Nutrient Cycle - PDF

UNIT 9: NUTRIENT CYCLE Presented by: Fadulla, Thricia Marie Failangca, D C Rey Gacita, Novem Marie Garcia, Rodmar More, Ryka Janelle Padernal, Mark Kevin Table of contents 01 02 03 Carbon, Humans and Nitrogen, and Other Nutrient Nutrient Sulfur Cycles Cycles Cycling INTRODUCTION What is Nutrient Cycle? The nutrient cycle, or biogeochemical cycle, is an essential ecological process that involves the movement and transformation of vital nutrients like carbon, nitrogen, phosphorus, and sulfur through the atmosphere, lithosphere, hydrosphere, and biosphere. These cycles are crucial for maintaining the health of ecosystems. For example, plants absorb nutrients from the soil, which are then consumed by herbivores. When these organisms die or produce waste, decomposers break down the organic matter, returning the nutrients to the soil, where the cycle begins again. This continuous ﬂow supports biodiversity, ecological balance, and the sustainability of life on Earth. Without the nutrient cycle, ecosystems would collapse, and life as we know it wouldn't be possible. 01 Carbon, Nitrogen, and Sulfur Cycles Carbon, Nitrogen, and Sulfur Cycles The key nutrients for life, including carbon, nitrogen, and phosphorus, are cycled by both microorganisms and macroorganisms, with microbial activities playing a dominant role in each cycle. Carbon cycle- microorganisms decompose organic matter, releasing carbon dioxide into the atmosphere and facilitating its uptake by plants through photosynthesis, which is crucial for sustaining life Nitrogen cycle- involves nitrogen-ﬁxing bacteria converting atmospheric nitrogen into forms usable by plants, while other microbes play roles in nitriﬁcation and denitriﬁcation, maintaining nitrogen availability in soils essential for plant growth Phosphorus cycle- microbes help solubilize phosphorus from organic and inorganic forms, making it accessible to plants, which is vital for energy transfer and photosynthesis The Carbon Cycle On a global basis, carbon (C) cycles serve as CO2 through all of Earth’s major carbon reservoirs: the atmosphere, the land, the oceans, freshwaters, sediments and rocks, and biomass. As we have already seen for freshwater environments, the carbon and oxygen cycles are intimately linked. All nutrient cycles link in some way to the carbon cycle, but the nitrogen (N) cycle links particularly strongly because, other than water (H2O), Carbon and Nitrogen make up the bulk of living organisms. The Carbon Cycle Figure 21.1 The carbon cycle. The carbon and oxygen cycles are closely connected, as oxygenic photosynthesis both removes CO2 and produces O2, and respiration both produces CO2 and removes O2. Carbon Reservoirs The largest carbon reservoir on Earth is the sediments and rocks of the Earth's crust, but the rate of carbon release from this reservoir as CO₂ is very slow, making it insigniﬁcant on a human timescale. A signiﬁcant amount of carbon is also found in land plants, which are key sites for photosynthetic CO₂ ﬁxation. Interestingly, more carbon exists in dead organic material, known as humus, than in living organisms. Humus, derived mainly from dead plants and microorganisms, is a complex mixture of organic materials that resist rapid decomposition. While some humic substances take decades to decompose, others break down much more quickly. Carbon Reservoirs The most rapid means of transfer of Carbon is via the atmosphere. Carbon dioxide is removed from the atmosphere primarily by photosynthesis of land plants and marine microorganisms and is returned to the atmosphere by respiration of animals and chemoorganotrophic microorganisms. The single most important contribution of CO2 to the atmosphere is by microbial decomposition of dead organic material. However, since the Industrial Revolution, human activities have increased atmospheric CO2 levels by nearly 40%, primarily from the combustion of fossil fuels. This rise in CO2, a major greenhouse gas, has triggered a period of steadily increasing global temperatures called global warming. Photosynthesis and Decomposition New organic compounds on Earth are exclusively produced through CO2 ﬁxation by phototrophs and chemolithotrophs. Most organic compounds originate in photosynthesis and thus phototrophic organisms are the foundation of the carbon cycle. However, phototrophic organisms are abundant in nature only in habitats where light is available. The deep sea, deep terrestrial subsurface, and other permanently dark habitats are devoid of indigenous phototrophs. There are two groups of oxygenic phototrophic organisms: - Plants: dominant phototrophic organisms of terrestrial environments - Microorganisms: dominate in aquatic environments Photosynthesis and Decomposition The redox cycle for Carbon begins with photosynthetic CO2 ﬁxation, driven by the energy of light: CO2 + H2O → (CH2O) + O2 Formaldehyde (CH2O) represents organic matter at the oxidation–reduction level of cell material. Phototrophic organisms also carry out respiration, both in the light and the dark. The overall equation for respiration is the reverse of oxygenic photosynthesis: (CH2O) + O2 → CO2 + H2O Photosynthesis and Decomposition Figure 21.2 Redox cycle for carbon. The diagram contrasts autotrophic processes (CO2 → organic compounds) and heterotrophic processes (organic compounds → CO2). Photosynthesis and Decomposition For organic matter to accumulate, photosynthesis must outpace respiration, allowing autotrophic organisms to convert CO2 into biomass. This biomass then provides carbon for heterotrophic organisms. While anoxygenic phototrophs and chemolithotrophs also generate organic compounds, their contributions are generally minor compared to those of oxygenic phototrophs, which beneﬁt from the abundant supply of water (H2O) as a reductant. Photosynthesis and Decomposition Organic compounds are degraded biologically to: Methane (CH4)= produced in anoxic environments by methanogens from the reduction of CO2 with hydrogen (H2) or from the splitting of acetate into methane (CH4) and carbon dioxide (CO2) Carbon Dioxide (CO2)= which is of microbial origin, is produced by aerobic and anaerobic respirations Photosynthesis and Decomposition However, any naturally occurring organic compound can eventually be converted to methane (CH4) from the cooperative activities of methanogens and various fermentative