Microbes and Land Use Change

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Introduction

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In the introduction, briefly describe the habitat that is the topic of this page. Introduce the habitat, its ecological significance, and the importance of microorganisms in this environment. (What processes do they carry out? What functions do they perform?)

Physical factors

Soil structure

Land use changes have many different effects on microbial communities and their habitats. One key one is through soil structure. Soil structure is the result of many years of natural factors and may have developed particular horizons formative of the ecosystem. Soil horizons may be drastically altered as a result of new land use regimes. In agricultural systems, plowing causes the creation of a defined plow layer (Ap) (1). Soil architecture can also be effected by excessive compaction, which reduces pore size and can limit the permeability of water, gas exchange, and root penetration, all of which have important consequences for microbes (2). Excess soil management, especially from agriculture and resource extraction, can break up this internal organization, resulting in erosion (1).

Hydrology

Hydrological regime shifts can also be associated with land use changes. In addition to soil permeability affects as mentioned above, land use changes may require that streams or rivers may be diverted or channelized, which may affect the hydrology of areas fed by these streams (3). Land use changes may exacerbate flood pulses, change flood intervals, or create new flood plains through the conversions of wetlands or by changing the flow of rivers (4). These hydrology changes resulting from land use change can also impact oxygen levels of the soil, as ecosystems like wetlands are characterized by oxygen poor soils resulting from constant saturation (5), and will affect microbial habitats through the creation or reduction of floodplain conditions. Additionally, soil moisture has an effect on temperature because the high heat capacity of water (6).

Chemical Factors

The chemical effects of land use changes have a huge importance with regard to microbial habitat. Nutrient content of the soil may be saturated or depleted through differing land use-related activities and can affect microbial metabolism, especially through alterations of the C/N ratio ( 7). Many anthropogenic processes or input from more developed areas can increase the soil content of heavy metals, hydrocarbons, or various other pollutants beyond their natural variation (8). Additional additives that change the pH from the soil can alter the availability of labile forms of nutrients and heavy metals. For example, at lower pHs, aluminium ions are more freely available while phosphorus is complexed by soil particles (9). Nutrients and pollutants in mobile forms can also be leached through erosion processes resulting from overworked soils (1).

Biological Factors

The planting of new or different species of plants as part of a land use change will have an affect on microbes in the context of land use change. Bringing in new species which have mutualistic associations with other microbes, such as arbuscular mycorrhizal fungi, resulting in increased competition for resources with new microbes. Plants themselves will also compete for nutrients against microbes (21). Additionally, the planting of allelopathic crops may inhibit microbial activity through the exudation of allelochemicals (22).

Microbial communities: Case Studies

Agriculture

Agriculture and forestry have similar types of effects in that these land conversions revolve mainly around direct resource utilization. The ecosystems typically converted to agriculture are either grasslands or slash and burn, which involves the burning and chopping down of trees. Studies of converted grasslands have determined through PFLA that most species in cultivated landscapes are Gram-negative, specifically Proteobacteria, Cytophaga-flavobacterium, and acidiobacteria, with little to no archea (7, 11). In terms of conversions from forests, microbial community structure is dominated predominately by acidiobacteria and proteobacteria (12). In both cases, the Glomus species of fungi was dominant (14).

Microbial community composition at individual plots in cultivated areas may or may not drop, depending on variation in environmental factors, such as nutrient availability and pH (12). In Steenwerth et al., comparisons between agricultural and grassland soils, microbial community composition was found to decrease (7), while Rodriges et al. found that conversion of the Amazon to cultivation results in an increase of microbial diversity (10). Jesus et al. confirms that this change in microbial community structure is moreso a function of pH and other factors (12). Microbial community structure does homogenization at greater spatial scales, however (12). This can be attributed to the selective pressures resulting from agricultural methods, such as tillage and inorganic fertilizers. There are specific OTUs of acidiobacteria and gamma-proteobacteria that correspond with inorganic fertilizers, explaining why diversity is reduced overall (13). With regards to fungi, arbuscular mycorrhizal species diversity also declined with shifts to more generalist species that reproduced via spores, indicating a shift to r-selected characteristics in response to these new conditions (14). The homogenous structure of these communities means that it possess less functional diversity and lower resilience to disturbances (7).

An Urban Brownfield

Brownfields/Polluted Areas

A consequence of urbanization and industrialization is the pollution of various areas through contaminants such as heavy metals and petroleum-based substrates. The same applies to heavy metals, and can even be found concurrently with petroleum substrates at sites (15). The microbes present depend upon the pollutants in question. In arsenic and cadmium contaminated soils, for example, fungi and proteobacteria appeared tolerant at the expense of other microbial species (16), while areas with zinc and mercury pollution were found to have more members of Acidiobacteria, such as Acidithiobacillus and Thiothrix (17). Fungal genera that can withstand heavy metal pollution include Geomyces, Pecilomyces, and Mortierella (18), and archeal phyla include Crenarchaeota (19). In petroleum contaminated soils, one can find Proteobacteria (Gammaproteobacteira, Epsilonproteobacteria) and archeal phyla (Crenarchaeota) (20).

