Chapter 2: LITERATURE REVIEW
2.3 FACTORS AFFECTING SOIL MICROBIAL DIVERSITY
2.3.2 Effects of land use
2.3.2.1 Arable agriculture
Land degradation reduces the productive capacity of arable agricultural soils causing a loss of biodiversity. However, land use management practices, such as tillage methods, crop residue management, application of fertilizers and manures, can help minimise this deterioration (Girvan et al., 2003).
Research evidence suggests that the microbial community under long-term arable soils differs from that under grasslands. To verify this, Garbeva et al. (2003) studied the diversity of Bacillus spp and related taxa in agricultural soil under three different management regimes, namely, short- and long-term arable land, and permanent grassland. The effects on the structure and diversity of Bacillus communities were marked, with samples from permanent grassland and those from short-term arable land having similar profiles. Samples from long-term arable land showed significant differences to those from short-term arable land as some grass remained in the latter, enhancing diversity in the short-term. The authors concluded that the long-term presence of grass in soil supported and maintained greater numbers and a higher diversity of Bacillus and related taxa than did long-term arable land.
Other research has suggested that within arable soils, the main factor affecting community composition is soil type rather than crop management. In a study by Wakelin et al. (2008a), habitat selective factors in agricultural soils influencing the structural composition and functional capacity of the autochthonous microbial communities were investigated. The authors characterized soils from seven field sites differing in long-term agricultural management regimes, by assessing the relationship between soil physicochemical properties and community structure and potential catabolic functions of both the soil bacteria and fungi. They concluded that soil type and not agricultural management practice was the key determinant of microbial community structure and catabolic function, with pH a primary driver of both microbial diversity and function in these soils. Thus agricultural practices had the effect of selectively shifting microbial populations and functions.
The major sources of substrate for microbial growth and activity in arable soils are litter and crop plant residues. Dilly et al. (2004) investigated bacterial diversity in agricultural soils during litter (crop residue) decomposition. Rye and wheat litter were buried in comparable soil types under different vegetation and exposed to different climates. Bacterial diversity increased with advancing litter decomposition and with decreasing substrate quality resulting from the loss of readily available carbon and the accumulation of refractory compounds. At different locations containing the same buried litter, differences in bacterial diversity were observed, indicating that climate,
vegetation and indigenous soil microorganisms, in addition to litter type, affected bacterial community development.
Reports that plants are important in regulating net decomposition rates of litter by directly affecting the quality thereof, led to research by Trinder et al. (2009). They investigated how plant cover and litter type affected fungal community structure and litter decomposition in a cutover peatland. Results showed that plant species did not affect fungal community structure but most litter types had a significant effect. The quantities of carbon entering the soil via rhizodeposition were insignificant for regulating the activity and diversity of the litter-degrading soil microbes in the peatland. The chemistry of the litter produced by the peatlands had a strong and more varied effect on both decomposition and fungal community structure. They concluded that the initial decomposition of litter and also the structure of the soil fungal community were regulated by the litter type and not by the plant cover.
The effects of stubble retention and applications of nitrogen fertilizer on functional gene abundance and the structure of dominant soil microbial communities under irrigated maize, was studied by Wakelin et al. (2007). Both stubble-retention and N addition had significant and long-term effects on microbial community structure and size, with stubble-retention being the strongest driver affecting species composition, particularly in the case of the fungal community. However, diversity estimates were little affected. The authors concluded that the sustained shifts in the size and structure of the soil microbial communities and the overall changes in N-based functional genes could have an impact on ecosystem function and on the productivity of subsequent crops.
The addition of mulches is a management practice that can be used to protect and add organic matter to the soil surface, as well as to conserve soil water. Yang et al. (2003) investigated the influence of different organic mulches on soil bacterial communities a year after application. Results showed that the long-term effect of organic mulches on the activity and structure of soil microbial populations depended on the type of mulch and was evident only in the top few centimetres of the soil profile. None of the mulches affected the species composition of the chemolithoautotrophic ammonia- oxidizing bacteria (AAOB). The authors concluded that in the long-term, repeated
mulch applications might result in changes in the microbial community and in species diversity because of the increase in soil organic matter content.