bacteria. Methane produced in anoxic habitats is insoluble and most often diffuses rapidly to oxic environments where it is either released to the atmosphere or oxidized to CO2 by methanotrophs. Hence, most of the Carbon in organic compounds eventually returns to CO2, and the links in the carbon cycle are closed. Methane Hydrates Although present in the atmosphere at levels lower than even CO2, methane (CH4) is a potent greenhouse gas that is over 20 times more effective in trapping heat than is CO2. Some CH4 enters the atmosphere from methanogenic production, but not all biologically produced CH4 is immediately consumed or released to the atmosphere. Huge amounts of CH4 derived primarily from past microbial activities are trapped underground or Figure 21.3 Burning methane under marine sediments as methane hydrates, hydrate. Frozen methane ice molecules of frozen CH4. retrieved from marine sediments is ignited. Methane Hydrates Methane hydrates form when sufficient methane (CH4) is present in environments of high pressure and low temperature such as beneath the permafrost in the Arctic and in marine sediments. These deposits can be up to several hundred meters thick and are estimated to contain 700–10,000 petagrams (1 petagram = 1015 g) of methane (CH4). Figure 21.3 Burning methane This exceeds other known methane (CH4) hydrate. Frozen methane ice retrieved from marine sediments is reserves on Earth by several orders of ignited. magnitude. Methane Hydrates Methane hydrates are highly dynamic, absorbing and releasing methane (CH4) in response to changes in pressure, temperature, and ﬂuid movement. Methane hydrates also fuel deep-water ecosystems, called cold seeps. The slow release of methane (CH4) from seaﬂoor hydrates nourishes not only anaerobic methane-oxidizing Archaea, but also animal Figure 21.4 Seasonal flares of methane communities that contain aerobic bubbling from methane hydrates. Methane methane-oxidizing endosymbionts that hydrates in shallow coastal sediments are sensitive to seasonal changes in bottom water oxidize methane (CH4) and release organic temperature. Flares of methane bubbles are matter to the animals. observed when water temperatures warm by as little as 1–2°C. Methane Hydrates Anaerobic oxidation of methane (CH4) is coupled to the reduction of sulfate (SO42-), nitrate (NO3-), and oxides of iron and manganese [e.g., FeO(OH)], dampening release of free methane. Although deep oceanic methane hydrates are stabilized by high pressure, hydrates in shallower coastal sediments are much more sensitive to small changes in temperature. Figure 21.4 Seasonal flares of methane Hydrates in shallow sediments are at the bubbling from methane hydrates. Methane hydrates in shallow coastal sediments are margin of what is called the gas hydrate sensitive to seasonal changes in bottom water temperature. Flares of methane bubbles are stability zone (GHSZ). observed when water temperatures warm by as little as 1–2°C. Methane Hydrates During periods of seasonally elevated water temperature, methane was observed to bubble freely (a phenomenon called methane ﬂares) from the sediments. In addition to the release of methane from marine hydrates, as permafrost melts, its huge reserve of organic Figure 21.4 Seasonal flares of methane matter could be catabolized by bubbling from methane hydrates. Methane hydrates in shallow coastal sediments are microbes, leading to the formation of sensitive to seasonal changes in bottom water temperature. Flares of methane bubbles are yet more methane. observed when water temperatures warm by as little as 1–2°C. Carbon Balances and Coupled Cycles While it's useful to view carbon cycling as distinct from other nutrient cycles, all nutrient cycles are interconnected, and changes in one can impact others. The carbon and nitrogen cycles are particularly closely linked due to the signiﬁcant amounts of carbon and nitrogen present in living organisms. The rate of primary productivity (CO2 ﬁxation) is controlled by several factors: magnitude of photosynthetic biomass and by available Nitrogen, often a limiting nutrient. Thus, large scale reductions in biomass, for instance by widespread deforestation, reduce rates of primary productivity and increase levels of CO2. Carbon Balances and Coupled Cycles High levels of organic Carbon stimulate microbial nitrogen ﬁxation (N2 → NH3) and this in turn adds more ﬁxed Nitrogen to the pool for primary producers. Low levels of organic Carbon have just the opposite effect. High levels of ammonia (NH3) stimulate primary production and nitriﬁcation, but inhibit nitrogen ﬁxation. High levels of nitrate (NO3-), an excellent Nitrogen source for plants and aquatic phototrophs, stimulate Figure 21.5 Coupled cycles. All nutrient primary production but also increase the rate of cycles are interconnected, but the carbon denitriﬁcation; the latter removes ﬁxed forms of and nitrogen cycles are intimately coupled. In the carbon cycle, CO2 supplies the Nitrogen from the environment and feeds back in a Carbon for carbon compounds. The negative way on primary production. Nitrogen cycle supplies nutrient for many biological compounds. Syntrophy and Methanogenesis Organic compounds are primarily oxidized by aerobic microbes. However, due to limited oxygen solubility and rapid consumption, much organic carbon ends up in anoxic environments. In anoxic conditions, methanogenesis becomes a major process, where Archaea (methanogens) produce CH₄ as they are strict anaerobes. Methanogenesis is signiﬁcant in anoxic ecosystems, helping convert organic carbon to methane. Syntrophy and Methanogenesis Most methanogens use CO₂ as a terminal electron acceptor in anaerobic respiration, reducing it to CH₄ with H₂ as the electron donor. Only a few substrates, primarily acetate, can be directly converted to CH₄ by methanogens. To convert most organic compounds to CH4, methanogens must team up with partner organisms called syntrophs that function to supply them with precursors for methanogenesis. ❏ Anoxic Decomposition and Syntrophy Organic compounds such as polysaccharides, proteins, lipids, and nucleic acids from dead organisms enter anoxic habitats, where they undergo catabolism. Through hydrolysis, these polymers release monomers that serve as key electron donors for energy metabolism in anaerobic environments. The breakdown of cellulose a typical polysaccharide