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PubMed2003

Investigating plant-plant interference by metabolic fingerprinting.

New analytical developments in post-genomic technologies are being introduced to the field of plant ecology. FT-IR fingerprinting coupled with chemometrics via cluster analysis is proposed as a tool for correlating global metabolic changes with abiotic or biotic perturbation and/or interactions. The current study concentrates on detecting chemical responses by inter-species competition between a monocotyledon Brachypodium distachyion and a dicotyledon Arabidopsis thaliana. Growth analysis of 42 days old plants showed differences in both species under competition. Clear changes in the FT-IR metabolic fingerprints of B. distachyion in competition with A. thaliana were observed, whilst there were no apparent chemical differences in the A. thaliana plant tissues. This study demonstrates the power of this approach in detecting changes in the global metabolic profiles of plants in response to biotic interactions, and we believe FT-IR is appropriate for rapid screening (10 s per sample) prior to targeted metabolite analyses.

Arabidopsis↗
PubMed2001

Biotic ligand model of the acute toxicity of metals. 1. Technical basis.

The biotic ligand model (BLM) of acute metal toxicity to aquatic organisms is based on the idea that mortality occurs when the metal-biotic ligand complex reaches a critical concentration. For fish, the biotic ligand is either known or suspected to be the sodium or calcium channel proteins in the gill surface that regulate the ionic composition of the blood. For other organisms, it is hypothesized that a biotic ligand exists and that mortality can be modeled in a similar way. The biotic ligand interacts with the metal cations in solution. The amount of metal that binds is determined by a competition for metal ions between the biotic ligand and the other aqueous ligands, particularly dissolved organic matter (DOM), and the competition for the biotic ligand between the toxic metal ion and the other metal cations in solution, for example, calcium. The model is a generalization of the free ion activity model that relates toxicity to the concentration of the divalent metal cation. The difference is the presence of competitive binding at the biotic ligand, which models the protective effects of other metal cations, and the direct influence of pH. The model is implemented using the Windermere humic aqueous model (WHAM) model of metal-DOM complexation. It is applied to copper and silver using gill complexation constants reported by R. Playle and coworkers. Initial application is made to the fathead minnow data set reported by R. Erickson and a water effects ratio data set by J. Diamond. The use of the BLM for determining total maximum daily loadings (TMDLs) and for regional risk assessments is discussed within a probabilistic framework. At first glance, it appears that a large amount of data are required for a successful application. However, the use of lognormal probability distributions reduces the required data to a manageable amount.

Animals↗
PubMed2001

Immune response to parasitism reduces resistance of Drosophila melanogaster to desiccation and starvation.

In natural populations, organisms experience simultaneously biotic (e.g., competitors and parasites) and abiotic (e.g., temperature and humidity) stresses. Thus, species must have the capacity to respond to combinations of stressors. How does interaction between biotic and abiotic stress affect organismal performance? To address this question, I studied stress resistance of adult Drosophila melanogaster that survived parasitic attack (as larvae) by the parasitoid Asobara tabida. To determine the impact of genotype on stress resistance. I measured survival under desiccation and starvation of flies within isofemale (genetic) lines. Survivors of parasitism had slightly reduced survivorship compared to unparasitized relatives when both were unstressed, and this difference was exacerbated by desiccation and starvation. These results indicate multiple stressors can compound each other's individual negative effects on fitness. Moreover, isofemale lines differed in their sensitivity to environmental stress and to parasitism. Consequently, genotypic differences in sensitivity to stress may reflect differences in investment priorities between traits that promote survival over other life-history characters.

Animals↗
PubMed2006

Integrating human impacts and ecological integrity into a risk-based protocol for conservation planning.

