scholarly journals The influence of the crowding assumptions in biofilm simulations

2021 ◽  
Vol 17 (7) ◽  
pp. e1009158
Author(s):  
Liliana Angeles-Martinez ◽  
Vassily Hatzimanikatis
Keyword(s):  
Environmental Conditions ◽  
Community Dynamics ◽  
Volume Fraction ◽  
Cell Metabolism ◽  
Microbial Dynamics ◽  
Nutrient Media ◽  
Nutrient Quality ◽  
Appearance Time ◽  
Temporal Modeling ◽  
Microbial Systems

Microorganisms are frequently organized into crowded structures that affect the nutrients diffusion. This reduction in metabolite diffusion could modify the microbial dynamics, meaning that computational methods for studying microbial systems need accurate ways to model the crowding conditions. We previously developed a computational framework, termed CROMICS, that incorporates the effect of the (time-dependent) crowding conditions on the spatio-temporal modeling of microbial communities, and we used it to demonstrate the crowding influence on the community dynamics. To further identify scenarios where crowding should be considered in microbial modeling, we herein applied and extended CROMICS to simulate several environmental conditions that could potentially boost or dampen the crowding influence in biofilms. We explore whether the nutrient supply (rich- or low-nutrient media), the cell-packing configuration (square or hexagonal spherical cell arrangement), or the cell growing conditions (planktonic state or biofilm) modify the crowding influence on the growth of Escherichia coli. Our results indicate that the growth rate, the abundance and appearance time of different cell phenotypes as well as the amount of by-products secreted to the medium are sensitive to some extent to the local crowding conditions in all scenarios tested, except in rich-nutrient media. Crowding conditions enhance the formation of nutrient gradient in biofilms, but its effect is only appreciated when cell metabolism is controlled by the nutrient limitation. Thus, as soon as biomass (and/or any other extracellular macromolecule) accumulates in a region, and cells occupy more than 14% of the volume fraction, the crowding effect must not be underestimated, as the microbial dynamics start to deviate from the ideal/expected behaviour that assumes volumeless cells or when a homogeneous (reduced) diffusion is applied in the simulation. The modeling and simulation of the interplay between the species diversity (cell shape and metabolism) and the environmental conditions (nutrient quality, crowding conditions) can help to design effective strategies for the optimization and control of microbial systems.

Distribution, abundance, and diversity of stream fishes under variable environmental conditions

2006 ◽  
Vol 63 (1) ◽  
pp. 43-54 ◽  
Author(s):  
Christopher M Taylor ◽  
Thomas L Holder ◽  
Riccardo A Fiorillo ◽  
Lance R Williams ◽  
R Brent Thomas ◽  
...  
Keyword(s):  
Species Richness ◽  
Environmental Conditions ◽  
Community Dynamics ◽  
Local Community ◽  
Fish Assemblages ◽  
Fish Distribution ◽  
Stream Fish ◽  
Spatial And Temporal Variability ◽  
Regional Patterns ◽  
Abundance And Diversity

The effects of stream size and flow regime on spatial and temporal variability of stream fish distribution, abundance, and diversity patterns were investigated. Assemblage variability and species richness were each significantly associated with a complex environmental gradient contrasting smaller, hydrologically variable stream localities with larger localities characterized by more stable flow regimes. Assemblages showing the least variability were the most species-rich and occurred in relatively large, stable environments. Theory suggests that species richness can be an important determinant of assemblage variability. Although this appears to be true in our system, we suggest that spatial and temporal heterogeneity in the environment largely determines both assemblage richness and variability, providing a more parsimonious explanation for the diversity–variability correlation. Changes in species richness of local assemblages across time were coordinated across the landscape, and assemblages formed spatially and temporally nested subset patterns. These results suggest an important link between local community dynamics and community-wide occurrence. At the species level, mean local persistence was significantly associated with regional occurrence. Thus, the more widespread a species was, the greater its local persistence. Our results illustrate how the integrity of local stream fish assemblages is dependent on local environmental conditions, regional patterns of species distribution, and landscape continuity.

scholarly journals DNA from lake sediments reveals the long-term dynamics and diversity of <i>Synechococcus</i> assemblages

2013 ◽  
Vol 10 (6) ◽  
pp. 3817-3838 ◽  
Author(s):  
I. Domaizon ◽  
O. Savichtcheva ◽  
D. Debroas ◽  
F. Arnaud ◽  
C. Villar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Environmental Conditions ◽  
Trophic Status ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Quantitative Polymerase Chain Reaction ◽  
Additive Models ◽  
Phosphorus Concentration ◽  
Rrna Gene

