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Soil science

Fire and soil microorganisms: where should we focus on?

Fire and soil microorganisms: where should we focus on?

Gema Bárcenas-Moreno
University of Seville, Sevilla, Spain

Currently, the complexity of soil microbial ecology on soil systems is a hot topic in the environmental sciences, since the scientific community has achieved a deep knowledge of the relevance of microorganisms in soil processes. After several decades of study of the effects of wildfires on soils, one of the main conclusions is that soil microbial populations are very sensitive to fire, which allows us to use them as a tool to assess the impact of fire on ecosystems.

Polysaccharides distribution due to microbial colonization in a soil microaggregate. Credit: Imaggeo/María Hernández-Soriano. Click the image for more information.

Polysaccharides distribution due to microbial colonization in a soil microaggregate. Credit: Imaggeo/María Hernández-Soriano. Click the image for more information.

Usually, soil is partly or completely sterilized after a fire, and it constitutes a new environment that organisms must recolonize and grow in. This is the reason why burning is followed immediately by a decrease of microbial abundance (which may be easily detected by assessment of microbial biomass or plate counting methods). Nevertheless, this decrease of microbial abundance in the post-fire is not always combined with a decrease in microbial activity or even bacterial growth (which may be related to increased concentrations of soluble organic carbon). Therefore, this is one of the many reasons that lead soil microbiologists to consider new parameters in their investigations. But the abundance and microbial activity are highly variable parameters that normally support deep seasonal changes under field conditions, even more intense than those caused by fire in most cases. This makes it necessary to analyse the composition of the microbial community in the post-fire to assess the real impact of the direct and indirect effects of fire on soil microorganisms and the main consequences for ecosystems.

It is possible to study changes in both the microbial community structure and functions through new methods such as phospholipids fatty acid analysis (PLFA), community DNA by restriction fragment length polymorphism (RFLP) or community level substrate utilization (CLSU). Each of these tests gives us important and abundant information, although it is difficult to interpret correctly.

With these suggestions, I do not pretend to discourage young soil microbiologists, but encourage them to find new targets. Currently, there are several lines of study of microbial soil responses after fire, focused on the evaluation of possible alterations of microbial functions and the impact on ecosystems. Other research groups have focused on searching for bio-indicators to monitor the recovery of fire-affected ecosystems. There are even several recent studies focused on the isolation and characterization of species with special ability to degrade recalcitrant or toxic compounds and so survive in burned soils.

At present, there are many gaps in the knowledge of microbial processes in fire-affected soils, but what really matters is to use the accumulated knowledge to ask the right questions.

 

This post has been simultaneusly published in G-Soil.

Sure can smell the rain

Fly, thought, on golden wings,
go alight on the cliffs, on the hills,
where the sweet airs of our
native soil smell soft and mild!

Chorus of the Hebrew slaves, Nabucco
Giuseppe Verdi

 

Have you ever noticed the smell of rain? Why does wet soil smell so good?

Bottled petricor. Picture by Kevin O-Mara.  Clinc the image to see the original picture at Flickr.

Bottled petrichor. Photo by Kevin O-Mara. Clinc the image to see the original picture at Flickr.

The smell of wet soil plants oils released into the soil during dry periods is due. These substances accumulate in the soil and mix with geosmin, produced and released by several groups of bacteria, including actinobacteria (eg, Streptomyces) and cyanobacteria. Geosmine (from Greek “geo”, earth, and “osmin”, smell) is a bicyclic alcohol derivative of decain, and was firstly described in the 1960s (Gerber and Lechevalier, 1965). When it rains, these chemicals are released into the atmosphere and cause a special smell which is known in English as petrichor (Greek “petros”, stone, and “ikhôr” liquid flowing through the veins of the gods).

Geosmin structural formulae.

Geosmin structural formulae.

Animals can detect extremely low concentrations of geosmin and other similar substances released by wet soil. It is well known that camels, for example, are able to find water in the desert from distances up to 80 km by smell.

Botanical garden in Coimbra (Portugal). Photo by Artemi Cerdà. Click the image to see the original picture and details at Imaggeo.

Apparently, the process is simple. You Sure? In fact, the mechanism by which these substances pass from the soil to the atmosphere was not known until now. Young Soo Joung and Cullen R. Buie from the Massachusetts Institute of Technology (MIT) have unveiled the process … and have recorded it on video!

