User:Alandmanson/draft article on SOM

Principles & factors to consider:
"This soil organic matter (SOM), operationally defined as humic substances, consists of relatively low-molecular-weight fragments of lignin, polysaccharides, polyphenols, lipids, peptidoglycan, peptides and other biomolecules (Simpson et al., 2007; Schmidt et al., 2011). The molecules associate with each other in supramolecular aggregates that are stabilized by hydrophobic interactions and hydrogen (H) bonding and by interactions with mineral particles (Kleber & Johnson, 2010; Kleber et al., 2015)".

"onion layering" model vs "snowflake" theory of humic materials
 * "onion layering" model whereby so-called humic substances are actually aggregates of smaller residues of decomposing microbial and plant cells held together by hydrophobic forces and hydrogen bonds; these are visualized as layers on mineral surfaces, with nitrogen-rich compounds bonding tightly to mineral surfaces; these are then bound to a layer of hydrophobic compounds (composed predominantly of non-polar organic groups) close to the mineral surface, and a hydrophilic layer (with many polar groups, such as carboxylate) in contact with the soil water.
 * "snowflake" theory Whereby humic substances composed of huge polymers with complex and varied composition, that were inherently resistant to decomposition.

Physical protection of SOM: SOC sequestration control mechanisms: (i) poor spatial access within aggregates, (ii) biochemical recalcitrance, and (iii) chemical protection - mineral surface interactions with SOM

"This supported the hypothesis that a significant part of organic C stabilized in these fractions is due to the presence of very stable clay-size aggregates (resistant to sonication) that encapsulate organic C". Fernández-Ugalde, O., Barré, P., Virto, I., Hubert, F., Billiou, D. and Chenu, C., 2016. Does phyllosilicate mineralogy explain organic matter stabilization in different particle-size fractions in a 19-year C 3/C 4 chronosequence in a temperate Cambisol?. Geoderma, 264, pp.171-178.

microbes and microbial by-products associated with mineral surfaces and likely physically protected by entrapment within very small microaggregates constitute the most important pool of OM stabilization and C sequestration in soils under NT.

Wet-dry cycles

Physical protection of SOM - how do wet-dry cycles improve access? On dessication, microbes store carbon as water-retaining "osmolytes"?

NT has more iPOM (intra-aggregate particulate OM) than CT (21% of extra SOM held by NT)

SOM released by crushing of macroaggregates is in a decomposed stage (than that decomposed without crushing) and mainly of microbial origin

Effect of NT on decreasing turnover is due to better aggregation:
 * physical disturbance of aggregates with tillage
 * more fauna & microbes (esp fungi) producing more binding agents (e.g. extracellular polysaccharides) and enmeshing hyphal networks Under NT increased microbial activity generates aggregating agents such as fungal hyphae, microbial by-products, and root exudates
 * conventional tillage exposed new soil to wet-dry cycles & freeze-thaw cycles
 * microbes and microbial by-products associated with mineral surfaces and likely physically protected by entrapment within very small microaggregates constitute the most important pool of OM stabilization and C sequestration in soils under NT.


 * Narrow pores can directly exclude extracellular enzymes, microbes, and soil micro-fauna. Pore size also indirectly affects decomposition by regulating fluxes that influence microbial activity, such as oxygen, heat, solutes, and water.

Both temperate and tropical soils have better aggregation under NT, but more C protected in temperate (low Fe) soils

Six, J., Bossuyt, H., Degryze, S. and Denef, K., 2004. A history of research on the link between (micro) aggregates, soil biota, and soil organic matter dynamics. Soil and Tillage Research, 79(1), pp.7-31.

The soil carbon dilemma: Shall we hoard it or use it?

Original article
Soil organic matter (SOM) is the organic matter component of soil, consisting of plant and animal residues at various stages of decomposition, cells and tissues of soil organisms, and substances synthesized by soil organisms. SOM exerts numerous positive effects on soil physical and chemical properties, as well as the soil’s capacity to provide regulatory ecosystem services. Particularly, the presence of SOM is regarded as being critical for soil function and soil quality.

The positive impacts of SOM result from a number of complex, interactive edaphic factors; a non-exhaustive list of SOM's effects on soil functioning includes improvements related to soil structure, aggregation, water retention, soil biodiversity, absorption and retention of pollutants, buffering capacity, and the cycling and storage of plant nutrients. SOM increases soil fertility by providing cation exchange sites and acting as reserve of plant nutrients, especially nitrogen (N), phosphorus (P), and sulfur (S), along with micronutrients, which are slowly released upon SOM mineralization. As such, there is a significant correlation between SOM content and soil fertility.

SOM also acts the major sink and source of soil carbon (C). Although the C content of SOM is known to vary considerably, SOM is typically estimated to contain 58% C, and the terms 'soil organic carbon' (SOC) and SOM are often used interchangeably, with measured SOC content often serving as a proxy for SOM. Soil represents one of the largest C sinks on the planet and plays a major role in the global carbon cycle. Therefore, SOM/SOC dynamics and the capacity of soils to provide the ecosystem service of carbon sequestration through SOM management have received considerable attention in recent years.

The concentration of SOM in soils generally ranges from 1% to 6% of the total topsoil mass for most upland soils. Soils whose upper horizons consist of less than 1% organic matter are mostly limited to desert areas, while the SOM content of soils in low-lying, wet areas can be as high as 90%. Soils containing 12-18% SOC are generally classified as organic soils.

It can be divided into three general pools: living biomass of microorganisms, fresh and partially decomposed residues, and humus: the highly stable (well-decomposed) organic material. Surface litter is generally not included as part of soil organic matter.

Role in carbon cycling
Soil plays a major role in the global carbon cycle, with the global soil carbon pool estimated at 2500 gigatons. This is 3.3 times the size of the atmospheric pool (750 gigatons) and 4.5 times the biotic pool (560 gigatons). The pool of organic carbon, which occurs primarily in the form of SOM, accounts roughly 1550 gigatons of the total global C pool, with the remainder accounted for by soil inorganic carbon (SIC). The pool of organic C exists in dynamic equilibrium between gains and losses; soil may therefore serve as either a sink or source of C, through sequestration or greenhouse gas emissions, respectively, depending on exogenous factors.

Humus
In stable soils, humus dominates the soil organic matter fraction. Thus most of the benefits and properties of soil organic matter relate specifically to humus.