Microbial community structure also appears to homogenize in these more extreme environments. In Nordgren, Baath, and Soderstrom, the diversity of fungal species decreased as the heavy metal gradient approached its source (18). Similarly, the diversity of petroleum microbes also decreased as conditions were exacerbated. The tolerant microbes are not only able to withstand these conditions but may even exacerbate conditions to limit competition. In Linton, Shotbolt, and Thomas, it was observed that surviving bacterial species in the highest concentration of heavy metals were related to acidophilic species that can oxidize iron and sulfur, reducing the pH and increasing the potency of these heavy metals (17). Similar characteristics can be found with species that can withstand high concentrations of petroleum (20).

Microbial processes

Decomposition

Decomposition is an important microbial process that is affected by conversions of land into agriculture and petroleum pollution. On the whole, there is a net loss in soil organic C in conversion to agriculture. The quality of the litter that agricultural crops will produce may not be equivalent to that of native vegetation and may be incorporated into microbial biomass too quickly if the C:N ratio is lower or may stick around for longer and accumulate as organic matter if the ratio is high (1, 13). Decomposition may also affect the availability of other nutrients, as easily decomposed organic matter will liberate much needed nitrogen and phosphorus for microbial biomass and metabolism (1). Decomposition rates are often higher because reductions of litter, over or understory cover results in a higher soil temperature that stimulates microbial activity. This is amplified by tillage, which increases the soil oxygen content and also increases decomposition (23). Decomposition is also important for microbes impacted by petroleum pollution because those that are adapted can use the hydrocarbons as a carbon substrate (20).

Diagram of decomposition, using compost as an example

Nitrification

Nitrification is one of the major processes that can be affected by land use changes. In agriculture, nitrogen amendments and fertilizers are added to the soil, meaning that microbes are rarely nitrogen deficient. However, since microbes receive an excess of nitrogen, they may further mineralize inorganic forms and convert them to nitrate, which is much more motile. Nitrate can leach from the soil via erosion and can result in nitrogen losses (24).

Lithotropy and Respiration

Rates of respiration are strongly effected by land use changes to brownfield sites because, for many microbes, the concentrations of heavy metals can interfere with essential enzymatic activity (16). Therefore, the microbes that can tolerate these extreme conditions. However, since there may be shortages of carbon substate at a brownfield site, many of these microbes are able to take their reducing equivalents from inorganic sources (17).

Current Research

Dong, X., Y. Huai-Ying, GE De-Yong, and H. Chang-Young. 2007. “Soil Microbial Structure in Diverse Land Use Systems: a Comparative Study Using Biolog, DGGE, and PFLA Analyses”. Pedosphere 18(5):653-663.

Using 3 different molecular methods, the soil microbial community compositions were observed in 3 tea gardens in decreasing age, a secondary growth forest, a “wasteland” consisting of an area populated lightly by grasses. It was found that there is a greater amount of metabolic diversity in the tea garden, followed by the forest, and then the wasteland. Additionally, there was the greatest amount of fungi in the tea garden system according to the fungal PLFA, indicating that land use change encourages increases in soil microbial community structure.

Ding, G-C, Y.M. Piceno, H. Heuer, N. Weinert, A.B. Dohrmann, A. Carrillo, G.L. Andersen, T. Castellanos, C.C. Tebbe, and K. Smalla. 2013. “Changes of Soil Bacterial Diversity as a Consequence of Land Use in a Semi-Arid Ecosystem”. PLOS One 8(3): e59497.

This study looked at the microbial community composition of farm fields that are the conversions of natural schrublands. A 50 year old Alfalfa and semi-arid desert sites were compared with DGGE and 16S rRNA gene fragments that were taken from the community DNA. The agricultural soils had less organic matter and phosphates but were more saline. There was an increase in alpha diversity with regards to the agricultural plots, but further analyses of the microbial communities and the physiochemical parameters reveal a decrease in beta diversity.

Hartman, W.H., C.J. Richardson, R. Vilgalys, and G.L. Bruland. 2008. “Environmental and anthropogenic controls over bacterial communities in wetland soils”. PNAS 105(46):17842-17847

This study looked at factors which dictate wetland soil bacterial abundances and distributions. Samples were taken from North Carolina swamps and bogs across a similar nutrient gradient. Bacterial diversity and community structure were most effected by soil pH, land use, and restoration status. Acidiobacteria and Proteobacteria, in particular, had visible variation that could be used for indicators of restoration and trophic status.

References

[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.

Edited by <your name>, a student of Angela Kent at the University of Illinois at Urbana-Champaign.