Sophia I. Passy

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Verified

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• PhD
• Faculty at The University of Texas at Arlington

Aim To examine species and trait composition in stream diatoms along environmental, climatic and spatial gradients and to ascertain if the use of different levels of biological organization is beneficial for investigating global environmental changes and the role of history in structuring communities. Location Global cover with datasets from the A...

The hollow-shaped species abundance distribution (SAD) and its allied rank abundance distribution (RAD)-showing that abundance is unevenly distributed among species-are some of the most studied patterns in ecology. To explain the nature of abundance inequality, I developed a novel framework identifying environmental favorability, which controls the...

The relationships of local population density (N) with body size (M) and distribution (D) have been extensively studied because they reveal how ecological and historical factors structure species communities; however, a unifying model explaining their joint behaviour, has not been developed. Here, I propose a theory that explores these relationship...

Aim Co-occurrence networks can be described in terms of topology (i.e., size and connectance) and node degree distribution (NDD). The NDD represents the frequency distribution of nodes (species) with k number of connections (degree). The shape of the NDD, single-scale, scale-free (power-law) or broad-scale, reveals if there are species with many co...

While resource enrichment can shape community structure and ecosystem functioning, how species diversity and biomass production respond to the input of multiple resources across habitats—particularly between terrestrial and aquatic ecosystems—remains poorly understood. Using a meta-analysis, we show that multiple resource addition consistently incr...

Aim: The influences of environmental and spatial processes on species composition have been at the center of metacommunity ecology. Conversely, the relative importance of these processes for species co-occurrences and taxonomic similarity has remained poorly understood. We hypothesized that at a subcontinental scale, shared environmental preference...

Motivation: Freshwater ecosystems have been heavily impacted by land-use changes, but data syntheses on these impacts are still limited. Here, we compiled a global database encompassing 241 studies with species abundance data (from multiple biological groups and geographic locations) across sites with different land-use categories. This compilation...

Motivation: Freshwater ecosystems have been heavily impacted by land-use changes, but data syntheses on these impacts are still limited. Here, we compiled a global database encompassing 241 studies with species abundance data (from multiplebiological groups and geographic locations) across sites with different land-use categories. This compilation...

Motivation: Freshwater ecosystems have been heavily impacted by land-use changes, but syntheses on the impacts on freshwater ecosystems are still limited. Here, we compiled a global database encompassing 248 studies with species abundance data (from multiple taxon groups and geographic locations) across sites with different land-use categories. Thi...

Motivation: Freshwater ecosystems have been heavily impacted by land-use changes, but syntheses on the impacts on freshwater ecosystems are still limited. Here, we compiled a global database encompassing 248 studies with species abundance data (from multiple taxon groups and geographic locations) across sites with different land-use categories. Thi...

Abstract Aim To evaluate the patterns of stream diatom beta diversity in islands vs. continents across scales, to relate community similarities with spatial and environmental distances and to investigate the role of island characteristics in shaping insular diatom beta diversity. Location Africa, America, Europe, and Pacific. Time period Present....

Recent research on diatom metacommunities has focused on disentangling the assembly mechanisms driving species and functional composition and biodiversity across space and time, including deterministic (environmental filtering and biotic interactions) and stochastic processes (dispersal and ecological drift). In this chapter, we provide an overview...

IInfluential ecological research in the 1980s, elucidating that local biodiversity (LB) is a function of local ecological factors and the size of the regional species pool (γ-diversity), has prompted numerous investigations on the local and regional origins of LB. These investigations, however, have been mostly limited to single scales and target g...

Aim: Understanding the roles of deterministic and stochastic processes in community assembly is essential for gaining insights into species biogeographical patterns. However, the way community assembly processes operate is still not fully understood, especially in oceanic islands. In this study, we examine the importance of assembly processes in sh...

S'il ne fait aucun doute que la biodiversité décline à l'échelle mondiale, il est surprenant de constater que les dynamiques locales peuvent être contrastées. Nous possédons une compréhension encore incomplète de la façon dont les écosystèmes évoluent sous l'effet du changement global. Ici, nous avons cherché à caractériser la dynamique temporelle...

The species–area relationship (SAR) has over a 150‐year‐long history in ecology, but how its shape and origins vary across scales and organisms remains incompletely understood. This is the first subcontinental freshwater study to examine both these properties of the SAR in a spatially explicit way across major organismal groups (diatoms, insects, a...

Aim Niche and dispersal processes influence biodiversity, but their relative importance along latitude is unclear. We predicted that: (a) niche processes would dominate at high latitudes due to increased climatic stress, consistent with the physiological tolerance hypothesis and the Dobzhansky–MacArthur hypothesis and (b) dispersal limitation would...

