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At least 19 recordsLinked to original sources
USGS2020

An overview of agent-based models in plant biology and ecology

Agent-based modeling (ABM) has become an established methodology in many areas of biology, ranging from the cellular to the ecological population and community levels. In plant science, two different scales have predominated in their use of ABM. One is the scale of populations and communities, through the modeling of collections of agents representing individual plants, interacting with each other and with the environment. The other is the scale of the individual plant, through the modeling, by functional-structural plant models (FSPMs), of agents representing plant building blocks, or metamers, to describe the development of plant architecture and functions within individual plants. The purpose of this review is to show key results and parallels in ABM for growth, mortality, carbon allocation, competition, and reproduction across the scales from the plant organ to populations and communities on a range of spatial scale to the whole landscape. Several areas of application of ABMs are reviewed, showing that some issues are addressed by both population-level ABMs and FSPMs. Continued increase in the relevance of ABM to environmental science and management will be helped by greater integration of ABMs across these two scales.

Annals of Botany↗
USGS2009

Untangling the biological contributions to soil stability in semiarid shrublands

Communities of plants, biological soil crusts (BSCs), and arbuscular mycorrhizal (AM) fungi are known to influence soil stability individually, but their relative contributions, interactions, and combined effects are not well understood, particularly in arid and semiarid ecosystems. In a landscape-scale field study we quantified plant, BSC, and AM fungal communities at 216 locations along a gradient of soil stability levels in southern Utah, USA. We used multivariate modeling to examine the relative influences of plants, BSCs, and AM fungi on surface and subsurface stability in a semiarid shrubland landscape. Models were found to be congruent with the data and explained 35% of the variation in surface stability and 54% of the variation in subsurface stability. The results support several tentative conclusions. While BSCs, plants, and AM fungi all contribute to surface stability, only plants and AM fungi contribute to subsurface stability. In both surface and subsurface models, the strongest contributions to soil stability are made by biological components of the system. Biological soil crust cover was found to have the strongest direct effect on surface soil stability (0.60; controlling for other factors). Surprisingly, AM fungi appeared to influence surface soil stability (0.37), even though they are not generally considered to exist in the top few millimeters of the soil. In the subsurface model, plant cover appeared to have the strongest direct influence on soil stability (0.42); in both models, results indicate that plant cover influences soil stability both directly (controlling for other factors) and indirectly through influences on other organisms. Soil organic matter was not found to have a direct contribution to surface or subsurface stability in this system. The relative influence of AM fungi on soil stability in these semiarid shrublands was similar to that reported for a mesic tallgrass prairie. Estimates of effects that BSCs, plants, and AM fungi have on soil stability in these models are used to suggest the relative amounts of resources that erosion control practitioners should devote to promoting these communities. This study highlights the need for system approaches in combating erosion, soil degradation, and arid-land desertification.

Utah↗
USGS2010

Adaptation and survival of plants in high stress habitats via fungal endophyte conferred stress tolerance

From the Arctic to the Antarctic, plants thrive in diverse habitats that impose different levels of adaptive pressures depending on the type and degree of biotic and abiotic stresses inherent to each habitat (Stevens, 1989). At any particular location, the abundance and distribution of individual plant species vary tremendously and is theorized to be based on the ability to tolerate a wide range of edaphic conditions and habitat-specific stresses (Pianka, 1966). The ability of individual plant species to thrive in diverse habitats is commonly referred to as phenotypic plasticity and is thought to involve adaptations based on changes in the plant genome (Givnish, 2002; Pan et al., 2006; Robe and Griffiths, 2000; Schurr et al., 2006). Habitats that impose high levels of abiotic stress are typically colonized with fewer plant species compared to habitats imposing low levels of stress. Moreover, high stress habitats have decreased levels of plant abundance compared to low stress habitats even though these habitats may occur in close proximity to one another (Perelman et al., 2007). This is particularly interesting because all plants are known to perceive, transmit signals, and respond to abiotic stresses such as drought, heat, and salinity (Bartels and Sunkar, 2005; Bohnert et al., 1995). Although there has been extensive research performed to determine the genetic, molecular, and physiological bases of how plants respond to and tolerate stress, the nature of plant adaptation to high stress habitats remains unresolved (Leone et al., 2003; Maggio et al., 2003; Tuberosa et al., 2003). However, recent evidence indicates that a ubiquitous aspect of plant biology (fungal symbiosis) is involved in the adaptation and survival of at least some plants in high stress habitats (Rodriguez et al., 2008).

