Microbial Ecology PDF

Microbial Ecology Fiona Doody Nov 2024 What is Microbial Ecology  The study of microbes and their interactions with the environment, with each other and with hosts.  Microbes are the tiniest creatures on Earth, yet despite their small size, they have a huge impa...

Microbial Ecology Fiona Doody Nov 2024 What is Microbial Ecology  The study of microbes and their interactions with the environment, with each other and with hosts.  Microbes are the tiniest creatures on Earth, yet despite their small size, they have a huge impact on us and on our environment.  Most types of microbes remain unknown.  It is estimated that we know fewer than 1% of the microbial species on Earth.  Microbes surround us everywhere - air, water, soil.  An average gram of soil contains one billion (1,000,000,000) microbes representing probably several thousand species.  Benefits from understanding microbial ecology In Bangladesh there is a very high incidence of cholera.  Reduction of the incidence by filtering water through old saris.  Vibrio cholera rarely exists for very long freely in water.  They colonise the surfaces of tiny invertebrates called copepods.  The copepods depend on the V. cholera to digest the chitin of their egg cases, releasing their young.  Copepods are much larger than V. cholerae, easier to filter, so by filtering out the copepods the communities indirectly reduced the exposure to V. cholerae. Microbes recycle organic material in aquatic, terrestrial ecosystems providing resources for plants and animals. Agricultural productivity is in a good part dependent on microbial activity in the soil. To preserve the health of the planet we will need to increase our understanding of microbial ecology. Microbial interactions with each other and their many diverse habitats on Earth  Of all the forms of life, microbes grow in the widest range of habitats.  Microbial communities (organisms in a given area) form the foundation of the Earths biosphere (the regions of the earth inhabited by living organisms).  Microbes shape the environments inhabited by plants and animals.  In the oceans, vast quantities of microbes are the primary producers that produce the biomass that ultimately feed fish and humans.  In forests and fields microbes are the main consumers; microbes decompose the majority of plant material, generating fertile soil.  Through their biochemistry, diverse microbes largely determine the quality of soil, air and water. Microbes in Ecosystems  All microbes live within ecosystems – (a community of living organisms in conjunction with the non living (abiotic) components of their environment).  Within an ecosystem, each population fills a specific niche.  Niche is the functional role and position of a species in its environment that describes how the species responds to the distribution of resources and competitors or predators.  For example, the niche of Synechococcus, a cyanobacterium, is that of a free- living marine organism, that fixes CO2 into biomass, while producing molecular oxygen utilised by huge numbers of heterotrophic bacilli.  The habitat of Synechococcus is the upper water layer of the ocean; it’s biomass produces food for protist predators, which in turn feed invertebrates and fish. Ecosystems In all ecosystems (ecosystem is a community of living organisms in conjunction with the non-living components of their environment) microbes associate with animals and plants. Microbes form elaborate symbiotic systems such as;  Mycorrhizae that support and connect roots of plants throughout the forest and fields.  Rhizobia that fix Nitrogen for legumes.  Algae that photosynthesise for the coral reefs  Anaerobes that digest complex plant fibres for termites, cattle and even humans.  Interaction between microbes and their ecosystems 1. Assimilation  Common kinds of assimilation reactions include CO2 fixation and nitrogen fixation.  Organisms that produce biomass (bodies of living things) from inorganic carbon (CO2) are called primary producers.  Primary producers are a key determinant of productivity for other members of an ecosystem.  When an environment lacks an organic source of N or Phosphorus, microbes can assimilate these elements from mineral sources.  Interaction between microbes and their ecosystems 2. Dissimilation  The process of breaking down organic nutrients to inorganic minerals such as Carbon Dioxide (CO2) and Nitrogen Dioxide (NO2-), usually through oxidation.  