Decomposition of Organic Matter

Decomposition of organic matter, root functions and microbial activity as a driving force for the exchange of CO2 between soil and atmosphere.

From: Advances in Organic Farming , 2021

SOIL BIOLOGY AND TREE GROWTH | Soil Organic Matter Forms and Functions

L.A. Morris , in Encyclopedia of Forest Sciences, 2004

Acid leaching

Decomposition of organic matter in forests results in formation of soluble organic acids that, over time, have a major impact on soil formation. Acids produced during decomposition of litter on the surface move down through the soil with percolating water removing base cations such as calcium (Ca 2+), magnesium (Mg2+), and potassium (K+) weathered from minerals. Charge balance is maintained through accumulation of H+ and concentration of acid forming aluminum (Al) in the process. This acid leaching creates soils that tend to be slightly (pHw 6.5) to very acidic (pHw 3.8) in the surface and contributes to development of distinct profile features associated with some forests. For instance, organic subsoil horizons resulting from leaching of organic acids from the surface and subsequent precipitation as organic–metal complexes deeper in the profile are characteristic of conifer stands grown on coarse textured soils throughout the world.

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METHANE

E. Dlugokencky , S. Houweling , in Encyclopedia of Atmospheric Sciences, 2003

Biological Production

Decomposition of organic matter by bacteria under anaerobic conditions in, for example, wetlands, flooded soils, sediments of lakes and oceans, sewage, and digestive tracts of ruminant animals, involves complex simultaneous processes that can produce methane as a byproduct. Three steps, each the responsibility of different types of organisms, are required: fermentation degrades organic matter into simple fatty acids and CO 2; other organisms convert the fatty acids into CO2 and H2; and methane-generating bacteria (methanogens) metabolize these substrates (e.g., by hydrogen reduction of acetate, formate, and CO2) and CH4 is produced as a byproduct. In wetland environments, methane that diffuses through the water column must pass through an oxic (oxygen-rich) layer at the surface. Most of the methane that diffuses to the surface is destroyed by methane-oxidizing bacteria (methanotrophs) at the water–atmosphere interface. Generally, the amount of methane released to the atmosphere depends on the production rate and the efficiency of transport through the oxic layer. In natural wetlands and rice paddies, methane can also reach the surface through bubbles and transport through the stems of plants; in contrast to diffusion, these modes of transport to the atmosphere are relatively efficient. Methanogens are also found in the digestive tracts of ruminant herbivores. The animals do not have the enzymes necessary to digest cellulose; rather, they have a symbiotic relationship with fermenting bacteria that produce short-chain fatty acids, vitamins, and protein used by the animal for growth. As a result, species such as cows, sheep, buffaloes, and termites are efficient methane producers, and they contribute ∼20% of total CH4 emissions to the atmosphere.

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Decomposition and Pedogenesis

Timothy D. Schowalter , in Insect Ecology (Fourth Edition), 2016

Abstract

Decomposition of organic matter involves four component processes: photo-oxidation, leaching, comminution, and mineralization. Arthropods are key factors influencing comminution and mineralization. Decomposition most commonly is measured as respiration rate, as the ratio of litter input to litter standing crop, or as the rate of litter disappearance. Isotopic tracers also provide data on decomposition rate. Decomposition rate typically is higher in mesic than in arid ecosystems. Decomposition generally can be modeled as a multiple negative exponential decay function over time, with decay constants proportional to the quality of litter components. Detritivores affect decomposition through comminution, effects on microbial biomass, and effects on mineralization. Comminution increases detrital surface area and facilitates colonization and decay by microflora. Not all organic material is converted to CO 2. The low oxygen concentrations characterizing warm, humid termite colonies favor incomplete reduction of organic molecules to methane and other trace gases. Detritivores often increase mineralization of nitrogen, but nitrogen released from detritus may be immobilized quickly by microorganisms. Burrowers affect soil development by redistributing soil and organic matter. Ants and termites, in particular, excavate large volumes of soil and accumulate organic material in their centralized nests, mixing soil with organic material and influencing the distribution of soil nutrients and organic matter. Surrounding soils may become depleted in soil carbon and nutrients. Detritivore and burrower effects on mineralization and soil composition can increase plant growth, alter vegetation structure, and increase herbivory.