To increase crop production, fertilizer applications are a common and important agricultural practice. However the effects of fertilizer on soil microbes, vital to agroecosystem health as residue decomposers and cyclers of nutrients, are not fully understood. Attempts to devise sound land management strategies led to a study by Ge et al. (2008) of the effects of long-term applications of inorganic and organic fertilizers on soil microbial communities under maize rotated with wheat. They showed that long-term fertilization regimes affected the structure and diversity of the microbial communities in the agricultural soils. The bacterial community structure in organic manure (OM) and phosphorus/potassium (PK) amended soils had a higher richness and diversity than those of the unfertilized control and the N-containing fertilizer combinations (NK, NP, NPK and ½ NPKOM). They suggested that N- fertilizer could be a key factor that countered the effects of other fertilizers on soil microbial communities.
Inorganic fertilizers and organic manures are routinely applied to arable soils to replace nutrients removed by the harvested crop. Organic manures also add organic carbon which acts as a microbial substrate. Marschner et al. (2003) studied the effects of long-term applications of organic and inorganic fertilizer at low rates, on the chemical and biological properties of soil. They concluded that these amendments significantly changed soil chemical properties, and that ratios of Gram positive to Gram negative bacteria and of bacteria to fungi, were higher in organic treatments than in inorganic treatments. Different amendments influenced bacterial and eukaryotic community composition through their effect on the organic Ccontent and C/N ratio in the soil. Dissolved organic carbon (DOC) concentration was also shown to influence bacterial community structure.
Several researchers have used the particle-size fractionation technique (Sessitsch et al., 2001; Poll et al., 2003) to investigate the effects of manures and fertilizers on microbial activity and diversity. Poll et al. (2003) studied the effect of long-term farmyard manure (FYM) additions in several particle-size fractions of soil, by comparing soil fertilized with FYM and an unfertilized control. Coarse sand fractions
were colonised by a fungal-dominated community, together with a simple bacterial community, but after applications of FYM, bacteria dominated. On the other hand, silt and clay fractions were colonised by complex bacterial communities. The addition of FYM increased organic matter content, total microbial biomass and enzyme activity in sand, whereas microbial communities in finer fractions were less influenced.
Concern over agricultural sustainability, arising from soil erosion and fertility decline, in the densely populated and intensively cropped subtropical highlands of the world, led to a study by Govaerts et al. (2007). They assessed the long-term effects of tillage/seeding practices, crop rotation and crop residue management on maize and wheat, grown under rainfed conditions. The authors concluded that, compared to common farming practices, cropping systems that included zero tillage, crop rotation and residue retention increased overall microbial biomass, activity and diversity.
However, long-term zero tillage without residue retention was an unsustainable practice that led to poor soil health.
Most economically important field crops, such as maize (Zea mays) or wheat (Triticum aestivum) in agricultural soils, are associated with mycorrhiza. In contrast to these beneficial organisms, some of the most important plant pathogens are also found among the fungi. Therefore fungal diversity in agricultural soils, in particular of biocontrol strains of Trichoderma spp., was investigated by Hagn et al. (2003). Soils from high- and low-yield areas of a winter wheat field under two different farming management practices were analysed. Results showed that the dormant soil fungal community was minimally influenced by the factors investigated, whereas active populations exhibited a clear response to changes in the environment.
Concern over increased atmospheric concentrations of greenhouse gases (especially CO2), agroecosystem transformation and sustaining land productivity, prompted Razafimbelo et al. (2006) to study the effect of sugarcane residue management on soil organic carbon (SOC). They reported that soils under pre-harvest burnt cane contained lower levels of SOC than those under green cane harvesting with trash retention. Soil bulk density was lower under residue mulching compared to pre- harvest burning. The authors hypothesized that the preferential enrichment of soil carbon observed in the fine (< 2 µ m) fractions resulted in long-term storage of carbon.
Galdos et al. (2009), also working with sugarcane, evaluated the effects of trash management on the carbon dynamics of a sugarcane crop, but on land previously converted from native forest. They studied two chronosequences in plots which had been replanted to sugarcane, with or without pre-harvest burning, 2, 6 and 8 years prior to sampling. They concluded that soils from the area converted to the unburnt management for 8 years, had higher levels of total C, microbial biomass C and particulate organic matter C than those from plots under residue burning.