Lecture 12 - Microbial Ecosystems PDF

BIOL371: Microbiology Lecture 12 – Microbial ecosystems 1 Topics of today 1. 2. 3. 4. Microbial ecology The microbial environment Terrestrial environment Aquatic environment Materials covered:  Chapters 20.1-20.16  Figures 20.1-20.4, 20.6, 20.8, 20.11, 20.13, 20.14, 20.16, 20.1820.22, 20.26,...

BIOL371: Microbiology Lecture 12 – Microbial ecosystems 1 Topics of today 1. 2. 3. 4. Microbial ecology The microbial environment Terrestrial environment Aquatic environment Materials covered:  Chapters 20.1-20.16  Figures 20.1-20.4, 20.6, 20.8, 20.11, 20.13, 20.14, 20.16, 20.1820.22, 20.26, 20.29, 20.32, 20.41-20.43  Table 20.1 2 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  An ecosystem contains many habitats  Microbes account of ~50% of all biomass 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  May be descendants of a single cell  Community: consists of populations living in association with other populations 3 Microbial diversity: richness vs abundance  Diversity of microbial species in an ecosystem is expressed in two ways  Species richness: total number of different species present  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 Collecting samples following a bloom of cyanobacteria High species: cyanobacteria, diatoms, green algae, flagellates, and bacteria Shift of community in (b) to low richness but high abundance following a bloom of cyanobacteria 4 Resources and conditions that govern microbial growth in nature 5 Populations, guilds and communities  Guilds: metabolically related microbial populations  sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem  Niche: habitat shared by a guild  Supplies nutrients and conditions for growth Example of a freshwater lake microbial ecosystem 6 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  Microorganisms play essential role in cycling elements C, N, S, and Fe between their different chemical forms  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 7 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 8 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 Contour map of O2 concentrations in a small soil particle 9 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  Microbial partnerships are particularly important for anoxic carbon cycling  Metabolic cooperation can also be seen in the activities of organisms that carry out complementary metabolisms 10 Surfaces are important microbial habitats  Surfaces: offer microbes greater access to nutrients and protection from predation and physicochemical disturbances  Nutrients adsorb to surfaces  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 Fluorescence photomicrograph of a natural microbial community living on plant roots in soil and stained with acridine orange Bacterial microcolonies developing on a microscope slide that was immersed in a river 11 Biofilms  Biofilms: assemblages of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells  The matrix is typically a mixture of polysaccharides  Biofilms trap nutrients for microbial growth and help prevent detachment of cells in flowing systems Confocal scanning laser microscopy through a natural biofilm on a leaf surface A cross-sectional view of an experimental biofilm composed of cells of Pseudomonas aeruginosa Phototrophic biofilms colonizing the rocky bottom of a stream 12 Implications of biofilms  Why bacteria form biofilms?  Self-defense: Biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, and penetration of toxins (e.g., antibiotics  Allows cells to remain in a favorable niche  Allows bacterial cells to live in close association with one another  Biofilms have been implicated in several medical and dental conditions  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  Few highly effective antibiofilm agents are available 13 Microbial mats  Microbial mats: thick biofilms  Built by phototrophic and/or chemolithotrophic bacteria  Phototrophic mats contain filamentous cyanobacteria  Chemolithotrophic mats contain filamentous sulfur-oxidizing bacteria Microbial mat core from an alkaline hot spring of Yellowstone National Park 14 Terrestrial environments 1. Soils 2. The terrestrial subsurface 15 Soils – layers  Loose outer materials of Earth’s surface  Mineral soils: derived from rock weathering and other inorganic materials  Organic soils: derived from sedimentation in bogs and marshes O horizon: surface with undecomposed plant material A horizon: most microbial growth; rich in organic material and nutrients B horizon: subsoil with organic material leached from A horizon; little microbial activity C horizon: base that is directly above bedrock 16 Soils – composition and microenvironment  Composition of soils by soil volume  Air and water – 50%  Inorganic mineral matter – 40%  Organic matter – 5%  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 17 Soils – formation  Soils are formed by interdependent physical, chemical, and biological processes  Carbon dioxide is formed by respiring organisms that form carbonic acid that breaks down rock  Physical processes such as freezing and thawing break apart rocks, allowing plant roots to penetrate and form an expanded rhizosphere  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 18 Arid soils  Arid soils: dry, limited plant growth  Make up ~5% of the Earth’s land mass  Extreme environments: low water availability and variable temperatures (>60°C and below – 24°C)  Home to microbial communities specialized for extreme conditions  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  Damage to biological soil crusts leads to decrease soil fertility Biological soil crust on the Colorado Plateau shown adjacent to lighter, disturbed soils. 