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Organic Matter Processing in Tropical Streams

Karl M. Wantzen , ... Catherine M. Pringle , in Tropical Stream Ecology, 2008

E. In-stream Decomposition Processes

Decomposition of organic matter in streams is caused by a number of interacting processes ( Fig. 4), and their joint effects are usually studied by measuring loss of detrital mass over time. This is not wholly satisfactory, since weight loss [or changes in ash-free dry weight (AFDW)] does not provide direct information on the fate of this material or its uptake and assimilation by consumers. Gessner et al. (1999) propose a more organism-centered perspective on leaf—litter breakdown, which acknowledges that ‚degradation' may begin even before leaves are shed. In tropical rainforests, many living leaves are colonized by epiphyllic algae and mosses. The surface characteristics and the chemistry of these leaves are also influenced by colonization of fungi and activity of herbivores. While parts of individual leaves may be killed when infected by pathogenic fungi, some fungi appear to maintain leaf activity in order to profit by the products of photosynthesis even after the onset of senescence of infected leaves (Butin, 1995). All these processes interfere with the quality of the leaves before they are shed and eventually reach the water. The term ‚leaching' describes the extraction of soluble compounds by water. Leaching rates are affected by the integrity of the leaf surface, and leaching may occur during rain when senescing leaves are still attached to the tree. Once fallen leaves enter the stream, osmotic breakage of dead cell walls, penetration by fungal hyphae, and softening of the structural elements by microbial enzymes combined with feeding by invertebrate shredders enhance leaching. Leaching rates generally peak 24–48 h after immersion (Fig. 4) but some leaching continues for weeks (France et al., 1997). The leachates (sugars, amino acids, etc.) are generally energy-rich and easily absorbed by bacteria (Strauss and Lamberti, 2002). Studies in temperate waters have shown that benthic decomposition of leaves enhanced microalgal biomass in the water column, demonstrating the role of allochthonous detritus as a nutrient source for primary production (Fazi and Rossi, 2000). The importance of epilithic algae growing on submerged litter in tropical streams has not been studied, but they could provide a significant enrichment of the food value of leaves consumed by invertebrates. As Fig. 4 shows, a temporary increase of dry weight during decomposition may be caused by the growth of biofilms on the leaf surface (as well as increased endophytic microbial biomass), as has been reported for Syzygium cordatum (Myrtaceae) litter by Mathooko et al. (2000b). Laboratory studies show that light favors biofilm quality on litter and thus the growth of temperate-zone invertebrate shredders (Franken et al., 2005), and there is no reason to assume that this effect does not occur in tropical streams.

FIGURE 4. Synthesis of processes acting during decomposition of plant litter in fresh water and their effects on weight loss. Note that a temporary increase of litter dry weight may be caused by growth of biofilms on the leaf surface (e). The relative contribution of individual processes (a)–(f) may differ between streams.

 Highly modified after Suberkropp (1998). Copyright © 1998

Fungi and bacteria growing on the leaf surface and inside the mesophyll produce enzymes that degrade structural polysaccharides, such as cellulose, resulting in a softening of leaf structure and an increase in food value for shredders (Kaushik and Hynes, 1971). Fungal biomass and reproduction generally peaks 1 or 2 weeks after immersion in temperate streams (Gessner and Chauvet, 1994). A few existing studies on tropical streams confirm this pattern (e.g. 10–20 days in Columbia; Mathuriau and Chauvet, 2002), or indicate that it may occur even more quickly (e.g. within 7 days in Costa Rica; Stallcup et al., 2006). Invertebrate shredders and large benthic omnivores (decapods, crabs, and fish) contribute to the comminution and consumption of the litter and associated microbes (see Section V) and, together with physical degradation by the water current, reduce the leaf particles to tiny fragments and fibres. Although the retention of coarse litter in some tropical headwaters appears generally high (Mathooko, 1995; Morara et al., 2003), large amounts of leaf material and fine fragments of organic material are transported to the lower course and floodplains especially, as described earlier, during spates and high-flow events. This organic material forms large accumulations in the deposition zone of rivers, often alternatively layered as sandy-loamy layers within ‚sand/debris dunes' (Fittkau, 1982; Wantzen et al., 2005).

