth. - **Microaerophilic species**: Thrive in environments with low oxygen levels. - **Facultatively aerobic species**: Can grow with or without oxygen. **Morphological Diversity** - **Proteobacteria display extensive morphological diversity**: - **Cell shapes** include: - Straight rods. - Curved rods. - Cocci (spherical cells). - Spirilla (spiral-shaped cells). - Filamentous forms. - Budding forms. - Appendaged forms. - Section 1.3 and Figure 1.8 provide visual examples of these diverse cell morphologies.  **Microbial Systematics: Overview** - Importance of understanding the hierarchy in microbial systematics: - **Domain** (Bacteria or Archaea) - **Phylum** - **Class** - **Order** - **Family** - **Genus** - **Species** - These terms will be frequently referenced in the chapter.  **Proteobacteria Phylum: Classification** - Divided into six classes based on 16S rRNA gene sequences: - **Alphaproteobacteria** - **Betaproteobacteria** - **Gammaproteobacteria** - **Deltaproteobacteria** - **Epsilonproteobacteria** - **Zetaproteobacteria** - Unique as it contains only a single characterized species: - **Mariprofundus ferrooxydans**: A marine iron-oxidizing bacterium.  **Metabolic Similarities Across Classes** - Despite phylogenetic differences, species in different classes often share similar metabolisms: - **Phototrophy** and **methylotrophy** occur in three different classes of Proteobacteria. - **Nitrifying bacteria** are found across four different classes of Proteobacteria. - This phenomenon suggests: - **Horizontal gene flow** has significantly influenced the metabolic diversity within Proteobacteria.  **Divergence Between Phenotype and Phylogeny** - The sharing of metabolic traits across different classes of Proteobacteria indicates: - **Phenotype** and **phylogeny** often provide different perspectives on prokaryotic diversity. - Emphasizes the importance of understanding both aspects when studying microbial diversity.  **References to Previous Sections** - **Section 13.12** and **Table 13.1**: For understanding the hierarchy of microbial systematics. - **Section 15.14**: Discusses Mariprofundus ferrooxydans in detail. - **Chapter 9** and **Section 13.9**: Cover horizontal gene flow. - **Section 15.1**: Discusses the differences between phenotype and phylogeny in prokaryotic diversity. - **Figure 15.1**: Illustrates the spread of metabolic traits across different classes of Proteobacteria. **16.1 *Alphaproteobacteria***  **Alphaproteobacteria Overview** - Comprises approximately **one thousand described species**. - Represents the **second largest class** of Proteobacteria. - **Figure References**: - **Figure 16.1b**: Visual representation of the Alphaproteobacteria class. - **Figure 16.2**: Illustrates the functional diversity within the Alphaproteobacteria. - **Figure 15.1**: Previously referenced figure related to functional diversity across Proteobacteria classes.  **Functional Diversity** - Alphaproteobacteria exhibit **extensive functional diversity**. - Many genera within this class have been discussed in **Chapters 14 and 15**. - The species within this class display a range of metabolic capabilities.  **Metabolic Characteristics** - Majority of species are either: - **Obligate aerobes**: Require oxygen for growth. - **Facultative aerobes**: Can grow with or without oxygen. - Many species are **oligotrophic**: - Thrive in environments with **low nutrient concentrations**.  **Orders within Alphaproteobacteria** - There are **10 well-characterized orders** within this class. - The majority of species are classified under the following orders: - **Rhizobiales** - **Rickettsiales** - **Rhodobacterales** - **Rhodospirillales** - **Caulobacterales** - **Sphingomonadales** - **Figure 16.3** and **Table 16.1**: - Provide additional details on the distribution and characteristics of these orders. ***Rhizobiales*** **KEY GENERA: *Bartonella, Methylobacterium, Pelagibacter,*** ***Rhizobium, Agrobacterium***  **Rhizobiales Overview** - Largest and most **metabolically diverse** order of Alphaproteobacteria. - Contains various metabolic types, including: - **Phototrophs** (e.g., *Rhodopseudomonas*) - **Chemolithotrophs** (e.g., *Nitrobacter*) - **Symbionts** (e.g., rhizobia) - **Free-living nitrogen-fixing bacteria** (e.g., *Beijerinckia*) - **Pathogens** of plants and animals - Diverse **chemoorganotrophs**  **Rhizobia: Naming and Characteristics** - The order Rhizobiales is named after **rhizobia**: - A **polyphyletic** group of genera that form **root nodules** and **fix nitrogen** in symbiosis with leguminous plants. - Referenced in **Section 23.4** for additional details.  **Rhizobial Genera** - Rhizobiales includes **nine genera** that contain rhizobia: - *Bradyrhizobium* - *Ochrobactrum* - *Azorhizobium* - *Devosia* - *Methylobacterium* - *Mesorhizobium* - *Phyllobacterium* - *Sinorhizobium* - *Rhizobium* - Characteristics of rhizobia: - Typically **chemoorganotrophs** - **Obligate aerobes** - Capable of **forming root nodules** through genes distributed by **horizontal gene transfer**.  **Nodulation Genes and Horizontal Gene Transfer** - Nodulation genes are often located on **large plasmids**. - These plasmids can be transferred between cells, spreading the ability to form root nodules. - This horizontal gene transfer is further discussed in **Section 23.4**.  **Host Specificity** - Each rhizobial genus has a **distinct range of plant hosts** that it can colonize. - Detailed information on host specificity is provided in **Table 23.1**.  **Isolation of Rhizobia** - Rhizobia can be isolated by: - **Crushing root nodules** and spreading the contents on **nutrient-rich solid media**. - Rhizobial colonies typically produce **copious amounts of exopolysaccharide slime**, as illustrated in **Figure 16.4**.  **Figure and Section References** - **Figure 16.3**: Provides visual representation of the Rhizobiales order. - **Section 23.4**: Discusses rhizobia in detail, including nodulation and gene transfer. - **Table 23.1**: Details the distinct range of plant hosts for each rhizobial genus. - **Figure 16.4**: Illustrates the exopolysaccharide slime produced by rhizobial colonies.   **Agrobacterium tumefaciens (Rhizobium radiobacter)** - **Relatedness**: - Closely related to root nodule *Rhizobium* species. - **Pathogenic Nature**: - A plant pathogen that causes **crown gall disease**. - Detailed discussion in **Section 23.6**. - **Differences from Rhizobium**: - Unlike *Rhizobium*, *A. tumefaciens* is **unable to form root nodules**. - The genes responsible for gall formation are found on a **plasmid**. - These **pathogenicity genes** are unrelated to the plasmid-borne genes responsible for nodule formation in symbiotic rhizobia.  **Genus Methylobacterium** - One of the **largest genera** within the Rhizobiales. - **Nickname**: - Often called **\"pink-pigmented facultative methylotrophs\"**. - Named for the **pink color** of their colonies. - Capable of **growing well on methanol** as a carbon source. - Reference to **Section 15.15** for more details on their characteristics. - **Habitat**: - Commonly found on the **surface of plants**. - Present in **soils** and **freshwater systems**. - Frequently encountered in **toilets** and **baths**: - Grow on **shower curtains**, **caulk**, and **toilet bowls**. - Their growth results in the formation of **pink-pigmented biofilms**. - **Isolation Method**: - Species of *Methylobacterium* can be isolated by: - Pressing the surface of a plant leaf onto an **agar Petri plate**. - The plate should contain **methanol** as the sole carbon source to encourage growth.  **Genus Bartonella** - **Classification**: - Bartonella is a notable genus within the **Rhizobiales**. - These organisms were **previously classified with the Rickettsiales**. - They are **intracellular pathogens** of humans and other vertebrates.  **Diseases Caused by Bartonella Species** - Bartonella species can cause a **variety of diseases** in humans and other animals. - **Bartonella quintana**: - Causative agent of **trench fever**. - Trench fever is named because it decimated soldiers during **World War I** trench warfare. - Other Bartonella species can cause: - **Bartonellosis** - **Cat scratch disease** - A variety of **inflammatory diseases**  **Disease Transmission** - Diseases caused by Bartonella species are mediated by **arthropod vectors** including: - **Fleas** - **Lice** - **Sand flies** - Further discussion on this topic can be found in **Chapter 32**.  **Cultivation and Growth Characteristics** - Bartonella species are **fastidious** and **difficult to cultivate**. - **Isolation Method**: - Most commonly achieved using **blood agar**. - **Growth in Tissue Culture**: - When growing in tissue culture, Bartonella cells grow on the **outside surface** of the eukaryotic host cells. - They do not grow within the **cytoplasm** or the **nucleus** of the host cells.  **Genus Pelagibacter** - **Classification**: - Belongs to the order **Rhizobiales**.  **Species: Pelagibacter ubique** - **Metabolic Characteristics**: - An **oligotroph**: - Thrives in environments with low nutrient concentrations. - An **obligately aerobic chemoorganotroph**: - Requires oxygen for growth and obtains energy by oxidizing organic compounds. - **Habitat**: - Inhabits the **photic zone** of Earth's oceans. - The photic zone is the upper layer of water where sunlight penetrates, allowing photosynthesis.  **Abundance and Ecological Significance** - *Pelagibacter ubique* can constitute up to **25% of bacterial cells** found at the ocean's surface. - In **temperate waters** during the summer, its population can reach up to **50% of cells**. - Due to its high abundance, *Pelagibacter ubique* is likely the **most abundant bacterial species on Earth**. - Further details on this are provided in **Section 20.12**. ***Rickettsiales*** **KEY GENERA: *Rickettsia, Wolbachia***  **Rhizobiales Overview** - **Classification**: - Belongs to the order **Alphaproteobacteria**. - **Largest and most metabolically diverse** order within this class. - **Figure Reference**: - Refer to **Figure 16.3** for a visual representation of the Rhizobiales.  **Metabolic Diversity** - Contains various types of organisms, including: - **Phototrophs**: - Example: *Rhodopseudomonas*. - **Chemolithotrophs**: - Example: *Nitrobacter*. - **Symbionts**: - Example: **Rhizobia**. - Forms **root nodules** and **fixes nitrogen** in a symbiotic association with leguminous plants. - **Free-living nitrogen-fixing bacteria**: - Example: *Beijerinckia*. - **Pathogens**: - A few species are pathogens of plants and animals. - **Chemoorganotrophs**: - Contains diverse species with this metabolic capability.  **Rhizobia** - The name **Rhizobiales** is derived from **rhizobia**: - A **polyphyletic** collection of genera. - Known for forming **root nodules**. - Fix nitrogen in a **symbiotic association** with leguminous plants. - Further details on rhizobia can be found in **Section 23.4**.  **Rhizobiales Genera Containing Rhizobia** - **Nine Genera**: - *Bradyrhizobium* - *Ochrobactrum* - *Azorhizobium* - *Devosia* - *Methylobacterium* - *Mesorhizobium* - *Phyllobacterium* - *Sinorhizobium* - *Rhizobium* - **Metabolic Characteristics**: - These genera are typically **chemoorganotrophs**. - They are generally **obligate aerobes**. - **Nodulation Genes**: - The ability to form root nodules is conveyed by **genes distributed through horizontal gene transfer**. - **Nodulation genes** are located on **large plasmids** that can be transferred between cells. - Further discussion can be found in **Section 23.4**. - **Host Specificity**: - Each rhizobial genus has a **distinct range of plant hosts** it can colonize. - Detailed information is available in **Table 23.1**. - **Isolation of Rhizobia**: - Rhizobia can be isolated by: - **Crushing root nodules**. - Spreading the contents on **nutrient-rich solid media**. - Colonies typically produce **copious amounts of exopolysaccharide slime**. - Visual representation of this can be seen in **Figure 16.4**.  **Agrobacterium tumefaciens (Rhizobium radiobacter)** - **Relatedness**: - Closely related to root nodule *Rhizobium* species. - **Pathogenic Nature**: - A plant pathogen that causes **crown gall disease**. - Further discussion in **Section 23.6**. - **Differences from Rhizobium**: - *A. tumefaciens* is **unable to form root nodules**. - The genes responsible for gall formation are found on a **plasmid**. - These **pathogenicity genes** are unrelated to the plasmid-borne genes that mediate nodule formation in symbiotic rhizobia.  **Genus Methylobacterium** - **Classification**: - One of the largest genera within the **Rhizobiales**. - **Nicknamed**: - Referred to as **"pink-pigmented facultative methylotrophs"**. - Named for the **pink color** of their colonies. - Thrive on **methanol** as a carbon source. - Detailed discussion in **Section 15.15**. - **Habitat**: - Commonly found on the **surface of plants**. - Present in **soils** and **freshwater systems**. - Frequently encountered in **toilets** and **baths**: - Can grow on **shower curtains**, **caulk**, and **toilet bowls**. - Their growth results in the formation of **pink-pigmented biofilms**. - **Isolation Method**: - *Methylobacterium* species can be isolated by: - Pressing the surface of a **plant leaf** onto an **agar Petri plate** containing methanol as the sole carbon source.  **Genus Bartonella** - **Classification**: - Another notable genus within the **Rhizobiales**. - Previously classified with the **Rickettsiales**. - **Pathogenicity**: - Intracellular pathogens of **humans** and other **vertebrate animals**. - Can cause a variety of diseases, including: - **Trench fever** caused by *Bartonella quintana*. - Named for its impact on soldiers during **World War I** trench warfare. - **Bartonellosis**. - **Cat scratch disease**. - Various **inflammatory diseases**. - **Transmission**: - These diseases are mediated by **arthropod vectors** including: - **Fleas**. - **Lice**. - **Sand flies**. - Further discussion in **Chapter 32**. - **Cultivation**: - Species of *Bartonella* are **fastidious** and **difficult to cultivate**. - **Isolation Method**: - Most commonly achieved using **blood agar**. - **Growth in Tissue Culture**: - *Bartonella* cells grow on the **outside surface** of eukaryotic host cells. - They do not grow within the **cytoplasm** or **nucleus**.  **Genus Pelagibacter** - **Classification**: - Belongs to the order **Rhizobiales**. - **Species: Pelagibacter ubique** - **Metabolic Characteristics**: - An **oligotroph**: - Thrives in environments with low nutrient concentrations. - An **obligately aerobic chemoorganotroph**: - Requires oxygen for growth and obtains energy by oxidizing organic compounds. - **Habitat**: - Inhabits the **photic zone** of Earth's oceans. - The photic zone is the upper layer of water where sunlight penetrates, allowing photosynthesis. - **Abundance**: - *Pelagibacter ubique* can constitute up to **25% of bacterial cells** found at the ocean's surface. - In **temperate waters** during the summer, its population can reach up to **50% of cells**. - Due to its high abundance, *Pelagibacter ubique* is likely the **most abundant bacterial species on Earth**. - Further details can be found in **Section 20.12**. Close-up of a group of clear gelatinous bubbles Description automatically generated ***Rickettsiales*** **KEY GENERA: *Rickettsia, Wolbachia***  **Rickettsiales Overview:** - Rickettsiales are all obligate intracellular parasites or mutualists of animals. - These organisms have not yet been successfully cultivated outside of host cells. - They must be grown in environments such as: - Chicken eggs - Host cell tissue culture - Typically, Rickettsiales are closely associated with arthropods.  **Transmission and Association with Arthropods:** - Genera that cause disease, such as *Rickettsia* and *Ehrlichia*, are transmitted via arthropod bites. - Other genera, such as *Wolbachia*, are obligate parasites or mutualists of insects and other arthropods.  **Species of the Genus Rickettsia:** - *Rickettsia* species are the causative agents of several human diseases, including: - **Typhus**: Caused by *Rickettsia prowazekii*. - **Spotted fever rickettsiosis** (commonly known as Rocky Mountain spotted fever): Caused by *Rickettsia rickettsii*. - These organisms are closely associated with arthropod vectors and can be transmitted by: - Ticks - Fleas - Lice - Mites  **Metabolic Specialization of Rickettsias:** - Most rickettsias are metabolically specialized. - They can oxidize only specific amino acids: - Glutamate - Glutamine - They are unable to oxidize: - Glucose - Organic acids - Rickettsias are unable to synthesize certain metabolites and must obtain them from host cells.  **Survival and Transmission:** - Rickettsias do not survive long outside their hosts. - This limited survival ability may explain why they require transmission from animal to animal via arthropod vectors.   **Electron Micrographs of Rickettsial Cells:** - Thin sections of rickettsial cells observed under electron micrographs reveal a typical prokaryotic morphology. - The rickettsial cells include a cell wall (as depicted in Figure 16.5b).  **Host Cell Penetration by Rickettsial Cells:** - The penetration of a host cell by a rickettsial cell is an active process. - This process requires both the host and the parasite to be viable and metabolically active.  **Intracellular Multiplication of Rickettsial Cells:** - Once inside the host cell: - The rickettsial bacteria multiply primarily in the cytoplasm. - The bacteria continue replicating until the host cell becomes loaded with parasites (illustrated in Figure 16.5; Figures 32.6 and 32.7). - Eventually, the host cell bursts, liberating the bacterial cells.  **The Genus Wolbachia:** - *Wolbachia* species are intracellular parasites. - These parasites are found within many arthropods and some nematodes (as shown in Figure 16.6).  **Infection and Effects of Wolbachia:** - *Wolbachia* species infect an enormous diversity of insect species. - Between 10--70% of individual insects in a susceptible species carry *Wolbachia*. - *Wolbachia* species can exert several effects on their insect hosts, including: - **Inducing Parthenogenesis**: Development of unfertilized eggs. - **Killing of Males**: Selective elimination of male insects. - **Feminization**: Conversion of male insects into females.  **Impact on Host Evolution:** - Due to their ability to alter host reproduction, *Wolbachia* species have a significant impact on the evolution of their insect hosts (discussed in Section 23.7).  **Wolbachia pipientis Overview:** - *Wolbachia pipientis* is the best-studied species within the genus *Wolbachia*.  **Colonization and Multiplication in Insect Eggs:** - *W. pipientis* cells colonize the insect egg (as illustrated in Figure 16.6). - The bacteria multiply in vacuoles within host cells. - These vacuoles are surrounded by a membrane of host origin.  **Cell Wall and Peptidoglycan Characteristics:** - *W. pipientis* lacks a cell wall. - *W. pipientis* is unable to produce peptidoglycan. - Peptidoglycan can trigger host immune responses (refer to Chapter 26). - The loss of genes for peptidoglycan synthesis aids *W. pipientis*, an obligate intracellular organism, in escaping host immune detection.  **Transmission to Offspring:** - Cells of *W. pipientis* are transmitted from an infected female to her offspring via infected eggs.  **Wolbachia-Induced Parthenogenesis:** - *Wolbachia*-induced parthenogenesis occurs in several species of wasps. - In the normal reproductive cycle of these insects: - Unfertilized (haploid) eggs develop into males. - Fertilized (diploid) eggs develop into females. - However, *Wolbachia* infection causes a doubling of chromosome number in haploid eggs. - As a result, an infected mother can only lay female eggs containing her own DNA.  **Effect of Antibiotics on Parthenogenesis:** - If female insects infected with *Wolbachia* are fed antibiotics that kill the bacteria, parthenogenesis ceases.  **Other Groups of *Alphaproteobacteria*** **KEY GENERA: *Rhodobacter, Acetobacter, Caulobacter,*** ***Sphingomonas***  **Orders Rhodobacterales and Rhodospirillales:** - These orders contain metabolically diverse organisms, including: - **Purple Nonsulfur Bacteria**: - Examples: *Rhodobacter* and *Rhodospirillum* - Discussed in Section 15.5. - **Aerobic Anoxygenic Phototrophs**: - Example: *Roseobacter* - Discussed in Section 15.5. - **Nitrogen-Fixing Bacteria**: - Example: *Azospirillum* - Discussed in Section 15.9. - **Denitrifiers**: - Example: *Paracoccus* - Discussed in Section 15.10. - **Magnetotactic Bacteria**: - Example: *Magnetospirillum* - Discussed in Section 15.20. - These organisms represent a variety of metabolic functions and ecological roles.  **Order Caulobacterales:** - Typically oligotrophic and strictly aerobic chemoorganotrophs. - Species often form prosthecae or stalks (discussed in Section 15.18). - Many species display asymmetric forms of cell division. - **Characteristic Genus: Caulobacter** - *Caulobacter* has a characteristic life cycle, which has been discussed previously (in Sections 8.8 and 15.18).  **Order Sphingomonadales:** - Includes a diverse range of organisms: - **Aerobic and Facultatively Aerobic Chemoorganotrophs**. - **Aerobic Anoxygenic Phototrophs**: - Example: *Erythrobacter*. - **Obligate Anaerobes**. - **Characteristic Genus: Sphingomonas**: - *Sphingomonas* consists of obligately aerobic and nutritionally versatile species. - Widespread in aquatic and terrestrial environments. - Notable for their ability to metabolize a wide range of organic compounds, including: - Aromatic compounds that are common environmental contaminants, such as: - Toluene - Nonylphenol - Dibenzo-p-dioxin - Naphthalene - Anthracene - Due to their metabolic versatility, sphingomonads have been widely studied as potential agents of bioremediation (discussed in Sections 22.4 and 22.5). - Typically easy to cultivate and grow well on a variety of complex culture media. **16.2 *Betaproteobacteria*** With about 500 described species, the *Betaproteobacteria* are the third largest class of *Proteobacteria* (Figure 16.1). The *Betaproteobacteria* contain an immense amount of functional diversity (Figure 16.2 and ◀ Figure 15.1), and many species in this group have already been considered in Chapter 15. A total of six orders of *Betaproteobacteria* have many characterized species: *Burkholderiales*, *Hydrogenophilales*, *Methylophilales*, *Neisseriales*, *Nitrosomonadales*, and *Rhodocyclales* (**Figure 16.7**), and we focus on these here. ***Burkholderiales*** **KEY GENUS: *Burkholderia***  **Order Burkholderiales Overview:** - Contains species with a wide range of metabolic and ecological characteristics. - Species include: - **Strictly Aerobic Chemoorganotrophs**. - **Facultatively Aerobic Chemoorganotrophs**. - **Obligately Anaerobic Chemoorganotrophs**. - **Anoxygenic Phototrophs**. - **Obligate and Facultative Chemolithotrophs**. - **Free-living Nitrogen Fixers**. - **Pathogens of Plants, Animals, and Humans**.  **Genus Burkholderia:** - **Type Genus for Burkholderiales**: - *Burkholderia* is the type genus of the order Burkholderiales. - Includes diverse species of chemoorganotrophs with strictly respiratory metabolism. - **Metabolic Characteristics:** - All species can grow aerobically. - Some species can also grow anaerobically by using nitrate as the electron acceptor. - Many strains are capable of nitrogen fixation (N2 fixation). - **Metabolic Versatility:** - *Burkholderia* species exhibit metabolic versatility, particularly with respect to organic and aromatic compounds. - This versatility has led to interest in their potential use in bioremediation (discussed in Section 22.4). - **Plant Growth Promotion:** - Certain strains of *Burkholderia* have been shown to promote plant growth. - **Pathogenic Potential:** - Many species of *Burkholderia* are potentially pathogenic to plants or animals. - **Notable Pathogenic Species:** - *Burkholderia cepacia* is one of the best-known pathogenic species (illustrated in Figure 16.8).  **Burkholderia cepacia Overview:** - *B. cepacia* is primarily a soil bacterium. - Also functions as an opportunistic pathogen.  **Ecological Role and Plant Interaction:** - Commonly found in the rhizosphere of plants. - *B. cepacia* produces antifungal and anti-nematodal compounds. - Its ability to colonize plant roots can provide: - **Disease Protection**. - **Promotion of Plant Growth**. - Despite its beneficial aspects, *B. cepacia* is also known as a plant pathogen under certain conditions. - It is a major cause of soft rot in onions.  **Opportunistic Pathogen in Humans:** - *B. cepacia* has emerged as a significant opportunistic hospital-acquired infection. - Known for its resilience and difficulty to eradicate from clinical settings.  **Infections in Immunocompromised Patients:** - *B. cepacia* can cause secondary lung infections, particularly in: - Immunocompromised patients. - Patients with pneumonia. - Patients with cystic fibrosis. - *B. cepacia* is dangerous for cystic fibrosis patients due to: - Its ability to form biofilms in the lungs. - Its natural resistance to many antibiotics. - *B. cepacia* is particularly hazardous when combined with *Pseudomonas aeruginosa* for cystic fibrosis patients (refer to Section 8.10 and Section 20.4). ***Rhodocyclales*** **KEY GENERA: *Rhodocyclus, Zoogloea***  **Order Rhodocyclales Overview:** - Like the Burkholderiales, Rhodocyclales contains species with diverse metabolic and ecological characteristics.  **Type Genus: Rhodocyclus** - *Rhodocyclus* is the type genus for the Rhodocyclales. - *Rhodocyclus* is a purple nonsulfur bacterium (discussed in Section 15.5). - **Growth Characteristics:** - *Rhodocyclus* species grow best as photoheterotrophs. - Most species can also grow as photoautotrophs, using H₂ as an electron acceptor. - Additionally, species can grow by respiration in darkness. - **Habitat:** - Typically found in illuminated anoxic environments where organic matter is present.  **Genus Zoogloea:** - Another important genus within the Rhodocyclales. - *Zoogloea* species are aerobic chemoorganotrophs. - **Distinctive Characteristics:** - Known for producing a thick gelatinous capsule. - This capsule binds cells together into a complex matrix with branching, fingerlike projections. - The gelatinous matrix can cause flocculation, which is the formation of macroscopic particles that settle out of solution.  **Zoogloea ramigera:** - *Z. ramigera* is particularly important in aerobic wastewater treatment (discussed in Section 22.6). - **Role in Wastewater Treatment:** - Degrades much of the organic carbon in the waste stream. - Promotes flocculation and settling, which are crucial steps in water purification. ***Neisseriales*** **KEY GENERA: *Chromobacterium, Neisseria***  **Order Neisseriales Overview:** - Contains at least 29 genera of diverse chemoorganotrophs. - The best-characterized species are in the genera *Neisseria* and *Chromobacterium*.  **Genus Neisseria:** - Commonly isolated from animals. - Some species are pathogenic. - **Morphology:** - *Neisseria* species are always cocci (illustrated in Figure 16.9a). - **Ecological Roles:** - Some *Neisseria* species are free-living saprophytes. - Reside in the oral cavity and other moist areas on the animal body. - **Pathogenic Species:** - **Neisseria meningitidis**: - Causes meningitis, a potentially fatal inflammation of the membranes lining the brain (discussed in Section 31.5). - **Neisseria gonorrhoeae**: - The causative agent of the sexually transmitted disease gonorrhea. - Discussed in detail in Section 31.5 (clinical microbiology) and Section 31.13 (pathogenesis of gonorrhea).  **Genus Chromobacterium:** - A close phylogenetic relative of *Neisseria*. - **Morphology:** - *Chromobacterium* is rod-shaped. - **Best-Known Species:** - **Chromobacterium violaceum**: - Purple-pigmented organism (illustrated in Figure 16.9b). - Found in soil and water. - Occasionally found in pus-forming wounds of humans and other animals. - **Pigment Production:** - Produces the purple pigment violacein (illustrated in Figure 16.9b). - Violacein is a water-insoluble pigment with antimicrobial and antioxidant properties. - **Metabolic Characteristics:** - *Chromobacterium* is a facultative aerobe. - Grows fermentatively on sugars. - Grows aerobically on various carbon sources. **Hydrogenophilales, *Methylophilales*,** **and *Nitrosomonadales*** **KEY GENERA: *Hydrogenophilus, Thiobacillus, Methylophilus,*** ***Nitrosomonas*** **General Metabolic Capabilities of the Three Orders** - These three orders contain organisms with specialized metabolic capabilities: - **Chemolithotrophs** (organisms that obtain energy by oxidizing inorganic compounds). - **Methylotrophs** (organisms that utilize one-carbon compounds, such as methanol, as carbon and energy sources). - **Most species are obligate aerobes** (require oxygen to survive). - **Many species are autotrophic** (capable of fixing carbon dioxide as a carbon source). **Order 1: Hydrogenophilales** - **Species: Hydrogenophilus thermoluteolus** - **Obligate aerobe**: - Requires oxygen for survival. - Capable of growing as a **chemolithotroph**: - Uses **H₂ as an electron donor** for respiration. - Engages the **Calvin cycle** to fix CO₂. - **Facultative chemolithotroph**: - Can also grow as a **chemoorganotroph** on simple carbon sources. - **Genus: Thiobacillus** - Metabolic Versatility: - Includes species that can function as **chemoorganotrophs** or **chemolithotrophs**. - **Chemolithotrophic Species**: - These species are **sulfur bacteria**: - Oxidize **reduced sulfur compounds** as electron donors. - Use either **aerobic respiration** or **denitrification** as energy-yielding processes. - **Relevant Sections**: - Details on sulfur bacteria: **Section 14.7** and **Section 15.12**. - Details on denitrification: **Section 14.11** and **Section 15.10**. - **CO₂ Fixation**: - Capable of fixing CO₂ using the **Calvin cycle**. - **Habitats**: - Commonly found in: - **Soils**. - **Sulfur springs**. - **Marine habitats**. - Other environments where **reduced sulfur compounds** are available. **Order 2: Methylophilales** - **Genus: Methylophilus** - **Methylotrophs**: - Includes species that are **obligate** and **facultative methylotrophs**. - Can grow on **methanol** and other **C₁ compounds**. - **Note**: These species do **not** grow on **CH₄** (methane). - **Facultative Species**: - Capable of growing as **chemoorganotrophs**: - Rely on **aerobic respiration** of simple sugars. - **Relevant Section**: - Details on methylotrophy: **Section 14.16**. **Order 3: Nitrosomonadales** - Contains metabolically specialized organisms that are **obligately chemolithotrophic**. - Specialize in **ammonia oxidation**. - **Key Genera**: - **Nitrosomonas**. - **Nitrosospira**. - **Relevant Section**: - Details on ammonia-oxidizing bacteria: **Section 15.10**. - **16.3 *Gammaproteobacteria:*** - ***Enterobacteriales*** - **KEY GENERA: *Enterobacter, Escherichia, Klebsiella, Proteus,*** - ***Salmonella, Serratia, Shigella*** **Overview of Gammaproteobacteria:** - The **Gammaproteobacteria** are: - The **largest and most diverse class** of Proteobacteria. - Contain **nearly half of all characterized species** in the phylum. - Include **more than 1500 characterized species**. - Comprise **at least 15 well-characterized orders** (Figure 16.10, Figure 16.1b). - **Metabolic and Ecological Characteristics**: - Species exhibit **diverse metabolic and ecological traits** (Figure 16.2 and Figure 15.1). - Includes many **well-known human pathogens**. - Species can be: - **Phototrophic** (including **purple sulfur bacteria**, see Section 15.4). - **Chemoorganotrophic**. - **Chemolithotrophic**. - Can have either: - **Respiratory metabolism**. - **Fermentative metabolism**. - **Laboratory Growth**: - Members often grow rapidly in laboratory media. - **Habitat Diversity**: - Can be isolated from a wide range of habitats. - **Focus on Enterobacteriales**: - One of the **largest and best-known orders** within the Gammaproteobacteria. **Enterobacteriales (Enteric Bacteria):** - **Homogeneous Phylogenetic Group**: - A **relatively homogeneous group** within the Gammaproteobacteria. - **General Characteristics**: - **Facultatively aerobic**. - **Gram-negative**. - **Nonsporulating rods**. - Can be either: - **Nonmotile**. - **Motile by peritrichous flagella** (Figure 16.11). - **Diagnostic Tests**: - Common assays used to characterize bacteria include: - **Oxidase Test**: - Assays for the presence of **cytochrome c oxidase** (an enzyme present in many respiring bacteria). - See Section 29.3 and Figure 29.6 for more details. - **Catalase Test**: - Assays for the enzyme **catalase**, which detoxifies hydrogen peroxide. - Catalase is commonly found in bacteria able to grow in the presence of oxygen. - See Section 4.16 and Figure 4.32 for more details. - **Enteric Bacteria**: - **Oxidase-negative**. - **Catalase-positive**. - **Metabolic Traits**: - Produce **acid from glucose**. - **Reduce nitrate**, but only to nitrite. - Have **relatively simple nutritional requirements**. - **Ferment sugars** to a variety of end products. **Pathogenic and Industrial Importance:** - **Pathogenic Species**: - Include many species pathogenic to: - Humans. - Other animals. - Plants. - **Escherichia coli (E. coli)**: - The **best-known organism** among enteric bacteria. - Serves as the **classic example of an enteric bacterium**. - **Characterization and Identification**: - Due to the medical importance of many enteric bacteria: - **Extremely large numbers** have been characterized. - **Numerous genera and species have been defined** for ease of identification in clinical microbiology. - **Genetic Similarity**: - Despite the large number of species, enteric bacteria are **genetically very closely related**. - This close genetic relationship often presents challenges in positive identification. - **Identification Techniques**: - In clinical laboratories, identification typically involves: - **Combined analysis of numerous diagnostic tests**. - Use of **miniaturized rapid diagnostic media kits**. - Integration of **immunological and genomic analyses** to identify signature proteins or genes specific to particular species (see Chapter 29). **Fermentation Patterns in Enteric Bacteria** **Taxonomic Characteristic: Type and Proportion of Fermentation Products** - **Primary Basis for Differentiation Among Genera of Enteric Bacteria**: - The type and proportion of fermentation products generated from the fermentation of glucose. - **Two Broad Patterns of Fermentation**: - **Mixed-Acid Fermentation**. - **2,3-Butanediol Fermentation** (Figure 16.12). **Mixed-Acid Fermentation** - **Major Fermentation Products**: - Significant amounts of: - **Acetic acid**. - **Lactic acid**. - **Succinic acid**. - Additionally produces: - **Ethanol**. - **CO₂**. - **H₂**. - **Does not produce butanediol**. - **Gas Production**: - Equal amounts of **CO₂** and **H₂** are produced. - **Reaction Mechanism**: - CO₂ production results from formic acid via the enzyme **formate hydrogenlyase**: - **Reaction**: HCOOH → H₂ + CO₂. - This reaction leads to the production of equal amounts of CO₂ and H₂. - **Bacterial Genera Exhibiting Mixed-Acid Fermentation**: - **Escherichia**. - **Salmonella**. - **Shigella**. - **Citrobacter**. - **Proteus**. - **Yersinia**. **2,3-Butanediol Fermentation** - **Major Fermentation Products**: - Smaller amounts of acids. - Main products include: - **Butanediol**. - **Ethanol**. - **CO₂**. - **H₂** (Figure 14.45). - **Gas Production**: - Considerably more **CO₂** than **H₂** is produced. - **Reaction Mechanism**: - Like mixed-acid fermenters, butanediol fermenters produce CO₂ and H₂ from formic acid. - Additionally, they produce two extra molecules of CO₂ during the formation of each molecule of butanediol (Figure 16.12b). - **Bacterial Genera Exhibiting Butanediol Fermentation**: - **Enterobacter**. - **Klebsiella**. - **Erwinia**. - **Serratia**.  **Mixed-Acid Fermenters: *Escherichia*, *Salmonella*,** ***Shigella*, and *Proteus*** **Species of Escherichia:** - **Habitat**: - Almost universal inhabitants of the **intestinal tract of humans** and other **warm-blooded animals**. - **Not the dominant organisms** in this habitat. - **Nutritional Role**: - May play a role in the **intestinal tract by synthesizing vitamins**, particularly **vitamin K**. - **Facultative Aerobe**: - Likely helps **consume O₂**, rendering the large intestine **anoxic**. - **Wild-Type Escherichia Strains**: - **Rarely show any growth-factor requirements**. - Able to grow on a wide variety of **carbon and energy sources**: - **Sugars**. - **Amino acids**. - **Organic acids**. **Pathogenicity and Health Implications:** - **Diarrheal Diseases**: - Some strains of Escherichia are **pathogenic** and are implicated in **diarrheal diseases**. - Diarrheal diseases are especially significant in **infants**. - These diseases are a **major public health problem in developing countries** (Sections 33.1, 33.2, 33.7, and 33.11). - **Urinary Tract Infections**: - Escherichia is a **major cause of urinary tract infections** in women. - **Enteropathogenic E. coli Strains**: - **Increasingly implicated** in **gastrointestinal infections** and **generalized fevers**. - **Enterohemorrhagic E. coli**: - Notable representative: **Strain O157** - Causes **sporadic outbreaks of severe foodborne disease**. - **Infection Sources**: - Infection primarily occurs through consumption of **contaminated foods**: - **Raw or undercooked ground beef**. - **Unpasteurized milk**. - **Contaminated water**. - **Life-Threatening Complication**: - In a small percentage of cases, **E. coli O157** **Relationship Between Salmonella and Escherichia:** - **Close Genetic Relationship**: - Salmonella and Escherichia are **closely related species**. - **Pathogenicity of Salmonella**: - **Contrasting with Escherichia**, Salmonella species are **almost always pathogenic**: - Pathogenic to **humans** and other **warm-blooded animals**. - Also found in the intestines of **cold-blooded animals** like turtles and lizards. - **Common Human Diseases Caused by Salmonella**: - **Typhoid fever**. - **Gastroenteritis** (Sections 33.5 and 33.10). **Relationship Between Shigella and Escherichia:** - **Close