begins with cellulolytic bacteria that hydrolyze it into glucose. Fermentative organisms then catabolize glucose into short-chain fatty acids (acetate, propionate, butyrate), alcohols (ethanol, butanol), and gases such as H₂ and CO₂. While methanogens can directly consume H₂ and acetate, they cannot directly break down fatty acids and alcohols. ❏ Anoxic Decomposition and Syntrophy Syntrophic bacteria step in to help catabolize the remaining fatty acids and alcohols, acting as secondary fermenters. These bacteria ferment the products of primary fermenters, producing H₂, CO₂, and acetate as byproducts. For example, Syntrophomonas wolfei oxidizes C₄ to C₈ fatty acids, yielding acetate and H₂ (and CO₂ when the fatty acid is C₅ or C₇). Other Syntrophomonas species can utilize longer fatty acids, up to C₁₈, including some unsaturated fatty acids. Syntrophobacter wolinii specializes in propionate (C₃) fermentation, generating acetate, CO₂, and H₂. Meanwhile, Syntrophus gentianae degrades aromatic compounds like benzoate, breaking them down into acetate, H₂, and CO₂, thus broadening the range of compounds metabolized in anoxic environments. ❏ Anoxic Decomposition and Syntrophy ❏ Anoxic Decomposition and Syntrophy Syntrophs have diverse metabolic abilities but cannot perform their reactions in pure culture; they rely on an H₂-consuming partner due to the unique bioenergetics of syntrophy. The presence of a partner organism is essential for syntrophic bacteria to grow, as it consumes H₂, thereby facilitating energy production. The association between H₂ producers and H₂ consumers can be very close, with some suggesting direct electron transfer via conductive structures instead of H₂ gas transfer. In standard conditions, the free-energy change (ΔG°) for syntrophic reactions with compounds like butyrate, propionate, ethanol, and benzoate is positive, meaning they would normally require energy rather than release it. However, H₂ consumption by the partner organism shifts the energetics to become favorable. With H₂ concentrations near zero, the reaction's free-energy change (ΔG) becomes negative, enabling the syntrophic bacterium to conserve energy and produce ATP. ❏ Anoxic Decomposition and Syntrophy The ﬁnal products of the syntrophic partnership are CO₂ and CH₄. Any organic compound entering a methanogenic habitat will ultimately be converted to these products, including complex aromatic and aliphatic hydrocarbons. While various organisms may participate in degradation, the process leads to the generation of fatty acids and alcohols, which are converted to methanogenic substrates by syntrophs. Acetate, produced by syntrophs and acetogenic bacteria (as noted in Figure 21.6 and Section 14.16), is a direct methanogenic substrate, which is then converted by methanogens into CO₂ and CH₄. ❏ Methanogenic Symbionts and Acetogens in Termites A variety of anaerobic protists, such as ciliates and ﬂagellates, thrive in strictly anoxic conditions and play a signiﬁcant role in the carbon cycle. Methanogenic Archaea inhabit some of these protist cells as H2-consuming endosymbionts. For instance, methanogens are found within trichomonal protists residing in the hindgut of termites , where methanogenesis and acetogenesis are key metabolic processes. The methanogenic symbionts in these protists belong to the genera Methanobacterium or Methanobrevibacter. ❏ Methanogenic Symbionts and Acetogens in Termites In the termite hindgut, endosymbiotic methanogens along with acetogenic bacteria are thought to beneﬁt their protist hosts by consuming H2 generated from glucose fermentation by cellulolytic protists. The acetogens are not endosymbionts but instead reside in the termite hindgut itself, consuming H2 from primary fermenters and reducing CO2 to make acetate. Unlike methanogens, acetogens can ferment glucose directly to acetate. Acetogens can also ferment methoxylated aromatic compounds to acetate. This is especially important in the termite hindgut because termites live on wood, which contains lignin, a complex polymer of methoxylated aromatic compounds. The acetate produced by acetogens in the termite hindgut is consumed by the insect as its primary carbon and energy source. ❏ Methanogenic Symbionts and Acetogens in Termites The Nitrogen Cycle Nitriﬁcation Ammoniﬁcation Denitriﬁcation Anammox Nitrogen Fixation Nitrogen Cycle Nitrogen is an essential element for all living organisms, primarily found in amino acids, nucleic acids, and proteins. It exists in various oxidation states, which are crucial for different biological processes. Nitrogen gas is the most stable form of N and is a major reservoir for N on Earth. However, only a relatively small number of Bacteria and Archaea are able to use N2 as a cellular N source by the process of nitrogen ﬁxation. The N recycled on Earth is mostly already "ﬁxed N"; that is, N in combination with other elements, such as in ammonia (NH3) or nitrate (NO3) In many environments, however, the short supply of ﬁxed N puts a premium on biological nitrogen ﬁxation, and in these habitats, nitrogen-ﬁxing bacteria ﬂourish. Key Processes in Nitrogen Cycle Nitriﬁcation The biological oxidation of ammonium (NH₄⁺) to nitrate (NO₃⁻). Stages: First Step: Ammonium is oxidized to nitrite (NO₂⁻) by bacteria such as Nitrosomonas and Nitrosopumilus (Archaea). Second Step: Nitrite is further oxidized to nitrate by bacteria like Nitrobacter. Environmental Role: Nitriﬁcation is crucial for converting ammonia, which can be toxic at high concentrations, into nitrate, which is more readily taken up by plants. Denitriﬁcation The process by which nitrates (NO₃⁻) are reduced to nitrogen gas (N₂) or nitrous oxide (N₂O). Key Organisms: Includes Bacillus, Pseudomonas, and Paracoccus. Process: - Under anaerobic conditions, denitrifying bacteria use nitrate as an electron acceptor, reducing it to gaseous forms. Environmental Consequences: - Negative Impacts: Can lead to the loss of ﬁxed nitrogen from soils, especially in waterlogged agricultural ﬁelds, potentially reducing soil fertility. - Positive Uses: In wastewater treatment, denitriﬁcation helps minimize ﬁxed nitrogen in discharge waters, reducing algal blooms caused by excess nutrients. - Greenhouse Gas Emission: Nitrous oxide (N₂O) contributes signiﬁcantly to global warming, being approximately 300 times more effective than CO₂ in trapping heat. Nitrogen Fixation