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Nature of the Belowground Ecosystem and Its Development during Pedogenesis

Richard John Haynes , in Advances in Agronomy, 2014

5.1 Indirect Effects

Decomposition of organic matter and mineralization of organic N, S, and P is performed by the combined effect of members of the detrital food web. The primary decomposers (bacteria and fungi) release extracellular hydrolytic enzymes into their immediate environment and these catalyze organic matter decomposition ( Berg and McClaugherty, 2008). The effect of microbial-feeding microfauna, such as protozoa and nematodes on microbial activity and C, N, and P mineralization are generally positive (Mikola et al., 2002). Enhanced C mineralization is due to increased cellular turnover rate, microbial activity, and respiration of the grazed community. This is because moderate levels of consumption of microbes by protozoa and invertebrates stimulates further microbial growth and turnover (Wall and Moore, 1999; Coleman et al., 2013). Increased N and P mineralization is due to direct animal excretion of excess N and P (Hunt et al., 1987; Bloem et al., 1988). That is, invertebrates consume more N (and sometimes P) than they require for growth and therefore their excreta is high in N and P. Hunt et al. (1987) calculated that in a short-grass prairie ecosystem bacteria mineralized about 4.5   g   N   m−2  year−1 and fungi 0.3   g   N   m−2  year−1, while fauna mineralized 2.9   g   N   m−2  year−1 (i.e., 38%). Most of the faunal-derived N was released at the second trophic level with amebae and bacterivorous nematodes accounting for 83% of the faunal mineralization. Similarly, Griffiths (1994) found that in a range of ecosystems approximately 30% of total net N mineralization was attributable to soil fauna. Soil fauna can also promote the decomposition rate through other mechanisms. For instance, invertebrate grazing of bacteria and fungi can disseminate microbes from one detrital source to another while comminution increases the surface area of detritus to microbial attack (Coleman et al., 2013).

A key aspect of the role of soil biota in natural ecosystems in nutrient mineralization/release is in the synchronization of nutrient release with plant demand so that nutrient losses are minimized (Myers et al., 1994; Matson et al., 1997). Indeed in natural ecosystems such as mature forests, losses of N via stream water and gaseous fluxes are often less than 10   kg   N   ha−1  year−1 and inputs of N as wet and dry deposition are of a similar magnitude (Haynes, 1986). By contrast, the flux of N through the decomposer subsystem, which is then reabsorbed by the trees often ranges from 50 to 130   kg   N   ha−1  year−1 (Johnson et al., 1982; Haynes, 1986; Butterbach-Bahl and Gundersen, 2011; Likens, 2013). A number of factors can contribute to efficient nutrient cycling. For example, the wide range of species in tropical rainforests means there is a fairly constant return of litter and nutrients over the year (rather than one large pulse) and a high rate of nutrient retranslocation prior to litter fall reduces litter quality (e.g., increases the C/N and C/P ratios) thus lowering the decomposition rate and resulting in N and P being temporarily stored (immobilized) in the microbial biomass during decomposition (Myers et al., 1994). It is now recognized that in many natural ecosystems degradation of N-containing organic compounds may often only proceed to monomers (e.g., amino acids) and that this dissolved organic N is then absorbed by both plants and microorganisms (Schimel and Bennett, 2004). This minimizes NO3 − concentrations in soil solution and thus N loss by NO3 − leaching and/or denitrification. In addition, as discussed in Section 5.2, Ericoid and ectomycorrhizal fungi can also use organic N and P thus recycling these nutrients without them being mineralized to inorganic form.

During litter decomposition soil humus is formed (Figure 2.3). The soil humus contributes indirectly to plant growth in a number of ways. It acts as a pool of potentially mineralizable (plant-available) N, S, and P, it increases soil cation exchange capacity (and the retention of Ca, Mg, and K), it can form chelates with micronutrients such as Cu, Zn, and Mn (thus increasing their mobility) and it increases soil water holding capacity (Stevenson, 1994). As noted previously, the linkage of soil humic material with clay minerals is the basis of the formation of soil microaggreates, which are then linked together to form macroaggregates and as a result soil structure is formed.