Genetic Relationship**: - Shigella is **genetically very closely related** to Escherichia. - **Horizontal Gene Transfer**: - Genomic analyses suggest **significant gene exchange** between Shigella and Escherichia through **horizontal gene flow**. - **Pathogenicity of Shigella**: - Unlike most Escherichia species, Shigella species are typically **pathogenic to humans**. - Causes severe gastroenteritis known as **bacillary dysentery**. - **Example: Shigella dysenteriae**: - Transmitted through **food- and waterborne routes**. - The bacterium contains **endotoxin** and invades **intestinal epithelial cells**. - Excretes a **neurotoxin** that leads to acute gastrointestinal distress. **Genus Proteus:** - **Motility and Enzyme Production**: - Proteus species typically contain **highly motile cells** (Figure 16.13). - Produce the enzyme **urease**. - **Distant Relationship to Escherichia**: - Unlike Salmonella and Shigella, Proteus shows only a **distant genetic relationship** to Escherichia. - **Pathogenicity and Human Infections**: - Proteus is a frequent cause of **urinary tract infections in humans**. - Benefits from its ability to **degrade urea** via urease. - **Swarming Phenotype on Agar Plates**: - Colonies often exhibit a **characteristic swarming phenotype** (Figure 16.13b). - **Motility Pattern**: - Cells at the edge of the growing colony are **more rapidly motile** than those in the center. - The edge cells move away in a mass, then **reduce motility**, settle down, and divide. - This forms a new population of motile cells that again **swarm**. - **Mature Colony Appearance**: - Appears as **concentric rings** with alternating higher and lower cell concentrations (Figure 16.13b). A diagram of different types of fermentation Description automatically generated **Butanediol Fermenters: *Enterobacter*,** ***Klebsiella*, and *Serratia*** **Genetic and Physiological Relationships** - **Butanediol Fermenters:** - Genetically more closely related to each other than to mixed-acid fermenters. - This relationship aligns with observed physiological differences (refer to Figure 16.12). **Enterobacter Genus** - **Enterobacter aerogenes:** - Commonly found in: - Water - Sewage - Intestinal tract of warm-blooded animals - Occasional cause of urinary tract infections. **Klebsiella Genus** - **Klebsiella pneumoniae:** - Occasional cause of pneumonia in humans. - Most Klebsiella species are commonly found in: - Soil - Water - **Nitrogen Fixation:** - Most strains of Klebsiella can fix nitrogen. - This property is not characteristic of other enteric bacteria. - Relevant sections for nitrogen fixation: Section 3.12 and Section 15.9. **Serratia Genus** - **Pigment Production:** - Produces red pyrrole-containing pigments called **prodigiosins**. - **Prodigiosin Characteristics:** - Formed during stationary phase as a secondary metabolite. - Contains a pyrrole ring, similar to pigments involved in energy transfer: - Porphyrins - Chlorophylls - Bacteriochlorophylls - Phycobilins - Relevant sections for energy transfer pigments: Section 14.3--14.5. - The exact function of prodigiosin is unknown. - Unclear if prodigiosin plays a role in energy transfer. - **Habitat and Occurrence:** - Species of Serratia can be isolated from: - Water - Soil - Gut of various insects and vertebrates - Occasionally found in the intestines of humans. - **Serratia marcescens:** - Human pathogen. - Can cause infections in multiple body sites. - Implicated in infections related to invasive medical procedures. - Occasionally contaminates intravenous fluids. A close-up of a petri dish Description automatically generated **16.4 *Gammaproteobacteria:*** ***Pseudomonadales* and *Vibrionales*** **KEY GENERA: *Aliivibrio, Pseudomonas, Vibrio*** The phylogenetic and metabolic diversity of the *Gammaproteobacteria* is remarkable (Figure 16.2 and ◀ Figure 15.1), making it difficult to select any particular species as characteristic of the class. We focus here on the *Pseudomonadales* and *Vibrionales*, since these groups (along with the *Enterobacteriales*) represent some of the most commonly encountered orders of *Gammaproteobacteria* (Figure 16.10). ***Pseudomonadales*** **Pseudomonadales Overview** - **Classification and Metabolism:** - The order **Pseudomonadales** contains exclusively chemoorganotrophs. - All species carry out respiratory metabolisms. - Species characteristics: - Can grow aerobically. - Typically oxidase- and catalase-positive. - Some species are capable of anaerobic respiration using nitrate as the electron acceptor. - **Carbon and Energy Sources:** - Most species can utilize a wide diversity of organic compounds as sources of carbon and energy for growth. - **Habitat and Ubiquity:** - These organisms are ubiquitous in soil and aquatic systems. - **Diseases and Pathogenicity:** - Many species cause diseases in plants and animals, including humans. - **Terminology:** - The term **pseudomonad** is often used to describe any: - Gram-negative - Polarly flagellated - Aerobic rod - Capable of using diverse carbon sources. - Pseudomonads can be found in several different groups of Proteobacteria. - The current focus is only on those organisms within the order **Pseudomonadales**. - The type genus for this order is **Pseudomonas**. **Pseudomonas Genus** - **Pathogenic Species:** - Several species of **Pseudomonas** are pathogenic. - **Pseudomonas aeruginosa:** - Frequently associated with infections of the urinary and respiratory tracts in humans. - Not an obligate pathogen but an opportunist. - Initiates infections in individuals with weakened immune systems. - Serves as a model organism for studying the development of microbial biofilms (refer to Sections 4.9 and 8.10). - **Pseudomonas aeruginosa and Nosocomial Infections:** - Due to its ability to readily colonize surfaces, it is a common cause of hospital-acquired (nosocomial) infections. - Common sources of nosocomial infections include: - Catheterizations - Tracheostomies - Lumbar punctures - Intravenous infusions. - **Pseudomonas aeruginosa and Vulnerable Patient Populations:** - Common pathogen in patients receiving treatment for severe burns or other traumatic skin damage. - Often infects patients undergoing prolonged treatment with immunosuppressive agents. - Frequently colonizes the lungs of individuals with cystic fibrosis. - **Pseudomonas aeruginosa and Systemic Infections:** - Can cause systemic infections, especially in individuals with extensive skin damage. **Pseudomonas aeruginosa: Antibiotic Resistance** - **Natural Resistance:** - P. aeruginosa is naturally resistant to many widely used antibiotics, making treatment of infections challenging. - **Resistance Mechanism:** - **Resistance Transfer Plasmid (R Plasmid):** - The resistance is typically due to an R plasmid. - Relevant sections: Section 6.2 and Section 28.7. - **Function of R Plasmid:** - The plasmid's genes encode proteins that: - Detoxify various antibiotics. - Pump antibiotics out of the cell. - **Enhanced Resistance:** - **Biofilm Growth:** - Resistance to antibiotics is further enhanced by the growth of P. aeruginosa in biofilms. - Relevant section: Section 8.10. - **Treatment Options:** - **Polymyxin:** - An antibiotic effective against P. aeruginosa. - Not ordinarily used in human therapy due to its toxicity. - Reserved for use in critical medical situations. **Pseudomonas as Plant Pathogens (Phytopathogens)** - **Notable Species:** - Certain species of Pseudomonas, such as **Pseudomonas syringae**, are well-known plant pathogens (phytopathogens). - **Habitat and Transmission:** - Phytopathogens often inhabit nonhost plants where disease symptoms are inapparent. - These nonhost plants serve as reservoirs from which the pathogen can be transmitted to host plants, initiating infection. - **Disease Symptoms:** - Disease symptoms vary considerably depending on the specific phytopathogen and host plant. - **Pathogen Activity:** - The pathogen releases various substances that destroy or distort plant tissue, releasing nutrients for the bacterium to use: - Plant toxins - Lytic enzymes - Plant growth factors - Other substances - **Disease Identification:** - In many cases, the disease symptoms help identify the specific phytopathogen. - **Examples:** - **Pseudomonas syringae:** - Typically isolated from leaves showing chlorotic (yellowing) lesions. - **Pseudomonas marginalis:** - A "soft-rot" pathogen. - Infects stems and shoots, but rarely infects leaves. ***Vibrionales*** **Vibrionales Overview** - **Classification and Metabolism:** - The order **Vibrionales** includes facultatively aerobic rods and curved rods. - These bacteria employ a fermentative metabolism. - **Key Differences with Other Bacteria:** - **Vibrio Group vs. Enteric Bacteria:** - **Vibrio:** Oxidase-positive. - **Enteric Bacteria:** Oxidase-negative. - **Vibrio vs. Pseudomonas Species:** - **Vibrio:** Oxidase-positive and fermentative. - **Pseudomonas:** Oxidase-positive but non-fermentative. - **Notable Genera:** - The best-known genera in this group are: - **Vibrio** - **Aliivibrio** - **Photobacterium** - Several species within these genera are bioluminescent (refer to Section 23.10). **Habitat and Distribution** - **Aquatic Habitats:** - Most vibrios and related bacteria are aquatic. - Found in: - Marine habitats - Brackish water - Freshwater environments **Pathogenic Species and Human Health** - **Vibrio cholerae:** - **Disease:** Causes cholera in humans. - **Transmission:** - Cholera is one of the most common infectious diseases in developing countries. - Transmitted almost exclusively via water. - **Host