Soil Chemical Analysis

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/6A4E3EB5D8D502B5571F591F5B705C47/S0953756201005196a.pdf/div-class-title-a-new-fungal-phylum-the-span-class-italic-glomeromycota-span-phylogeny-and-evolution-div.pdf

A new fungal phylum, the Glomeromycota: phylogeny and evolution

https://www2.clarku.edu/faculty/dhibbett/Reprints%20PDFs/Taylor%20et%20al%202000%20FGB.pdf

Phylogenetic Species Recognition and Species Concepts in Fungi

Soil bacteria are very important in biogeochemical cycles and have been used for crop production for decades. Plant–bacterial interactions in the rhizosphere are the determinants of plant health and soil fertility. Free-living soil bacteria beneficial to plant growth, usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. PGPR are also termed plant health promoting rhizobacteria (PHPR) or nodule promoting rhizobacteria (NPR). These are associated with the rhizosphere, which is an important soil ecological environment for plant–microbe interactions. Symbiotic nitrogen-fixing bacteria include the cyanobacteria of the genera Rhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium, Sinorhizobium and Mesorhizobium. Free-living nitrogen-fixing bacteria or associative nitrogen fixers, for example bacteria belonging to the species Azospirillum, Enterobacter, Klebsiella and Pseudomonas, have been shown to attach to the root and efficiently colonize root surfaces. PGPR have the potential to contribute to sustainable plant growth promotion. Generally, PGPR function in three different ways: synthesizing particular compounds for the plants, facilitating the uptake of certain nutrients from the soil, and lessening or preventing the plants from diseases. Plant growth promotion and development can be facilitated both directly and indirectly. Indirect plant growth promotion includes the prevention of the deleterious effects of phytopathogenic organisms. This can be achieved by the production of siderophores, i.e. small metal-binding molecules. Biological control of soil-borne plant pathogens and the synthesis of antibiotics have also been reported in several bacterial species. Another mechanism by which PGPR can inhibit phytopathogens is the production of hydrogen cyanide (HCN) and/or fungal cell wall degrading enzymes, e.g., chitinase and s-1,3-glucanase. Direct plant growth promotion includes symbiotic and non-symbiotic PGPR which function through production of plant hormones such as auxins, cytokinins, gibberellins, ethylene and abscisic acid. Production of indole-3-ethanol or indole-3-acetic acid (IAA), the compounds belonging to auxins, have been reported for several bacterial genera. Some PGPR function as a sink for 1-aminocyclopropane-1-carboxylate (ACC), the immediate precursor of ethylene in higher plants, by hydrolyzing it into α-ketobutyrate and ammonia, and in this way promote root growth by lowering indigenous ethylene levels in the micro-rhizo environment. PGPR also help in solubilization of mineral phosphates and other nutrients, enhance resistance to stress, stabilize soil aggregates, and improve soil structure and organic matter content. PGPR retain more soil organic N, and other nutrients in the plant–soil system, thus reducing the need for fertilizer N and P and enhancing release of the nutrients.

Soil beneficial bacteria and their role in plant growth promotion: a review

Summary Here, the coevolution of mycorrhizal fungi and roots is assessed in the light of evidence now available, from palaeobotanical and morphological studies and the analysis of DNA-based phylogenies. The first bryophyte-like land plants, in the early Devonian (400 million years ago), had endophytic associations resembling vesicular‐ arbuscular mycorrhizas (VAM) even before roots evolved. Mycorrhizal evolution would have progressed from endophytic hyphae towards balanced associations where partners were interdependent due to the exchange of limiting energy and nutrient resources. Most mycorrhizas are mutualistic, but in some cases the trend for increasing plant control of fungi culminates in the exploitative mycorrhizas of achlorophyllous, mycoheterotrophic plants. Ectomycorrhizal, ericoid and orchid mycorrhizas, as well as nonmycorrhizal roots, evolved during the period of rapid angiosperm radiation in the Cretaceous. It is hypothesised that roots gradually evolved from rhizomes to provide more suitable habitats for mycorrhizal fungi and provide plants with complex branching and leaves with water and nutrients. Selection pressures have caused the morphological divergence of roots with different types of mycorrizas. Root cortex thickness and exodermis suberization are greatest in obligately mycorrhizal plants, while nonmycorrhizal plants tend to have fine roots, with more roots hairs and relatively advanced chemical defences. Major coevolutionary trends and the relative success of plants with different root types are discussed.

