{1} Introduction to Microbial Ecology.pdf

Introduction to Microbial Ecology Prof. Rhenz Cedrick Cequeña, Msc. MICROBIAL ECOLOGY MICROBIAL FOSSILS AND EARLY LIFE Scope: From individual cells to complex stems Crucial for understanding evolution, but w exist Stud...

Introduction to Microbial Ecology Prof. Rhenz Cedrick Cequeña, Msc. MICROBIAL ECOLOGY MICROBIAL FOSSILS AND EARLY LIFE Scope: From individual cells to complex stems Crucial for understanding evolution, but w exist Study approach: Pure Cultures vs. Unique for microorganisms. Environments Electron microscopy revealed cell-like Focus of Microbial Ecology structures. o Microbial Community Structure: Early evolutionary development is divided. to High interest in understanding three phases: pre-Darwinian (before cell o Identification Methods: Molecular formation), proto-Darwinian (first cell methods for uncultivated microbes formation), and Darwinian (selective pressures favoring diverse forms of life). QUESTIONS IN MICROBIAL ECOLOGY Key Questions: Which microbes are present? What is the role of each species? What interactions occur in the microbial environment? How do microbes change the environment? HISTORY OF MICROBIAL ECOLOGY Founders of Microbial Ecology Sergei Winogradsky (1845-1916): Nutrient cycles, chemolithotrophy Martinus Beijerinck (1851-1931): Enrichment culture technique, virology PRE-CELLULAR WORLD WINOGRADSKY COLUMN Different theories exist about energy sources and sites for organic molecule synthesis: Used to demonstrate microbial interaction and o Wächtershäuser (1990): Organic biochemical cycle. macromolecules produced on NATURAL HISTORY clay-like surfaces. o Koch (1985) and Deamer (1997): Prokaryotic cells were ideal for early life e to Vesicles with membrane-like rapid genetic evolution and horizontal gene structures involved in organic transfer. molecule formation. Some prokaryotic organisms evolved to o Some theories suggest life arose produce eukaryotic organisms and from a "primordial soup" in a lake or decomposed prehistoric forms. from a subsurface spring. Microorganisms are crucial for nutrient These theories highlight the interplay of cycling, community structure, and geochemical processes leading to biological interactions with other life forms. activity. THE FIRST CELL Organic compounds likely accumulated in the prebiotic environment, leading to early cell development. Membrane formation was crucial for cell-like structures to manage energy and substances, with non-living vesicles possibly having catalytic abilities. The RNA world hypothesis suggests that RNA- based life preceded DNA-based life, with ribozymes being central to metabolism and replication processes. 1 Introduction to Microbial Ecology Prof. Rhenz Cedrick Cequeña, Msc. The transition from RNA to DNA allowed for more EVOLUTION OF METABOLIC PATHWAYS stable genetic material storage and more efficient enzymes, which could have been Ancestral cells had few genes, no gene facilitated by ribozymes. regulation, and no mobile genetic elements compared to current prokaryotic cells. The "patchwork" hypothesis suggests that genes encoding low-specificity enzymes were duplicated and evolved into genes for highly specific enzymes. Gene duplication and horizontal gene transfer expanded metabolic capabilities and established regulatory mechanisms in primordial cells. Efficient metabolic pathways were selected through population growth pressures, leading to interconnected biogeochemical cycles. MITOCHONDRIA AND CHLOROPLAST Bacterial and archaeal species evolved through mutations and horizontal gene transfer, adapting to environmental changes. Theories suggest eukaryotic cells formed through endosymbiosis, with the nucleus developing before mitochondria and CELL SHAPE AND ECOLOGY chloroplasts. The genome fusion hypothesis explains the Microbial cells have precise structural eukaryotic nucleus formation from archaeal organization, reflected in molecular alignment and bacterial genes. in membranes, ribosomes, cell walls, DNA, and The endosymbiotic hypothesis and hydrogen other macromolecules. hypothesis address the origins of mitochondria and chloroplasts, with endosymbionts providing benefits to host cells. ENERGY AND GROWTH Electron flow from donors to acceptors is a hallmark of living systems, observed in both aerobic and anaerobic cultures. 