Specificity:** Does not normally cause disease in other hosts. - Relevant sections: Section 30.8 and Section 33.3. - **Vibrio parahaemolyticus:** - **Habitat:** Inhabits the marine environment. - **Disease:** - Major cause of gastroenteritis in Japan, where raw fish is widely consumed. - Also implicated in outbreaks of gastroenteritis in other parts of the world, including the United States. - **Isolation Sources:** - Can be isolated from seawater, shellfish, and crustaceans. - **Primary Habitat:** Likely marine animals, with humans being an accidental host. **16.5 *Deltaproteobacteria* and** ***Epsilonproteobacteria*** These classes of *Proteobacteria* contain fewer species and less functional diversity than we have encountered in the *Alpha*-*, Beta*-, and *Gammaproteobacteria* (Figure 16.2 and ◀ Figure 15.1). The *Deltaproteobacteria* are primarily sulfate- and sulfur-reducing bacteria (◀ Sections 14.12, 15.11), dissimilative iron-reducers (◀ Section 15.13), and bacterial predators (◀ Section 15.16). *Epsilonproteobacteria*, by contrast, contain many species that oxidize the H2S produced by the sulfate and sulfur reducers (◀ Sections 14.7, 15.12). The final class of *Proteobacteria*, the *Zetaproteobacteria*, contains only one characterized species (the iron oxidizer *Mariprofundus ferrooxydans*)and was considered earlier (◀ Section 15.14). ***Deltaproteobacteria*** **KEY GENERA: *Bdellovibrio, Myxococcus, Desulfovibrio,*** ***Geobacter, Syntrophobacter*** **Overview of Deltaproteobacteria** - **Characterized Orders:** - Eight orders within the Deltaproteobacteria have been well characterized (refer to Figure 16.16). **Notable Bacterial Predators** - **Myxococcales and Bdellovibrionales:** - These orders contain notable genera of bacterial predators. - Relevant section: Section 15.16. **Metal- and Sulfur-Reducing Genera** - **Desulfuromonadales:** - Contains diverse species of metal- and sulfur-reducing genera, such as **Geobacter**. - Relevant sections: Section 14.13 and Section 15.13. - Like other genera in the Deltaproteobacteria, many are associated with the reduction of sulfur compounds. **Sulfate-Reducing Orders** - **Desulfovibrionales:** - The largest and most common order containing sulfate reducers. - **Habitat:** - These organisms are readily cultivated from marine sediments and nutrient-rich anoxic environments that contain sulfate. - **Metabolic Characteristics:** - Typically incomplete oxidizers. - Relevant section: Section 15.11. - All species use sulfate as the terminal electron acceptor. - Require small organic compounds, such as lactate, as a source of carbon and energy for growth. - **Desulfobacterales and Desulfarculales:** - These orders also typically reduce sulfate. - **Oxidation Capabilities:** - In contrast to Desulfovibrionales, species in these orders can be either complete or incomplete acetate oxidizers. - Relevant section: Section 15.11. - **Additional Reduction Capabilities:** - In addition to sulfate, some species in these orders can reduce: - Sulfite - Thiosulfate - Nitrate - **Fermentation:** - Some species are also capable of certain types of fermentation. **Syntrophobacterales Overview** - **Sulfate Reduction:** - The Syntrophobacterales is the final order containing sulfate reducers within the Deltaproteobacteria. - **Species Variability:** - Some, but not all, species of Syntrophobacterales are able to reduce sulfate. **Syntrophy and Metabolic Partnerships** - **Primary Interaction:** - In nature, species of Syntrophobacterales primarily interact with hydrogen (H₂)-consuming bacteria in a metabolic partnership known as syntrophy. - Relevant section: Section 14.22. - **Example of Syntrophic Species:** - **Syntrophobacter wolinii:** - **Propionate Oxidation:** - Oxidizes propionate, producing: - Acetate - CO₂ - H₂ - Such growth is only possible when an H₂-consuming partner is present. - **Sulfate Reduction:** - If sulfate is present, S. wolinii can grow as a sulfate reducer without needing a partner. - **Fermentation Capabilities:** - S. wolinii can also grow independently (without a partner) by fermenting: - Pyruvate - Fumarate - Malate ***Epsilonproteobacteria*** **KEY GENERA: *Campylobacter, Helicobacter*** **Epsilonproteobacteria Overview** - **Initial Definition:** - Epsilonproteobacteria were initially defined by pathogenic species within the genera **Campylobacter** and **Helicobacter**. - Relevant reference: Figure 16.16. - **Pathogenic Species:** - **Campylobacter** and **Helicobacter** are the best-characterized species within this phylum. - **Environmental Diversity:** - **Marine and Terrestrial Habitats:** - Environmental studies have revealed a wide diversity of Epsilonproteobacteria in various marine and terrestrial microbial habitats. - **Sulfur Metabolism:** - **Sulfur Compound Metabolism:** - Nearly all environmental Epsilonproteobacteria metabolize sulfur compounds in some manner. - **Common Metabolic Traits:** - **Chemolithotrophy and Autotrophy:** - Many Epsilonproteobacteria are chemolithotrophs and autotrophs. - **Associations with Hosts:** - **Pathogens and Symbionts:** - Many Epsilonproteobacteria are associated with hosts, functioning either as pathogens or symbionts. ***Campylobacter* and *Helicobacter*** **Shared Characteristics of Campylobacter and Helicobacter (Epsilonproteobacteria)** - **Gram-Negative:** - Both **Campylobacter** and **Helicobacter** species are gram-negative bacteria. - **Oxidase and Catalase Positive:** - These genera are oxidase-positive and catalase-positive. - **Motility:** - Both are motile spirilla. - **Pathogenicity:** - Most species within these genera are pathogenic to humans or other animals. - **Microaerophilic Nature:** - These organisms are microaerophilic, meaning they require low oxygen levels to grow. - Relevant section: Section 4.16. - **Culturing Conditions:** - Must be cultured from clinical specimens at: - Low oxygen levels (3--15% O₂). - High carbon dioxide levels (3--10% CO₂). **Campylobacter Species** - **Species Diversity:** - Over a dozen species of **Campylobacter** have been described. - **Disease Caused:** - **Campylobacter** species cause acute gastroenteritis. - **Symptoms:** - The gastroenteritis typically results in bloody diarrhea. - **Pathogenesis:** - Pathogenesis is due to several factors, including: - An enterotoxin related to cholera toxin. **Helicobacter pylori** - **Pathogenicity:** - **Helicobacter pylori** is a pathogen known to cause both chronic and acute gastritis. - **Disease Progression:** - The gastritis caused by **H. pylori** can lead to the formation of peptic ulcers. - **Further Details:** - Diseases caused by **Helicobacter pylori**, including modes of transmission and clinical symptoms, are discussed in more detail in Section 31.10. **Sulfur-Metabolizing *Epsilonproteobacteria*** **Ubiquity of Epsilonproteobacteria in the Environment** - **Recognition Through Environmental Studies:** - Species of Epsilonproteobacteria are recognized as ubiquitous in marine and terrestrial environments. - Discovery aided by environmental sequencing studies and ongoing cultivation efforts. - Relevant sections: Sections 19.6 and 19.8. **Abundance in Sulfur-Cycling Environments** - **Sulfur-Rich Habitats:** - Epsilonproteobacteria are particularly abundant in environments where sulfur-cycling activities are prominent. - **Key Habitats:** - Deep-sea hydrothermal vent habitats. - Marine sediments where sulfide-rich and oxygenated waters mix. - Relevant sections: Sections 20.15 and 20.16. **Thermophilicity and Habitat Prevalence** - **Thermophilic Species:** - Common within this class, contributing to their prevalence in hydrothermal systems. - Relevant section: Section 20.16. **Metabolic Characteristics** - **Chemolithotrophy and Autotrophy:** - Widespread among Epsilonproteobacteria. - **Autotrophy Mechanism:** - Uses the reverse TCA cycle for CO₂ fixation. - Relevant section: Section 14.2. - **Respiration:** - Can grow aerobically or anaerobically. - Anaerobic growth involves using oxidized nitrogen or sulfur compounds as electron acceptors. - **Electron Donors:** - Inorganic electron donors such as reduced sulfur compounds or H₂. **Ecological Roles and Environmental Distribution** - **Surface Attachment:** - Especially abundant when attached to surfaces at oxic-anoxic interfaces in sulfur-rich environments. - Play major roles in the oxidation of sulfur compounds in nature. **CO₂ Fixation and Symbiosis** - **CO₂ Fixation:** - Crucial for many animals in sulfur-rich environments. - Example: Epsilonproteobacteria can account for up to 85% of microbial biomass on hydrothermal vent chimneys. - Relevant section: Section 20.16 and Figure 20.44. - **Symbiotic Relationships:** - Epsilonproteobacteria grow as ectosymbionts and endosymbionts of various animals. - **Host Animals:** - Oligochaete and polychaete worms, snails, and shrimp. - **Roles of Symbionts:** - Provide nutrition to the host. - Help detoxify H₂S, which would otherwise be harmful to the host. - Relevant section: Section 23.11. **Future Research Directions** - **Exploration of Phylogeny, Metabolic Activities, and Ecological Roles:** - Further research is likely to uncover new aspects of prokaryotic diversity among Epsilonproteobacteria. **II *Firmicutes*, *Tenericutes*,** **and *Actinobacteria*** T**he *Firmicutes* and *Actinobacteria* contain gram-positive** ***Bacteria* and include many well-characterized bacteria. The** ***Tenericutes* include species such as *Mycoplasma* that have lost** **the ability to make peptidoglycan and a cell wall of any kind.