Conservation planning aims to protect biodiversity by sustainng the natural physical, chemical, and biological processes within representative ecosystems. Often data to measure these components are inadequate or unavailable. The impact of human activities on ecosystem processes complicates integrity assessments and might alter ecosystem organization at multiple spatial scales. Freshwater conservation targets, such as populations and communities, are influenced by both intrinsic aquatic properties and the surrounding landscape, and locally collected data might not accurately reflect potential impacts. We suggest that changes in five major biotic drivers-energy sources, physical habitat, flow regime, water quality, and biotic interactions-might be used as surrogates to inform conservation planners of the ecological integrity of freshwater ecosystems. Threats to freshwater systems might be evaluated based on their impact to these drivers to provide an overview of potential risk to conservation targets. We developed a risk-based protocol, the Ecological Risk Index (ERI), to identify watersheds with least/most risk to conservation targets. Our protocol combines risk-based components, specifically the frequency and severity of human-induced stressors, with biotic drivers and mappable land- and water-use data to provide a summary of relative risk to watersheds. We illustrate application of our protocol with a case study of the upper Tennessee River basin, USA. Differences in risk patterns among the major drainages in the basin reflect dominant land uses, such as mining and agriculture. A principal components analysis showed that localized, moderately severe threats accounted for most of the threat composition differences among our watersheds. We also found that the relative importance of threats is sensitive to the spatial grain of the analysis. Our case study demonstrates that the ERI is useful for evaluating the frequency and severity of ecosystem-wide risk, which can inform local and regional conservation planning.

Agriculture↗
PubMed2004

Geographic variation in patterns of nestedness among local stream fish assemblages in Virginia.

Nestedness of faunal assemblages is a multi-scale phenomenon, potentially influenced by a variety of factors. Prior small-scale studies have found freshwater fish species assemblages to be nested along stream courses as a result of either selective colonization or extinction. However, within-stream gradients in temperature and other factors are correlated with the distributions of many fish species and may also contribute to nestedness. At a regional level, strongly nested patterns would require a consistent set of structuring mechanisms across streams, and correlation among species' tolerances of the environmental factors that influence distribution. Thus, nestedness should be negatively associated with the spatial extent of the region analyzed and positively associated with elevational gradients (a correlate of temperature and other environmental factors). We examined these relationships for the freshwater fishes of Virginia. Regions were defined within a spatial hierarchy and included whole river drainages, portions of drainages within physiographic provinces, and smaller subdrainages. In most cases, nestedness was significantly stronger in regions of smaller spatial extent and in regions characterized by greater topographic relief. Analysis of hydrologic variability and patterns of faunal turnover provided no evidence that inter-annual colonization/extinction dynamics contributed to elevational differences in nestedness. These results suggest that, at regional scales, nestedness is influenced by interactions between biotic and abiotic factors, and that the strongest nestedness is likely to occur where a small number of organizational processes predominate, i.show $132#e., over small spatial extents and regions exhibiting strong environmental gradients.

Animals↗
PubMed2006

Egg components, egg size, and hatchling size in leatherback turtles.

Relationships between egg size, egg components, and neonate size have been investigated across a wide range of oviparous taxa. Differences in egg traits among taxa reflect not only phylogenetic differences, but also interactions between biotic (i.e., maternal resource allocation) and abiotic (i.e. nest environment conditions) factors. We examined relationships between egg mass, egg composition, and hatchling size in leatherback turtles (Dermochelys coriacea) because of the unique egg and reproductive characteristics of this species and of sea turtles in general. Albumen comprised 63.0%+/-2.8% (mean+/-S.D.) of egg mass and explained most of the variation in egg mass, whereas yolk comprised only 33.0%+/-2.7%. Additionally, leatherback albumen dry mass was approximately 16% of albumen wet mass. Whereas hatchling mass increased significantly with egg mass (n = 218 clutches), hatchling mass increased by only approximately 2 g for each 10 g increase in egg mass and was approximately 10-20 g greater than yolk mass. Taken together, our results indicate that albumen might play a particularly significant role in leatherback embryonic development, and that leatherback eggs are both capable of water uptake from the nest substrate and also possess a large reservoir of water in the albumen. Relationships between egg mass and egg components, such as variation in egg mass being largely explained by variation in albumen mass and egg mass containing a relatively high proportion of albumen solids, are more similar to bird eggs than to eggs of other non-avian reptiles. However, hatchling mass correlates more with yolk mass than with albumen mass, unlike patterns observed in bird eggs of similar composition.

