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Soil (土壌)

Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

[soil formation process, duff, litter, decomposition rate]
[belowground, gardening]

Soil science

The study of soil as natural resources including the properties, formation, classification and mapping. It is tightly related to ecology, forestry and agriculture

Pedology (基礎土壌学): pedogenesis + soil morphology + soil classification ≈ soil science
Edaphology (応用土壌学/農業土壌学): the way soils influence plants, fungi and others

Soil: The top layer of the Earth's surface, containing unconsolidated rock and mineral particles mixed with organic material.

soil_→ → climate
___← animal ↵
rock ← plant__

Pedosphere (土壌圏)
The outermost layer of the earth that is composed of soil and subject to soil formation processes → geosphere

Soil properties (土壌特性)

particles (solid) + water (liquid) + air (gas)
Soil texture (土壌粒径): sand > sild > clay

Soil texture
The particle sizes determine soil properties, such as water-holding capacity, CEC, etc. (Hillel 2008)

muddy with much water
hard when dry
contained in muddy water

The structural units of aluminosilicate clay minerals (left) a tetrahedron of oxygen atoms surrounding a silicon ion, (right) an octahedron oxygens or hydroxyls enclosing an aluminum ion

Hexahedral network of tetrahedra forming a silica sheet
Structural network of octahedra forming an alumina sheet

Soil profile (土壌断面)

Soil profile refers to the layers of soil, horizons (L, F, H,) A, B, and C. Each layer is subdivided to the sublayers if needed.
L : litter
F : fermentation
H : humus
A : made of highly decomposed organic matter
C : mostly bedrock
[1] at Poker Flat, AK, on May 18 2005. The ground surface was covered with Picea mariana and Sphagnum spp. [2] near UAF. Fairbanks, on August 5 2013. We can see tough roots! [3] un-develped soil profile taken on August 4, 2015, on the southwestern slope of Mount Koma, southern Hokkaido, after the 1929 eruptions.

Ground surface covered
by Cinnamomum

Duff (腐葉層)

Organic matter layer (O layer) is divided into two indistinct layers
Litter (L):
consists of the loosely packed, largely unaltered dead remains of animals and plants usually recently cast.
Duff (D)
Consisting of two layers
(F) = an upper F layer: consisting of litter which has recently begun to decompose but with the particles still recognizable as to their origins
(H) = a lower H layer: is made of well-decomposed organic matter (= humus) which can not be recognized as to its origin.

(Johnson 1992)

Soil classification (土壌分類)

0. Sand, silt, peat and humus
1. V.V. Dokchaen (1900)
A: Zonal soil distribution
B1. Successional soil
B2. Azonal soil (edaphic soil)
3. Comprehensive soil group (USDA 1960)
Nomenclature of soil taxonomy (12th revision, 2014)
The history of soil classification after 1960
1960 Seventh Approximation published by US soil survey staff

ISSS Congress asks FAO to prepare world soil map

1967 Russian classification updated (Ivanova and Rozov)
1972 Soil Taxonomy published by Soil Survey Staff

French soil classification system (CPCS)

1974 Legend of the world soil map (FAO/UNESCO)
1980 Last volume and map sheet soil map of the world
1982 the international reference base (IRB) for soil resources (ISSS) 1988 revised legend of the soil map of the world (FAO/ISRIC/UNESCO) 1992 IRB Working Group decides

to use the revised legend of the world soil map as a basis for the ISSS system. IRB working group renamed as WRB

1994 WRB produces draft world reference base at ISSS Congress

Draft topsoil characterization presented

1995 FAO produces digital world soil map and

decides together with ISRIC and UNEP to undertake an update of the map using the principles of the SOTER manual

1996 Australian soil classification system revised (Isbell)
1998 WRB working group produces

the world reference base for soil resources in three volumes endorsed and adopted by IUSS as the official soil correlation system of the international union of soil scientists
soil saxonomy (2nd edn.) published
référentiel pédologique published in English (Baise)

1999 European soil bureau adopts

WRB as correlation system for Europeean soil map

2000 SOTER adopts WRB as a reference system to classify soil profiles
ISSS: International Society of Soil Science
WRB: World Reference Base for Soil Resources