The soil biota are strongly involved in formation of soil structure (aggregation and porosity). As already noted, the microbial community plays a central role in aggregation through the enmeshing effect of fungal hyphae and the glueing effect of extracellular polysaccharide gels produced by both bacteria and fungi. The macrofaunal ecological engineers continually move large quantities of soil and organic residues and mix them together and promote aggregation and porosity. For example, earthworms ingest large amounts of organic litter as well as soil and their casts have a higher organic matter content, microbial activity, and stability than bulk soil (Blair et al., 1995; Blanchard et al., 1999; Laossi et al., 2010). In temperate grassland soils it has been suggested that more than 50% of structural aggregates are recognizable as earthworm casts (Lee and Foster, 1991). Earthworms also greatly influence soil porosity since their burrowing activity increases the proportion of macropores present. Anecic earthworms form surface connected biopores to depth while endogeic species tend to burrow horizontally within the top 15   cm thus increasing macroporosity within the A horizon. These effects on soil structure improve the soil volume as a rooting medium for plants through improved aeration, water holding capacity, infiltration capacity and drainage, and a medium more conducive for root growth and function (Blanchard et al., 1999).

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Ecosystem services in paddy rice systems

P. Chivenge PhD , ... S. Johnson-Beebout PhD , in The Role of Ecosystem Services in Sustainable Food Systems, 2020

Carbon regulation and maintenance

Soil submergence favors anaerobic decomposition of organic matter, which is slower than aerobic decomposition, resulting in soil organic carbon build-up. Shirato and Yokozawa (2005) effectively modeled soil carbon in rice paddies by simply decreasing the decomposition rates in Roth-C, a model that was developed and parameterized for arable topsoil carbon dynamics for upland soils (Coleman and Jenkinson, 1996). Alberto et al. (2015) showed cumulative effect of continuous residue incorporation in a lowland rice soil, likely due to slower organic matter decomposition. In an analysis of four long-term experiments in the Philippines with two or three irrigated rice crops per year, Pampolino et al. (2008) showed positive changes in soil organic carbon even with no fertilization, although greater concentrations were observed with full fertilization. In that study, soil organic carbon slightly increased even where straw was removed, suggesting that continuous soil submergence contributes to soil organic carbon build up. This is in contrast to systems where rice is rotated with an upland crop, e.g., Majumder et al. (2008) observed a decline in soil organic carbon when no residues were added under rice-wheat cropping system in India.

Although rice paddy ecosystems are known carbon source, rather than sink, soil carbon apparently has longer residence in these systems as these long-term experiments demonstrated. This becomes an advantage in maintaining water and nutrients within the rootzone, depending on how irrigation is managed during the cropping season.

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Oribatid mite biodiversity in agroecosystems: role for bioindication

Valerie M. Behan-Pelletier , in Invertebrate Biodiversity as Bioindicators of Sustainable Landscapes, 1999

2 General ecology

Oribatida are actively involved in decomposition of organic matter, in nutrient cycling and in soil formation. All active instars of these mites feed on a wide variety of material, including living and dead plants and fungi, moss, lichens and carrion; many species are intermediate hosts of tapeworms, some species are predaceous, none is parasitic ( Krantz, 1978). Oribatid mites are particulate feeders; chelicera and other structures of the mouthparts are used together to cut or tear particles into sizes suitable for intake (Norton, 1990). Species studied in in vitro experiments show fungal preferences, with dermatiaceous microfungi preferred (Klironomos and Kendrick, 1996). Oribatida influence decomposition and soil structure by comminuting organic matter; their fecal pellets provide a large surface area for decomposition, and are in turn an integral component of soil structure in organic horizons. They are the most important group of arachnids from the standpoint of direct and indirect effects on the formation and maintenance of soil structure (Norton, 1986a; Moore et al., 1988). Oribatid mites disperse bacteria and fungi, both externally on their body surface, or by feeding on spores that survive passage through their alimentary tracts. They can enhance endomycorrhizal colonization (Klironomos and Kendrick, 1995). Many species sequester calcium and other minerals in their thickened cuticle (Norton and Behan-Pelletier, 1991). Thus, their bodies may form important 'sinks' for nutrients, especially in nutrient limited environments (Crossley, 1977).

