Biol 371 Class Notes (27-39) PDF

lOMoARcPSD|14412004 o Can be highly specific to species, or multiple species or genera. o Used in microbial ecology food industry and clinical diagnostics. - Can be modified to measure gene expression or translational activity. PCR methods of microbial community analysis - Specific genes can be us...

lOMoARcPSD|14412004 o Can be highly specific to species, or multiple species or genera. o Used in microbial ecology food industry and clinical diagnostics. - Can be modified to measure gene expression or translational activity. PCR methods of microbial community analysis - Specific genes can be used as a measure of diversity. Isolate DNA from environmental samples. o PCR (polymerase chain reaction) amplification of specific genes; typically, rRNA genes. o Analysis of the amplified genes  Molecular cloning  Electrophoresis  Restriction enzyme digestion  Sequencing Phylogenetic analysis: massively parallel DNA sequencing - - Multiple sequencing technologies available o Do not require molecular cloning. o Generates billions of sequences reads. o Allows the detection of minor phylotypes. Results of phylogenetic analysis o rRNA sequences differ from those of all known laboratory cultures. o New phylogenetic distinct prokaryotes. o Fewer than 0.1% of bacteria have been cultured, enrichment bias a real problem in environmental microbiology. Geochip-functional gene microarray - DNA microarray containing gene probes that encompass most major biogeochemical processes. Fluorescently labelled environmental DNA and hybridize to Geochip. o Relatively fast and easy analyze. o Provides functional information to correlate with phylogenetic analysis. Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 Environmental multi-omics - - More complete understanding of how a microorganism functions requires and integrated accounting of all central cellular processes. These include integrative knowledge on: o Genomics – genes, gene function and gene regulation. o Transcriptomics- global gene expression under different conditions. o Proteomics- accumulation of proteins under different conditions. o Metabolomics- dynamics of accumulation of metabolites. Expand the analysis to community level: metagenomics, meta transcriptomics, metaproteomic, and metametabolomics. Environmental genomic (metagenomics) - DNA extracted from environmental samples. - Sequence, assemble and annotate – mostly partial genomes assembled. - Identify as many genes as possible. o Detect genes not amplified by available PCR primers. o Powerful tool for assessing the phylogenetic and metabolic diversity of an environment. Meta transcriptomics Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 - Analysis of community mRNA o Remove rRNA before sequencing (>90% of total RNA are rRNA) o Reveals genes in a community that are active. o Reveals level of gene expression Metaproteomic and metabolomics - Metaproteomic: measures the diversity and abundance of different proteins in a community. o Current state of technology can only detect the most abundant proteins - Metabolomics: the comprehensive analysis of cellular and extracellular metabolites of a microbial community Direct chemical measurements of metabolites - For many studies, direct chemical measurements are sufficient, e.g., lactate and H S can 2 be measured with high sensitivity by chemical assay - For some processes, higher sensitivity can be achieved with radioisotopes. Microsensors - Microsensors available to measure a wide range of activity. o Small glass electrodes that can be inserted into the habitat. Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 Isotopic fractionation - Stable isotopes: an element can have multiple nonradioactive stable isotopes, e.g., 13 and C. - Isotopic fractionation: biological reactions prefer lighter isotopes; hence cellular 12 13 materials are enriched in C and depleted in C relative to inorganic carbon. 12 C 12 13 o The ratio of C and C can be used to trace the biological or geological origin of ancient environment. Stable isotope probing - Stable isotope probing: feed microorganisms with substrate labelled with stable heavy 13 isotope, e.g., C-benzoate. o Microorganisms that can utilize benzoate will incorporate 13 C into their DNA. o The heavier DNA can be separated by ultracentrifugation.  13 Compare the C-labelled DNA sequence with metagenomics data will identify microorganisms that can utilize benzoate in the microbial community. Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 Lecture 12 | Microbial Ecosystems General ecological concepts - Ecosystem: the sum total of all organisms and abiotic (physical rather than biological) factors in a particular environment - Habitat: portion of an ecosystem where a community could reside o An ecosystem contains many habitats. o Microbes account of ~50% of all biomasses on Earth, on the surface and deep within - Population: a group of microorganisms of the same species that reside in the same place at the same time o May be descendants of a single cell. - Community: consists of populations living in association with other populations Microbial diversity: richness vs abundance - Diversity of microbial species in an ecosystem is expressed in two ways o Species richness: total number of different species present o Species abundance: proportion of each species in an ecosystem - Microbial species richness and abundance are functions of the kinds and amounts of nutrients available in a given habitat. Resources and conditions that govern microbial growth in nature. Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 Populations, guilds and communities - Guilds: metabolically related microbial populations o sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem. - Niche: habitat shared by a guild o Supplies nutrients and conditions for growth Biogeochemistry and nutrient cycles - Biogeochemistry: the study of biologically mediated chemical transformations - A biogeochemical cycle defines the transformations of a key element by biological or chemical agents. Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 o Microorganisms play essential role in cycling elements C, N, S, and Fe between their different chemical forms. o Typically proceed by oxidation–reduction reactions - Microbes play critical roles in energy transformations and biogeochemical processes that result in the recycling of elements to living systems. The microbial environment - Growth of microbes depends on resources and growth conditions. - Differences in the type and quantity of resources and the physiochemical conditions of a habitat define the niche for each microbe. - Fundamental niche: Full range of environmental conditions under which an organism can exist. - Realized niche or prime niche: for each organism, there exists at least one niche in which that organism is most successful. Microenvironment - Microenvironment: the immediate environmental surrounding of a microbial cell or groups of cells - Soil particles contain many microenvironments - Physiochemical conditions in a microenvironment are subject to rapid change, both spatially and temporally - Resources in natural environments are highly variable, and many microbes in nature face a feast-or-famine existence - Growth rates of microbes in nature are usually well below maximum growth rates defined in the laboratory Competition and cooperation - Competition and cooperation occur between microbes in natural systems. - Syntrophy: microbes work together to carry out transformations that neither can accomplish alone. o Microbial partnerships are particularly important for anoxic carbon cycling Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 o Metabolic cooperation can also be seen in the activities of organisms that carry out complementary metabolisms. Surfaces are important microbial habitats. - Surfaces: offer microbes greater access to nutrients and protection from predation and physicochemical disturbances o Nutrients adsorb to surfaces. o Attachment to a surface also offers cells a means to remain in a favorable habitat, modify the habitat by their own activities, and not be washed away Biofilms - Biofilms: assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells o The matrix is typically a mixture of polysaccharides. o Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems. Implications of biofilms - - Why bacteria form biofilms? o Self-defense: Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics o Allows cells to remain in a favorable niche. o Allows bacterial cells to live in close association with one another. Biofilms have been implicated in several medical and dental conditions. o Periodontal disease, kidney stones, tuberculosis, Legionnaires’ disease, Staphylococcus infections - In industrial settings, biofilms can slow the flow of liquids through pipelines and accelerate corrosion. - Surface colonization and biodegradation of plastic alters the surface chemistry, density, and sinking rates of microplastics. Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 - Few highly effective antibiofilm agents are available Microbial mats - Microbial mats: thick biofilms o Built by phototrophic and/or chemolithotrophic bacteria. o Phototrophic mats contain filamentous cyanobacteria. o Chemolithotrophic mats contain filamentous sulfur-oxidizing bacteria. Soils-layers - Loose outer materials of Earth’s surface o Mineral soils: derived from rock weathering and other inorganic materials o Organic soils: derived from sedimentation in bogs and marshes Soil-composition and microenvironment - Composition of soils by soil volume o Air and water – 50%s o Inorganic mineral matter – 40% o Organic matter – 5% o Microorganisms and macroorganisms – 5% - Most microbial growth takes place on the surfaces of soil particles - Soil aggregates contain many different microenvironments supporting the growth of multiple types of microbes Soils-formation - Soils are formed by interdependent physical, chemical, and biological processes o Carbon dioxide is formed by respiring organisms that form carbonic acid that breaks down rock o Physical processes such as freezing and thawing break apart rocks, allowing plant roots to penetrate and form an expanded rhizosphere Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 o The rhizosphere, the area around plant roots where plants secrete sugars and other compounds, is rich in organic matter and microbial life - Water availability is variable and dependent on rainfall, plant coverage, drainage, and soil composition - Soil water has many dissolved materials and is called a soil solution - Well-drained soils have oxygen available, while waterlogged soils are typically anoxic, with the oxygen being consumed by soil microbiota Arid soils - Arid soils: dry, limited