Animals↗
PubMed2004

Effect of light, temperature, and pH on the accumulation of phenol by Selenastrum capricornutum, a green alga.

The role of light, temperature, and pH was evaluated on the accumulation of phenol by the green alga, Selenastrum capricornutum. All three environmental variables had a significant effect on the accumulation of phenol. Differences in phenol accumulation were observed in algae that were cultured under light or dark conditions. In the light tests, the accumulation of phenol over a temperature range of 12-28 degrees C was unimodal while in the dark test accumulation exhibited a monotonic relationship with temperature. Differences in accumulation were not simply a function of algal growth or biomass. A unimodal relationship was also observed in the pH experiments with the maximal phenol accumulation in algae occurring at pH 6 and the least at pH 10. Temperature also influenced the accumulation of phenol by algae in the pH tests. As was determined in the light tests, biomass or cell growth was not a significant factor in determining the extent of accumulation in these studies. The results from this study demonstrate that accumulation of organics by algae is not simply a partitioning process but one that can be influenced by the interaction of biotic and abiotic variables.

Analysis of Variance↗
PubMed2004

Occurrence of spruce bark beetles in forest stands at different levels of air pollution stress.

The spruce bark beetle, Ips typographus (L.) is the most serious pest of mature spruce stands, mainly Norway spruce, Picea abies (L.) Karst. throughout Eurasia. A complex of weather-related events and other environmental stresses are reported to predispose spruce stands to bark beetle attack and subsequent tree mortality; however the possible role of industrial pollution as a predisposing factor to attack by this species is poorly understood. The abundance and dynamics of I. typographus populations was evaluated in 60-80 year old Norway spruce stands occurring on 10 x 50 ha sites in five countries within the Carpathian range that were selected in proximity to established ozone measurement sites. Data were recorded on several parameters including the volume of infested trees, captures of adult beetles in pheromone traps, number of attacks, and the presence and relative abundance of associated bark beetle species. In several cases, stands adjacent to sites with higher ozone values were associated with higher bark beetle populations. The volume of sanitary cuttings, a reflection of tree mortality, and the mean daily capture of beetles in pheromone traps were significantly higher at sites where the O(3) level was higher. However, the mean infestation density on trees was higher in plots associated with lower O(3) levels. Captures of beetles in pheromone traps and infestation densities were higher in the zone above 800 m. However, none of the relationships was conclusive, suggesting that spruce bark beetle dynamics are driven by a complex interaction of biotic and abiotic factors and not by a single parameter such as air pollution.

Air Pollution↗
PubMed1994

Disruption of the structure of larval foraging behaviour in interspecific hybrids in Drosophila.

Larval foraging behaviour in two sibling species, Drosophila pavani and Drosophila gaucha belonging to the mesophragmatica species group, is described. Interspecific hybrid larvae derived from both reciprocal crosses of the parent species show disruption in the organization of their behaviour, leading to lower mean feeding rates. This, together with interactions involving biotic residues, described elsewhere, is likely under competitive conditions to contribute to reduced fitness of the hybrids relative to the parent species.

Animals↗
PubMed1994

Assessment of human exposure to chemicals from Superfund sites.