The feeding habits of oribatid mites are traditionally categorized based on analysis of their gut contents (Schuster, 1956; Luxton, 1972). Macrophytophages (including xylophages feeding on woody tissue, and phyllophages feeding on non-vascular tissue) feed on higher plant material. Microphytophages (including mycophages feeding on fungi, phycophages feeding on algae, and bacteriophages feeding on bacteria) feed on the soil microflora. Panphytophages feed on both microbial and higher plant material, either concurrently, or at different stages in the life cycle. Walter (1987) noted that many Oribatida that have been considered mycophagous, also graze on algae and act as predators of nematodes; he defines these species as polyphagous.

Astigmatic mites also facilitate the humification process, fragmenting organic material and providing a greater surface area for subsequent attack by other organisms (Philips, 1990). Astigmata free living in soil feed on plant material, fungi and algae, preferably of high protein content, and also consume the liquified products of decaying organic material (Philips, 1990). Species of Schwiebia and Tyrophagus are omnivorous, attacking detrital, microbial and animal prey. Tyrophagus putrescentiae is an effective predator of the southern corn root worm under no-tillage conditions, and may be a significant over-wintering mortality factor for this pest (Stinner and House, 1990). A species of Histiostoma feeds on earthworm eggs (Krantz, 1978), whereas a congener filter feeds on fine organic material and its associated microbes (Walter and Kaplan, 1990). Few soil astigmatic mites are phytophagous, but species of Tyrophagus and Rhizoglyphus can be significant plant pests, feeding on bulbs and roots (Hughes, 1976).

Recently, oribatid mites, including the astigmatic Tyrophagus similis Volgin, have been divided into feeding guilds on the basis of their carbohydrase activity (Siepel and de Ruiter-Dijkman, 1993). Herbivorous grazers show cellulase activity only and can feed on the cell wall and cell content of green plants (both living and dead) and algae. Fungivorous grazers show chitinase and trehalase activity, and can digest both cell walls and cell contents of living and dead fungi. Fungivorous browsers show trehalose activity only and can digest cell contents of living fungi. Herbo-fungivorous grazers are able to digest both green plants and fungi. Opportunistic herbo-fungivores can digest cellulose in litter and cell walls of living green plants, and trehalose in fungi. Omnivores show cellulase and chitinase activity and can feed on components of plants, fungi and arthropods. Species which lack carbohydrase activity entirely probably are predators, or carrion feeders and/or bacteria feeders. Studies on gut content analysis and those on enzyme activity (e.g., Luxton, 1979; Siepel and de Ruiter-Dijkman, 1993; Urbášek and Starŷ, 1994) highlight the range of feeding habits in any oribatid lineage; for example, the Desmonomata includes herbivorous grazers, herbo-fungivorous grazers and opportunistic herbo-fungivores.

Culturing oribatid and astigmatic mites can present a more complete picture of their food requirements and preferences. Tyrophagus similis, a fungivorous browser (Siepel and de Ruiter-Dijkman, 1993), developed at similar rates on fungal only or nematode only diets (Walter, 1987). Pilogalumna tenuiclaves is a herbo-fungivorous grazer based on carbohydrase activity, but egg clutches of a congener (P. cozadensis) were doubled in size when nematodes were added to a diet of fungi and algae (Walter, 1987).

Many digestive enzymes, including cellulase and chitinase, are produced by the diverse and very active gut microflora of oribatid species, which is a subset of the microflora of the surrounding environment rather than a specialized obligate flora (Stefaniak and Seniczak, 1976; Stefaniak, 1981; Norton, 1994). Perhaps, as Norton (1986a) suggests, microorganisms capable of continued enzymic production in the gut are those resistant to digestion. The ability of oribatid mites to adjust to forced changes in diet, and the evidence that gut contents of a given species can vary with site and season (Anderson, 1975; Behan-Pelletier and Hill, 1983) or at different stages in the life cycle (Siepel, 1990a) may reflect changes in this active gut microflora (Norton, 1986a).