2 Introduction to Microbial Ecology Prof. Rhenz Cedrick Cequeña, Msc. Electron transfer is mediated by cytochromes, Microbiologists used phenotypic quinones, and iron-sulfur proteins, with characteristics and metabolism to discern variability distinguishing prokaryotes from species, but 16S rDNA studies revealed mitochondria-containing life forms. limitations. Growth in bacteria, archaea, and single-cell Proposed species definitions include ≥70% protists generally means an increase in cell whole genome DNA-DNA reassociation and similar G-C ratios, or 97-99% 16S rRNA gene sequence identity. TREE OF LIFE Initially, life was classified into five kingdoms: Animalia, Plantae, Fungi, Monera, and Protista. Woese and Fox (1977) proposed a new division, Archaea, as one of three major lines of descent. Woese et al. (1990) classified life into three domains: Bacteria (Eubacteria), Archaea (Archaebacteria), and Eukarya (Eukarya). Sequencing of the small subunit (SSU) of the ribosome revealed greater diversity in bacteria and archaea than in eukaryotes. Researchers use whole genomes to identify universal protein gene sequences, refining relationships among the three domains and revealing greater metabolic diversity in microorganisms. MICROBIAL ADAPTATION Microorganisms respond to environmental changes to maintain near-optimal growth and physiological processes. Extreme changes favor cells with genetic content enabling growth in harsh conditions, leading to new species with special traits. Metabolic changes occur in response to chemical environment changes, with gene MICROECOLOGY VS. MACROECOLOGY expression modulated to conserve energy. Microorganisms have adapted to Earth's Ecological and epidemiological theories have changing environment, impacting microbial been successful in predicting and controlling activities and microbe-host interactions. emerging diseases like Ebola and rabies. Two factors limit theory development in CLASSIFICAION AND TAXONOMY: THE SPECIES CONCEPT microbial ecology: lack of distinguishing microbial characteristics and slow progress in Classical species definition based on shared incorporating general ecological theory. traits and interbreeding is problematic for Microbial model systems help understand asexual microorganisms. natural systems and predict future interactions, exploring key ecological questions. 3 Introduction to Microbial Ecology Prof. Rhenz Cedrick Cequeña, Msc. TRENDS IN MICROBIAL ECOLOGY Interest expanded to include microorganisms' contributions to global nutrient cycling, bioremediation, greenhouse gases, and climate change. System-based technologies, or "omic" technologies, are now used to evaluate microbial ecology, relying on sensitive analytical Instrumentation. New approaches are being developed to evaluate microbial relationships using DNA and protein sequences. MOLECULAR MICROBIAL ECOLOGY Less than 1% of microorganisms samples could be grown using standard media. C Carl Woese and Norm Pace developed methods to identify and compare environmental organisms using small-subunit ribosomal RNA genes, measuring evolutionary distance. TABLE 1.4. ‘‘OMIC’’ TECHNOLOGIES WITH APPLICATIONS TO MICROBIAL ECOLOGY TERMS-CHARACTERISTICS Genomics- Analysis of gene content of an organism by sequencing and mapping of genomes (chromosomes of eukaryotes or nucleoid of prokaryotes) Metagenomics- Analysis of gene content of all organisms in a specific environment Transcriptomics- Study evaluating the production of mRNA produced at a specific time by a cultured organism Proteomics- Study of protein structure and protein regulation of an organism Metaproteomics- Analysis of all proteins produced by all the organisms in a specific environment Metabiomics- Study of small molecules and intermediate compounds produced from metabolism; frequently this includes the end products of metabolism Metallomics- Study of the various metal ions and their activities in a biological cell Biolomics- Study of all the biological systems and biochemical components of cellular system Microbiomics- Study including all the microorganisms and their interactions with the immediate environment. 4