Book chapter↗
USGS1997

Fungal life-styles and ecosystem dynamics: Biological aspects of plant pathogens, plant endophytes and saprophytes

This chapter discusses various biochemical, genetic, ecological, and evolutionary aspects of fungi that express either symbiotic or saprophytic life-styles. An enormous pool of potential pathogens exists in both agricultural and natural ecosystems, and virtually all plant species are susceptible to one or more fungal pathogens. Fungal pathogens have the potential to impact on the genetic structure of populations of individual plant species, the composition of plant communities and the process of plant succession. Endophytic fungi exist for at least part of their life cycles within the tissues of a plant host. This group of fungi is distinguished from plant pathogens because they do not elicit significant disease symptoms. However, endophytes do maintain the genetic and biochemical mechanisms required for infection and colonization of plant hosts. Fungi that obtain chemical nutrients from dead organic matter are known as saprophytes and are critical to the dynamics and resilience of ecosystems. There are two modes of saprophytic growth: one in which biomolecules that are amenable to transport across cell walls and membranes are directly absorbed, and another in which fungi must actively convert complex biopolymers into subunit forms amenable to transportation into cells. Regardless of life-style, fungi employ similar biochemical mechanisms for the acquisition and conversion of nutrients into complex biomolecules that are necessary for vegetative growth, production and dissemination of progeny, organismal competition, and survival during periods of nutrient deprivation or environmental inclemency.

Advances in Botanical Research↗
USGS2023

Plant size, latitude, and phylogeny explain within-population variability in herbivory

Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.

Science↗
USGS2009

Impact of biological soil crusts and desert plants on soil microfaunal community composition

Carbon and nitrogen are supplied by a variety of sources in the desert food web; both vascular and non-vascular plants and cyanobacteria supply carbon, and cyanobacteria and plant-associated rhizosphere bacteria are sources of biological nitrogen fixation. The objective of this study was to compare the relative influence of vascular plants and biological soil crusts on desert soil nematode and protozoan abundance and community composition. In the first experiment, biological soil crusts were removed by physical trampling. Treatments with crust removed had fewer nematodes and a greater relative ratio of bacterivores to microphytophages than treatments with intact crust. However, protozoa composition was similar with or without the presence of crusts. In a second experiment, nematode community composition was characterized along a spatial gradient away from stems of grasses or shrubs. Although nematodes generally occurred in increasing abundance nearer to plant stems, some genera (such as the enrichment-type Panagrolaimus) increased disproportionately more than others (such as the stress-tolerant Acromoldavicus). We propose that the impact of biological soil crusts and desert plants on soil microfauna, as reflected in the community composition of microbivorous nematodes, is a combination of carbon input, microclimate amelioration, and altered soil hydrology. ?? Springer Science + Business Media B.V. 2009.

Plant and Soil↗
USGS2020

Components and predictors of biological soil crusts vary at the regional vs. plant community scales