19 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 20 The terrestrial subsurface  Microbial life extends at least 3,000 metres below surface  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 nutrientlimited environment  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 21 Aquatic environments 1. 2. 3. 4. 5. 6. 7. 8. Freshwaters Oxygen relationships in the marine environment Major marine phototrophs Pelagic bacteria and archaea Pelagic marine viruses The deep sea Deep-sea sediments Hydrothermal vents 22 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  Produce oxygen and organic material  They can be either planktonic (free floating) or benthic (attached to the bottom or sides of a lake or stream  Heterotrophic microbes in aquatic systems are highly dependent upon the activity of the primary producers  Oxygen has limited solubility in water  Concentrations are dependent on the amount of organic matter present and the physical mixing of the system  Deep layers of freshwater lakes can become anoxic once oxygen is consumed 23 Stratification of water column in temperate lakes  In many temperate lakes, the water column becomes stratified during the summer  Epilimnion: warmer, less dense surface water  Hypolimnion: cooler, denser water at the bottom of a lake or pond  Thermocline: zone separating the epilimnion and the hypolimnion  These layers vary greatly in temperature, oxygen availability, and chemical composition 24 Influx of organic-rich wastewaters into aquatic systems  Biochemical oxygen demand: the microbial oxygen-consuming capacity of a body of water  Increases with the influx of organic material (e.g., from sewage), then decreases over time Distribution of oxygen and nutrients in a river following an input of wastewater Nutrient-rich lake showing algae, cyanobacteria and aquatic plants 25 Prokaryotic diversity of freshwater lakes  Phylogenetic sampling: 16S rRNA genes sequencing  High microbial diversity reflects dynamic character of lake  Seasonally variable inputs of endogenous and exogenous nutrients sustains a phylogenetically and metabolically complex community of bacteria and a few groups of archaea 26 Differences between freshwater and marine environments  With the exception of oxygen, open ocean as compared to freshwater is:  Saline  Low in nutrients, especially nitrogen, phosphorus, and iron  Cooler  Lower microbial activity (~106/mL as compared to ~107/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 27 Phototrophic microorganisms in near-shore waters  Terrestrial runoff, retention of nutrients, and upwelling of nutrient-rich waters combine to support higher populations of phototrophic microorganisms in nearshore waters than in pelagic waters The eastern coastline of the Northeast. Areas rich in phototrophic plankton are shown in red. 28 Diversity of marine systems  Eutrophication resulting from nutrient inputs can lead to the waters becoming intermittently anoxic from the removal of oxygen by respiration and the production of H2S by sulfate-reducing bacteria  Oxygen minimum zones: regions of oxygen-depleted waters at intermediate depths (100-1,000 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  Excessive oxygen consumption by chemoorganotrophs and the formation oxygendepleted water 29 Major marine phototroph – Prochlorococcus  Most of the primary productivity in the open oceans is due to photosynthesis by prochlorophytes  Prochlorococcus accounts for >40 percent of the biomass of marine phototrophs and ~50% of the net primary production  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 30 Distribution of bacteria and archaea in marine water  Abundant small planktonic heterotrophic prokaryotes  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  Bacteria and archaea are roughly equal in deeper waters 31 Marine viruses  Viruses are typically 10X more abundant than microorganisms in the ocean  Highly diverse  Mostly affecting prokaryotic populations A water sample collected on 20-nm pore size filter is stained with SYBR Green and viewed by fluorescence microscopy. The tiny green dots are viruses while the larger, brighter dots are prokaryotes 32 The deep sea  Deep sea: lying between 1000 and 6000 metres  >75% of all ocean water  Organisms that inhabit the deep sea must deal with:  Low temperature (psychrophilic or psychrotolerant)  High pressure (piezophilic or piezotolerant)  Low nutrient levels  Must be chemotrophic because deep-sea water is completely dark 33 Deep-sea sediments  Deep-sea core samples are harvested by drilling the ocean floor  Archaeal and bacterial populations occur at depths >2000 metres  Fewer deep-sea microbes at greater depths than are found closer to the surface of the rock layer  Proteobacteria dominate  Novel phyla of archaea are widespread in deep subsurface Depth-related cell abundance from the analysis of one coastal sediment (filled circles) and the global average for all sampled ocean sediments (dashed 34 regression line) based on cell count data. Hydrothermal vents  Chemolithotrophic bacteria dominate at vent  Utilize inorganic materials from vents  Thermophiles and hyperthermophiles present  More diversity in bacteria than in archaea 35