Ecology Of Soil Fungi Research Articles

Landscape-scale mapping of soil fungal distribution: proposing a new NGS-based approach

Soil fungi play an indispensable role in the functioning of terrestrial habitats. Most landscape-scale studies of soil fungal diversity try to identify the fungal taxa present at a study site and define the relationships between their abundance and environmental factors. The specific spatial distribution of these fungi over the site, however, is not addressed. Our study’s main objective is to propose a novel approach to landscape-scale mapping of soil fungi distribution using next generation sequencing and geographic information system applications. Furthermore, to test the proposed approach and discuss its performance, we aimed to conduct a case study mapping the spatial distribution of soil fungi on the Wielka Żuława island. The case study was performed on the Wielka Żuława island in northern Poland, where soil samples were collected every 100 m in an even grid. The fungal taxa and their relative abundance in each sample were assessed using the Illumina platform. Using the data obtained for the sampled points, maps of soil fungi spatial distribution were generated using three common interpolators: inverted distance weighted (IDW), B-spline, and ordinary Kriging. The proposed approach succeeded in creating maps of fungal distribution on Wielka Żuława. The most abundant groups of soil fungi were Penicillium on the genus level, Aspergillaceae on the family level, and ectomycorrhizal fungi on the trophic group level. Ordinary Kriging proved to be the most accurate at predicting relative abundance values for the groups of fungi significantly spatially autocorrelated at the sampled scale. For the groups of fungi not displaying spatial autocorrelation at the sampled scale, IDW provided the most accurate predictions of their relative abundance. Although less accurate at predicting exact relative abundance values, B-spline performed best in delineating the spatial patterns of soil fungi distribution. The proposed approach to landscape-scale mapping of soil fungi distribution could provide new insights into the ecology of soil fungi and terrestrial ecosystems in general. Producing maps of predicted fungal distribution in landscape-scale soil fungi diversity studies would also facilitate the reusability and replicability of the results. Outside the area of research, mapping the distribution of soil fungi could prove helpful in areas such as agriculture and forestry, nature conservation, and urban planning.

Diversity of Trichoderma species associated with soil in the Zoige alpine wetland of Southwest China

The ecology of soil fungi is poorly understood, and recent comprehensive reports on Trichoderma are unavailable for any region, including the Zoige alpine wetland ecological region in China. One hundred soil samples were collected from different soil types and soil layers in Zoige alpine wetland ecological regions. Using the traditional suspension plating method, 80 Trichoderma strains were chosen to analyze species diversity. After a preliminary classification of morphological characteristics and the genes glyceraldehyde-3-phosphate dehydrogenase (gpd), 57 representative strains were selected and eventually identified as seven species via phylogenetic analyses of multilocus sequences based on the genes transcription elongation factor 1 alpha (tef1), encoding RNA polymerase II subunit B (rpb2) and ATP citrate lyase (acl1). Among them, T. harzianum was the dominant species isolated from five soil layers and four soil types, and had the highest isolation frequency (23%) in this zone, while T. polysporum and T. pyramidale were rare species, with isolation frequencies of less than 1%. Our detailed morphological observation and molecular phylogenetic analyses support the recognition of Trichoderma zoigense was described for the first time as a new species, while T. atrobrunneum as a new record for China was found. Our results will be used as a reference for a greater understanding of soil microbial resources, ecological rehabilitation and reconstructions in the Zoige alpine wetland.

Biodiversity and ecology of soil fungi in a primary succession of a temperate coastal dune system

Soil fungal communities were studied in an actively developing coastal dune system at Goeree Island, the Netherlands. A shore to inland sampling transect was laid out, extending from coastal brackish marshes to recently formed foredunes to older dune pastures to adjacent woodlands. Soil samples from these biotopes were thoroughly characterized by analyzing physicochemical and microbial characteristics. Soil fungal community structure and composition were analysed by a combination of different phenotypic and genotypic methodologies (isolation of microfungi via a specialized soil washing technique and in situ observation of macrofungi, versus DGGE profiling and sequencing of multi-locus rDNA clone libraries). The results showed that fungal biomass tended to increase land-inwards along the gradient of maturity. The community structure was significantly correlated with progressive soil acidification land-inwards and with the exposure to brackish water in the coastal sites. Comparison between isolation and molecular datasets revealed that both methods were biased towards specific functional or phylogenetic groups. Most of the isolated fungi were common soil saprotrophic ascomycetes, while specialized fungi (biotrophic plant symbionts and pathogens, primary decomposers of recalcitrant organic matter, etc.) were only detected by molecular means. Phylogenetic specificity of PCR-based DNA profiling, on the other hand, strongly depended on primer selection. In spite of the relatively low number of common species that were identified among the isolated cultures and by clone library sequencing, as well as the potential biases of each characterization method, multivariate analysis on both isolation and molecular datasets yielded similar correlation patterns with the environment.

