Academic literature on the topic 'Edaphic niche'

SynopsisThis assessment of selected literature on pteridophyte edaphic adaptation is presented in three parts: (1) pH and general soil nutrient background, (2) growth responses to specific inorganic ions and frond mineral content, and (3) collected works on Pteridium aquilinum edaphic adaptations. In this report, a case is made for the overriding effect of both soil pH and inorganic ion content in determining pteridophyte occurrence. Recommendations are made for more field and laboratory co-ordinated studies, especially as they pertain to the determination of species-specific amplitudes of adaptation, and for the initiation of physiological and metabolic investigations into the basis of these edaphic adaptations.

The ecological niche of Vallonia pulchella (Muller, 1774) was investigated by means of the general factor analysis of GNESFA. It was revealed that the ecological niche of a micromollusk is determined by both edaphic factors and ecological features of vegetation. Ecological niche optima may be presented by integral variables such as marginality and specialization axes and may be plotted in geographic space. The spatial distribution of the Vallonia pulchella habitat suitability index (HSI) within the Technosols (sod-lithogenic soils on red-brown clays) is shown, which allows predicting the optimal conditions for the existence of the species.

The ecological niche is the keystone conception of theoretical ecology. But for its use methodical difficulties appears which can be solved with the help of the number of statistical techniques which includes OMI-analyses. This procedure has given the possibility of visualization of the ecological niche of soil animal community of the sod-lithogenic soils on the red-brown clays. The phenomenon of differentiation of the ecological niche demands the explanation of structuring ecological space and detects of dominant factors which have influenced for the physiognomy of communities of soil animals. The important problem is also to evaluate the role of ecological specialization of animals, which expresses in the terms ecomorphical structure. The usage of RLQ-analyses has permitted to quantity estimate the influence of vegetation features and edaphic factors on the spatial distribution of soil mesofauna. The researching polygon is characterized both the presence of patch with optimal vital activity terms, and with unfavorable conditions. Mesopedobionts within researching polygon have been established as not being ecologically homogeneous. The functional groups A and B embrace in the majority of endogeic animals such as larvae of beetles. The ecologically diverse ecomorphic properties of these groups with high density of the animal community may be determined by the axis number 1. These groups concentrate within 3–4 meters diameter patches with most favorable conditions for vital activity. Such patches are marginal for this polygon. The functional group C is presented by gerpetobiont animals which are able to migrate and relatively tolerant to edaphic factors. That is why centroid of given group is most closely located to the typical condition of this polygon. Considered indicators of soil as environment of living organisms permit to estimate the community’s ecological niche. The quantity characteristics of species ecological niches within researching polygon such as specialization and marginality have been estimated. At first for the characteristics of soil animals’ ecological niches have been used phytoindicator scales and ecomorphical analyses of the vegetations structure and also physiognomy types of it. The selection of functional groups of soil animals and applied for them ecomorphical characteristics are present high information values and conformity of indicator scales for the description of real current types of conditions of ecosystems.

The aim of our work is to describe the ecological niche of the land snail Brephulopsis cylindrica (Menke, 1828) in terms of the edaphic properties and properties of the vegetation cover and to show the spatial features of the variation of the habitat preference index within the artificial soil body – technosols (soddy-lithogenic soils on loess-like clays) using the ecological niche factor analysis (ENFA). The research was carried out at the Research Centre of the Dnipro Agrarian and Economic University in Pokrov. Sampling was carried out on a variant of artificial soil (technozems) formed on loess-like clays. The test site where the sampling was conducted consists of 7 transects of 15 samples each. Test points form a regular grid with a mesh size of 3 m. Soil mechanical impedance, aggregate-size distribution, soil electrical conductivity, vegetation physiognomic characteristics, and Didukh phytoindication scales were used as ecogeographic predictors of the mollusc’s ecological niche properties. Phytoindication assessment indicates that the technosol ecological regimes are favourable for sub-mesophytes, hemi-hydrocontrastophiles, neutrophiles, semi-eutrophs. The test for statistical significance showed that an axis of marginality of the ecological niche of B. cylindrica and axes of specialization are significantly different from the random distribution. We found that the ecological niche of the mollusc is determined by both edaphic factors and ecological features of vegetation. The marginality of B. cylindrica ecological niche over the entire period of study is determined mainly by preferences for physiognomic vegetation types, higher values of the continentality and thermality regimes. Often greater content in the soil of aggregates 1–3 mm in size coincides with greater numbers of B. cylindrica individuals. Individuals of this species avoid physiognomic type III and areas with higher soil alkalinity and mineralization detected both by means of the phytoindication approach and soil electrical conductivity data. Ecological niche optima may be presented by integral variables such as marginality and specialization axes and plotted in geographic space. The spatial distribution of the B. cylindrica habitat suitability index (HSI) within the technosols is shown, which makes it possible to predict the optimal conditions for the existence of the species.

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

Vegetation–environment relationships are well understood for boreal lichen woodlands, but the mechanistic basis for small-scale understory patchiness (patches dominated by lichen, mosses, and vascular plants), and its implications for the prevalence of niche vs. neutral processes driving understory development, have not been explored. We asked whether predictable vegetation–environment associations exist at the microsite scale, with the goal of informing caribou range management. We sampled canopy and edaphic variables in patches of lichen, feathermoss, and vascular plants in subalpine lodgepole pine (Pinus contorta var. latifolia Engelm. ex S.Wats.) forests, in north-central British Columbia, Canada. Lichens positively associate with microsites that have high light and heat, and low moisture and nutrient availability; vascular plants positively associate with base-cation availability, sulphur and phosphorus availability, fine-textured soils, thick organic layers, and high light; feathermosses positively associate with low light and heat, and nitrogen availability. Understory composition is most strongly associated with canopy characteristics, but is also related to edaphic properties in predictable ways; soil and canopy attributes may further interact to define distinct intra-stand niches. The viability of caribou winter ranges can likely be extended by partially thinning or burning the canopy and organic layers, but the longevity of a lichen-dominant stage may ultimately depend on the soil texture, due to its influence on vascular plant growth.

The thesis starts in the continental context of the White Carpathians Protected Landscape Area and UNESCO Biosphere Reserve (Czech Republic), a protected area famous for its grasslands with the globally highest fine-scale plant species richness. The effects of management on species richness and composition of both plants and animals were tested in relation to different management practices (mowing, grazing, abandonment and mixed management) for several years at several sites, clarifying the disagreements that have occurred among conservationists and practitioners to date. The thesis continues with a focus on the Mediterranean context. Here, the distribution patterns of understorey assemblages of coastal pine stands on sand dunes were studied, given the scarcity of literature due to scholarly disdain. Using more than a hundred plots along Italian coastlines in different pine forest types, community similarity and specificity was assessed in order to provide lacking management clues. Subsequently, focusing on a pine forest stand located in Southern Tuscany, the thesis aimed to solve another pivotal question, namely by investigating the concordance of species assemblages between vascular plants, oribatid mites and soil chemical properties with special attention to the role of vegetation structure (i.e. tree, shrub and herbaceous cover) for biological components. This part provides new answers about congruence among communities and following appropriate management practices to be fulfilled for communities. The last part, performed along a wide range of Tuscan coasts, deals with one of the most extreme habitats in the Mediterranean basin: coastal dunes. Here, the understanding of the response of plant species to soil factors was estimated. This provides concrete proposals for the effective conservation of coastal habitats.

Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report