Microbial dissimilation in soil releases minerals for uptake by plants, and it provides the basis of wastewater treatment (secondary biological treatment). Food webs and Trophic levels  Microbes play very important roles in food webs.  Food web’ shows the links between primary producers (assimilators that produce biomass), consumers and decomposers (dissimilators)  To obtain energy and materials to form biomass, all organisms participate in food webs.  A food web describes the ways in which various organisms consume each other.  The trophic level of an organism is the number of steps it is from the start of the food chain beginning with primary producers.  A food chain is a sequence of organisms through which nutrients and energy pass as one organism eats another. Food web and Trophic Levels  A food chain follows one path of energy and materials between species.  A food web is more complex and is a whole system of connected food chains. In a food web, organisms are placed into different trophic levels.  Trophic levels include different categories of organisms such as producers, consumers, and decomposers Phytoplankton, also known as microalgae, are similar to terrestrial plants in that they contain chlorophyll and require sunlight in order to live and grow. Most phytoplankton are buoyant and float in the upper part of the ocean, where sunlight penetrates the water. Phytoplankton also require inorganic nutrients such as nitrates, phosphates, and sulfur which they convert into proteins, fats, and carbohydrates. Dinoflagellates Diatoms Food web and Trophic Levels  The two main classes of phytoplankton are  dinoflagellates and  diatoms.  Dinoflagellates use a whip-like tail, or flagella, to move through the water and their bodies are covered with complex shells.  Diatoms also have shells, but they are made of a different substance and their structure is rigid and made of interlocking parts.  Diatoms do not rely on flagella to move through the water and instead rely on ocean currents to travel through the water.  In a balanced ecosystem, phytoplankton provide food for a wide range of sea creatures including shrimp, snails, and jellyfish. When too many nutrients are available, phytoplankton may grow out of control and form harmful algal blooms (HABs). These blooms can produce extremely toxic compounds that have harmful effects on fish, shellfish, mammals, birds, andHarmful evenalgal people. blooms of dinoflagellates or diatoms are often called red tides because they can make the water appear red. Dinoflagellates are the most common cause of algal blooms in salt water. Dinoflagellates and diatoms can cause harm to people and animals by making toxins or growing too dense. Trophic levels (number of steps an organism is away from the primary producers)  Trophic levels illustrated in a trophic pyramid where organisms are grouped by the role they play in the food web.  The 1st level in the oceans form the base of the pyramid and is made up of producers (Cyanobacteria, algae and plants).  The 2nd level is made up of herbivorous consumers generally called grazers and directly feed on producers.  The next level of consumers are called predators, feed on grazers.  At each trophic level, some of the organisms die, their bodies are consumed by decomposers, returning carbon and minerals back to the environment to be used by producers. Decomposers are ALL microbes (bacteria and Fungi). Without microbial decomposers carbon and minerals needed by producers (phototrophs) would be locked away in an ever increasing mounds of dead biomass. Instead, all the biomass is recycled. Trophic Levels  On average, only 10% of the energy (calories) from an organism is transferred to its consumer in the next trophic level.  The rest of the energy is lost as waste, movement energy, heat energy and so on.  In the oceans each trophic level supports a smaller number of organisms above it.  This means that a top-level consumer, such as a shark, is supported by millions of primary producers from the base of the food web or trophic pyramid.  Food webs throughout the world all have the same basic trophic levels.  The number and type of species that make up each level varies greatly between different areas and different ecosystems. Trophic Levels  A top-level consumer, such as a tuna, is supported by millions of primary producers from the base of the food web or trophic pyramid. Trophic Levels  Some species in a food web are described as ‘keystone’ species.  A keystone species is one that has a greater impact on a food web than you would expect in relation to their abundance.  