Although biological soil crusts (biocrusts) occur globally in arid and semi-arid environments, most of our knowledge of biocrust cover and ecology is from a relatively small number of locations worldwide. Some plant communities are known to have high cover of biocrusts, but the abundance of biocrusts is largely undocumented in most plant communities. Using a data driven approach, we identified 16 plant communities based on plant cover from the Assessment, Inventory, and Monitoring Strategy data from the Bureau of Land Management (AIM, 5,200 plots). We found that abundance of lichens and mosses varies among communities, but that both components of biocrusts are present in all plant communities. Biocrusts are indicators of two of these communities: one that is defined by high cover of mosses and basin big sagebrush and one that is defined by high cover of lichens and shadscale saltbush. Using non-parametric multiplicative regression, we evaluated a suite of abiotic and disturbance variables to assess the degree to which climate and soils are associated with the abundance of lichens and mosses at the regional scale. At the regional scale, soil depth and maximum vapor pressure deficit were found to be strongly associated with the abundance of lichens and January minimum temperature dictated the abundance of mosses. At the scale of plant communities, community specific metrics of soils and climate were better able to explain the abundance of biocrusts. Our demonstration of the presence of biocrusts across the western US suggests that studies on ecosystem function could include these organisms because they are present in all plant communities, maintain arguably stronger associations with climatic variation, are directly associated with soils, and contribute to ecosystem functions that are not solely maintained by vascular plants.

Frontiers in Ecology and Evolution↗
USGS2015

Growth responses of five desert plants as influenced by biological soil crusts from a temperate desert, China

In almost all dryland systems, biological soil crusts (biocrusts) coexist alongside herbaceous and woody vegetation, creating landscape mosaics of vegetated and biocrusted patches. Results from past studies on the interaction between biocrusts and vascular plants have been contradictory. In the Gurbantunggut desert, a large temperate desert in northwestern China, well-developed lichen-dominated crusts dominate the areas at the base and between the sand dunes. We examined the influence of these lichen-dominated biocrusts on the germination, growth, biomass accumulation, and elemental content of five common plants in this desert: two shrubs ( Haloxylon persicum , Ephedra distachya ) and three herbaceous plants ( Ceratocarpus arenarius , Malcolmia africana and Lappula semiglabra ) under greenhouse conditions. The influence of biocrusts on seed germination was species-specific. Biocrusts did not affect percent germination in plants with smooth seeds, but inhibited germination of seeds with appendages that reduced or eliminated contact with the soil surface or prevented seeds from slipping into soil cracks. Once seeds had germinated, biocrusts had different influences on growth of shrub and herbaceous plants. The presence of biocrusts increased concentrations of nitrogen but did not affect phosphorus or potassium in tissue of all tested species, while the uptake of the other tested nutrients was species-specific. Our study showed that biocrusts can serve as a biological filter during seed germination and also can influence growth and elemental uptake. Therefore, they may be an important trigger for determining desert plant diversity and community composition in deserts.

Ecological Research↗
USGS2020

Biological control of Aedes mosquito larvae with carnivorous aquatic plant, Utricularia macrorhiza

Background Biological controls with predators of larval mosquito vectors have historically focused almost exclusively on insectivorous animals, with few studies examining predatory plants as potential larvacidal agents. In this study, we experimentally evaluate a generalist plant predator of North America, Utricularia macrorhiza, the common bladderwort, and evaluate its larvacidal efficiency for the mosquito vectors Aedes aegypti and Aedes albopictus in no-choice, laboratory experiments. We sought to determine first, whether U. macrorhiza is a competent predator of container-breeding mosquitoes, and second, its predation efficiency for early and late instar larvae of each mosquito species. Methods Newly hatched, first instar Aedes albopictus and Aedes aegypti larvae were separately exposed in cohorts of 10 to field collected U. macrorhiza cuttings. Data on development time and larval survival were collected on a daily basis to ascertain the effectiveness of U. macrorhiza as a larval predator. Survival models were used to assess differences in larval survival between cohorts that were exposed to U. macrorhiza and those that were not. A permutation analysis was used to investigate whether storing U. macrorhiza in laboratory conditions for extended periods of time (1 month vs. 6 months) affected its predation efficiency. Results Our results indicated a 100% and 95% reduction of survival of Ae. aegypti and Ae. albopictus larvae respectively, in the presence of U. macrorhiza relative to controls within five days, with peak larvacidal efficiency in plant cuttings from ponds collected in August. Utricularia macrorhiza cuttings, which were prey-deprived, and maintained in laboratory conditions for 6 months were more effective larval predators than cuttings, which were maintained prey-free for 1 month. Conclusions Due to the combination of high predation efficiency and the unique biological feature of facultative predation, we suggest that U. macrorhiza warrants further development as a method for larval mosquito control.