Aim The species–area relationship (SAR) is one of the most distinctive biogeographic patterns, but global comparisons of the SARs between island and mainland are lacking for microbial taxa. Here, we explore whether the form of the SAR and the drivers of species richness, including area, environmental heterogeneity, climate and physico‐chemistry, di...

Globally, freshwater systems are threatened by climate change, so projections under various climate change scenarios are needed to inform efforts to protect and conserve already vulnerable taxa. Here, the change in distribution of stream vertebrates was investigated under different greenhouse gas emission scenarios. Using occurrence data from multi...

While it is recognized that biodiversity currently declines at a global scale, we still have an incomplete understanding of local biodiversity trends under global change. To address this deficiency, we examined the recent decadal trends in water quality and biodiversity (taxonomic and functional) of key river organisms (diatoms, macroinvertebrates...

The amounts and ratios of nutrients (nitrogen and phosphorus) are important determinants of producer community biodiversity and composition and their responses to climate and dispersal. However, the nutrient effects on co‐occurrence network topology, particularly in freshwaters, are understudied. Here, we investigate 1) whether nutrient supply and...

Bioassessment is widely used to measure ecological integrity of natural habitats following anthropogenic disturbances and modifications. Traditionally, bioassessment has been based exclusively on species-environment interactions, i.e. niche processes. However, dispersal processes, and in particular mass effect, could mask the influence of niche pro...

Aim Biodiversity on Earth is threatened by climate change. Despite the vulnerability of freshwater habitats to human impacts, most climate change projections have focused on terrestrial systems. Here, we examined how current distributions and biodiversity of stream taxa may change under mitigated, stabilizing, and increasing greenhouse gas emission...

Patterns in community composition are scale‐dependent and generally difficult to distinguish. Therefore, quantifying the main assembly processes in various systems and across different datasets has remained challenging. Building on the PER‐SIMPER method, we propose a new metric, the dispersal–niche continuum index (DNCI), which estimates whether di...

Aim Biodiversity on Earth is threatened by climate change. Despite the vulnerability of freshwater habitats to human impacts, most climate change projections have focused on terrestrial systems. Here, we examined how the current distributions and biodiversity of stream taxa might change under mitigated, stabilizing and increasing greenhouse gas emi...

Mass effect, allowing species to persist in unfavourable habitats, and dispersal limitation, preventing species from reaching favourable habitats, are the two major dispersal processes. While dispersal limitation can be detected by experimental or modelling techniques, mass effect is more challenging to evaluate, which hampers our ability to disent...

We developed a framework for the hierarchical pathways of bottom‐up (niche dimensionality) and top‐down control (herbivory) on biomass of stream algae via changes in guild composition (relative abundance of low profile, high profile, and motile guilds), species richness, and evenness. We further tested (1) the contrasting predictions of resource co...

Aim The interaction of land use with local versus regional processes driving biological homogenization (β‐diversity loss) is poorly understood. We explored: (a) stream β‐diversity responses to land cover (forest versus agriculture) in terms of physicochemistry and physicochemical heterogeneity; (b) whether these responses were constrained by the re...

Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consis- tent with NC includes similar niche properties across geographically distant regions. We investigated whet...

Aim To quantify the relative contributions of local community assembly processes versus γ‐diversity to β‐diversity, and to assess how spatial scale and anthropogenic disturbance (i.e. nutrient enrichment) interact to dictate which driver dominates. Location France and the United States. Time period 1993–2011. Major taxa studied Freshwater stream...

Aim Severity and heterogeneity of stress are major constraints of beta diversity, but their relative influence is poorly understood. Here, we addressed this question by examining the patterns of beta diversity in stress‐sensitive versus stress‐tolerant stream diatoms and their response to local versus regional factors along gradients of stress seve...

In this intercontinental study of stream diatoms, we asked three important but still unresolved ecological questions: (1) What factors drive the biogeography of species richness and species abundance distribution (SAD)? (2) Are climate-related hypotheses, which have dominated the research on the latitudinal and altitudinal diversity gradients, adeq...

Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whethe...

Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whethe...

Cyanobacteria-dominated harmful algal blooms are increasing in occurrence. Many of the taxa contributing to these blooms are capable of fixing atmospheric nitrogen and should be favored under conditions of low nitrogen availability. Yet, synthesizing nitrogenase, the enzyme responsible for nitrogen fixation, is energetically expensive and requires...

To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the...

Species data Guild affiliation, absolute, and relative abundance for all species in each of the studied guilds across the three groups where the shared preference (Table 1), the distinct preference (Table 2), and the facilitative mode (Table 3) were tested.

Sample data Spatial, environmental, and biotic data for samples in groups where the shared preference (Table 1), the distinct preference (Table 2), and the facilitative mode (Table 3) were tested. For each sample, the sample ID, station ID, study unit, and time of collection are also provided.