For this they used high-speed cameras. They have observed that raindrops may behave differently if they impact a homogeneous and smooth or an irregular and porous surface (eg, soil). In the latter case, droplets can trap small bubbles of air at the point of impact. Within the drop, the bubbles move up and explode on the surface. Thus, each bubble releases a small cloud of soil particles into the atmosphere.

Joung and Buie (2015) have also studied that the amount of these substances which may be sprayed strongly depends on variables such as rainfall intensity and permeability and porosity of the contact surface. During their experiment, they observed and recorded for the first time the impact of simulated raindrops on different wettable surfaces (engineering materials or soil naturally) using high-speed cameras. At the time of impact, small bubbles form in the solid/liquid interface, cross up the water body and are released into the atmosphere. Immediately after, they have also watched wind carrying and subsequently dispersing the cloud of released substances. In total, the whole process lasts a few microseconds. They suggest that this process can also contribute to the transport of other substances and even microorganisms, explaining, for example, the spread of diseases such as E. coli.

Aerosol generation from droplets hitting soils and porous surfaces. Click the image to access the original image in the article.

 

References

 

This post has been simultaneously published in G-Soil.

A dark future sprouting from sealed soil

A view of Quito (Ecuador). Credit: Martin Mergili. Click on the image to see the original picture and details in Imaggeo.

Every year in Europe, soils covering an area larger than the city of Berlin are lost to urban sprawl and transport infrastructure. This unsustainable trend threatens the availability of fertile soils and groundwater reservoirs for future generations. A new report made public today by the European Commission recommends a three-tiered approach focused on limiting the progression of soil sealing, mitigating its effects and compensating valuable soil losses by action in other areas.

Environment: Soil sealing in the EU threatens the availability of ecosystem services. European Commission – IP/11/624   23/05/2011

You live on sealed soil

Look out your window. If you do not live isolated in the countryside, it will be difficult that most of which you can see is not sealed floor. Most land around you is covered by buildings or pavement. It is normal, you live in a town or a village. There is much more space out there! Is there much space out there?

Decay. Credit: Marcel Van Oijen. Click on the image to see the original picture and details in Imaggeo.

Soil sealing occurs when it is covered with impervious surfaces such as asphalt or concrete. These materials are necessary for construction of buildings and road materials, but its use implies the disappearance of agricultural resources and food production, significant changes in the hydrological processes at catchment scales as well as the loss the most important soil functions as habitat and biological support, biomass production, gene pool, sink of greenhouse gases, filtration and transformation of substances and protection of groundwater and the food chain …

Organic farming. Credit: Kristof Van Oost. Click on the image to see the original picture and details in Imaggeo.

Soil products. Credit: Artemi Cerdà. Click on the image to see the original picture and details in Imaggeo.

Even in cities, unsealed floor areas are necessary. because rain water can not flow through paved surfaces, and the ability of the sewerage system is overloaded.

A problem linked to social inequality

The rapid occupation of land for buildings has become one of the most important environmental problems. Due to migration from rural areas to the big cities and the intense changes of use from the second half of the twentieth century until now, the area of ​​land devoted to agriculture or natural vegetation is declining. And the reasons are obvious: the private economic benefit obtained from construction is much higher than from farming. Besides food products can be imported from other countries. But … is this a sustainable policy? How long?

Just one example: in Andalusia, where I live, land consumption per capita has increased by 4 in the last 50 years, from 87 m2 in 1956 to more than 337 m2 in 2007. Although causes vary from one region to another (industrial and commercial growth, infrastructure construction, mining activities, landfills, etc.), in all cases urban expansion is the main cause of soil sealing.

Rural roads change the landscape. Credit: Artemi Cerdà. Click on the image to see the original picture and details in Imaggeo.

And it’s not just a problem in the south of Europe. In small countries like Austria, only one third of the land can be used for construction. But urban and industrial expansion continues (the Viennese population grows at a rate of 20,000 people per year), so that in many parts of the country there is not much space and urban planning should be seriously analyzed.

Land abandonment is a key factor of Mediterranean Landscapes. Credit: Artemi Cerdà. Click on the image to see the original picture and details in Imaggeo.

In the EU, At least 275 ha of soil per day were lost, amounting to 1,000 km² per year Between 1990 and 2000, although this trend has been reduced to 252 ha per day in recent years, but the rate of land consumption is still worrying. Between 2000 and 2006, the EU average increase in artificial areas was 3%, with increases attaining 14% in Ireland and Cyprus and 15% in Spain (read more here).

May we get rid of soil sealing?