**  **Overview of Phylogenetic Bacterial Diversity:** - Continuing the exploration of gram-positive bacteria. - Focus on the following phyla: - **Actinobacteria** - **Firmicutes** - **Tenericutes** - These three phyla collectively encompass nearly half of all characterized species of Bacteria.  **Phylum: Actinobacteria** - **Actinomycetes:** - A vast group of primarily filamentous soil bacteria. - **Distinguishing Feature:** - Genomic DNA of Actinobacteria typically has a high frequency of GC base pairs. - Due to their high GC content, Actinobacteria are also referred to as **\"high G+C gram-positive bacteria.\"**  **Phylum: Firmicutes** - **General Characteristics:** - Includes endospore-forming bacteria, lactic acid bacteria, and several other groups. - **Genomic Feature:** - In contrast to Actinobacteria, Firmicutes generally have a low GC content in their genomes. - Due to their low GC content, Firmicutes are also known as **\"low G+C gram-positive bacteria.\"**  **Phylum: Tenericutes** - **Cell Wall Characteristics:** - Includes cells that lack a cell wall, distinguishing them from other gram-positive bacteria.  **Focus on Firmicutes:** - The examination begins with **Firmicutes that do not form endospores.** **16.6 *Firmicutes: Lactobacillales*** **KEY GENERA: *Lactobacillus, Streptococcus*** - **Order: Lactobacillales** - **Lactic Acid Bacteria:** - Fermentative organisms that produce lactic acid as a major end product of metabolism. - Widely used in food production and preservation. - Reference: Section 1.6. - **Characteristics:** - Nonsporulating bacteria. - Oxidase-negative and catalase-negative. - Morphology: - Can be rods or cocci. - Metabolism: - Exclusively fermentative metabolism. - All members produce lactic acid as a major or sole fermentation product. - Reference: Sections 3.7, 14.18. - **Lack of Porphyrins and Cytochromes:** - Do not carry out oxidative phosphorylation. - Obtain energy only by substrate-level phosphorylation. - **Aerotolerance:** - Despite being anaerobes, they are not sensitive to oxygen (O₂). - Capable of growing in the presence of oxygen. - Classified as **aerotolerant anaerobes.** - Reference: Section 4.16. - **Energy and Nutritional Requirements:** - **Energy Source:** - Primarily obtain energy from the metabolism of sugars. - Usually restricted to habitats where sugars are present. - **Nutritional Limitations:** - Limited biosynthetic abilities. - Require complex nutritional inputs, including: - Amino acids. - Vitamins. - Purines. - Pyrimidines. - Example: Nutritional needs for Leuconostoc mesenteroides. - Reference: Table 4.2. - **Fermentation Patterns in Lactic Acid Bacteria:** - **Homofermentative Group:** - Produces a single fermentation product: lactic acid. - **Heterofermentative Group:** - Produces multiple fermentation products, including: - Ethanol. - CO₂. - Lactate. - Reference: Section 14.18 and Figure 14.44. ***Lactobacillus***  **Lactobacilli Overview:** - **Morphology:** - Typically rod-shaped bacteria. - Grow in chains, with variation in shape: - Some are long and slender rods. - Others are short, bent rods. - Visual reference: Figure 16.18. - **Fermentation Type:** - Most Lactobacilli are **homofermentative**.  **Habitat and Usage:** - **Common Presence:** - Frequently found in dairy products. - **Industrial and Food Production Uses:** - **Lactobacillus acidophilus:** - Used in the production of acidophilus milk. - Visual reference: Figure 16.18a. - **Lactobacillus delbrueckii:** - Used in the preparation of yogurt. - Visual reference: Figure 16.18c. - Other species of Lactobacilli: - Used in the production of sauerkraut, silage, and pickles. - Reference: Section 33.6.  **Acid Resistance:** - **Comparison with Other Lactic Acid Bacteria:** - Lactobacilli are more resistant to acidic conditions than other lactic acid bacteria. - **Growth Conditions:** - Capable of growing well at pH values as low as 4. - **Selective Enrichment:** - Due to their acid resistance, Lactobacilli can be selectively enriched from: - Dairy products. - Fermenting plant material. - Grown on acidic carbohydrate-containing media.  **Role in Lactic Acid Fermentations:** - **Growth During Fermentation:** - Their acid resistance enables Lactobacilli to continue growing during natural lactic fermentations. - Able to grow even when pH drops too low for other lactic acid bacteria. - **Final Stages of Fermentation:** - Typically responsible for the final stages of most lactic acid fermentations.  **Pathogenicity:** - **Rare Pathogenicity:** - Lactobacilli are rarely, if ever, pathogenic. ***Streptococcus* and Other Cocci** **Genera: Lactococcus and Streptococcus** - **General Characteristics:** - Both genera contain homofermentative, coccoid-shaped lactic acid bacteria. - These bacteria have distinct habitats and activities. - Of significant practical importance to humans. - **Pathogenicity:** - Some species within these genera are pathogenic to humans and animals. - Reference: Section 31.2. **Streptococcus Genus** - **Morphology:** - Characteristic cell morphology: cocci arranged in chains or tetrads. - Easily distinguishable from rod-shaped lactobacilli. - Visual reference: Figure 16.19a. - **Role in Fermentation and Disease:** - **Lactic Acid Production:** - Important roles in the production of: - Buttermilk. - Silage. - Other fermented products. - Reference: Section 33.6. - **Dental Caries Formation:** - Certain species play a major role in dental caries formation. - References: Sections 24.3 and 25.1. - **Subgroups of Streptococci:** - **Pyogenes Subgroup:** - Characterized by **Streptococcus pyogenes**. - Cause of strep throat. - Reference: Section 31.2. - **Viridans Subgroup:** - Characterized by **Streptococcus mutans**. - Major cause of dental caries. - References: Sections 24.3 and 25.1. - **Hemolysis on Blood Agar:** - **Beta (β)-Hemolysis:** - Species producing virulence factors **streptolysin O** or **streptolysin S**: - Form colonies surrounded by a large zone of complete red blood cell hemolysis. - This condition is known as β-hemolysis. - β-hemolysis is diagnostic for streptococci in the pyogenes subgroup. - Visual references: Figures 25.17a, 31.4b, and 31.8. - **Alpha (α)-Hemolysis:** - Streptococci in the viridans subgroup cause incomplete hemolysis: - Leads to greening of the agar under colonies. - **Immunological Grouping:** - **Grouping Based on Specific Carbohydrate Antigens:** - Streptococci are divided into immunological groups, designated by letters: - A, B, C, F, G. - **Group A Antigen:** - Typically found in β-hemolytic streptococci found in humans. - **Group D Antigen:** - Found in enterococci. **Lactococcus Genus** - **Characteristics:** - Contains streptococci of dairy significance. - Visual reference: Figure 16.19b. **Enterococcus Genus** - **Characteristics:** - Includes streptococci primarily of fecal origin. - Some species can be human pathogens. **Other Homofermentative Cocci:** - **Peptococcus** and **Peptostreptococcus** Genera: - Obligate anaerobes. - Ferment proteins rather than sugars. **Genus: Leuconostoc** - **Heterofermentative Lactococci:** - **Classification:** - Reside in the genus **Leuconostoc**. - **Flavoring Ingredients Production:** - **Diacetyl and Acetoin:** - Produced from the catabolism of citrate by Leuconostoc strains. - **Application:** - Used as starter cultures in dairy fermentations. - **Polysaccharide Production:** - **Glucose or Fructose Polysaccharide Slimes:** - Some Leuconostoc strains produce large amounts of these polysaccharides. - Production is especially significant when cultured on sucrose as the carbon and energy source. - Visual reference: Figure 16.19c. - **Medical Application:** - **Plasma Extenders:** - Certain polysaccharide polymers produced by Leuconostoc have found medical use. - Used as plasma extenders in blood transfusions. - **16.7 *Firmicutes:* Nonsporulating *Bacillales*** - **and *Clostridiales*** - **KEY GENERA: *Listeria, Staphylococcus, Sarcina*** - *Firmicutes* that form endospores reside in the orders *Bacillales* and - *Clostridiales*. However, numerous *Bacillales* and *Clostridiales* are - unable to form endospores, and we consider some of these here. ***Listeria*** **Order: Bacillales** - **General Characteristics:** - Typically contains **aerobic** and **facultatively aerobic** chemoorganotrophs. - Members of this order are widespread and particularly common in soils. **Genus: Listeria** - **Habitat and Distribution:** - Found widely in soils. - Known as an **opportunistic pathogen**. - A common cause of foodborne illness. - **Morphological and Metabolic Characteristics:** - **Gram-positive** bacteria. - **Catalase-positive**. - **Rod-shaped**. - **Facultatively aerobic** chemoorganotrophs. - **Noteworthy Species:** - **Listeria monocytogenes:** - Most noteworthy species in the genus. - Causes a major foodborne illness known as **listeriosis**. - Reference: Section 33.13. - **Transmission:** - Transmitted through contaminated, usually ready-to-eat foods. - Examples of such foods: - **Cheese**. - **Sausages**. - **Clinical Impact:** - Listeriosis can range from a mild illness to a fatal form of meningitis. - **Growth Characteristics:** - Species of Listeria often grow well at low temperatures. - Capable of growth in refrigerated foods. ***Staphylococcus*** **Genus: Staphylococcus** - **Metabolic Characteristics:** - **Facultative aerobe** with a typical respiratory metabolism. - Can also grow fermentatively. - Produces acid from glucose both **aerobically** and **anaerobically**. - **Morphological Characteristics:** - Cells typically grow in clusters. - Staphylococcus species are **catalase-positive**. - This trait distinguishes