Microbial habitat Biotechnology 1121.pptx

Microbial habitat

1. Env Microbiology SWE-531 Microbial habitat

2. Within ecosystems, there are a variety of areas, called habitats , where particular microorganisms reside, which are characterized by a given set of chemical, physical, and biological conditions. Microorganisms occupy and adapt to niches within habitats in much the same way that animals and plants do, but their ability to acquire new metabolic functions through horizontal gene transfer can lead to dynamic niche boundaries. Major habitat types (aqueous, soil, rock, atmospheric, intracellular ) differ in fairly substantial ways, which leads to differences in microbial composition. Topics to be discussed

3. Habitats are composed of many microenvironments that differ in abiotic conditions, such as oxygen level, pH, temperature, moisture content, nutrient availability, and light. Some habitats within these categories are extreme in terms of pH, temperature, and ultraviolet radiation. Aquatic habitats are common with approximately 71% of Earth’s surface being occupied by oceans, rivers, streams, and lakes. Key aquatic microbial players include phototrophs that generate primary productivity and heterotrophs that are key cyclers of carbon. Topics to be discussed

4. Soil habitats are widespread and important microbial habitats, where nitrogen fixing and other microorganisms play key roles in plant nutrition. Rock habitats, such as rock surfaces and endolithic environments , offer niches for phototrophs and other microorganisms, while subsurface habitats such as caves and deep subsurface pore spaces within Earth’s crust offer environments where organisms use molecular hydrogen, and reduced sulfur and iron species for energy. Many microbial species, including several pathogens , are transported over long distances through the atmospheric habitat, to colonize new habitats. Topics to be discussed

5. Niche: the sum of the environmental factors that affect the ability of a species to live and reproduce within a environment. Fundamental Niche: Represents all ecological factors Realized Niche: Actual Niche which take into account biotic interactions Niche

6. Aquatic habitats range from the vast ocean reaches to lakes and flowing bodies of water Major microbial players in aquatic habitats include phototrophs, which are critical to primary production, and heterotrophs, which participate in the cycling of carbon in aquatic habitats . such as rivers and streams. Environmental and physicochemical conditions differ greatly across these aquatic environments for example movement of water Aquatic Habitats

7. Aquatic Habitats Physico -chemical factors, such as pH, oxygen availability, salinity (Table 4.2), phosphorus, nitrogen, sulfur, and carbon availability, and macro- and micronutrient availability may differ widely within and across these different habitats.

8. Aquatic Habitats Predation, particularly by protists, and lysis by viruses are two of the major factors that cause mortality in aquatic environment The amount of virus burden has been estimated at 5–25% of the bacterioplankton in aquatic systems, with higher levels recorded for anoxic waters and sediments, where viruses appear to be more important agents of mortality Viruses play a strong role in the regeneration of dissolved organic matter in aquatic systems as they lyse their prey, transforming the carbon and other nutrients in the bodies of their prey

9. The United States Geological Survey (USGS) defines freshwater as water that contains less than 1000 mg/L of dissolved solids. Lakes: Oxygen gradient, Oligotrophic (Low Vegetation) Eutropich (High Nutrient load and may experience oxygen Depletion) The river habitat is made up of several different components, including the horizontal components of (1) the active channel, which in some rivers and streams may go dry part of the year and (2) the riparian zone, which forms a transition zone between the terrestrial and aquatic ecosystems. Vertically, rivers and streams are characterized by (1) surface waters; (2) the hyporheic zone, which lies beneath the surface water; and (3) the phreatic zone, which contains the groundwater. Aquatic Habitats

10. Aquatic Habitats Hot Springs : Hot springs are springs of geothermally heated water, groundwater that comes in contact with hot rocks, or in volcanically active regions, magma, which emerge from Earth’s crust worldwide. Hot springs vent a variety of dissolved gases, providing a range of electron donors such as molecular hydrogen and reduced iron and sulfur compounds Archaeal species find hot springs a prime habitat. Ocean: The ocean’s habitats change with distance from shore and vertical depth . As you move deeper into the ocean you move from the surface or epipelagic zone to the mesopelagic zone (200–1000 m) to the bathypelagic zone (1000–4000 m), to the abyssal zone (4000–6000 m), and finally to the hadean zone (<6000 m). viruses exist in greater numbers than do bacteria and help control the species diversity of bacteria. The role of archaea in the oceans remains largely a mystery.