Obviously, people need to be fed. And for that we need transport infrastructures and consequent soil sealing. We also need infrastructures for the processing of raw materials. As a colleague says, “processes generate structures“. Therefore, we can not do without soil sealing. But we can achieve a balance.

How to? Discovering the causes

The poor generally have access only to areas that have higher risk for health and income generation. And they generally lack the resources to reduce the exposure to the risk or to invest in alleviating the causes of such risk. Environmental degradation therefore can affect the health and nutrition status of the poor and lower their productivity. This can happen both directly through, for example, lower yields per unit of labor or land because of reduced soil quality, and indirectly through the reduced physical capacity of labor to produce because of malnutrition and poor health. Even in cases where the poor are healthy labor productivity can be low due to increased time being allocated to less-productive activities such as fuel wood collection and away from agriculture and other income generating activities.

Consultative Group on International Agricultural Research. CGIAR research priorities for marginal lands. Document No.:SDR/TAC:IAR/99/12.

Zooming in community. Credit: Veilo Coviello. Click on the image to see the original picture and details in Imaggeo.

In current systems, urban population, for which most of these infrastructures are intended, is mostly concentrated in points far from the sources of production. The rural population migrates to cities due to low access to education, health care and, above all, low incomes and job expectations.

Ploughing in Central rift valley, Ethiopia. Credit: Saskia Keesstra. Click on the image to see the original picture and details in Imaggeo.

Although the consequences of this migration are not as severe (they are) in the so-called First World, the urban agglomeration does not solve these problems. More, it contributes to create large pockets of poverty in the periphery of cities. Here we have an interesting political issue. Are we heading towards a future of smart cities for the ruling class surrounded by belts of hunger, poverty and insecurity?

Getting crowded. Credit: Albin Hammerle. Click on the image to see the original picture and details in Imaggeo.

Read more

 

This post has been also published in gsoil.wordpress.com.

Lightening the clay (II)

 

According to the previous post, tetrahedral and octahedral sheets combine to form layers, and we can find two main types of clay structures: structure 1:1 (one tetrahedron sheet and one octahedral sheet) and 2:1 (two tetrahedral sheets and one octahedral sheet).

The basic structure of clays is this:

Basic structure of clays.

Basic structure of clays.

Substitutions between cations may occur in the tetrahedral and octahedral sheets, resulting in different charge deficits. These negative charges attract cations which are inserted between the layers, in the so-called interlayer space.

Depending on these substitutions, composition of the tetrahedral and octahedral sheets changes, and the resulting layer will have no charge, or will have a net negative charge. Depending on the amount of negative charge, the place where it occurs (the tetrahedral or octahedral sheet) and the type of cations, different mineral species may appear: kaolinite, serpentine, mica (muscovite, biotite, illite), smectite (montmorillonite), vermiculite, chlorite, sepiolite and vermiculite, mainly. Let’s have a look at them.

2-sheet minerals (1:1 structure)

Some examples of 2-sheets minerals are kaolinite, dickite and nacrite (wich are polymorphs of Al2Si2O5(OH)4. Halloysite, a hydrated form of kaolinite, can be found in some Tropical soils.The structure of kaolinite is the following:

Structure of kaolinite.

Structure of kaolinite.

Layers of kaolinite are formed by a tetrahedral sheet of SiO44- on another sheet of AlOH66- octahedra, with shared vertices. The interlayer space is about 7.2 Å thick and non expandable due to strong hydrogen bonds. This union does not allow water molecules or ions to enter the structure. Particle size ranges from 0.2 to 2 µm and the effective surface area is limited (10 – 30 m2/g), as only external surfaces are available.

Kaolinite. Credit: M. Roe, Macaulay Institute. Click to see the original image and details at the Mineralogical Society website.

Halloysite (hollow tubes). Credit: Ömer Işik Ece, Istanbul Technical University. Click to see the original image and details at the Mineralogical Society website.

Kaolinite. Credit: Ray Frost, Macaulay Institute. Click to see the original image and details at the Mineralogical Society website.

In kaolinites, Si is never replaced. So, the elementary particle is electrically neutral and the cation exchange capacity (CEC) very low (1-10 cmol (+) / kg), which explains the low fertility of soils rich in kaolinite.

The name “kaolinite” is derived from Chinese Kao-Ling, a mountain from Jiangxi province (China) were this mineral was extracted.

Kaollinite-rich soil in Faro (Portugal). Credit: A. Jordán. Click to see the original image and details in Imaggeo.