them from **Streptococcus** and other genera of lactic acid bacteria. - **Environmental Resistance:** - **Relatively resistant** to reduced water potential. - Tolerant to **drying** and **high salt (NaCl)** conditions. - Can grow in media containing salt, providing a selective means for isolation. - Example: When a skin swab, dry soil, or room dust is spread on a rich-medium agar plate containing 7.5% NaCl and incubated aerobically, gram-positive cocci often form the predominant colonies. - **Pigmentation:** - Many species are **pigmented**, aiding in the selection of gram-positive cocci. - **Ecological Role:** - Common **commensals** and **parasites** of humans and animals. - Occasionally cause serious infections. **Major Species in Humans:** - **Staphylococcus epidermidis:** - **Nonpigmented**. - **Nonpathogenic**. - Usually found on the **skin** or **mucous membranes**. - **Staphylococcus aureus:** - **Yellow-pigmented** species. - Most commonly associated with pathological conditions in humans: - **Boils**. - **Pimples**. - **Pneumonia**. - **Osteomyelitis**. - **Meningitis**. - **Arthritis**. - **Antibiotic Resistance:** - Some strains are resistant to multiple antibiotics, known as **MRSA (Methicillin-resistant Staphylococcus aureus)**. - MRSA strains are fierce pathogens that can cause extensive tissue damage. - Reference: **Figure 31.9**. - Further discussion on the pathogenesis of MRSA and other strains of **S. aureus**: - Sections **24.5**, **29.2**, and **31.9**. ***Sarcina*** **Genus: Sarcina** - **Classification:** - Belongs to the order **Clostridiales**. - Contains **obligate anaerobes**. - **Catalase-negative**. - **Morphological Characteristics:** - **Cell Division:** - Sarcina species divide in three perpendicular planes. - This division yields packets of eight or more cells. - Notable for this unique morphology. - Visual reference: **Figure 16.21**. - **Cell Structure:** - Cells of **Sarcina ventriculi** have a thick, fibrous layer of cellulose surrounding the cell wall. - **Cellulose Layers:** - The cellulose layers of adjacent cells become attached. - Functions as a cementing material to hold together packets of **S. ventriculi** cells. - Visual reference: **Figure 16.21b**. - **Environmental Tolerance:** - **Extremely acid-tolerant**. - Capable of fermenting sugars and growing in environments with a pH as low as 2. - **Habitat and Distribution:** - Sarcina species can be isolated from: - **Soil**. - **Mud**. - **Feces**. - **Stomach contents**. - **Sarcina ventriculi:** - One of the few bacteria capable of inhabiting and growing in the stomach of humans and other monogastric animals. - **Clinical Relevance:** - **Sarcina ventriculi** is associated with certain gastrointestinal disorders in humans: - For example, **pyloric ulcerations**. - In these conditions, rapid growth of **S. ventriculi** is observed in the stomach. - **Pathological Impact:** - These disorders retard the flow of food to the intestine. - Often require surgery to correct. **16.8 *Firmicutes****:* **Sporulating *Bacillales*** **and *Clostridiales*** **KEY GENERA: *Bacillus, Clostridium, Sporosarcina***  **All endospore-forming bacteria**: - Belong to **Gram-positive species** of the orders **Bacillales** and **Clostridiales**.  **Evolutionary origin of endospores**: - The ability to form endospores evolved **only once** in a **common ancestor** of the following groups: - **Bacillales** - **Clostridiales** - **Lactobacillales**. - **Not all members** of Bacillales, Clostridiales, or Lactobacillales can form endospores. - Many **Bacillales** and **Clostridiales** have **lost** the ability to form endospores. - The **entire order Lactobacillales** is unable to form endospores.  **Genetic requirements for endospore formation**: - Requires **many genes** (refer to Sections 2.8 and 8.6 for more details). - **Endospore formation has not** been acquired through **horizontal gene transfer**. - The **phylogenetic distribution** of endospores suggests **many losses** of this ability during evolution.  **Distinguishing features of endospore-forming bacteria**: - Based on: - **Cell morphology** - **Shape** of the endospore - **Cellular position** of the endospore (refer to Figure 16.22). - **Relationship to O₂**. - **Energy metabolism**.  **Key genera of endospore-forming bacteria**: - **Bacillus**: - Species are **aerobic** or **facultatively aerobic**. - **Clostridium**: - Species are **obligately anaerobic** and **fermentative**.  **Ecological relationship of endospore-forming bacteria**: - All are primarily found in **soil**. - Even **pathogenic species** (to humans or other animals) are primarily **saprophytic soil organisms**. - These pathogens infect animals **incidentally**. - The ability to produce **endospores** is advantageous for a **soil microorganism** because: - Soil is a **highly variable environment**. - Variability includes **nutrient levels**, **temperature**, and **water activity**.  **Isolation of endospore-forming bacteria**: - Endospore-forming bacteria can be **selectively isolated** from samples such as: - **Soil** - **Food** - **Dust** - Other materials. - Isolation technique: - Heat the sample to **80°C for 10 minutes**. - This treatment kills **vegetative cells** while leaving **endospores viable**. - The heat-treated sample is then streaked on plates with **appropriate medium**. - Incubate the sample: - **Aerobically** to yield **Bacillus species**. - **Anaerobically** to yield **Clostridium species**. ***Bacillus* and *Paenibacillus***  **Growth of Bacillus and Paenibacillus species**: - These species grow well on **defined media** that contain a variety of **carbon sources**. - Many **bacilli** produce **extracellular hydrolytic enzymes**, which: - Break down **complex polymers** such as: - **Polysaccharides** - **Nucleic acids** - **Lipids** - This breakdown allows the organisms to use the resulting products as **carbon sources** and **electron donors**.  **Antibiotic production by bacilli**: - Many **bacilli** produce antibiotics, including: - **Bacitracin** - **Polymyxin** - **Tyrocidine** - **Gramicidin** - **Circulin** - In most cases, antibiotics are released when the culture enters the **stationary phase of growth** and is **committed to sporulation**.  **Insecticidal properties of certain bacilli**: - Some bacilli produce **toxic insecticidal proteins**, notably: - **Paenibacillus popilliae** - **Bacillus thuringiensis** - **Paenibacillus popilliae**: - Produces a toxic protein that causes **milky disease** in: - **Japanese beetle larvae** - Larvae of beetles in the family **Scarabaeidae**. - **Bacillus thuringiensis**: - Produces a protein that causes a **fatal disease** in many different groups of **insects**. - Both **P. popilliae** and **B. thuringiensis** produce a **crystalline protein** during sporulation called the **parasporal body**, which: - Is deposited within the **sporangium** but outside the **endospore proper** (refer to Figure 16.23).  **Mechanism of action of B. thuringiensis toxin**: - The **parasporal body** produced by B. thuringiensis is a **protoxin**. - The protoxin is converted to a **toxin** in the **insect gut**. - The toxin: - Binds to **specific receptors** in the **intestinal epithelial cells** of certain insects. - Induces **pore formation**, causing **leakage of the host cell cytoplasm**. - This leads to **lysis** (destruction) of the host cell. - **Diverse strains** of **B. thuringiensis** produce different types of toxin that are specific to **different groups of insects**.  **Commercial applications of insecticidal proteins**: - **Endospore preparations** derived from **B. thuringiensis** and **P. popilliae** are commercially available as **biological insecticides**.  **Cry genes and genetically modified crops**: - The **cry genes** that encode **crystal proteins** have been **isolated** from several strains of **B. thuringiensis**. - The genes for the **B. thuringiensis crystal protein** (commercially known as \"**Bt toxin**\") have been introduced into **genetically modified crops**, such as: - **Maize** - **Soybeans** - **Cotton** - These genetically modified crops are called **Bt crops** and are **resistant to insects**. - **Bt crops** are widely used **around the world**. ***Clostridium***  **Clostridia lack a respiratory chain**: - Unlike **Bacillus species**, **Clostridia** do not have a respiratory chain. - **Clostridia** obtain **ATP** through **substrate-level phosphorylation**.  **Anaerobic energy-yielding mechanisms in Clostridia**: - Many anaerobic energy mechanisms exist within Clostridia (refer to Section 14.19). - The separation of the **genus Clostridium** into subgroups is primarily based on: - Their **anaerobic energy-yielding mechanisms**. - The type of **fermentable substrate** used.  **Saccharolytic Clostridia**: - Many Clostridia are **saccharolytic** and ferment **sugars**. - The primary end product of sugar fermentation is **butyric acid**. - Some saccharolytic Clostridia also produce **acetone** and **butanol**, such as: - **Clostridium pasteurianum**. - This species is also a vigorous **nitrogen-fixing bacterium** (refer to Sections 3.12 and 15.9).  **Cellulolytic Clostridia**: - Some Clostridia ferment **cellulose** to produce **acids** and **alcohols**. - Species in this group include: - **C. thermocellum** - **C. cellulolyticum** - **C. cellulovorans**. - These species are likely the major organisms that **decompose cellulose** in **anoxic environments** such as: - **Rumen** (part of the digestive system of certain animals). - **Sediments**. - **Cellulolytic Clostridia** possess **cellulosomes**, whic