Assessing human exposure to chemicals from Superfund sites requires knowledge of basic physical, chemical, and biological processes occurring in the environment and specific information about the local environment and population in the vicinity of sites of interest. Although progress is being made in both areas, there is still a tremendous amount to be done. Participants at this meeting have identified several of the areas in need of greater understanding, and they are listed below. Movement of dissolved and volatile organics, especially NAPLs, in the subsurface environment. This includes study of the partitioning of compounds between NAPLs, air, water, and soil. Partitioning of volatilized chemicals between gaseous and aerosol components of the atmosphere. This includes understanding how these components influence both wet and dry deposition. Long-term movement from sediments into biota and how these affect chronic toxicity to sediment biota. Broad validation of PBPK models describing partitioning of compounds from sediment and water into fish. Reactions of chemicals sorbed to atmospheric particles. This includes application of laboratory models to real and varied atmospheric conditions. Interactions between biotic and abiotic transformations in soil and sediment. Applicability of physiological pharmacokinetic models developed in laboratory studies of experimental animals and clinical investigations of humans to environmental chemicals, concentrations, and routes of exposure in humans. Use of human and wildlife behavioral and biomonitoring information to estimate exposure. This includes better understanding of human variability and the applicability of information gathered from particular wildlife species. To successfully address these gaps in our knowledge, much more analytical data must be collected.(ABSTRACT TRUNCATED AT 250 WORDS)

Air Pollutants↗
PubMed2001

Environmental and developmental regulation of the wound-induced cell wall protein WI12 in the halophyte ice plant.

A wounded gene WI12 was used as a marker to examine the interaction between biotic stress (wounding) and abiotic stress (high salt) in the facultative halophyte ice plant (Mesembryanthemum crystallinum). The deduced WI12 amino acid sequence has 68% similarity to WUN1, a known potato (Solanum tuberosum) wound-induced protein. Wounding, methyl jasmonate, and pathogen infection induced local WI12 expression. Upon wounding, the expression of WI12 reached a maximum level after 3 h in 4-week-old juvenile leaves, whereas the maximum expression was after 24 h in 8-week-old adult leaves. The temporal expression of WI12 in salt-stressed juvenile leaves was similar to that of adult leaves. The result suggests that a salt-induced switch from C3 to Crassulacean acid metabolism has a great influence on the ice plant's response to wounding. The expression of WI12 and the accumulation of WI12 protein were constitutively found in phloem and in wounded mesophyll cells. At the reproductive stage, WI12 was constitutively found in petals and styles, and developmentally regulated in the placenta and developing seeds. The histochemical analysis showed that the appearance of WI12 is controlled by both environmental and developmental factors. Immunogold labeling showed WI12 preferentially accumulates in the cell wall, suggesting its role in the reinforcement of cell wall composition after wounding and during plant development.

Acetates↗
PubMed2006

Biotic habitat complexity controls species diversity and nutrient effects on net biomass production.

Canopy-forming plants and algae commonly contribute to spatial variation in habitat complexity for associated organisms and thereby create a biotic patchiness of communities. In this study, we tested for interaction effects between biotic habitat complexity and resource availability on net biomass production and species diversity of understory macroalgae by factorial field manipulations of light, nutrients, and algal canopy cover in a subtidal rocky-shore community. Presence of algal canopy cover and/or artificial shadings limited net biomass production and facilitated species diversity. Artificial shadings reduced light to levels similar to those under canopy cover, and net biomass production was significantly and positively correlated to light availability. Considering the comparable and dependent experimental effects from shadings and canopy cover, the results strongly suggest that canopy cover controlled net biomass production and species diversity by limiting light and thereby limiting resource availability for community production. Canopy cover also controlled experimental nutrient effects by preventing a significant increase in net biomass production from nutrient enrichment recorded in ambient light (no shading). Changes in species diversity were mediated by changes in species dominance patterns and species evenness, where canopy cover and shadings facilitated slow-growing crust-forming species and suppressed spatial dominance by Fucus vesiculosus, which was the main contributor to net production of algal biomass. The demonstrated impacts of biotic habitat complexity on biomass production and local diversity contribute significantly to understanding the importance of functionally important species and biodiversity for ecosystem processes. In particular, this study demonstrates how loss of a dominant species and decreased habitat complexity change the response of the remaining assembly to resource loading. This is of potential significance for marine conservation since resource loading often promotes low habitat complexity and canopy species are among the first groups lost in degraded aquatic systems.