The removal of a keystone species characteristically results in a major change, in the same way that removing a keystone from an arch or bridge could cause the structure to collapse.  In Fiordland, the New Zealand sea star is a keystone species that controls the numbers of the species it feeds on, for example, mussels. If the sea star is removed, this can cause a large increase in the numbers of mussels, and this has flow-on effects throughout the food web.  Many scientists investigate food webs in order to better understand how they may be affected by human impacts such as fishing, pollution and tourism. Aquatic Inhabitants Marine environments range from - Deep sea to shallower coastal regions, nutrients are scare in deep sea and abundant in shallower regions. - Seawater contains high salt concentrations, supports growth of halophilic organisms. - Ocean waters are usually oligotrophic, low nutrient levels, limits growth of microorganisms. - Ecology of inshore not as stable as deep oceans, dramatically influenced by nutrient rich runoff, consequence algae and cyanobacteria flourish. Oxygen is consumed and areas become hypoxic. Freshwater microbial communities  Large undisturbed lakes are usually oligotrophic-low in nutrients.  The warm upper layer called the Epilimnion is well mixed, oxygenated relative to the lower layers of water.  It supports oxygenic phototrophs such as algae and cyanobacteria. It reaches about 10m in depth.  At the edge of the lake where the water becomes shallow enough for plants to root is the littoral zone.  A lake that receives large concentrations of runoff from agriculture or septic tanks, becomes eutrophic.  In a eutrophic lake the nutrients support the growth of algae causing an algal bloom.  The algal bloom is consumed by heterotrophic bacteria whose aerobic respiration uses up the dissolved oxygen. This results in anoxic conditions. In a eutrophic lake fish die because of lack of oxygen which heterotrophic microbes have consumed. Such a lake is said to have a high B.O.D. Soil and subsurface microbiology  In soil the major producers are terrestrial plants in contrast to oceans.  Soil is a complex mixture of decaying organic and mineral matter that feeds vast communities of microbes.  The surface or O layer is the organic layer. This layer is in the earliest stage of decomposition,  By primarily fungi and bacteria such as actinomycetes.  The A zone, the aerated zone, the organic particles are in a more advanced stage of decomposition and combine with minerals from levels below.  Decomposers here will have broken down some of the more difficult to digest plant structural components such as lignin.  In well drained soils both the O zone and A zone are well oxygenated and full of nutrients liberated by the decomposers and used by plants.  In between the soil particles in the O and a zones ar air spaces that provide access to oxygen, allowing aerobic respiration. Soil and subsurface microbiology  Each particle of soil supports miniature colonies, biofilms, and filamentous bacteria and fungi that interact with each other and the roots of plants.  Below the aerated layers is the eluviated E horizon which experiences periods of water saturation from rain.  Rainwater leaches (dissolves and removes) some of the organic and mineral nutrients from the upper layers.  Below the E horizon lie increasing proportions of mineral and rock fragments broken off from the bedrock below.  These lower layers experience increased water saturation, forming the water table.  Prolonged water saturation generates anoxic conditions.  The anoxic, water saturated layer contains mainly lithotrophs and anaerobic heterotrophs.  The soil layers final end in bedrock, a source of mineral nutrients such as carbonates and iron.  Bedrock is actually permeated with endolithic microbes (down 3km). Soil and subsurface microbiology Soil Food Web  Top horizons feature complex food webs.  Major producers are green plants.  Their leaves generate a detritus that is decomposed by fungi, such as Mycena species, and bacteria like actinomycetes.  The actinomycetes include Streptomycetes.  Besides fallen leaves another source of organic matter for plants is the rhizosphere, the region surrounding the plant roots.  The rhizosphere contains proteins and sugars released by the roots as well as sloughed-off plant cells.  These materials feed large numbers of bacteria, which then cycle minerals back to the plant.  Bacteria in the rhizosphere may also discourage plant pathogens by producing antibiotics.  