Table S1 Water chemistry variability across the three studied groups of streams, where the shared preference (group 1), the distinct preference (group 2), and the facilitative mode (group 3) were tested. The concentrations of NO2 + NO3 and PO4 were measured in mg L−1. SD = standard deviation; and n= number of stream localities. A different letter i...

We examined the relationship between species richness (S) and evenness (J) within a novel, community assembly framework. We hypothesized that environmental stress leads to filtering (increasing the proportional abundance of tolerant species) and taxonomic dispersion (decreasing the number of species within genera and families). Environmental filter...

The role of the number of limiting resources (NLR) on species richness has been the subject of much theoretical and experimental work. However, how the NLR controls temporal beta diversity and the processes of community assembly is not well understood. To address this knowledge gap, we initiated a series of laboratory microcosm experiments, exposin...

The current paradigm that stream producers are under exclusive macronutrient control was recently challenged by continental studies, demonstrating that iron supply constrained diatom biodiversity. Using algal abundance and water chemistry data from the National Water-Quality Assessment Program, we determined for the first time community thresholds...

For over 40 years, acid deposition has been recognized as a serious international environmental problem, but efforts to restore acidified streams and biota have had limited success. The need to better understand the effects of different sources of acidity on streams has become more pressing with the recent increases in surface water organic acids,...

The accumulation of new and taxonomically diverse species is a marked feature of community development but the role of the environment in this process is not well understood. To address this problem, we subjected periphyton in laboratory streams to low (10 cm⋅sec(-1)), high (30 cm⋅sec(-1)), and variable (9-32 cm⋅sec(-1)) current velocity and low vs...

In an effort to identify the causes and patterns of temporal change in periphytic communities, we examined biomass accumulation, taxonomic and functional composition, rate of species turnover, and pairwise species correlations in response to variability in current velocity and nutrient supply in artificial stream flumes. Divergent patterns in commu...

Biological diversity comprises both species richness, i.e., the number of species in a community, and evenness, measuring how similar species are in their abundances. The relationship between species richness and evenness (RRE) across communities remains, however, a controversial issue in ecology because no consistent pattern has been reported. We...

Background/Question/Methods Streams in the Adirondack region of New York are acidified by both inorganic acid deposition and organic acidity in the form of dissolved organic carbon (DOC), but the impacts of these two types of acidity on biological communities are not well understood. Acid deposition mobilizes aluminum in streams to toxic levels,...

The century-long research on succession has bestowed us with a number of theories, but little agreement on what causes species replacements through time. The majority of studies has explored the temporal trends of individual species in plant and much less so in microbial communities, arguing that interspecific interactions, especially competition,...

For over 200 years, scientists have recognized the nearly ubiquitous poleward decline of species richness, but none of the theories explaining its occurrence has been widely accepted. In this continental study of U.S. running waters, I report an exception to this general pattern, i.e., a U-shaped latitudinal distribution of diatom richness (DR), eq...

Aim In this continental study, species richness at local (LSR) and regional (RSR) scales was correlated and examined as a function of stream (local) and watershed (regional) environment in an effort to elucidate what factors control diatom biodiversity across scales. Location Conterminous United States. Methods Data on diatom richness, stream condi...

Biodiversity of both terrestrial ecosystems and lacustrine phytoplankton increases with niche dimensionality, which can be determined by the number of limiting resources (NLR) in the environment. In the present continental study, I tested whether niche dimensionality and, with this species, richness scale positively with NLR in running waters. Diat...

Diatom material from South Africa and Swaziland was examined with light and scanning electron microscopy. Five new taxa are proposed: Gomphonema crocodilei, G. quasicrocodilei, G. venusta, G. latistigmata, and G. cholnokyi. Gomphonema venusta has been previously misidentified as Gomphonema clevei Fricke and G. cholnokyi as G. subclavatum (Grunow) G...

The morphology of initial frustules of Gomphoneis mesta Passy-Tolar & Lowe was studied with light and scanning electron microscopy The structure of the raphe, central nodule, stigma, striae, and apical pore field in post-auxospore generations was described. Discovery of internal chambers and an axial plate in very early stages of the life cycle of...

Atmospheric acid deposition has decreased in the northeastern United States since the 1970s, resulting in modest increases in pH, acid-neutralizing capacity (ANC), and decreases in inorganic monomeric aluminum (AlIM) concentrations since stream chemistry monitoring began in the 1980s in the acid-sensitive upper Neversink River basin in the Catskill...

Among the most studied relationships in ecology are those of population density with (1) body size and (2) species distribution. The first relationship, in conjunction with metabolic rate, determines the energy flows through species communities, whereas the second relationship shows how local communities are influenced by the species history of dis...

The relationship between species richness and body size is one of the most thoroughly studied subjects in animal ecology; however, this relationship and its underlying mechanisms are largely unknown in photosynthetic organisms, especially protists. In this continental study, I first examined the number of diatom species across the cell size spectru...

