18.1 - Soil aeration, redox chemistry, soil toxins and changes in nutrients


Table 18.1. List of chemical changes in two soils and a linked graph of when they occurred during 100 days of waterlogging. One soil is a sandy loam containing little organic matter at 18 °C from Muresk, Western Australia, the other a clay soil high in organic matter at 35 °C from the International Rice Research Institute (IRRI) in the Philippines. Based on Setter and Belford (1990).

In drained soils, diffusion in the gas phase of the bulk soil sustains the O2 supply needed for roots to respire at optimal rates. Soil flooding impedes O2 movement into soils, and so roots experience hypoxia (sub-optimal O2) and anoxia (absence of O2). O2 is the terminal electron acceptor of mitochondrial electron transport, so anoxia inhibits respiration and the resulting energy deficit has major implications for roots. In addition, decreases in soil redox potential result in significant changes to the soil elemental profile. The sequence of events following soil flooding are listed in Table 18.1, which also shows the rates of change measured in two soil types differing in temperature and organic matter contents. The impeded gas exchange during soil waterlogging leads to root hypoxia or anoxia, high CO2 in the root zone, and phytotoxins in reduced soils, all with consequences for root metabolism, nutrient acquisition, and growth of roots and shoots.

As soon as O2 is depleted, NO3- is used by some soil microorganisms as an alternative electron acceptor in their respiration; NO3- is reduced to NH4+, so it becomes the main form of mineral nitrogen in waterlogged soils. In the rhizosphere of roots with radial O2 loss (ROL), however, NH4+ can be converted back to NO3-, with both these forms of mineral nitrogen absorbed by roots. Manganese oxides are the next electron acceptors used by anaerobic microorganisms, followed by iron oxides resulting, respectively, in elevated concentrations of Mn2+ and Fe2+ in the soil solution; these soluble forms often increase to levels that are toxic to plants. Further decrease in the redox potential results in the reduction of SO42- to H2S, which is also potentially toxic. In addition to these inorganic phytotoxins (Fe2+, Mn2+, or H2S), various short-chain fatty acids can also accumulate in waterlogged soils. In addition to phytotoxins, some nutrients change in availability in flooded soils; e.g., P becomes more available, whereas Zn becomes less available (reviewed in Ismail et al., 2007).

High concentrations of both Mn2+ and Fe2+ are considered to be major constraints for growing sensitive cultivars of wheat in waterlogging-prone areas of Australia (Khabaz-Saberi et al. 2010); these elemental toxicities also limit rice yields in many flooded areas around the globe. Also detrimental to plants is the accumulation of metabolites (e.g. acetic acid, butyric acid, propionic acid) produced as a result of anaerobic metabolism by microorganisms in waterlogged soils. The types and amounts of these organic compounds depends upon the fermentative character of the microorganisms, the organic matter in the soil, and on soil conditions such as pH and temperature. These compounds can have adverse effects on root growth (e.g. cell division and viability) and nutrient acquisition (e.g. activity of various membrane transporters, membrane permeability) and, ultimately, shoot growth (Shabala 2011).

Of particular interest is the finding that the function of root plasma membrane transporters may be affected by these phytotoxins or secondary metabolites in waterlogged soils. Transporters located at the root-rhizosphere interface would be exposed to these toxins in waterlogged soils. Ion flux kinetics for plant roots changed rapidly upon exposure to secondary metabolites (Pang et al. 2007), and uptake of phytotoxins per se may be mediated by membrane transporters. Whether wetland plant roots, as compared with waterlogging-sensitive crops, posses membrane transporters more resistant to these toxins is an important question for future research, with possible implications for improving waterlogging tolerance in crops.

Case Study 18.1: Rice ecotypes and systems

Abdelbagi M. Ismail, International Rice Research Institute, The Philippines

The genus Oryza constitutes about 24 species, 20 of which are wild and only O. sativa and O. glaberrima are cultivated. O. sativa is grown worldwide, whereas O. glaberrima is restricted mostly to West Africa. Ecological and geographic distribution of these species is largely determined by temperature and water availability. O. sativa is cultivated on about 144 million ha worldwide, from 50° N in North China to 35° S in Australia (New South Wales) and in Argentina. It is also grown from 3 m below sea level in Kerala, India, to as high as 3000 m in Nepal and Bhutan. Two broad categories are generally identified within O. sativa, with some overlaps; japonica varieties are mostly grown in temperate regions, while indica varieties are grown in tropical and subtropical areas. A third category― tropical-japonica ― is mostly grown in the uplands of the tropics and subtropics. Japonica types are known for their better tolerance of low temperatures compared with indica types, and japonica types also have shorter, thicker grains that are softer and stickier when cooked.