Role of Prosopis cineraria on the ecology of soil fungi in Indian desert

Abstract An investigation was carried out to assess the effect of Prosopis cineraria on some ecological parameters of soil microfungi in an arid region of western Rajasthan. Nine soil samplings were done from the undercanopy of the tree and from the open areas for 2 years. Undercanopy soil of the tree possessed higher population of fungi and fungal biomass as compared to open field. Fungal parameters varied among different sampling periods. Soil samples analysed during different seasons for soil mycoflora revealed maximum fungal populations in rainy months. Fungal biomass and fungal population are directly proportional to organic matter ( r = 0·78;·0·78, respectively). The population of fungi is linearly related to fungal biomass with higher ( r = 0·92) correlation at undercanopy as compared to open area ( r = 0·72). Soil and climatic factors are responsible for enormous variation in fungal biomass. Organic carbon in the undercanopy is the critical factor that explained 76% variation in fungal biomass. Climatic factors did not affect undercanopy fungal biomass to any measurable extent; however, fungal biomass in the open area varied significantly due to rainfall and the model explained 73% variations in fungal biomass.

Role of Prosopis cineraria on the ecology of soil fungi in Indian desert

An investigation was carried out to assess the effect of Prosopis cineraria on some ecological parameters of soil microfungi in an arid region of western Rajasthan. Nine soil samplings were done from the undercanopy of the tree and from the open areas for 2 years. Undercanopy soil of the tree possessed higher population of fungi and fungal biomass as compared to open field. Fungal parameters varied among different sampling periods. Soil samples analysed during different seasons for soil mycoflora revealed maximum fungal populations in rainy months. Fungal biomass and fungal population are directly proportional to organic matter ( r= 0·78;·0·78, respectively). The population of fungi is linearly related to fungal biomass with higher ( r= 0·92) correlation at undercanopy as compared to open area ( r= 0·72). Soil and climatic factors are responsible for enormous variation in fungal biomass. Organic carbon in the undercanopy is the critical factor that explained 76% variation in fungal biomass. Climatic factors did not affect undercanopy fungal biomass to any measurable extent; however, fungal biomass in the open area varied significantly due to rainfall and the model explained 73% variations in fungal biomass.

Use of cotton strips to relate fungal community structure to cellulose decomposition rates in the field

Studies on the ecology of soil fungi have traditionally been concerned with the distribution of taxa in the soil, and the influence of the environment on community structure and composition. Relatively little emphasis has been placed on the role of the fungal community and the effects of community composition on decomposition processes, even though it is recognized that the decomposition of natural compounds is a major function of the fungal community. One approach to defining the role of soil fungi in the decomposition process is to take an inventory of the fungi in the soil, evaluate their enzymatic capacity under laboratory conditions and then use these data to make inferences about the role of the community in decomposition of natural substrates, as has been done by Flanagan and Scarborough (1974) and Gochenaur (1984). Using this approach, and comparing soils, Flanagan (198 1) concluded that “it appears that taxonomic differences in fungal communities between ecosystems do not significantly influence the decay rate of plant remains between sites. The biomass of fungi is related to quantity and quality of organic matter, and the decay rate of a given organic matter is controlled primarily by climates”. Although such studies provide useful information, they suffer from the fact that soil fungi are being tested under artificial conditions for their potential for decomposing specific substrates. To interpret the role of fungal community structure on actual decomposition rates, it would be better to examine fungi actually colonizing particular substrates, from the soil, and to monitor simultaneously the amount of decomposition that is taking place. An opportunity to do this arose as part of an ongoing study on the effects of amendments on the decomposition of cotton (cellulose) strips, buried in a Scottish moorland soil. Cotton strips of uniform weave, 1Ocm wide by 30 cm, were prepared (Latter and Howson, 1977) and inserted into an acid (pH 4.345) Scottish moorland soil near Banchory (Grid Ref. No. 637903). The general area of the study has been described in detail by Miles (1973). The top segments of the strips were placed in the old litter/F horizon, the side segments in the variable O/H/Ah horizon, and the bottom segments in the E/Es horizons (nomenclature according to Hodgson, 1974) using the method of French and Howson (1982). On 25 August 1981, five replicate strips were placed randomly in each of three plots that had been amended as follows: (i) N aDDlied as NH.NO, at a rate of 40 am-‘: (ii) P applied as KH;FCJ, at 60 gm-*, (iii) Ca applied& Ca;cb; at 100 g m-*. A further 5 strips were distributed between three plots treated with a 1: 1 mixture of glucose and potato starch: two in a plot treated at 4 g m-*, one in a plot treated at 16gm-* and the remaining two in a plot treated at 40 g m-*. Data from these three plots were combined as a single “carbohydrate” treatment. All amendments had been applied on three occasions during 1979; on 19 September, 15 October and 30 October. Five strips were also inserted in unamended control plots. The strips were removed on 8 December 198 1 and the side segments were cut, frayed and tested for tensile strength (Latter and Howson, 1977). Unburied control strips were simultaneously tested for tensile strength and the percent tensile strength loss for test strips was calculated as follows:

Ecology of Soil Fungi

Ecology of Soil Fungi

Ecology of Soil Fungi.