The conversion of atmospheric nitrogen (N₂) into ammonia (NH₃). Key Organisms: - Bacteria such as Rhizobium (symbiotic with legumes), Azotobacter, and cyanobacteria. Process: - Nitrogen-ﬁxing bacteria possess the enzyme nitrogenase, which facilitates the conversion of N₂ into NH₃, making nitrogen available to plants. Importance: Essential in ecosystems where nitrogen is limited, allowing for the growth of nitrogen-dependent organisms. Ammoniﬁcation The process of converting organic nitrogen compounds (e.g., from dead organisms) back into ammonium (NH₄⁺). Key Processes: - Occurs during the decomposition of organic matter, such as amino acids and nucleotides. - Involves various microorganisms, including bacteria and fungi. Role in the Cycle: Ammoniﬁcation returns nitrogen to the soil, making it available for nitriﬁcation and plant uptake. Anammox (Anaerobic Ammonium Oxidation) A process that converts ammonium (NH₄⁺) and nitrite (NO₂⁻) directly into nitrogen gas (N₂). Key Organisms: Bacteria such as Brocadia. Signiﬁcance: Anammox is an important process in nitrogen removal in wastewater treatment, helping to reduce nitrogen loading in aquatic systems. Ammonia Fluxes Release of Ammonia: Ammonia (NH₃) is generated during the decomposition of organic nitrogen compounds. Volatility: NH₃ is volatile and can be lost to the atmosphere, particularly in alkaline soils or areas with high animal populations (e.g., cattle feedlots). Global Contribution: On a global scale, ammonia represents about 15% of the nitrogen released into the atmosphere, with the majority being nitrogen gas (N₂) or nitrous oxide (N₂O) from denitriﬁcation. Environmental Impacts of the Nitrogen Cycle Global Warming: The release of nitrous oxide (N₂O) from denitriﬁcation contributes to climate change due to its high global warming potential. Ozone Layer Depletion: Nitric oxide (NO) produced during denitriﬁcation reacts with ozone (O₃) in the upper atmosphere, leading to the formation of nitrite (NO₂) and contributing to ozone depletion. Soil Acidity: Increased nitrogen deposition can lead to soil acidiﬁcation, which affects microbial communities and alters soil fertility, impacting plant diversity and agricultural productivity. The Sulfur Cycle Sulfur Cycle The sulfur cycle involves complex microbial transformations of sulfur (S), which are more intricate than those of nitrogen (N) due to the numerous oxidation states of sulfur. Key processes include both biotic and abiotic transformations, including chemolithotrophic oxidation and sulfate reduction. Key Oxidation States of Sulfur −2: Sulfhydryl (R-SH) and sulﬁde (HS⁻) 0: Elemental sulfur (S⁰) +6: Sulfate (SO₄²⁻) The majority of sulfur on Earth is found in minerals like gypsum (CaSO₄) and sulﬁde minerals (e.g., pyrite, FeS₂). Oceans are the primary reservoir of sulfate (SO₄²⁻), while human activities, particularly fossil fuel combustion, introduce sulfur dioxide (SO₂) into the cycle. Hydrogen Sulﬁde and Sulfate Reduction Hydrogen Sulﬁde (H₂S): A major volatile sulfur gas produced through bacterial sulfate reduction or geochemical processes from sulﬁde springs and volcanoes. pH Inﬂuence: H₂S predominates below pH 7. - Non-volatile HS⁻ and S²⁻ dominate above pH 7. - These forms are collectively referred to as "sulﬁde." Sulfate-Reducing Bacteria A diverse group crucial for sulfate reduction, especially in anoxic environments like freshwater sediments. Sulfate reduction is limited by the availability of sulfate (SO₄²⁻) and requires organic electron donors. Environmental Impact Sulfate Reduction in Marine Sediments: Typically carbon-limited, but can be increased by organic matter inﬂux, which may result from sewage disposal. Toxicity of Hydrogen Sulﬁde: H₂S is harmful to many organisms as it inhibits respiration by binding with iron in cytochromes. It is often detoxiﬁed by forming insoluble minerals like FeS (pyrrhotite) and FeS₂ (pyrite), which contribute to the black coloration of sulﬁdic sediments. Sulﬁde and Elemental Sulfur Oxidation–Reduction Oxidation of Sulﬁde Oxic Conditions: Under aerobic conditions, sulﬁde (H₂S) rapidly oxidizes spontaneously at neutral pH. Catalysis by Bacteria: Sulfur-oxidizing chemolithotrophic bacteria, primarily aerobic, facilitate this oxidation process. Microbial Signiﬁcance: Microbial oxidation of sulﬁde is particularly signiﬁcant in areas where H₂S from anoxic environments comes into contact with air. Anoxic Oxidation Phototrophic Bacteria: In light-available conditions, anoxic oxidation of sulﬁde can occur, catalyzed by phototrophic purple and green sulfur bacteria. Environmental Impact of S⁰ Oxidation Formation of Sulfuric Acid: The oxidation of S⁰ leads to the production of sulfuric acid (H₂SO₄), which signiﬁcantly lowers the pH of the environment. Soil Acidiﬁcation: Small amounts of S⁰ can be added to alkaline soils as a natural method to lower pH, utilizing sulfur chemolithotrophs for the acidiﬁcation process. Reduction of Elemental Sulfur Anaerobic Respiration: S⁰ can also be reduced to sulﬁde (HS⁻), a process important for some bacteria and hyperthermophilic archaea. Specialized Sulfur Reducers: While sulfate-reducing bacteria can reduce S⁰, most reduction occurs via specialized sulfur reducers that do not reduce sulfate (SO₄²⁻). Ecological Guild: The habitats of sulfur reducers typically overlap with those of sulfate reducers, creating a metabolic guild uniﬁed by the production of hydrogen sulﬁde (H₂S). Important Points Oxidation and Reduction Dynamics: The processes of oxidation and reduction of sulﬁde and elemental sulfur are crucial for sulfur cycling in various environments. Role of Microbial Communities: Bacterial communities play a vital role in both the oxidation of sulﬁde and the reduction of elemental sulfur, inﬂuencing ecological and environmental dynamics. pH Modiﬁcation: The oxidation of S⁰ can signiﬁcantly affect soil pH, making it a useful tool for agricultural practices aimed at soil acidiﬁcation. Iron and Manganese Cycle Iron and Manganese Cycle Overview of Iron (Fe): Abundant element in Earth's crust. Exists primarily in two oxidation states: ○ Ferrous (Fe²⁺ or Fe(II)) ○ Ferric (Fe³⁺ or Fe(III)) A third state, Fe⁰, is found in Earth’s core and is produced by human activities (e.g., smelting iron ores). Iron Cycling: Iron cycles mainly between Fe²⁺ and Fe³⁺. Redox transitions involve one-electron oxidations and reductions: ○ Ferric iron (Fe³⁺) can be reduced chemically or through anaerobic respiration. ○ Ferrous iron (Fe²⁺) can be oxidized chemically or through chemolithotrophic metabolism. Iron and Manganese Cycle Overview of Manganese (Mn) Abundance: Manganese is present at 5- to 10-fold lesser abundance than iron in the near-surface environment. Exists primarily in two states: ○ Manganese (Mn²⁺) ○ Manganese (Mn⁴⁺) Key Features of Iron and Manganese Cycles: Solubility Differences: ○ Reduced forms (Fe²⁺ and Mn²⁺) are soluble. ○ Oxidized forms (iron oxides like Fe(OH)₃, Fe₂O₃ and manganese oxide MnO₂) are insoluble and settle in aquatic environments. Sediment Composition: ○ Oxidized minerals can comprise several percent of marine and freshwater sediments. ○ They act as significant electron acceptors in anoxic systems. Bacterial Reduction of Iron and Manganese Oxides Certain Bacteria and Archaea can utilize ferric iron (Fe³⁺) as an electron acceptor during anaerobic respiration. Many of these organisms are also capable of using manganese (Mn⁴⁺) and, in some cases, reducing oxidized uranium. Common Environments: ○ Ferric iron and manganese oxide reduction typically occurs in waterlogged soils, bogs, and anoxic lake sediments. ○ In these environments, microorganisms facilitate the transformation of these metals through reduction processes. When soluble reduced iron and manganese reach oxic regions, for example, through diffusion from anoxic regions of sediments, they are oxidized chemically or microbiologically The chemical oxidation of Fe2+ is very rapid at near-neutral pH. Although the spontaneous oxidation of Mn2+ is very slow at neutral pH, the rate of oxidation can be increased up to five orders of magnitude by a variety of manganese-oxidizing bacteria and even fungi. Precipitation and Recycling Precipitation: ○ The oxidized metal oxides and hydroxides precipitate out of solution, returning to sediments. ○ This process completes the cycle, allowing metals to once again act as electron acceptors. Bacterial Reduction of Iron and Manganese Oxides Reactivity of Oxidized Metals: ○ Ferric Iron (Fe³⁺) and Manganese (Mn⁴⁺) are highly reactive. ○ Phosphate Trapping: Oxidized iron can form insoluble ferric phosphate, effectively trapping phosphates. ○ Manganese oxides can oxidize refractory organic compounds, potentially releasing more accessible carbon sources for microbial growth. Interactions with Other Metals Other metals (e.g., Cu, Cd, Co, Pb, As) can form insoluble complexes with iron and manganese oxides. Upon reduction of these oxides, bound phosphates and soluble forms of these metals can be released back into the environment. Bacterial Reduction of Iron and Manganese Oxides Conductive Properties of Bacterial Cells Some bacteria, such as Geobacter, exhibit electrically conductive surfaces and appendages that can function as “nanowires.” This allows for efficient electron transfer in microbial habitats, essentially creating a form of electricity. Potential applications include commercial power generation. Role of Humic Substances Humic substances can facilitate microbial metal reduction: ○ Some components of humics can alternate between oxidized and reduced forms, acting as electron shuttles. ○ This enhances the efficiency of the reduction process, linking the microbial community to metal transformations. Microbial Oxidation of Reduced Iron and Manganese Ferrous Iron (Fe²⁺) Oxidation: ○ At neutral pH, Fe²⁺ is rapidly oxidized abiotically in oxic environments. ○ In acidic conditions (pH < 4), Fe²⁺ does not oxidize spontaneously, leading to research focused on acidophilic environments. Key Microorganisms: ○ Acidophilic chemolithotrophs, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, are known for oxidizing Fe²⁺ to Fe³⁺. Energy Dynamics The oxidation of Fe²⁺ to Fe³⁺ produces a single electron, which means: ○ Very little energy can be conserved, necessitating the oxidation of large quantities of Fe²⁺ for microbial growth. ○ Despite the low energy yield, even small populations of these bacteria can precipitate significant amounts of iron minerals. Alternative Electron Acceptors: While O₂ is the primary electron acceptor, Fe²⁺ oxidation can also couple with nitrate (NO₃⁻) reduction in some anaerobic microbes. In photosynthesis, Fe²⁺ can function as an electron donor for certain anoxygenic phototrophs. Microbial Oxidation of Reduced Iron and Manganese Manganese Oxidation Mn²⁺ to Mn⁴⁺: ○ Although the oxidation of Mn²⁺ to Mn⁴⁺ can be energetically favorable, no organisms have been conclusively shown to derive energy directly from this process. Habitat Preferences Iron-oxidizing bacteria in non-acidic environments are limited to specific microoxic habitats, where ferrous iron-rich waters meet oxygenated water. Common Habitats Include: ○ Freshwater and coastal sediments ○ Slow-moving streams ○ Ferrous iron-rich spring waters ○ Hydrothermal vents Example of Interaction: ○ When ferrous iron-rich groundwater is exposed to air, Fe²⁺ is oxidized at the interface of anoxic and oxic zones by bacteria such as Leptothrix and Gallionella. Microbial Oxidation of Reduced Iron and Manganese Physiological Adaptations Bacteria like Leptothrix and Gallionella have evolved mechanisms to maintain their position in narrow redox zones, although the specifics of this behavior are not fully understood. Structural Adaptations: ○ Iron oxidizers often possess sheath and stalk structures that may aid in positioning and attachment. Electron Transfer Mechanisms Electron Transfer: ○ Organisms that reduce metal oxides can use conductive structures like pili for electron transfer. ○ Similarly, iron and manganese oxidizers utilize surface-associated electron transfer proteins to ensure oxidation occurs outside the cell. Cytochrome Functionality: ○ Cytochromes are involved in both iron reduction and oxidation. ○ Genomes of metal-oxidizing species (e.g., Gallionella, Sideroxydans) encode periplasmic c-type cytochromes, suggesting similar pathways for electron transfer. Microbial Oxidation of Reduced Iron and Manganese Prevention of Encasement Metal oxidizers face the challenge of becoming encased in iron oxide shells due to their metabolic processes. To prevent this, they produce extracellular organic material that sequesters metal oxides away from the cell. Strategies for Sequestration: ○ Gallionella: Produces long organic stalks that become