Soil for gardening (用土)

≈ Potting soil
Combination of organic and inorganic materials used to provide the basic requirements for plant growth (often used for )
Also used for various experiments in fields and greenhouses
  • Hold water
  • Hold nutrients
  • Permit gas exchange to and from roots
  • Support plant
Role: drain well, hold water, hold nutrients, have ideal pH that can be adjusted, produce vigorous plants, suppress disease, reduce nutrient leaching, not accumulate salts, be inexpensive, be readily (and preferably locally) available, be ultra lightweight for shipping and ease of moving nursery crops, facilitate plant establishment in the landscape
  • leaf mold: compost produced by the decay of plant materiasl
  • peat moss
  • pumicetephra (テフラ)

    Kanuma pumice (鹿沼土)

Organic components
Inorganic components
  • Mineral soil
  • Sand or grit
  • Perlite
  • Vermiculite
  • Polystyrene beads
  • Rockwool
Hydrophilic gels (or hydrogels)
= superabsorbents: crosslinked polymers that can 400-1500 times their dry weight in water - diapers, oil recovery, food processing, water purification and wound dressings
  1. Naturally occurring polymers are starch-based polysaccarides that are made from grain crops such as corn and wheat. Commonly used in the food industry as thickening agents
  2. Semi-synthetic polymers are derived from cellulose, which is chemically combined with petrochemicals. One of the first hydrogels specifically designed for horticulture was a polyethylene polymer combined with sawdust (Erazo 1987)
  3. Synthetic polymers are made from petrochemicals and polyacrylamides (PAMs) are one of the most popular polymers that are chemically linked to prevent them from dissolving in solution. Linear chain polyacrylamides are used for erosion control, canal sealing, and water clarification whereas crosslinked polyacrylamide hydrogels are most commonly used in horticulture (Peterson 2002)
Bolier 1-2-3®: inorganic Polymer (additives: mycorrhizal spores and biostimulant)
Bio-Organics®: inorganic Polymer (mycorrhizal spores)
Soil Mist®: polyacrylamide (some contain mycorrhizal spores, and one contains slow-release fertilizer)
Stockosorb®: polyacrylamide (none)
Viterra®: inorganic polymer (none)
Zeba®: starch polymer (none)

Soil texture (土壌粒径)

[protocol, プロトコル]

Soil analysis (土壌分析)

Nitrogen (窒素)

NH4+ in soil
A ppm (mg/L) of NH4 data
A is obtained from the solution which includes B gram of dry soil and 50-ml KCl
This means:
"A mg/L" is obtained when the solution includes B × (1 L / 50 ml) gram of soil in 1 L (the ratio between soil amount and solution is same with above)
Then the amount of NH4 in 1000 kg of dry soil is obtained
What we need to do is:

A × (1000 / (B × 20)) = C mg NH4 per 1 kg of dry soil.
B is calculated as:
(Wet soil weight - Dry soil weight) / (Wet soil weight) × 100

(3 to 60 mg/kg in mineral soil with 0-10cm deep on natural forests in Hokkaido)

Phosphorus (リン)

Phosphorus: P
Phosphate: An inorganic chemical (a salt of phosphoric acid)

Essential element for all living organisms

Quantification of phosphate

The principle of P quantification is how stain phosphate by ammonium molybdate.
Quantitative analysis of inorganic phosphoric acids (無機態リン酸)
Allen's variative analysis

Pi + 12(NH4)2MoO4
↓ Ammonium molybdate (NH4)3Mo12O4·Pi
↓ Ab. 460-550 nm (color is correspondent to phoshpric acid quantity)
↓ - add reductant Molybdenum bule: Ab. 560-730 nm


1. Standard phosphoric acid solution / KH2

= 1.0967 g/ 250 ml (# mg/ml) strictly!