3-sheet minerals (2:1 structure)

Smectites

Smectites are a group of clay minerals including pyrophyllite, montmorillonite, nontronite, beidellite and saponite. Montmorillonite is hydrated sodium calcium aluminium magnesium silicate hydroxide (Na,Ca)0.33(Al,Mg)2(Si4O10)(OH)2·nH2O. Charge is very negative due to isomorphous substitutions of Si. Crystallization of montmorillonites is not stable, since the layers are bonded only by Van der Waals forces, weak O-O bonds and cation-O bonds, what makes the interlayer space very variable. This allows easy expansion of the crystal and the entry of water molecules and cations. On average, the spacing between adjacent layers is around 14.2 Å, but it may easily expand due to swelling in contact with water. During the dry season, water loss reduces the interlayer space, contraction of soil aggregates and development of cracks in the soil surface.As the internal surface of layers is available for interactions, the effective surface area is very high (up to 600 – 800 m2/g).

Structure of smectite

Structure of smectite

Montmorillonite. Credit: Emilia García-Romero, Universidad Complutense de Madrid. Click to see the original image and details at the Mineralogical Society website.

Smectite, nontronitic. Credit: Michael Velbel (Michigan State University) and William Barker, (University of Wisconsin-Madison). Click to see the original image and details at the Mineralogical Society website.

Summer cracks at the surface of a montmorillonite-rich soil from the Doñana Natural Park, Spain. Credit: A. Jordán. Click to see the original image and details at Imaggeo.

Structure of mica.

Structure of mica.

Micas

Micas are also three-layer minerals, but quite different from montmorillonites. Micas and illites (see below) are a group characterized the presence of trivalent cations in the octahedral sheet and potassium in the tetrahedral and octahedral seets. This allows them to have a greater CEC.

The unit cell is negatively charged, but is compensated by the entry of K+ ions. Mica crystallizes from magma, and isomorphous substitution of Al+3 for Si4+ is intense. Consequently, there is a highly net negative charge. K+ cations are strongly retained in the interlayer space, which can not expand or pick up other cations. CEC is low, and the interlayer spacing is constant (10 Å).

In addition to cations forming the crystal structure (Al, Si, Mg and Fe), there are also others between the layers, which confer give specific characteristics. These variations are the origin of muscovite (native of Moscow, Russia), biotite (in honour of the French physicist Jean-Baptiste Biot) and phlogopite (from a Greek word meaning “like fire”).

Illites

Illites are three-layer minerals derived from pyrophyllites, where the substitution of Si4+ by Al3+ is less intense, and the global negative net charge is smaller.

With less negative charge, K+ cations are not strongly bonded, so other cations of similar size (or smaller but hydrated cations) can enter the structure. Therefore, the space between layers is slightly variable (not as much as in montmorillonites), 10 Å on average. The effective surface area is smilar to montmorillonite’s, but CEC is smaller (20 – 40 cmol(+)/kg).

Fibrous illite. Credit: M. Roe, Macaulay Institute. Click to see the original image and details at the Mineralogical Society website.

Chlorites

The chlorite has many isomorphic substitutions in the tetrahedral and octahedral layers (Al3+ instead of Si4+ and Mg2+ instead of Al3+). The negative charge is compensated by a stable positively charged octahedral sheet of Mg, Fe and Al hydroxides sandwiched between the tetrahedral sheets. The expansion of the network is difficult, and the entry of water molecules and cations is limited. The effective surface area is small (70 – 100 m2/g).

Structure of clorite.

Structure of clorite.

Fe-rich chlorite from an alpine fissure. Credit: Michal Skiba, Institute of Geological Sciences, Jagiellonian University. Click to see the original image and details at the Mineralogical Society website.

Vermiculites

Vermiculites are not very frequent. These clay minerals are intermediate froms between chlorites and micas. Intense weathering removed some  K+ cations, which are replaced by other hydrated cations. Expansion of the network is easy (10 – 15 Å), allowing the entry of water and cations replacing Mg2+. Net hegative charge is very high and CEC is . The effective surface area is 600 – 800 m2/g, similar to smectites.

Structure of vermiculite.

Structure of vermiculite.

Vermiculite. Credit: Steve Hillier and David Riley. Click to see the original image and details at the Mineralogical Society website. See video footage at the begining of the text, showing time lapse of hydrogen peroxide exfoliation process over 7 hours real time. Note bubbles in early stages when peroxide is still covering the particle, and relaxation as the process completes.

 

This post has been also published in gsoil.wordpress.com.