Coevolution of roots and mycorrhizas of land plants

AMONG the Eukaryota, the true fungi comprise four divisions (Chytridiomycota, Zymogomycota, Ascomycota and Basidio-mycota) that constitute a natural group which is thought to have diverged about 1 billion (109) years ago, believed also to be the time of divergence between metaphyta and metazoa lineages1. The endosymbionts responsible for the most prevalent plant root symbiosis, the vesicular–arbuscular mycorrhizae (VAM) or, more appropriately, arbuscular mycorrhizae, comprise 130 species of fungi classified in the Zygomycotina, order Glomales2–4. The arbuscular endomycorrhizae are considered to be ecologically important for most vascular plants5–8 in view of their beneficial effects on plant growth and survival. They are one of the few plant-fungus associations with a fossil record and may even have facilitated the origin of land flora. But the biochemical and genetic characterization of these microsymbionts has been hampered by the inability to grow them in pure culture. To investigate the origin and clarify the phylogenetic relationships of these organisms, we have sequenced ribosomal DNA genes from twelve species. Our phylogenetic analyses confirm the existence of three families within arbuscular fungi on the basis of morphological characters. We obtain approximate dates for the divergence of major branche's on the phylogenetic tree. These include an estimate for the origin of VAM-like fungi of 353–462 Myr ago, which is consistent with the hypothesis that VAM were instrumental in the colonization of land by ancient plants.

Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants

The first DNA sequences obtained from arbuscular endomycorrhizal fungi are reported. They were obtained by directly sequencing overlapping amplified fragments of the nuclear genes coding for the small subunit rRNA. These sequences were used to develop a polymerase chain reaction primer (VANS1) that enables the specific amplification of a portion of the vesicular-arbuscular endomycorrhizal fungus small subunit rRNA directly from a mixture of plant and fungal tissues. The specificity of this primer for arbuscular endomycorrhizal fungi was demonstrated by testing it on a number of organisms and by sequencing the fragment amplified from colonized leek (Allium porum) roots. This approach, coupled with other molecular techniques, will facilitate rapid detection, identification, and possibly quantitation of arbuscular endomycorrhizal fungi.

Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots.

A simple protocol for the extraction of total DNA from minute amounts of tissues and subsequent amplification of specific sequences by polymerase chain reaction is presented. The method is applicab...

DNA amplification from vegetative and sexual tissues of trees using polymerase chain reaction

A method to identify arbuscular endomycorrhizal fungi based on the amplification of portions of the nuclear gene coding for the small subunit rRNA is presented. By coupling the sensitivity of the polymerase chain reaction and the specificity afforded by taxon-specific primers, a variety of samples can be analyzed, including small amounts of colonized roots. Family-specific primers as well as generic primers are described and can be used to amplify small subunit rRNA fragments from endomycorrhizal fungi by polymerase chain reaction. The amplified products are then subjected to single-strand conformation polymorphism analysis to detect sequence differences. Among the advantages of this approach is the possibility of directly identifying the fungi inside field-collected roots, without having to rely on the fortuitous presence of spores. This technique should have obvious applications in the study of arbuscular endomycorrhizal fungi populations and allow closer examination of their host specificity.

https://aem.asm.org/content/aem/59/12/4211.full.pdf

Identification of endomycorrhizal fungi colonizing roots by fluorescent single-strand conformation polymorphism-polymerase chain reaction

The encapsulation material surrounding the endophyte of Alnus crispa var. mollis Fern. root nodule was studied by means of a variety of staining methods in light and in electron microscopy. The enzymatic degradation of the capsular material was obtained and the degradation products were studied by thin-layer chromatography. The endophyte capsule was composed mainly of granular and fibrillar non-sulfated and de-esterified polygalacturonic acid or its salts. An endophyte pectic capsule was also demonstrated in 11 additional species of non-leguminous root nodules. Small secretory vesicles, containing electron-dense material similar to that of the endophyte capsule, occurred in free multivesicular bodies throughout the host cell cytoplasm. Ultrastructural observations are consistent with the view that these bodies migrate to the host membrane envelope surrounding the endophyte, fuse with it, and deposit the contents of the small vesicles toward the endophyte cell wall. These small secretory vesicles appeared ...

Maurice Lalonde

Papers

Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants

Specific amplification of 18S fungal ribosomal genes from vesicular-arbuscular endomycorrhizal fungi colonizing roots.

DNA amplification from vegetative and sexual tissues of trees using polymerase chain reaction

Identification of endomycorrhizal fungi colonizing roots by fluorescent single-strand conformation polymorphism-polymerase chain reaction

Ultrastructure, composition, and biogenesis of the encapsulation material surrounding the endophyte in Alnus crispa var. mollis root nodules