11. The word soil refers to the loose outer material of Earth’s surface, a layer distinct from the bedrock that lies underneath Soils can be divided into two broad groups : Mineral soils are derived from the weathering of rock and other inorganic materials and organic soils are derived from sedimentation in bogs and marshes. Vegetated soils have at least four components . These include(1) inorganic mineral matter, typically 40% or so of the soil volume;(2) organic matter, usually about 5%; (3) air and water, roughly 50%; and (4) microorganisms and macroorganisms , about 5%. Soil Habitats

12. Depending on size Soil can be divided: Particles range of 0.1–2 mm in diameter are called sand, those between 0.002 and 0.1 mm silt, and those less than 0.002 mm clay. Freezing, thawing, and other physical processes assist in soil formation by forming cracks in the rocks. When the plants die, their remains are added to the soil and become nutrients for more extensive microbial development . Minerals are rendered soluble, and as water percolates, it carries some of these substances deeper into the soil. Soil Habitats

13. Soil Habitats The depth of these layers can vary dramatically , Areas where heavy rainfalls occur, such as the tropics, have nutrient-poor soils because the rains leach nutrients from the soils over time. Permeability of the soil can affect the degree to which nutrients and microorganisms can move around.

14. Each gram of soil has10 9 bacterial cells on average, representing up to 5000 or even 10,000 species of bacteria Microbial abundance in soil varies with physical and chemical characteristics of the microenvironment, including moisture content, abundance of organic matter, and size of soil aggregates. Bacteria in soil have considerable genetic diversity, and many of the physiological groups have yet to be cultivated in the laboratory. Thus, for analysis of the soil community, molecular techniques produce more information than traditional plating exercises. Soil Habitats

15. Two key, major groups of bacteria in soil that have been studied extensively are symbiotic nitrogen fixers and mycorrhizae, which provide 5–20% of grassland and savannah nitrogen and 80% of nitrogen in temperate and boreal forests. At least 20,000 plant species depend on nitrogen and phosphorus derived from symbiotic microorganisms Soil Habitats

16. Rhizobia, including Azorhizobium , Bradyrhizobium , and Rhizobium, are chemoheterotrophs, free-living in the soil or in association with a wide variety of legumes including alfalfa, clover lupines, and soybeans. Plants release chemical compounds to attract soil rhizobia to infect them. Most of the nodules form on root hairs, but some form on stems. Nodules can utilize 7–12% of the plant’s photosynthetic output while active (Coyne 1999), but the return in the form of fixed nitrogen available to the plant is well worth the cost. Soil Habitats

17. Arid Soil: some soils are so dry that plant coverage is greatly limited and only special microbial communities can thrive. These are arid soils, and approximately 35% of Earth’s landmass is permanently or seasonally arid. Arid soils are among the most extreme environments on Earth, with temperature highs in excess of 60°C and lows of -24°C, high insolation (exposure to solar rays), and low water activity. The dominant microorganisms present in these carbon-limited environments are cyanobacteria, with lesser numbers of green algae, fungi, heterotrophic bacteria, lichens, and mosses. Soil Habitats

18. Dryland microbial habitats include biological soil crusts (BSCs) ventral surfaces of translucent stones ( hypolithic colonists), exposed rock surfaces (epilithic colonists), and the interior pore spaces, cracks, and fissures of rocks (endolithic colonists). The soil crusts are dominated by cyanobacterial Microcoleus species, whereas coccoid Chroococcidiopsis species are the predominant endolithic population. The rock colonists play an important role in weathering and soil formation The disruption of BSCs is a major contributor to desertification, a process exacerbated by climate change and human activities. Soil Habitats

19. Endolithic Habitats. Living within the rock seems like a rather unimaginable place to find life, but the pore spaces within rocks are a widespread habitat for microorganisms, which are termed endolithic microorganisms. Radiation from the sun, especially ultraviolet radiation, desiccation, and large variations in temperature are important environmental stressors, which living within rock helps to minimize. Mineral composition of the rock, the nature of the pore spaces, nutrient sources, and climate in which the rocks occur, particularly the frequency of precipitation, influence the nature of the microbial communities that live within the rock. In hot deserts, water often results from overnight condensation, as dew, of moisture in the air, which is absorbed by rocks. Microorganisms colonize a few millimeters to centimeters from the surface of rocks, depending on different abiotic factors, with photosynthetic organisms preferring regions near the surface that receive more light. Rock Habitats

20. Atmospheric Habitats The microbial community of the atmosphere is potentially a vehicle for pathogen transport, but little research has been carried out on this important habitat. Dust storms loft desert soil particles, often with attached microorganisms, high into the air. Many have thought that ultraviolet light, temperature, and desiccation would kill transported microorganisms Various bacteria have been found in atmospherically transported dust, including species of Bacillus, a spore former, genera of Actinobacteria Because of their strong resistance to environmental stresses, many fungal spores are found associated with atmospherically transported dust.

21. Reference