2. 60% PCA (perchloric acid): hereafter, i.e., [A]
3. Amidol sodium sulfate (as reductant)

Sodium hydrogen sulfate - 8.0 g
Add these reagents in water and fill up finally100 ml: i.e., [B]
Thereafter, those are put into brown glass bottle and keep in cool and dark

4. 3.3% (w/w) ammonium molybdate: i.e., [C]


1. put 0.1 ml standard solution in graduated test tube
2. add 0.9 ml [A]
3. add 0.1 ml of [B] and [C], respectively
4. add water and adjuct finally 10 ml
5. incubate in water bath at 20C for 20 min.

       5 μg  10 μg  20 μg  40 μg  60 μg  80 μg

    A  0.078   0.172   0.315   0.610    0.95    1.20
    B  0.075   0.160   0.282   0.570    0.85    1.04

Quantification of available P in soil

Bray II (ブレイII)
Soil: grassland, rice field, etc. Ex. 20 samples

Extract: 20 × 20 = 400 (prepare 500 ml)
Dye: 8 × 20 = 160 (prepare 200 ml)
Boracic acid: 15 × 20 = 300 (prepare 400 ml)

Phosphate in lipids extracted from litter (Prototype)

Basically written by Otaki M

Solvents and chemicals are of highly-quality grade
Glassware is washed by phosphate-free detergent, rinsed 10 times with hot tap water, and then 2 times with deionized water
Lipid extract for lipids
Chloroform : Methanol : Deionized water = 1 : 2 : 0.8, v/v/v)
Fiske-Subbarow reagent
0.25% 1-amino-2-naphthol-4-sulfonic acid
13.7% sodium metabisulfite
3% sodium sulfite
Phosphate standard 1.2 mM phenyl phosphate disodium salt
Adjust 0 to 98 nmol phosphorus before use
Extraction of total lipids from litter
Total lipids are extracted on the basis of a method proposed by Bligh and Dyer (1959) with modification (White et al. 1979). A total amount of 1.0 g litter si bottled into a 40-ml screw-capped centrifuge tube, and then 19.0-ml extract is poured into the tube and mixed with litter. Thereafter, 5-ml chloroform and 5-ml deionized water are added into the tube. After the samples are vortexed and centrifuged at 2000 rpm for 5 min (Kubota KS-5000), two layers are developed in the tube. The lower layer (bottom phase) that contained lipids is transferred into a new test tube.
Quantification of phosphate in the lipids
H Each 1/10 amount of total lipid extract is digested by perchloric acid. After the lower layer sample is evaporated and condensed, the sample is mixed with 500 μl 60% perchloric acid. The mixed samples were then heated at 190 °C for 30 minutes. During the digestion, the lipid extract colors black and contains particulates. These two signals indicate that the organic compounds are digested and leak phosphate ions. To the sample, 2300 μl 1.78 mM ammonium molybdate solution and 100 μl of Fiske-Subbarow reagent are added (Fiske and Subbarow 1925). Then the samples in tubes are heated at 90°C for 10 minutes on dry bath. Absorbance at 815 nm that reflects the amount of blue-colored PMo12O407- reacted with phosphate was measured using a spectrophotometer (U-1800, Hitachi). The absorbance of standard solutions and the samples are measured at 815 nm using a spectrophotometer. The content of phosphorus ions on each sample is calibrated by the standard curve ranging from 0 to 98 nmol phosphorus ions.


Litter sample = 1.0 g freeze-dried and grinded litter
↓ put into 40-mL screw-capped glass tube
[Total lipids extracted by Bligh-Dyer method]
↓ 19 mL single-phased extract mixed with 10-mL methanol, 5-mL chloroform and 4 mL deionized water
↓ 29-mL two-phased extract mixed with 5-mL chloroform and 5-mL deionized water
↓ Lipid-contained lower layer istransferred into another tube
↓ The lower layer sample evapolated by jet nitrogen flow

(1/10 amount of total lipid extract in the sample was used for quantifying phosphate content)

[Fiske-Subbarow colorimetric determination of phosphorus]
↓ add 500 μl 60% perchloric acid to the sample

Phospholipids containing the total lipids are separated into organic compounds and phosphate ions