Rhode Island↗
USGS2019

Cohesive framework for modeling plant cover class data

The study of plant distribution and abundance is a fundamental pursuit in ecology and conservation biology. Measuring plant abundance by visually assessing percent cover and recording a cover class is a common field method that yields ordinal data. Statistical models for ordinal data exist but entail cumbersome interpretations and sometimes restrictive assumptions. We propose a Bayesian hierarchical framework for analysing cover class data that allows for linking ordinal observations to a latent beta distribution and accounts for zero inflation. Harnessing a latent beta distribution supports interpreting changes in abundance in terms of mean percent cover rather than odds ratios of cumulative cover classes as for cumulative link models. The zero augmentation allows for simultaneous inferences on both occurrence (distribution) and abundance. We show how our model can account for true and false zeros, misclassification of cover classes, multiple species and hierarchical sampling designs, using empirical examples and simulations. Simulated observation errors, when ignored, led to models overestimating abundance and underestimating occurrence. Based on simulations, we found no substantial difference between mean percent cover estimates when analyzing ordinal cover classes versus continuous percent cover as the response. Our empirical datasets displayed high probability of detection (>0.85 on average for all species), likely due to the sampling design used and training of observers. Probability of occurrence was slightly underestimated for bare ground, Artemisia tridentata , Elycap medusae , and Poa secunda using a model that ignored imperfect detection. Estimated mean percent cover was not substantially impacted by ignoring measurement error for five plant species and bare ground. Our modelling framework for cover class data allows for an explicit separation of distribution from abundance and, importantly, allows for interpreting species–environment relationships in terms of variation in mean percent cover as compared to cumulative odds ratios. The beta distribution inherently accommodates heteroscedasticity and skewness, statistical properties that are a consequence of spatially aggregated patterns common to plant survey data. Recording cover classes provides a reliable, efficient way to measure plants and our simulations suggest little loss of information compared to assuming continuous percent cover. We provide JAGS and Stan model code for implementation.

Methods in Ecology and Evolution↗
USGS2016

Germination and growth of native and invasive plants on soil associated with biological control of tamarisk (Tamarix spp.)

Introductions of biocontrol beetles (tamarisk beetles) are causing dieback of exotic tamarisk in riparian zones across the western United States, yet factors that determine plant communities that follow tamarisk dieback are poorly understood. Tamarisk-dominated soils are generally higher in nutrients, organic matter, and salts than nearby soils, and these soil attributes might influence the trajectory of community change. To assess physical and chemical drivers of plant colonization after beetle-induced tamarisk dieback, we conducted separate germination and growth experiments using soil and litter collected beneath defoliated tamarisk trees. Focal species were two common native (red threeawn, sand dropseed) and two common invasive exotic plants (Russian knapweed, downy brome), planted alone and in combination. Nutrient, salinity, wood chip, and litter manipulations examined how tamarisk litter affects the growth of other species in a context of riparian zone management. Tamarisk litter, tamarisk litter leachate, and fertilization with inorganic nutrients increased growth in all species, but the effect was larger on the exotic plants. Salinity of 4 dS m −1 benefitted Russian knapweed, which also showed the largest positive responses to added nutrients. Litter and wood chips generally delayed and decreased germination; however, a thinner layer of wood chips increased growth slightly. Time to germination was lengthened by most treatments for natives, was not affected in exotic Russian knapweed, and was sometimes decreased in downy brome. Because natives showed only small positive responses to litter and fertilization and large negative responses to competition, Russian knapweed and downy brome are likely to perform better than these two native species following tamarisk dieback.