Ecology of Soil Fungi.

Ecology of Soil Fungi

Ecology of Soil Fungi

Book reviews: Ecology of Soil Fungi.

Book reviews: Ecology of Soil Fungi.

Book Review - Ecology of Soil Fungi by D.M. Griffin. Chapman and Hall, London.

Book Review - Ecology of Soil Fungi by D.M. Griffin. Chapman and Hall, London.

Reviews

Book Reviewed in this article: Ecology of Soil Fungi. By D. M. Griffin. Ecology of Tropical and Subtropical Vegetation. By H. Walter. Shoot Organization in Vascular Plants. By K. J. Dormer. The Biology and Chemistry of the Umbelliferae. Ed. by V. H. Heywood. Chloroplasts and Mitochondria. By M. A. Tribe and P. A. Whittaker. Plant Metabolism. By H. E. Street and W. Cockburn. L'thylene Metabolisme et Activite Metabolique. By Chon‐Ton Phan.

Ecology of Soil Fungi

Ecology of Soil Fungi

Ecology of soil fungi of a sal forest with emphasis on fungistasis

An ecological study of the soil micro-fungi in three forest regions of different age was undertaken. The pH of the soil varied from 6.6 to 6.9. Soil samples were collected from three different depthsviz 0–6, 7–12, and 13–18 inches with aseptic precautions and were studied by a dilution-plate method using peptone-dextrose agar with rose bengal for the fungal analysis. Determinations were made of physico-chemical characters of soil such as organic matter, total nitrogen, phosphorus, water-holding capacity and pH of the soil. The organic matter and nitrogen favoured the growth of fungi in the soil. The upper horizon contained more of the organic matter, nitrogen, phosphorus, and perhaps other elements, which in turn favoured the growth of fungi in soil. The number of fungi decreased according to increase in depth of the soil samples. The frequency and abundance of some dominant fungi have been calculated and the fungal population has been represented both qualitatively and quantitatively.

The Ecology of Soil-Borne Fungal Disease

The behaviour in soil of root-infecting fungi is sometimes considered to be a complex subject, and the inherent principles and implications are indeed commonly misunderstood by plant pathologists not specialist in this field. There has, of course, been no shortage of reviews recently on various aspects of the ecology of fungi in soil. Yet despite, or perhaps even because of the extent of this literature, confusion is still common. From the large field avail­ able two works can best be recommended. Firstly Garrett's 1956 book (1), which provides a considered and balanced account of the relative importance of work up to that date and presents the theoretical concepts important in fully understanding the subject. Secondly the account of the 1958 Liverpool International Symposium (2) since it includes much recent work that indi­ cates the trend of current work and thought, some of it more controversial than others. The apparent complexity of the biology in soil of plant pathogens is partly the result of the soil's opacity, which makes observations difficult and necessitates the use of indirect methods, the interpretation of which is some­ times ambiguous. But another potent source of difficulty is the presence in the soil of an established population of microorganisms with their own biology without any necessary connection with a host plant. This situation contrasts markedly with the simple one existing for most air-borne diseases, in which not only is observation of the host-pathogen interaction relatively easy but also the system is a simple two-component one with two pathways of interac­ tion, and can be represented: H;:=P. This biological system is affected by the inorganic environment acting directly on both components which can then adjust the equilibrium as indicated by the arrows. The variations within this system are limited, and, using the symbolic signs for neutral, positive and negative effects (3), the pathogen may show 0 or towards the suscept, and the suscept +,0, or towards the pathogen. Little difficulty attends under­ standing the possibilities in such a system. Occasionally air-borne diseases may involve more than two components as in the synergistic production of disease in the white blister rust of cabbage, and there is also the possibility that the phyllosphere (4) might affect the outcome as has been recorded by Bamberg (5) and Koch (6), but there is no indication that such phenomena are either general or generally considered in air-borne disease. In soil, by contrast, it is the simple condition, H;:=P, that is uncommon, even rare. It occurs occasionally, owing to bad technique in hydroponics or in plant culture in sterilized composts. Where such a situation is allowed to develop disease is often exceptionally severe, and even organisms not

Ecology of soil fungi of rice fields 1. Succession of fungi on rice roots 2. Association of soil fungi with organic matter