Analysis of Variance↗
PubMed2025

Order among chaos: High throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system.

The likelihood that a host will be susceptible to infection is influenced by the interaction of diverse biotic and abiotic factors. As a result, substantial experimental replication and scalability are required to identify the contributions of and interactions between the host, the environment, and biotic factors such as the microbiome. For example, pathogen infection success is known to vary by host genotype, bacterial strain identity and dose, and pathogen dose. Elucidating the interactions between these factors in vivo has been challenging because testing combinations of these variables quickly becomes experimentally intractable. Here, we describe a novel high throughput plant growth system (MYCroplanters) to test how multiple host, non-pathogenic bacteria, and pathogen variables predict host health. Using an Arabidopsis-Pseudomonas host-microbe model, we found that host genotype and bacterial strain order of arrival predict host susceptibility to infection, but pathogen and non-pathogenic bacterial dose can overwhelm these effects. Host susceptibility to infection is therefore driven by complex interactions between multiple factors that can both mask and compensate for each other. However, regardless of host or inoculation conditions, the ratio of pathogen to non-pathogen emerged as a consistent correlate of disease. Our results demonstrate that high-throughput tools like MYCroplanters can isolate interacting drivers of host susceptibility to disease. Increasing the scale at which we can screen drivers of disease, such as microbiome community structure, will facilitate both disease predictions and treatments for medicine and agricultural applications.

Arabidopsis↗
PubMed2006

Tall herb herbivory resistance reflects historic exposure to leaf beetles in a boreal archipelago age-gradient.

In this paper, we introduce the coevolution-by-coexistence hypothesis which predicts that the strength of a coevolutionary adaptation will become increasingly apparent as long as the corresponding selection from an interacting counterpart continues. Hence, evolutionary interactions between plants and their herbivores can be studied by comparing discrete plant populations with known history of herbivore colonization. We studied populations of the host plant, Filipendula ulmaria (meadow sweet), on six islands, in a Bothnian archipelago subject to isostatic rebound, that represent a spatio-temporal gradient of coexistence with its two major herbivores, the specialist leaf beetles Galerucella tenella and Altica engstroemi. Regression analyses showed that a number of traits important for insect-plant interactions (leaf concentrations of individual phenolics and condensed tannins, plant height, G. tenella adult feeding and oviposition) were significantly correlated with island age. First, leaf concentrations of condensed tannins and individual phenolics were positively correlated with island age, suggesting that plant resistance increased after herbivore colonization and continued to increase in parallel to increasing time of past coexistence, while plant height showed a reverse negative correlation. Second, a multi-choice experiment with G. tenella showed that both oviposition and leaf consumption of the host plants were negatively correlated with island age. Third, larvae performed poorly on well-defended, older host populations and well on less-defended, younger populations. Thus, no parameter assessed in this study falsifies the coevolution-by-coexistence hypothesis. We conclude that spatio-temporal gradients present in rising archipelagos offer unique opportunities to address evolutionary interactions, but care has to be taken as abiotic (and other biotic) factors may interact in a complicated way.

Animals↗
PubMed2001

Biotic ligand model of the acute toxicity of metals. 2. Application to acute copper toxicity in freshwater fish and Daphnia.

The biotic ligand model (BLM) was developed to explain and predict the effects of water chemistry on the acute toxicity of metals to aquatic organisms. The biotic ligand is defined as a specific receptor within an organism where metal complexation leads to acute toxicity. The BLM is designed to predict metal interactions at the biotic ligand within the context of aqueous metal speciation and competitive binding of protective cations such as calcium. Toxicity is defined as accumulation of metal at the biotic ligand at or above a critical threshold concentration. This modeling framework provides mechanistic explanations for the observed effects of aqueous ligands, such as natural organic matter, and water hardness on metal toxicity. In this paper, the development of a copper version of the BLM is described. The calibrated model is then used to calculate LC50 (the lethal concentration for 50% of test organisms) and is evaluated by comparison with published toxicity data sets for freshwater fish (fathead minnow, Pimephales promelas) and Daphnia.