encrusted with metal oxides, positioned away from the cell. ○ Leptothrix: Forms an organic sheath around cells that becomes coated with metal oxides, allowing cells to move out while leaving the crust behind. Conclusion While not all metal oxidizers develop prominent structures, it is believed that most produce some form of extracellular organic material to manage insoluble byproducts of their metabolism. This organic matter may also influence the physical and chemical properties of the resulting metal oxides. Microbially Wired Respiration and Electron Transfer: Bacteria generate electricity during respiration by oxidizing electron donors (organic or inorganic) and separating electrons from protons. The process involves transferring electrons to an electron acceptor, generating a proton motive force for energy conservation. Role of Iron in Electron Transfer: Ferric iron (Fe³⁺) acts as an electron acceptor under anoxic conditions. Bacteria like Geobacter sulfurreducens can reduce Fe³⁺, which is typically found as insoluble minerals (e.g., iron oxides) outside the cell. The reduction of Fe³⁺ occurs at the bacterial cell surface, which functions like an electrical anode, enabling electron transfer from the electron donor to the anode. Nanowires in Bacterial Communication: Geobacter species have electrically conductive pili, functioning as nanowires, which facilitate direct electrical connections with insoluble materials or other bacterial cells. These structures enable electron shuttling over distances greater than the cell itself, enhancing the efficiency of electron transfer in microbial communities. Microbially Wired Large-Scale Electron Shuttling: Research shows that electron transfer can occur over considerable distances; for instance, in anoxic marine sediments, bacteria can oxidize hydrogen sulfide (H₂S) deep in the sediment and reduce oxygen (O₂) at the sediment-water interface, 2.5 cm away. Filamentous Bacteria: Filamentous bacteria affiliated with the Desulfobulbaceae family have unique surface structures that facilitate electron transfer, similar to the nanowires of Geobacter. These structures allow for the transfer of electrons from sulfide oxidation at one end of the filament to O₂ reduction at the other end. Ecological Significance and Applications: Electrical communication between bacterial cells may play a critical role in shuttling electrons from anoxic to oxic regions in ecosystems. The concept of microbial electricity has potential applications in microbial fuel cells, where bacteria could be used to oxidize waste and toxic compounds while generating electricity, contributing to sustainable energy solutions. The Phosphorus, Calcium and Silica Cycles Phosphorus, Calcium and Silica Cycles Key elements: - Phosphorus (P) - Calcium (Ca) - Silica (Si) The cycling of these elements is important in aquatic environments, particularly in the oceans, which are major reservoirs of Ca and Si. Large amounts of Ca and Si are incorporated into the exoskeletons of certain microbes. Unlike the carbon (C), nitrogen (N), and sulfur (S) cycles, the Ca and Si cycles do not involve redox changes or gaseous forms that can escape and alter Earth’s atmospheric chemistry. In recent discoveries, diﬀerent redox states of phosphorus been discovered to be biogeochemical signiﬁcant. Keeping these cycles in balance particularly in calcium is important for maintaining sustainable life on Earth. Phosphorus Phosphorus Type exists as organic and inorganic phosphates in nature, primarily found in phosphate-containing minerals in rocks, dissolved phosphates in freshwater and marine waters, and in the nucleic acids and phospholipids of living organisms. Most environmental phosphates are in the +5 oxidation state (e.g., inorganic phosphate HPO4²⁻). However, phosphorus can also exist in lower oxidation states. Most environmental phosphates are in the +5 oxidation state (e.g., inorganic phosphate HPO4²⁻). However, phosphorus can also exist in lower oxidation states. Phosphorus In marine environments, a fraction of dissolved phosphorus is organic, existing as phosphate esters and phosphonates. Phosphonates are organo-phosphate compounds with a direct bond between phosphorus and carbon, and they are more reduced (+3 oxidation state) than phosphate (+5 oxidation state). They are produced by certain microorganisms and make up about 25% of the organic phosphorus pool. Availability of Phosphonates Many organisms find phosphonates to be a less available source of phosphorus due to the lack of necessary enzymes to degrade them, leading to phosphorus limitation even when phosphonates are present. Phosphorus Reduced Inorganic Phosphorus Forms Phosphorus also exists in reduced inorganic forms, such as phosphite (H₂PO₃⁻, +3 oxidation state) and hypophosphite (H₂PO₂⁻, +1 oxidation state), which are rapidly cycled in marine environments by producers and consumers. Importance of Alternative Phosphorus Cycle This alternative phosphorus cycle is significant for organisms in phosphorus-depleted environments that can utilize these reduced forms. Methylphosphonate Production The production of methylphosphonate (CH₄O₃P⁻) by some marine microorganisms may explain the high levels of methane (CH₄) found in oxygenated surface waters, despite methanogenic Archaea being strict anaerobes, which raises questions about the presence of methane in these environments. Calcium The major global reservoirs of calcium (Ca) include calcareous rocks and the oceans, where dissolved calcium exists as Ca²⁺. In the oceans, calcium cycling is a highly dynamic process, maintaining a constant concentration of about 10 mM. Several marine phototrophic microorganisms, such as coccolithophores and foraminifera, take up Ca²⁺ to form calcareous exoskeletons. The calcium-cycling activities of these planktonic phototrophs are closely linked to the inorganic components of the carbon cycle. The precipitation of calcium carbonate (CaCO₃) for shell formation controls CO₂ flux into ocean surface water and influences inorganic carbon transport to the deep ocean and sediments. Calcium Effects on Bicarbonate and CO₂ Levels This process depletes surface dissolved bicarbonate (HCO₃⁻) while increasing dissolved CO₂ levels, which reduces the influx of atmospheric CO₂ into surface waters and helps maintain the slightly alkaline pH of the oceans. When these calcareous organisms