Invasive Plant Science and Management↗
USGS2011

Endocrine active chemicals, pharmaceuticals, and other chemicals of concern in surface water, wastewater-treatment plant effluent, and bed sediment, and biological characteristics in selected streams, Minnesota: Design, methods, and data, 2009

This report presents the study design, environmental data, and quality-assurance data for an integrated chemical and biological study of selected streams or lakes that receive wastewater-treatment plant effluent in Minnesota. This study was a cooperative effort of the U.S. Geological Survey, the Minnesota Pollution Control Agency, St. Cloud State University, the University of St. Thomas, and the University of Colorado. The objective of the study was to identify distribution patterns of endocrine active chemicals, pharmaceuticals, and other organic and inorganic chemicals of concern indicative of wastewater effluent, and to identify biological characteristics of estrogenicity and fish responses in the same streams. The U.S. Geological Survey collected and analyzed water, bed-sediment, and quality-assurance samples, and measured or recorded streamflow once at each sampling location from September through November 2009. Sampling locations included surface water and wastewater-treatment plant effluent. Twenty-five wastewater-treatment plants were selected to include continuous flow and periodic release facilities with differing processing steps (activated sludge or trickling filters) and plant design flows ranging from 0.002 to 10.9 cubic meters per second (0.04 to 251 million gallons per day) throughout Minnesota in varying land-use settings. Water samples were collected from the treated effluent of the 25 wastewater-treatment plants and at one point upstream from and one point downstream from wastewater-treatment plant effluent discharges. Bed-sediment samples also were collected at each of the stream or lake locations. Water samples were analyzed for major ions, nutrients, trace elements, pharmaceuticals, phytoestrogens and pharmaceuticals, alkylphenols and other neutral organic chemicals, carboxylic acids, and steroidal hormones. A subset (25 samples) of the bed-sediment samples were analyzed for carbon, wastewater-indicator chemicals, and steroidal hormones; the remaining samples were archived. Biological characteristics were determined by using an in-vitro bioassay to determine total estrogenicity in water samples and a caged fish study to determine characteristics of fish from experiments that exposed fish to wastewater effluent in 2009. St. Cloud State University deployed and processed caged fathead minnows at 13 stream sites during September 2009 for the caged fish study. Measured fish data included length, weight, body condition factor, and vitellogenin concentrations.

Minnesota↗
USGS2018

Resiliency of biological soil crusts and vascular plants varies among morphogroups with disturbance intensity

Background and aims Disturbance affects the ability of organisms to persist on a site, and disturbance history acts as a filter of community composition. This is true for vascular plants and morphological groups of biocrusts, which respond differently to disturbance. Although functioning arid ecosystems include both groups , filtering of morphological groups of biocrusts has not previously been compared simultaneously with the responses of vascular plants. Methods Using a chronosequence approach, cover of vascular plants and biocrusts was examined across chronic disturbance gradients related to invasion by exotic species and grazing by livestock, following the acute disturbance of fire using paired burned and unburned plots in Wyoming big sagebrush on 99 plots. Results Cover of vascular plants and biocrusts was related to disturbance more so than abiotic factors of precipitation following fire, soil chemistry, percent coarse fragment and heat load index. Over time since fire of 12–23 years, we saw recovery of early successional groups: short mosses, shallow-rooted perennial grasses and annual forbs. Cover of deep and shallow-rooted perennial grasses and annual forbs increased in cover with intermediate levels of disturbance. Perennial forbs lacked a clear relationship with disturbance. Biocrusts decreased in cover with less disturbance when compared with perennial herbaceous plants but differed in sensitivities. Tall mosses were less sensitive to disturbance compared with lichens. Short mosses increased with some disturbance. Conclusions Morphological groups of biocrusts and vascular plants are eliminated with increasing variability in the size of gaps between perennials represented by the standard deviation of gaps between perennials. The inclusion of both groups in assessments of ecosystem recovery following disturbance addresses the fact that recovery of either group does not happen in isolation from the other but with interacting contributions to ecosystem functions.