At the next trophic level, bacteria feeding on leaf detritus and root exudates are preyed upon by protists and nematodes.  Diverse predators such as nematodes, fungi and protists exhibit different preferences for bacteria, fungi or protists as prey.  Vampirella protists drill holes in the hyphae of fungi and suck out the nutrients Soil Food Web  Parasitic fungi prey on plants  Besides predation there also exists mutualistic relationships like the mycorrhizal association of fungi with plant roots.  Microorganisms co-operate with each other to form microbial mats and biofilms.  They ultimately feed invertebrates, which feed larger invertebrates and predators like earthworms,. Such predators enhance the soil quality by turning over the matter, aerating soil the soil particles etc. Decomposition of lignin to humus  A critical role of fungal decomposers (saprophytes) is the breakdown of extremely complex structural components of vascular plants such as grass and trees. Trees in particular store vast reserves of biomass in a form that is difficult to digest called lignin.  Lignins are particularly important in the formation of cell walls, especially in wood and bark, because they lend rigidity and do not rot easily  Fungal and bacterial decomposers have the enzymes to digest lignin. Examples, white rot fungi and actinomycete soil bacteria.  The prevalence of lignin is one reason why fungi play a bigger role in terrestrial ecosystems than in marine ecosystems.  Lignin is broken down into phenolic molecules called humus.  Humus degrades slowly and provides a steady slow release supply of nutrients for plant growth.  The first phase of lignin degradation occurs within a year of deposition in the soil, the remaining components degrade at a rate of 5% per year. The rhizosphere is the narrow zone of soil surrounding plant roots that is characterised by root exudation and an abundance of saprophytic, pathogenic and symbiotic bacteria and fungi. These include rhizobia that form nodules, and arbuscular mycorrhizal fungi (AMF). The rhizoplane describes the root surface in contact with the soil. Microbes associated with roots.  The environment surrounding a plant root can be divided into two regions, The rhizosphere (5mm) and the rhizoplane, the root surface.  The rhizosphere, the region of soil outside the root but influenced by root exudates.  Particular bacterial species are adapted to these environments.  The rhizosphere is the narrow zone of soil surrounding plant roots that is characterised by root exudation and an abundance of micro-organisms which can be beneficial or harmful to plants, or have no effect on root growth and function.  The roots of around 90% of higher plants form a symbiotic association with mycorrhizal fungi.  These fungi colonise roots, with the colonised root being termed a “mycorrhiza”.  The fungi benefit from the provision of plant carbon.  The host plant may benefit in many ways, but the primary benefit is most often the ability to access inorganic nutrients from soil beyond the rhizosphere due to their transport into the root by hyphae of the fungi.  Mycorrhizal associations are present in plants in both natural ecosystems and modern agricultural systems; although their occurrence in the latter may be reduced by common management practices, especially the addition of fertiliser.  Microbes associated with roots. The rhizosphere is the narrow zone of soil surrounding plant roots that is characterised by root exudation and an abundance of saprophytic, pathogenic and symbiotic bacteria and fungi. These include rhizobia that form nodules, and arbuscular mycorrhizal fungi (AMF). The rhizoplane describes the root surface in contact with the soil. Mycorrhiza – The Fungal Internet  Fungal mycelia that associate intimately with plant roots, extending access to minerals while in return obtaining energy rich products of plant photosynthesis.  Ectomycorrhizae colonise the rhizoplane, the surface of the rootlets but never penetrate the root. Ectomycorrhizal fungi include ascomycetes such as truffles, and basidiomycetes such as stinkhorns.  Plants with ectomycorrhizae invest less of their body mass in roots and more in the above ground stems and leaves.  Endomycorrhizae penetrate plant cells deep within the cortex (outer layer of a stem or root in a plant, lying below the epidermis but outside the vascular bundles).  They exist entirely underground (do not form fruiting bodies) and completely lack a Sexual cycle.  They acquire around 2% of the photosynthetic product of their host in exchange for tremendous expansion and access to soil resources.