An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil functions This review focuses on recent data relating how plant type, soil type, and soil management regime affect the microbial diversity of soil and the implication for the soil's disease suppressiveness The two main drivers of soil microbial community structure, ie, plant type and soil type, are thought to exert their function in a complex manner We propose that the fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to the complexity of the microbial interactions in soil, including interactions between microorganisms and soil and microorganisms and plants A conceptual framework, based on the relative strengths of the shaping forces exerted by plant and soil versus the ecological behavior of microorganisms, is proposed

Microbial diversity in soil: Selection of microbial populations by plant and soil type and implications for disease suppressiveness

Summary • Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). • Here, we assessed the fungal diversity in six different forest soils using tagencoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. • Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. • This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

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454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

Fungi fulfil a range of important ecological functions, yet current understanding of fungal biodiversity in soil is limited. Direct DNA extraction from soil, coupled with polymerase chain reaction amplification and community profiling techniques, has proved successful in investigations of bacterial ecology and shows great promise for elucidating the taxonomic and functional characteristics of soil fungal communities. These community profiling techniques include denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism (SSCP), terminal restriction fragment length polymorphism (T-RFLP), amplified rDNA restriction analysis (ARDRA), amplified ribosomal intergenic spacer analysis (ARISA) and cloning, and are generally coupled with DNA sequencing. The techniques and their potential limitations are discussed, along with recent advances that have been made possible through their application in soil fungal ecology. It is unlikely that a single approach will be universally applicable for assessing fungal diversity in all soils or circumstances. However, judicious selection of the methodology, keeping the experimental aims in mind, and the exploitation of emerging technologies will undoubtedly increase our understanding of soil fungal communities in the future.

Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques

Unravelling rhizosphere–microbial interactions: opportunities and limitations

Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants.

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

A greenhouse investigation was conducted to determine the effect of arbuscular mycorrhiza and drought on the growth of two tropical hedgerow legume trees (Gliricidia sepium and Leucaena leucocephala) under simulated eroded soil conditions. It was a factorial design with two levels of watering regime (adequate watering and drought), inoculation with Glomus deserticola (with and without), and two soil types (0–30 cm topsoil and 30–60 cm subsoil). Each treatment was replicated 3 times. After ten drought cycles, the growth of Gliricidia sepium in the subsoil was enhanced by mycorrhizal inoculation under both watering regimes whereas there was no significant contribution of mycorrhizal inoculation to the growth of L. leucocephala in both soil types under the two watering regimes. Drought stress significantly reduced most growth parameters for the two tree species in both soils with or without fungal inoculation. The N-fixing activity of Gliricidia sepium benefited from Glomus deserticola inoculation while that of L. leucocephala was not significantly affected in the topsoil. Mycorrhizal colonization was reduced for both tree species in the subsoil compared to the topsoil while it was significantly increased for both species in the subsoil when compared to the uninoculated subsoil counterpart. In the subsoil, inoculation of Gliricidia sepium with the mycorrhizal fungus increased root colonization by 89% and 73% under adequate watering and drought, respectively, whereas L. leucocephala had only a 38% and 42% increase in root colonization under comparative conditions in the subsoil. Thus Glomus deserticola inoculation may be beneficial to the growth of Gliricidia sepium in a badly eroded site where topsoil is missing.

Effects of drought stress and arbuscular mycorrhiza on the growth of Gliricidia sepium (Jacq). Walp, and Leucaena leucocephala (Lam.) de Wit. in simulated eroded soil conditions

A field trial on alley-cropping was conducted at the University of Ibadan research farm in the 1990/91 cropping season to assess the contributions of arbuscular mycorrhizal (AM) fungi and hedgerow woody legumes to the yield and nutrient uptake of cassava (Manihot esculenta Crantz) as an intercrop in an infertile soil. The trial also investigated the influence of AM fungi on the interplanting of a non-nodulating woody legume Senna siamea (syn. Cassia siamea) with a nodulating woody legume (Leucaena leucocephala). AM contributions to cassava were greater than the hedgerow contributions, which demonstrated that AM associations are an essential component in the nutrition of cassava. In contrast to cassava, AM inoculation only influenced the leaf dry weight and uptake of nutrients of non-interplanted woody legumes but not the above-ground biomass and P uptake of interplanted woody legumes. However, non-inoculated interplanted Leucaena benefited more from indigenous AM fungi than the competing Senna. The negative contributions to the nutrient uptake (K, Ca and Mg) of cassava by hedgerows and the lack of response to AM inoculation in interplanted hedgerow woody legumes could be attributed to root competition among the different plant species growing in close proximity to each other. The present results show that cassava benefits more from AM association than Leucaena which in turn benefits more than Senna in an alley-cropping system.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0021859698005516

Contribution of arbuscular mycorrhizal (AM) fungi and hedgerow trees to the yield and nutrient uptake of cassava in an alley-cropping system

The effect of inoculation with Glomus clarum, a vesicular-arbuscular mycorrhiza fungus, and alley-cropping on the growth of the cassava cultivar, TMS 30572, was investigated under field conditions in a low nutrient tropical soil. Cassava was grown either interplanted between two hedgerow tree species (alley-cropped) or sole-cropped. Sub-plots were either inoculated with G. clarum or were not inoculated. No effort was made to destroy the indigenous mycorrhizal fungi. Three months after planting, no significant influence of G. clarum inoculation was observed on the growth of roots, shoots or leaf area index (LAI). However, with time, inoculation and system of cropping enhanced these growth parameters. Nine months after planting, the total biomass of alley-cropped cassava was significantly higher than that of inoculated and non-inoculated sole-cropped cassava. Inoculation had led to an increase in the fresh tuber yield of both the alley- and sole-cropped cassava 12 months after planting. The LAI of both alley- and sole-cropped cassava inoculated with G. clarum increased.

Growth of cassava cultivar TMS 30572 as affected by alley-cropping and mycorrhizal inoculation

An article published by Journal of Food, Agriculture & Environment Vol.6(2) : 227 - 233 ,2008

Olajire Fagbola

Papers

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

Effects of drought stress and arbuscular mycorrhiza on the growth of Gliricidia sepium (Jacq). Walp, and Leucaena leucocephala (Lam.) de Wit. in simulated eroded soil conditions

Contribution of arbuscular mycorrhizal (AM) fungi and hedgerow trees to the yield and nutrient uptake of cassava in an alley-cropping system

Growth of cassava cultivar TMS 30572 as affected by alley-cropping and mycorrhizal inoculation

Genetic variation and genotype × environment interaction in yams (Dioscorea spp.) for root colonization by arbuscular mycorrhiza