plant growth o Make up ~5% of the Earth’s land mass o Extreme environments: low water availability and variable temperatures (>60°C and below – 24°C) o Home to microbial communities specialized for extreme conditions o Arid soils are slow to form and are subject to desertification - Biological soil crusts made up of photosynthetic cyanobacteria and filamentous fungi that stabilize the soil o Damage to biological soil crusts leads to decrease soil fertility Soil bacterial and archaeal diversity - Phylogenetic sampling – pooled analysis from multiple studies of 16S rRNA gene sequencing - Microbial diversity varies with soil type and geographical location - Undisturbed, unpolluted soils support very high prokaryotic diversity - Soil perturbations and environmental changes trigger measurable shifts in community composition The terrestrial subsurface - Microbial life extends at least 3,000 metres below surface Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 - Microbial diversity of relatively shallow subsurface areas is similar to that of surface soils, but abundance is lower - Subsurface microbial life grows in an extremely nutrient- limited environment o Small microbial cells (<1 μM) are common - Few archaea are found in surface soils - Deep subsurface is home to the Asgard group of archaea that are most closely related to eukaryotes Freshwaters - Freshwater environments: highly variable in the resources and conditions available for microbial growth - The balance between photosynthesis and respiration controls the oxygen and carbon cycles - Oxygenic phototrophs, including algae and cyanobacteria, are the primary producers o Produce oxygen and organic material o They can be either planktonic (free floating) or benthic (attached to the bottom or sides of a lake or stream o Heterotrophic microbes in aquatic systems are highly dependent upon the activity of the primary producers - Oxygen has limited solubility in water o Concentrations are dependent on the amount of organic matter present and the physical mixing of the system o Deep layers of freshwater lakes can become anoxic once oxygen is consumed Stratification of water column in temperate lakes - In many temperate lakes, the water column becomes stratified during the summer o Epilimnion: warmer, less dense surface water o Hypolimnion: cooler, denser water at the bottom of a lake or pond o Thermocline: zone separating the epilimnion and the hypolimnion Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 - These layers vary greatly in temperature, oxygen availability, and chemical composition Influx of organic-rich wastewaters into aquatic systems - Biochemical oxygen demand: the microbial oxygen-consuming capacity of a body of water o Increases with the influx of organic material (e.g., from sewage), then decreases over time Prokaryotic diversity of freshwater lakes - Phylogenetic sampling: 16S rRNA genes sequencing - High microbial diversity reflects dynamic character of lake o Seasonally variable inputs of endogenous and exogenous nutrients sustains a phylogenetically and metabolically complex community of bacteria and a few groups of archaea Differences between freshwater and marine environments - With the exception of oxygen, open ocean as compared to freshwater is: o Saline o Low in nutrients, especially nitrogen, phosphorus, and iron o Cooler 6 7 o Lower microbial activity (~10 /mL as compared to ~10 /mL for freshwater) - Because of the size of the oceans, the microbial activities taking place in them are major factors in Earth’s carbon balance Phototrophic microorganisms in near-shore waters Downloaded by Raghad Abushahin ([email protected]) lOMoARcPSD|14412004 - Terrestrial runoff, retention of nutrients, and upwelling of nutrient-rich waters combine to support higher populations of phototrophic microorganisms in near- shore waters than in pelagic waters Diversity of marine systems all mute -excime - Eutrophication resulting from nutrient inputs can lead to the waters becoming intermittently anoxic from the removal of oxygen by respiration and the production of H S by sulfate-reducing bacteria 2 - Oxygen minimum zones: regions of oxygen-depleted waters at intermediate depths (1001,000 metres) and extend over large expanses of the ocean - Marine dead zone: example, an area of 6,000-8,000 square miles of seasonal oxygen depletion in the Gulf of Mexico associated with agricultural runoff of the Mississippi River o Excessive oxygen consumption by chemoorganotrophs and the formation oxygendepleted water Major marine phototroph- Prochlorococcus - Most of the primary productivity in the open oceans is due to photosynthesis by prochlorophytes o Prochlorococcus accounts for >40 percent of the biomass of marine phototrophs and ~50% of the net primary production o Abundance of different genotypes correlates with seasonal changes in temperature, light, nutrients, and predators (e.g., bacteriophage)  Each strain has about 2,000 genes with a core genome of 1,100 genes Distribution of bacteria and archaea in marine water - Abundant small planktonic heterotrophic prokaryotes o Pelagibacter: the most abundant marine heterotrophs  Contain proteorhodopsin, a form of rhodopsin that captures light energy to drive ATP synthesis - Prokaryote densities decrease with depth - Bacterial species dominate in surface waters Downloaded by Raghad Abushahin ([email protected])