The composition of the fungal community associated with the roots changes with the ageing of the crop. In the early stages of growth species of Aspergillus and Penicillium are common isolates, but specialized root inhabitants like Thielavia angulata Das and Humicola sp. occur dominantly on mature roots. Trichoderma viride Pers. ex Fr. and Cephalosporium sp. may be associated with roots of all ages to a more or less varying degree, but they tend to become prominent only on dead and decomposing roots left in the field after harvesting, when only a minimum number of species is present. These roots are almost exhausted by March and only the more resistant parts left. Dominant fungi isolated in March and April were mainly sterile and could not be identified, though Aspergillus and Penicillium species reappeared with lesser frequency. In the second part the composition of the fungus population of a paddy field soil in relation to soil factors and amendments, cover crops and weather is described. Most of the fungi capable of growing on malt agar plates may be isolated either by the dilution plate method or by plating washed organic matter picked up from soil samples, but indication of their activities in soil is better secured by the latter technique. Of thirty-two fungi only nine were more or less dominant, occurring in almost every month, the rest were rather rare. Marked seasonal variation of the dominant fungi occurred, but soil treatments affected only a few of them. It is suggested that the greater frequency of isolation of some fungi from washed organic matter is due to their greater saprophytic ability to colonize organic debris in this soil.

Soil moisture and the ecology of soil fungi.

SummarySome basic concepts concerning soil physical factors have been briefly discussed. The importance of evaluation of the total soil moisture stress, as indicative of the energy which must be used by an organism to gain water from the soil, is shown. This total stress can be divided into tensiometric and osmotic components, of which the latter is important only in saline or heavily fertilized soils and is but briefly mentioned. Tensiometric suction is discussed and shown to be best described along with a measure of the texture and structure of the soil by means of the moisture characteristic. From such a characteristic, additional information concerning porosity and aeration can be obtained.Although there are few published experiments in which suction has been measured, none suggests a limitation of fungal growth directly due to suction factors in the soils between saturation and the permanent wilting point of mesophytic higher plants. Evidence derived from controlled humidity experiments reveals that most fungi can exert sufficient force to absorb water from atmospheres at a lower relative humidity than those in equilibrium with soil at the permanent wilting point. It is then suggested that absorption of soil water per unit area of absorptive surface will need to occur much less rapidly in the case of soil fungi than of higher plants, so that the growth of the former will not be limited to the same extent by reduction in the hydraulic conductivity of the soil. The conclusion is drawn that the majority of fungi will probably be able to grow in soils somewhat, or even considerably, drier than the permanent wilting point of higher plants.From an examination of the evidence it is concluded that in a compact soil spores are dispersed by the soil water only when that water is moving through a nearly saturated soil. In natural soils, however, where cracks, root channels, etc., are present, rapid movement of water, and thus of spores, may take place to a considerable depth even when the general soil mass is far from saturated.The literature reveals that such factors as moisture content, texture and structure, which affect soil aeration, have a profound influence on fungal activity and it is postulated that aeration is, in fact, the effective agent. Although the evidence is far from adequate, it appears that both excess of carbon dioxide and an insufficiency of oxygen are implicated as inhibitors.I wish to pay particular tribute to Professor N. Collis‐George who provided the initial stimulus for me to begin investigations in the field which forms the topic of this article and who has been of much assistance to me in discussion. I also wish to thank Dr E. C. Childs and Dr S. D. Garrett for discussion and for reading and criticizing various sections of the manuscript and to thank Dr D. J. Greenwood for advice concerning soil aeration. I am grateful to Professor H. Godwin for providing accommodation for me at the Botany School, Cambridge, for a period during which this article was written.

The Ecology of Soil Fungi

The Ecology of Soil Fungi

Ecology of Soil Fungi

The Ecology of Soil Fungi An International Symposium. Edited by D. Parkinson and J. S. Waid. Pp. xi + 324. (Liverpool: The University Press, 1960.) 42s. 6d. net.

REVIEWS

Review in this article: Drawings of British Plants. Part XIV. Adoxaceae‐Dipsacaceae. By Stella Ross‐Craig. Darwin's Biological Work: Some Aspects Reconsidered. Edited by P. R. Bell. Flora of the British Isles, Illustrations, Part II, Rosaceae‐Polemoniaceae. By A. R. Clapham, T. G. Tutin and E. F. Warburg. Drawings by Sybil J. Roles. Protoplasmic Streaming. Protoplasmatologia. Handbuch der Protoplasmaforschung. Edited by L. V. Heilbrunn and F. Weber. The Ecology of Soil Fungi. An International Symposium. Edited by D. Parkinson and J. S. Waid. Marine Algae of the Eastern Tropical and Subtropical Coasts of the Americas. By William Randolph Taylor. Introduction to Plant Geography. By Nicholas Polunin. Frost, Drought and Heat Resistance. By J. Levitt.