(minerals, water).  Nutrient Cycles – Biogeochemical Cycling  The ways in which an element—or compound such as water—moves between its various living and nonliving forms and locations in the biosphere is called a biogeochemical cycle.  Biogeochemical cycles important to living organisms include the water, carbon, nitrogen, phosphorus, and sulfur cycles.  Energy flows directionally through Earth’s ecosystems, typically entering in the form of sunlight and exiting in the form of heat.  The ways in which an element—or, in some cases, a compound such as water—moves between its various living and nonliving forms and locations is called a biogeochemical cycle.  Carbon Cycle  Carbon exists in the air largely as carbon dioxide—gas (CO2), which dissolves in water and reacts with water molecules to produce bicarbonate—(HCO-).  Photosynthesis by land plants, bacteria, and algae converts carbon dioxide or bicarbonate into organic molecules. Organic molecules made by photosynthesizers are passed through food chains, and cellular respiration converts the organic carbon back into carbon dioxide gas.  Carbon enters all food webs, both terrestrial and aquatic, through autotrophs, or self-feeders. Almost all of these autotrophs are photosynthesizers, such as plants or algae.  Autotrophs capture carbon dioxide from the air or bicarbonate ions from the water and use them to make organic compounds such as glucose. Heterotrophs, or other-feeders, such as humans, consume the organic molecules, and the organic carbon is passed through food chains and webs. How does carbon cycle back to the atmosphere or ocean? To release the energy stored in carbon-containing molecules, such as sugars, autotrophs and heterotrophs break these molecules down in a process called cellular respiration. In this process, the carbons of the molecule are released as carbon dioxide. Decomposers also release organic compounds and carbon dioxide when they break down dead organisms and waste products.  Nitrogen Cycle  Nitrogen is a key component of the bodies of living organisms. Nitrogen atoms are found in all proteins and DNA.  Nitrogen exists in the atmosphere as N2 gas. In nitrogen fixation, bacteria convert N2into ammonia, a form of nitrogen usable by plants. When animals eat the plants, they acquire usable nitrogen compounds.  Nitrogen is a common limiting nutrient in nature, and agriculture. A limiting nutrient is the nutrient that's in shortest supply and limits growth. Bacteria play a key role in the nitrogen cycle.  Nitrogen enters the living world by way of bacteria and other single-celled prokaryotes, which convert atmospheric nitrogen(N2) into biologically usable forms in a process called nitrogen fixation.  Some species of nitrogen-fixing bacteria are free-living in soil or water, while others are beneficial symbionts that live inside of plants. Examples  Photosynthetic cyanobacteria are found in most aquatic ecosystems that get sunlight, and they play a key role in nitrogen fixation.  Another type of bacteria, Rhizobium, live symbiotically in the roots of legume plants—like peas, beans, and peanuts—and provide them with fixed nitrogen.  Free-living bacteria in the genus Azotobacter are also key nitrogen fixers in terrestrial—land-based—ecosystems.  Nitrogen Cycle Nitrogen-fixing microorganisms capture atmospheric nitrogen by converting it to ammonia—NH3 which can be taken up by plants and used to make organic molecules.  The nitrogen-containing molecules are passed to animals when the plants are eaten. They may be incorporated into the animal's body or broken down and excreted as waste, such as the urea found in urine.  Nitrogen doesn't remain forever in the bodies of living organisms. Instead, it's converted from organic nitrogen back into N2 gas by bacteria.  This process often involves several steps in terrestrial—land—ecosystems. Nitrogenous compounds from dead organisms or wastes are converted into ammonia(NH3) by bacteria, and the ammonia is converted into nitrites and nitrates.  In the end, the nitrates are made into gas by denitrifying prokaryotes. Phosphorus Cycle  Phosphorus is found mostly in the form of phosphate ions—PO34  Phosphate compounds are found in sedimentary rocks, and as the rocks weather—wear down over long time periods—the phosphorus they contain slowly leaches into surface water and soils. Volcanic ash, aerosols, and mineral dust can also be significant phosphate sources, though phosphorus has no real gas phase, unlike other elements such as carbon, nitrogen, and sulfur.