↓ Heated at 190°C for 30 minutes.
↓ Mixed with 2300 μl 1.78 mM ammonium molybdate
↓ The anion was then reduced by 100-μl Fiske-Subbarow reagent

(to form the blue colored β-keggin ion (PMo12O407-)

↓ Measuring absorbance at 815 nm

Litter (リター, 落葉落枝)

Decomposition is physical and chemical brerakdown of detritus
Detritus (デトリタス, 有機堆積物)
Geology: particles produced by weathering
Biology: dead materials, derived from plants, animals, and microbial organisms
Speech: trash
Usage: Litter decomposition

[Litter decomposition pattern on Mount Usu]

Litter decomposition (リター分解)


  • Leaching: performed mostly by water that dissolves ions and other chemical components
  • Fragmentation: physically and/or biologically destroyed - that promotes the establishment of micro-organisms, such as fungi and bacteria

    Fungi and bacteria are the major decomposers that explain the 95% of biomass and respiration of decomposers.
    Bacteria: the smallest decomposers that dissolve litter (widespread) and are widespread (cosmopolitan) → they move more passively than fungi


    Fungi: the second smallest decomposers that also dissolve litter + developing hyphal networks that promote nutrient transfer [compared with bacteria, the habitat is limited]
    Protozoans is in microfuana - functioning as an litter predator
    Earthworm is in macrofauna - as an ecosystem engineer that physically changes litter and soil (e.g., tunnels, creating mounds and aggregated soil structure, and wormcast)

  • Chemical alteration: chemical components are altered mostly by microbial activities (+ photodegradation)

    Exoenzymes (= enzymes secreted by decomposer microbes)
    The enzymes produced by microorganisms decompose litter in the outside of m.o., because they are too small to uptake the litter into the bodies

Note that these three processes often occur simultaneously.

Effects of moisture and temperature on litter decomposition

Moisture: litter decomposition increases with increasing moisture (until excess water)

Excess water: anaerobic bacteria may be happy

(High) temperature

Short-term: affecting microbial activities (respiration and decomposition)
Long-term: considering indirect effects that reduce litter decomposition

Acclimation to temperature → reducing microbial activities (r.m.a.)
High respiration decreases oxygen → r.m.a.
Reducing water content in soil (by evapotranspiration) → r.m.a.

Litter decomposition rate (リター分解率)

Single and double exponential models best describe the loss of mass over time with an element of biological realism (Wieder & Lang 1982)
Single exponential equation: y/y0 = e-kt

y: remaining at time t, y0: initial mass, k: decay constant, or decomposition rate

A popular method to measure litter decomposition

controversial (e.g., mesh size)


C/N ratio (C:N ratio, C/N比)
Chemicals in substance (soil) and initial C:N ratio
Low C/N ratio → fast decomposition → good predictor
However we must consider lignin:nitrogen ratio (L/N ratio): express the ratio of nitrogen that consists of lignin

Lignin is persistent
To predict the decomposition rate, L/N is a good parameter
→ litter is persistent when the ratio is high

Note that these are also related to litter quality (species)
C → comsumed more by bacteria
N:P ratio
foligate < fresh litter < decompsed litter

Phospholipid fatty acids (PLFAs) for estimating litter decomposition

[ phosphate | qunatification | protocol ]

Table 2. PLFAs used as biomarkers for microbial groups. *: (Bossio & Scow 1998, Frostegard et al. 1993, Waldrop et al. 2000)
GroupPLFA groupMarker PLFAs (*)
Bacteriamultiple groupsum of the all of bacteria
Gram-positive bacteriaBranched PLFAsi14:0, a14:0, i15:0, a15:0, i16:0, i17:0, a17:0
Gram-negative bacteriaCyclopropyl and mono PLFAscy17:0, cy19:0
Hydroxy (2OH-14:0, 3OH-14:0, 2OH-16:0)
Actinomycetes10Me-PLFAs10Me16:0, 10Me18:0
FungiPolyunsaturated PLFAs 18:2ω6, 18:2ω9
ProtozoanPolyunsaturated PLFAs20:2ω6, 20:4ω6
Micro-eukaryotesPolyunsaturated PLFAs18:3, 20:4