Plant and Soil↗
USGS2021

Biological and practical tradeoffs in planting techniques for submerged aquatic vegetation

Global loss of submerged aquatic vegetation (SAV) and associated ecosystem function has prompted an interest in SAV revegetation, particularly where underlying stressors such as nutrient enrichment are mitigated, yet natural recruitment remains low. Typically, SAV is hand-planted, but alternative reliable and practically scalable SAV planting techniques are needed. In mesocosms, we evaluated five planting techniques: 1) hand planting, anchoring using 2) fishing weights and 3) plaster blocks, and sediment-added methods using 4) peat pots and 5) burlap-wraps (“burritos”). Anchoring and sediment-added techniques were also field evaluated at four locations within a single lake. In mesocosms, all techniques effectively established two common North American SAV species, Vallisneria americana and Potamogeton illinoensis . Sediment-added techniques had species-specific benefits, e.g. burritos produced taller Vallisneria leaves, and greater Potamogeton biomass, while peat pots encouraged rapid Vallisneria shoot production. However, no treatment was universally beneficial across all growth metrics. In the field, all techniques were effective at two sites, but at two other sites, no techniques were successful. Results show that under favorable mesocosm and field conditions, all techniques promote establishment; however, subtle differences in technique-driven plant traits (height, density, nutrients) suggest that under specific environmental conditions, some techniques may be more favorable. Also, no technique offers practical advantages in every scenario, but each offers situation-specific advantages. Guidance emerging from this work is that all techniques are potentially effective, but small-scale tests in site-specific restoration scenarios, along with consideration of feasibility constraints, are recommended to inform large-scale plantings.

Aquatic Botany↗
USGS2015

Global land cover mapping using Earth observation satellite data: Recent progresses and challenges

Land cover is an important variable for many studies involving the Earth surface, such as climate, food security, hydrology, soil erosion, atmospheric quality, conservation biology, and plant functioning. Land cover not only changes with human caused land use changes, but also changes with nature. Therefore, the state of land cover is highly dynamic. In winter snow shields underneath various other land cover types in higher latitudes. Floods may persist for a long period in a year over low land areas in the tropical and subtropical regions. Forest maybe burnt or clear cut in a few days and changes to bare land. Within several months, the coverage of crops may vary from bare land to nearly 100% crops and then back to bare land following harvest. The highly dynamic nature of land cover creates a challenge in mapping and monitoring which remains to be adequately addressed. As economic globalization continues to intensify, there is an increasing trend of land cover/land use change, environmental pollution, land degradation, biodiversity loss at the global scale, timely and reliable information on global land cover and its changes is urgently needed to mitigate the negative impact of global environment change.

ISPRS Journal of Photogrammetry and Remote Sensing↗
USGS2008

Reduced fecundity in small populations of the rare plant Gentianopsis ciliate (Gentianaceae)

Habitat destruction is the main cause for the biodiversity crisis. Surviving populations are often fragmented, i.e., small and isolated from each other. Reproduction of plants in small populations is often reduced, and this has been attributed to inbreeding depression, reduced attractiveness for pollinators, and reduced habitat quality in small populations. Here we present data on the effects of fragmentation on the rare, self-compatible perennial herb Gentianopsis ciliata (Gentianaceae), a species with very small and presumably well-dispersed seeds. We studied the relationship between population size, plant size, and the number of flowers produced in 63 populations from 1996-1998. In one of the years, leaf and flower size and the number of seeds produced per fruit was studied in a subset of 25 populations. Plant size, flower size, and the number of seeds per fruit and per plant increased with population size, whereas leaf length and the number of flowers per plant did not. The effects of population size on reproduction and on flower size remained significant if the effects were adjusted for differences in plant size, indicating that they could not be explained by differences in habitat quality. The strongly reduced reproduction in small populations may be due to pollination limitation, while the reduced flower size could indicate genetic effects.

Plant Biology↗