Rice is grown on a variety of soils, but the physical ability of the soil to hold water is an important property, so medium- and heavier-textured soils are typically favoured over light-textured sandy soils. It is also grown under variable water regimes and hydrological conditions, from aerobic soils as in uplands, to flooded soils in irrigated and rainfed lowlands, to long-duration flooded conditions in flood-prone areas (Figure 1).


Figure 1. Rice ecologies and ecosystems based on local hydrology. (Diagram courtesy M. A. Ismail)


Figure 2. Rice terraces of Madagascar. A typical example where rice is grown under different ecologies, from uplands at the top of the slope, to more favourable rainfed and irrigated areas midway, to flood prone areas at the bottom of the slope. Farmers normally grow different varieties based on adaptation to each condition. (Photograph courtesy A. M. Ismail)

The enormous plasticity in rice to adapt to these diverse ecologies led to the development of substantial numbers of rice cultivars with diverse morphology, phenology and other adaptive and grain characteristics. The Genetic Resource Center of the International Rice Research Institute hosts over 117,000 accessions collected worldwide (http://irri.org/our-work/research/genetic-diversity/international-rice-genebank).

This peculiar diversity within Oryza species made rice one of the most widely grown crops over an extreme range of habitats, and a spectacular model for plant ecophysiological and genetic studies. Various types of models were used to classify rice types based on field ecologies. The most widely used classification distinguishes four broad categories; upland, irrigated lowland, rainfed lowland and flood-prone ecosystems (Maclean et al., 2002). Characters of varieties suitable for each ecology are mostly determined by local hydrology, and in some cases multiple systems co-exist based on the toposequence (Figure 2).

Upland rice is grown in aerobic unbunded soils with topographies ranging from undulating and steep sloping lands with high runoff, to low-laying valleys and well-drained flat lands. Soils vary considerably in texture, fertility and water holding capacity; from poor highly leached soils of West Africa, to fertile soils in Southeast Asia. About 13% of the world rice is grown in uplands, but with low yields of about 1 t ha-1, and farmers are among the poorest. Upland varieties are mostly short maturing, with deeper roots (drought avoidance) and with higher tolerance of acid soils.

Irrigated ecosystem is the largest rice production system, covering 55% of the world rice area and producing over 75% of world rice grains. Fields have assured water supply and rice is grown in puddled soil in bunded fields with water depths of 2.5-10 cm through most of the season, and with 1-3 crops per year depending on location and farming systems. Dwarf high yielding varieties that are responsive to high use of fertilizers are predominant, and yields are usually high, averaging over 5 t ha-1.

Rainfed lowlands constitute about one quarter of rice world lands and contribute about 18% of rice production. These areas are generally densely populated with poor communities, and are prone to both drought and submergence because of lack of water control, besides adverse soils, inhibiting adoption of high-yielding varieties and use of high-cost fertilizer inputs. Local landraces with yields of less than 2 t ha-1 still dominate in most areas; however, new high-yielding varieties tolerant of prevailing abiotic factors are becoming available over recent years and are gradually replacing existing local landraces.

Flood-prone rice ecosystems are subjected to uncontrolled floods, ranging from transient flash-floods causing complete submergence, to longer term floods of 0.5 m to over 4.0 m for most of the season, and sometimes associated with excess salinity, acid sulfates and drought. Over 15 million ha in South and Southeast Asia are annually affected by uncontrolled floods. Yields are low, averaging 1.5 t ha-1, and yet these areas support over 100 million people. Traditional varieties still dominate because they are better adapted to water fluctuations than modern varieties. Recently, varieties that tolerate complete submergence are becoming available through the incorporation of the SUB1A gene (see also main text). These varieties tolerate 1-2 weeks of complete submergence and considerable yield benefits have been achieved in farmers’ fields, with yield advantages of 1 to over 3 t ha-1 (Mackill et al., 2012).

The extreme diversity in adaptation to various ecological and hydraulic conditions made rice one of the most widely grown cereal crops worldwide; and an interesting model for crop improvement research. Currently, rice is the most important food crop in developing word and the stable food for over half of the world population.

Further reading on this topic:

Maclean JL, Dawe DC, Hardy B, Hettel GP (2002) Rice Almanac. Los Banos (Philippines): International Rice Research Institute, pp 16-24 http://books.irri.org/0851996361_content.pdf

Mackill DJ, Ismail AM, Singh US, Labios RV, Paris TR (2012) Development and rapid adoption of submergence-tolerant (Sub1) rice varieties. Adv Agron 115: 303-356.