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Enzymes in rhizosphere engineering

Areeb Inamdar , ... Nitin Adhapure , in Rhizosphere Engineering, 2022

Abstract

Soil enzymes play prominent role in the decomposition of organic matter and nutrient recycling by oxidation (dehydrogenase, hydrolase, glucosidase) and mineralization (protease, amidase, urease, phosphatase, and sulfatase). Therefore, these enzymes can be collectively referred to as "rhizozymes" ( Rhizo means root, and zymes means enzymes). Rhizozymes are influenced by soil factors, such as cropping history, organic matter content, soil depth/horizons, agricultural practices, heavy metal, and factors like temperature, pH, and water availability. Reports suggest that enzyme secretion and activities depend on multiple factors like type and species of crop, their growth stages, seasons, CO2 level, crop rotation, precursor(s) available, chemical nature of root exudates, etc. Each factor has a different and cumulative effect on enzymes present in soil rather than microbial load.

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Biofuel production

Nathaskia Silva Pereira Nunes , ... Gustavo Graciano Fonseca , in Microalgae, 2021

3.6 Biogas

Biogas is one of the products of decomposition of organic matter. Coal, agro-industrial waste, algal biomass, petroleum coke, among others, can be used as raw material for the production of biogas ( Toro, Pérez, & Alzate, 2018). Among the processes for obtaining biogas are gasification and anaerobic digestion. Obtaining biogas through the gasification process involves several steps, such as feeding the gasification system with the microalgae biomass, with the temperature increase up to 1200°C. As the temperature of this process increases, the water evaporates, thus causing partial oxidation of the biomass, eventually producing biogas, which in this process can also be called synthesis gas (Patinvoh, Osadolor, Chandolias, Horváth, & Taherzadeh, 2016). Biogas obtained through anaerobic digestion can be produced with different substrates such as organic matter and biomass. For the process of obtaining biogas occur, chemical reactions take place at different stages, such as hydrolysis, acidification, acetate production, and methane production. From this chemical process, the biogas formed consists of methane and carbon dioxide (Toro et al., 2018). However, other traces of different gases can be found, such as hydrogen sulfide, ammonia, hydrogen, carbon monoxide, among others.

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Nitrogen Cycle

D.M. Karl , A.F. Michaels , in Encyclopedia of Ocean Sciences, 2001

Nitrogen Cycle and Ocean Productivity

Because nitrogen transformations include both the formation and decomposition of organic matter, much of the nitrogen used in photosynthesis is locally recycled back to NH 4 + or NO3 − to support another pass through the cycle. The net removal of nitrogen in particulate, dissolved, or gaseous form can cause the cycle to slow down or even terminate unless new nitrogen is imported from an external source. A unifying concept in the study of nutrient dynamics in the sea is the 'new' versus 'regenerated' nitrogen dichotomy (Figure 7). New nitrogen is imported from surrounding regions (e.g., NO3 − injection from below) or locally created (e.g., NH4 +/organic N from N2 fixation). Regenerated nitrogen is locally recycled (e.g., NH4 + from ammonification, NO2 −/ NO3 − from nitrification, or DON from grazing or cell lysis). Under steady-state conditions, the amount of new nitrogen entering an ecosystem will determine the total amount that can be exported without the system running down.

Figure 7. Schematic representation of the major pools and transformations/fluxes of nitrogen in a typical open ocean ecosystem. New sources of bioavailable N (NO3 − and N2 in this presentation) continuously resupply nitrogen that is lost via DON and PON export. These interactions and ocean processes form the conceptual framework for the 'new' versus 'regenerated' paradigm of nitrogen dynamics in the sea that was originally proposed by R. Dugdale and J. Goering.

In shallow, coastal regions runoff from land or movement upward from the sediments are potentially major sources of NH4 +, NO3 − and DON for water column processes. In certain regions, atmospheric deposition (both wet and dry) may also supply bioavailable nitrogen to the system. However, in most open ocean environments, new sources of nitrogen required to balance the net losses from the euphotic zone are restricted to upward diffusion or mixing of NO3 − from deep water and to local fixation of N2 gas. In a balanced steady state, the importation rate of new sources of bioavailable nitrogen will constrain the export of nitrogen (including fisheries production and harvesting). If all other required nutrients are available, export-rich ecosystems are those characterized by high bioavailable nitrogen loading such as coastal and open ocean upwelling regions. These are also the major regions of fish production in the sea.

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