Animals↗
PubMed1987

Scaling of biological community structure: a systems approach to community complexity.

Local community dynamics are determined by the interaction of environmental variation and the biotic properties of communities. This interaction occurs on many spatial and temporal scales, hence the expectation is that community dynamics will be complex. Previous theoretical approaches to communities have assumed linear, near equilibrium dynamics. An alternative approach suggests that community dynamics are the result of the balance between energy use by the community and its tendency to move towards thermodynamic equilibrium, in this case extinction of all species in the community. Because this balance will be imprecise, community dynamics should be oscillatory. Furthermore, because energy use by a community can be broken down into a hierarchical set of processes occurring on different time scales, community dynamics should reflect multiple periodicities. The above theoretical treatment suggests that since community dynamics are scaled, a hierarchical observational approach should help resolve important aspects of community structure. This approach of scaling community observations provides a technique for evaluation of community responses to environmental change, including human induced perturbations. A thermodynamic approach to community dynamics can also provide the basis for new theoretical and empricial discoveries about biological communities.

Animals↗
PubMed2006

Phylogeny of arbuscular mycorrhizal fungi predicts community composition of symbiosis-associated bacteria.

Many physicochemical and biotic aspects of the soil environment determine the community composition of bacteria. In this study, we examined the effects of arbuscular mycorrhizal fungi, common symbionts of higher plants, on the composition of bacterial communities after long-term (7-8 years) enrichment culture in the presence of a plant host. We showed that the phylogeny of arbuscular mycorrhizal fungal isolates was a highly significant predictor of bacterial community composition, as assessed by cluster analysis, redundancy analysis and linear discriminant analysis of phospholipid fatty acid patterns. Numerous phospholipid fatty acids differed between the phylogenetic groupings; this pattern also held for fungal-origin phospholipid fatty acids and in a combined bacterial/fungal analysis, suggesting that categorizing phospholipid fatty acids into predominantly bacterial and fungal origin did not affect the overall outcome. The mechanisms underlying this observation could include substrate quality (and quantity) effects, interactions mediated by the host plant (e.g. rhizodeposition) and direct biotic interactions between arbuscular mycorrhizal fungi and bacterial populations. Our results suggest that aspects of arbuscular mycorrhizal fungal functions may be partially explained by the symbiosis-accompanying bacterial communities, a possibility that should be explicitly considered in studies examining the roles of arbuscular mycorrhizal fungal species diversity in soil and ecosystem processes.

Bacteria↗
PubMed2026

Unlocking the Full Potential of Spatial Omics in Plants: Practical Challenges, Solutions, and a Path Forward.

Spatial omics technologies are providing new opportunities for plant biology by enabling molecular profiling within structurally intact tissues, revealing spatially organised cell states, developmental gradients, and regulatory interactions. While spatial transcriptomics has driven early advances, the field is rapidly expanding toward integrated spatial multi-omics by combining single-cell and spatial transcriptomic, epigenomic, proteomic, and metabolomic data. These approaches offer new opportunities to study development, physiology, and plant biotic and abiotic interactions in spatially preserved cellular contexts. However, despite rapid adoption, the field remains constrained by plant-specific challenges when applying technologies largely developed for animal systems. Compared with animal systems, plant tissues pose additional challenges due to rigid cell walls, and diverse chemistries, complicating sample preparation, cell and subcellular segmentation, signal detection, and data integration. As a result, many studies rely on bespoke protocols and analysis pipelines that are often difficult to reproduce or generalise. Here, we provide a practical, solution-oriented synthesis of current bottlenecks across experimental and computational pipelines, highlight emerging strategies to overcome these limitations, and propose a roadmap for community-driven protocol sharing, benchmarking, and integration across spatial and multi-omics modalities. Addressing these challenges will be essential to establish spatial omics as a routine and scalable tool for plant biology.

Journal Article↗