die and sink, Ca²⁺ and inorganic and organic carbon are transported to the deep ocean, where they are slowly released over long periods. Balance in Shell Formation The formation of CaCO₃ exoskeletons relies on a delicate balance between Ca²⁺ and carbon, making it sensitive to changes in atmospheric CO₂ levels. Calcium Impact of Increased Atmospheric CO₂ Increased atmospheric CO₂ leads to the formation of carbonic acid (H₂CO₃), which dissociates into HCO₃⁻ and H⁺, causing CaCO₃ to dissolve and decreasing seawater pH. Ecological Implications This greater ocean acidity is predicted to reduce the rate of calcareous shell formation, potentially affecting other microbial nutrient cycles and plant and animal communities. Silica The marine silicon (Si) cycle is primarily controlled by unicellular eukaryotes, including diatoms, silicoflagellates, and radiolarians. These organisms build ornate external cell skeletons called frustules, which are made of opal (SiO₂) rather than calcium carbonate (CaCO₃) like coccolithophores. The formation of frustules begins with the uptake of dissolved silicic acid by the cell. Diatoms are rapidly growing phototrophic eukaryotes that often dominate blooms of phytoplankton in coastal and open ocean waters. Unlike other major phytoplankton groups, diatoms require silicon (Si) and can become silica-limited during bloom development.Control of the Marine Si Cycle: The marine Due to their large size, diatom cells tend to sink faster than other organic particles, significantly contributing to the return of silicon and carbon (C) to deeper ocean waters. Silica Biological Pump The transport of organic material produced through primary production in near-surface waters to deeper ocean waters, primarily by sinking particles, is known as the biological pump. This process is crucial for carbon burial and mineralization in marine environments. In addition to major nutrients (CO₂, N, P, Fe), diatoms require sufficient dissolved silicon, which primarily originates from the skeletons of dead diatoms. Although silicon is released fairly rapidly after cell death, during periods of high diatom production in shallow waters, a significant fraction of dissolved silicon can be buried in sediments and remain there for millions of years. Consequences for Diatom Growth This burial of silicon has implications for continued diatom growth and their phototrophic consumption of dissolved CO₂ from ocean waters. Coupling of Si and C Cycles The flux of CO₂ into and out of ocean water affects its pH, linking the silicon and carbon cycles in a manner similar to the relationship observed between the calcium and carbon cycles. III. Human and Nutrient Cycle Mercury Transformations Mercury Transformations Mercury (Hg) is not a biological nutrient, but microbes can transform mercuric compounds to detoxify toxic forms. Widely used in various industries, especially in electronics. Active ingredient in pesticides and a pollutant from: ○ Chemical and mining industries. ○ Combustion of coal and municipal waste. Common contaminant in aquatic ecosystems and wetlands. Accumulates in living tissues, making it environmentally significant. In the atmosphere, mercury exists mostly as elemental mercury (Hg0). Elemental mercury is volatile and gets oxidized to mercuric ion (Hg2+) through photochemical reactions. Aquatic environments are often exposed to mercury as Hg2+. Microbial Redox Cycle for Mercury Mercuric ion (Hg2+) easily attaches to particulate matter. In anoxic environments (e.g., lake or marine sediments), Hg2+ can be metabolized by anaerobic microbes. Microbial activity methylates Hg2+: ○ Forms methylmercury (CH3Hg+). ○ Can be further methylated to dimethylmercury (CH3—Hg—CH3). Methylmercury and dimethylmercury: ○ Forms methylmercury (CH3Hg+). ○ Highly toxic to animals, easily absorbed through the skin, and potent neurotoxins. ○ Methylmercury (CH3Hg+) is soluble and concentrates in the food chain through biomagnification. ○ Accumulates primarily in fish muscle tissue and increases in concentration at higher trophic levels. ○ Particularly dangerous for humans who consume fish. Microbial Redox Cycle for Mercury Methylmercury is about 100 times more toxic than elemental mercury (Hg0) or mercuric ion (Hg2+). Accumulation is acute in freshwater lakes and marine coastal waters, where high levels of CH3Hg+ are found in fish. Mercuric compounds can cause liver and kidney damage in humans and animals. Methylation of mercury was initially linked to sulfate-reducing and iron-reducing bacteria. Recently, the enzyme systems responsible for this process have been identified: ○ Forms methylmercury (CH3Hg+). ○ Requires two genes: hgcA (encodes a methyltransferase corrinoid protein) and hgcB (encodes a [4Fe-4S] ferredoxin). Methyl group transfer process: ○ HgcA transfers a methyl group to inorganic Hg2+. ○ HgcB regenerates the reduced form of HgcA to accept a new methyl group from methyl-tetrahydrofolate (THF). Mercury Resistance Toxicity of Hg2+ and CH3Hg+: ○ High concentrations of Hg2+ and CH3Hg+ are toxic to both microorganisms and macroorganisms. Mercury-resistant bacteria: ○ Found in both gram-positive and gram-negative bacteria. ○ Use enzymes to convert toxic mercury forms into less toxic or nontoxic forms: Organomercury lyase degrades CH3Hg+ to Hg2+ and methane (CH4). Mercuric reductase (NADPH or NADH-linked) reduces Hg2+ to volatile elemental mercury (Hg0), which can escape from the cell. Genetic basis of mercury resistance: ○ Genes for mercury resistance (mer genes) are typically located on plasmids or transposons. ○ MerR protein regulates these genes: Repressor function: In the absence of Hg2+, MerR prevents transcription by binding to the mer operon operator region. Activator function: In the presence of Hg2+, MerR binds to Hg2+, activates transcription of mer structural genes (merTPABD). Human Impacts on the Carbon and Nitrogen Cycles Human Impacts on the Carbon and Nitrogen Cycles Human activities significantly affect the carbon and nitrogen cycles, impacting planetary health. The Anthropocene: ○ Informal term for a new geological epoch marked by human influence on nutrient cycles. ○ Began with the Industrial Revolution. Major human impacts include: ○ Carbon cycle: CO2 release from fossil fuel burning (oil, gas, coal). Deforestation contributes to increased CO2 levels. ○ Nitrogen cycle: Profoundly affected by