Diatom assemblages from 83 epilithic samples taken from the Mesta River, Bulgaria, were regressed against three sets of predictor variables, i.e. environmental, spatial, and temporal. Redundancy analysis (RDA) of species and environmental data explained 36% of the diatom variance and extracted several important gradients of species distribution, as...

Human-mediated geomorphic degradation of streams and rivers is a serious environmental problem with negative effects on aquatic biota and social infrastructure. Billions of dollars are spent for stream restoration in the USA alone, but it is still unknown how algal diversity is affected by these efforts. In this investigation, we studied a geomorph...

Three diatom ecological guilds were distinguished based on their potential to tolerate nutrient limitation and physical disturbance, i.e. a low profile, high profile, and motile guild. The guild distributions were examined along nutrient and flow disturbance gradients and across habitats in two extensively sampled streams. The guilds showed distinc...

The relationship between algal species richness and diversity, and pH is controversial. Furthermore, it is still unknown how episodic stream acidification following atmospheric deposition affects species richness and diversity. Here we analyzed water chemistry and diatom epiphyton dynamics and showed their contrasting behavior in chronically vs. ep...

Aim In this continental‐scale study, the biodiversity of benthic and planktonic algal communities was explored. A recent analysis of extinct and extant tree communities by Enquist et al . (2002) showed that richness of higher taxa was a power function of species richness, invariant across temporal and spatial scales. Here we examined whether the re...

In this continental-scale study, we show that in major benthic and planktonic stream habitats, algal biovolume--a proxy measure of biomass--is a unimodal function of species richness (SR). The biovolume peak is observed at intermediate to high SR in the benthos but at low richness in the phytoplankton. The unimodal nature of the biomass-diversity r...

Community dynamics of epiphytic diatoms were studied for 3 years in a chronically and an episodically acidified tributary of Buck Creek, Adirondacks. Both streams experienced pulses of acidity during hydrologic events but these pulses were more pronounced in the episodically acidified stream, where pH decreased over two units (between 4.53 and 6.62...

A new technique for spectral fingerprinting of major algal groups in the freshwater periphyton (i.e. cyanobacteria, green algae, and diatoms) was developed using confocal laser scanning microscopy. This technique used the differential spectral emission signatures of photosynthetic algae and allowed their spatially explicit quantification and commun...

ABSTRACTA new species from the diatom genus Gomphoneis, G. mesta, was described following morphological and ultra-structural analyses of its frustules by light and scanning electron microscopy. The valve striation consisting of double rows of areolae and the presence of longitudinal lines dictate the systematic position of this taxon in the genus G...

A new index, diatom model affinity (DMA) was erected as a reference-based community metric, derived from generic and species composition. DMA provides an assessment of water quality by the calculation of percent similarity to a model community, which can be viewed as a reference standard. High similarity to the model indicates communities that are...

Community response to environmental gradients operating at hierarchical scales was assessed in studies of benthic diatoms, macroinvertebrates and fish from 44 stream sites in the New York City watershed. Hierarchical cluster analysis (TWINSPAN) of diatoms and fish partitioned the study sites into four groups, i.e., acid streams, reservoir outlets a...

The morphology and distribution of six benthic colonial diatoms were investigated from the perspective of fractal geometry and stream ecology to test whether colonial complexity of benthic diatoms is associated with a tolerance to environmental variability, that is, if a random force, such as the unpredictability of current velocity, could be respo...

Spatial distributional patterns of benthic diatoms and their relation to current velocity were investigated in an unshaded cobble-bottom reach of White Creek (Washington County, NY). On 27 August 1999, diatoms were sampled and current velocity and depth were measured on a regular square sampling grid with a grain size of 0.01 m2, interval of 0.5 m,...

The bacterial RecA protein has been the most intensively studied enzyme in homologous genetic recombination. The core of RecA is structurally homologous to that of the F1-ATPase and helicases. Like the F1-ATPase and ring helicases, RecA forms a hexameric ring. The human Dmc1 (hDmc1) protein, a meiosis-specific recombinase, is homologous to RecA. We...

The beta protein of bacteriophage lambda acts in homologous genetic recombination by catalyzing the annealing of complementary single-stranded DNA produced by the lambda exonuclease. It has been shown that the beta protein binds to the products of the annealing reaction more tightly than to the initial substrates. We find that beta protein exists i...

Epilithon, epiphyton, epipelon, epipsammon and plocon diatom samples and water chemistry samples were collected bimonthly from 11 stations along the Mesta River, Bulgaria between December 1989 and April 1991. Principal component analysis (PCA), correlation, and dominance analysis were employed for describing the seasonal dynamics of diatom assembla...

Thesis (Ph. D.)--Bowling Green State University, 1997. Includes bibliographical references.