human activity, though not as visibly as the carbon cycle. Biogeochemical consequences: ○ Human alteration of these cycles has projected long-term effects on ecosystem balance and health. CO2, Other Trace Gases, and Global Warming Increase in Atmospheric CO₂: ○ CO₂ levels have risen 40% since the Industrial Revolution and are now the highest in 800,000 years. ○ CO₂, along with other trace gases (e.g., water vapor, CH₄, N₂O), contributes to the greenhouse effect by trapping infrared radiation, warming the Earth. Ocean Acidification: ○ Anthropogenic CO₂ dissolves in oceans, decreasing the pH by 0.1 units since the Industrial Revolution. ○ Projected further decrease in pH by 0.3–0.4 units by 2100. Consequences of Acidification ○ Reduces carbonate (CO₃²⁻) concentration, harming marine organisms that build CaCO₃ shells/skeletons (e.g., corals, foraminifera, coccolithophores). ○ Lower CO₃²⁻ may lead to dissolution of existing CaCO₃, releasing more CO₂ and reducing ocean capacity to absorb atmospheric CO₂. ○ Coral reefs may not survive naturally if CO₂ emissions continue at the current rate. CO2, Other Trace Gases, and Global Warming Impact on the Carbon Cycle: ○ Acidification affects calcifying organisms, leading to reduced CaCO₃ in oceans and disrupting the carbon cycle in potentially significant, unpredictable ways. Additional Effects: ○ Expansion of oxygen minimum zones (OMZs) in oceans, excluding animals and enhancing anaerobic microbial processes (e.g., denitrification, anammox) that produce N₂O, a potent greenhouse gas. ○ Melting Arctic permafrost may release more methane, amplifying climate change effects. Methane and Global Warming Contribution to Radiative Forcing: ○ Methane contributes about one-fifth of the increase in radiative forcing since 1750. ○ Two-thirds of methane emissions are due to industrial activities, such as coal mining, natural gas extraction, pipelines, and fracking. Sources of Methane: ○ Major natural sources include wetlands, ruminants, thawing permafrost, and methane hydrates. ○ Wetlands are now the largest natural source of atmospheric methane, with recent increases attributed to changes in tropical climates. ○ Increased methane release is also linked to tropical climate changes. Trends in Methane Emissions: ○ Atmospheric methane levels slowed in the 1990s, remained constant from 1999 to 2006, and began increasing again in 2007. ○ Stable isotopic analysis indicates recent growth is due to increased release from tropical wetlands. Methane and Global Warming Arctic Amplification and Sea Ice Loss: ○ The Arctic is warming twice as fast as lower latitudes due to a feedback mechanism called Arctic amplification. ○ Rapid loss of summer sea ice (down by 11% since 1979) increases the absorption of sunlight by dark open water, enhancing local warming. ○ Warmer Arctic temperatures accelerate methane release from hydrates and thawing permafrost. Positive Climate Feedback from Methane Release: ○ Thawing permafrost releases stored carbon as methane and CO₂, creating a positive climate feedback loop that could accelerate global warming. ○ Permafrost holds approximately 50% of global soil carbon, which could be released with ongoing warming. Methane and Global Warming Changes in Methanogenic Microbes: ○ Studies show shifts in methanogenic community structure (from H₂-oxidizing to partly acetate-oxidizing methanogens) in the Arctic due to vegetation and permafrost changes. ○ Understanding microbial methane sources is crucial for predicting future climate impacts. Impact on Weather Patterns: ○ The reduced temperature differential between the Arctic and midlatitudes weakens west-to-east winds and slows the jet stream, causing "meandering" patterns. ○ This meandering jet stream is associated with more frequent extreme weather events in midlatitude regions. Anthropogenic Eﬀects on the Nitrogen Cycle Industrial Nitrogen Production: ○ Haber–Bosch process synthesizes ammonia (NH₃) from nitrogen (N₂) and hydrogen (H₂) under high temperature and pressure. ○ Annual industrial nitrogen production now matches the amount of nitrogen fixed by natural biological processes. Fertilizer Use and Runoff: ○ Most industrial nitrogen is applied as fertilizers on farmland, but some runs off into oceans, contributing to coastal eutrophication (nutrient pollution that leads to algal blooms and oxygen depletion in water). Nitrogen Loss and Emissions: ○ Significant nitrogen is lost as gaseous nitrogen compounds (N₂, N₂O, NO) through nitrification and denitrification. ○ N₂O emissions are increasing by 0.2–0.3% per year, with about 80% of these emissions in the U.S. coming from agriculture (manure and urine breakdown). ○ Lesser amounts of N₂O come from motor vehicles and nitrogen-based industrial processes. Anthropogenic Eﬀects on the Nitrogen Cycle Atmospheric Nitrogen Deposition: ○ Industrial nitrogen also enters the atmosphere, fertilizing terrestrial and marine ecosystems when deposited back. ○ Atmospheric nitrogen deposition in oceans now equals natural nitrogen fixation levels, impacting marine ecosystems. Ecological Consequences and Unknowns: ○ Additional nitrogen may suppress microbial nitrogen fixation but can also enhance primary production in the presence of other nutrients like iron. ○ Potential impacts on the carbon cycle are significant but unpredictable. Interlinked Nutrient Cycles: ○ Changes in the nitrogen and carbon cycles affect other nutrient cycles (e.g., phosphorus, sulfur), potentially disrupting Earth's natural balance of nutrient cycles. ○ These disruptions may have negative consequences for ecosystems, affecting plants, animals, and humans. References BYJUS. (n.d.). Nutrient Cycle: Definition, Examples and Importance. BYJUS. https://byjus.com/neet/nutrient-cycle/ BYJU'S. (2018, July 5). Nitrogen Cycle. BYJUS; Byju’s. https://byjus.com/biology/nitrogen-cycle/ BYJU'S. (2023). Phosphorus Cycle - Steps and Importance of Phosphorus Cycle. BYJUS. https://byjus.com/biology/phosphorus-cycle/ National Oceanic and Atmospheric Administration. (2023, March 2). What Is the Carbon cycle? Noaa.gov; NOAA. https://oceanservice.noaa.gov/facts/carbon-cycle.html#transcript University of California Museum of Paleontology. (2022). Carbon cycle. Understanding Global Change. https://ugc.berkeley.edu/background-content/carbon-cycle/ END OF PRESENTATION

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