Abstract. While picocyanobacteria (PC) are important actors in carbon and nutrient cycles in aquatic systems, factors controlling their interannual dynamics and diversity are poorly known due to the general lack of long-term monitoring surveys. This study intended to fill this gap by applying a DNA-based paleolimnological approach to sediment records from a deep subalpine lake that has experienced dramatic changes in environmental conditions during the last century (eutrophication, re-oligotrophication and large-scale climate changes). In particular, we investigated the long-term (100 yr) diversity and dynamics of Synechococcus,, PC that have presumably been affected by both the lake trophic status changes and global warming. The lake's morphological and environmental conditions provided the ideal conditions for DNA preservation in the sediment archives. Generalised additive models applied to quantitative PCR (qPCR; quantitative Polymerase Chain Reaction) results highlighted that an increase in summer temperature could have a significant positive impact on the relative abundance of Synechococcus, (fraction of Synechococcus, in total cyanobacteria). The diversity of Synechococcus, in Lake Bourget was studied by phylogenetic analyses of the 16S rRNA gene and the following internally transcribed spacer (ITS). Up to 23 different OTUs (based on 16S rRNA), which fell into various cosmopolitan or endemic clusters, were identified in samples from the past 100 yr. Moreover, the study of ITS revealed a higher diversity within the major 16S rRNA-defined OTUs. Changes in PC diversity were related to the lake's trophic status. Overall, qPCR and sequencing results showed that environmental changes (in temperature and phosphorus concentration) affected Synechococcus, community dynamics and structure, translating into changes in genotype composition. These results also helped to re-evaluate the geographical distribution of some Synechococcus, clusters. Providing such novel insights into the long-term history of an important group of primary producers, this study illustrates the promising approach that consists in coupling molecular tools and paleolimnology to reconstruct a lake's biodiversity history.

scholarly journals Landscape-level DNA metabarcoding study in the Pannonian forests reveals differential effects of slope aspect on taxonomic and functional groups of fungi

2018 ◽  
Author(s):  
József Geml
Keyword(s):  
Functional Groups ◽  
Community Composition ◽  
Fungal Community ◽  
Environmental Conditions ◽  
Community Dynamics ◽  
Fungal Communities ◽  
Slope Aspect ◽  
Fungal Community Composition ◽  
Dna Metabarcoding ◽  
Landscape Level

AbstractIn temperate regions, slope aspect is one of the most influential drivers of environmental conditions at landscape level. The effect of aspect on vegetation has been well studied, but virtually nothing is known about how fungal communities are shaped by aspect-driven environmental conditions. I carried out DNA metabarcoding of fungi from soil samples taken in a selected study area of Pannonian forests to compare richness and community composition of taxonomic and functional groups of fungi between slopes of predominantly southerly vs. northerly aspect and to assess the influence of selected environmental variables on fungal community composition. The deep sequence data presented here (i.e. 980 766 quality-filtered sequences) indicate that both niche (environmental filtering) and neutral (stochastic) processes shape fungal community composition at landscape level. Fungal community composition correlated strongly with aspect, with many fungi showing preference for either south-facing or north-facing slopes. Several taxonomic and functional groups showed significant differences in richness between north-and south-facing slopes and strong compositional differences were observed in all functional groups. The effect of aspect on fungal communities likely is mediated through contrasting mesoclimatic conditions, that in turn influence edaphic processes as well as vegetation. Finally, the data presented here provide an unprecedented insight into the diversity and landscape-level community dynamics of fungi in the Pannonian forests.

scholarly journals Monitoring biofilm Co2 production in response to antibiotic exposures

2021 ◽  
Author(s):  
Lindsay Jackson
Keyword(s):  
Environmental Conditions ◽  
Community Dynamics ◽  
Antibiotic Resistance Genes ◽  
Metagenomic Analysis ◽  
Co2 Production ◽  
High Dose ◽  
Neutral Ph ◽  
Susceptibility Tests ◽  
Biofilm Development ◽  
Multispecies Biofilms

Bacteria commonly exist in nature as biofilms which help protect them from harsh environmental conditions, thus increasing their ability to adapt and survive. In clinical settings antibiotic treatments based on planktonic susceptibility tests are ineffective against biofilm infections, as biofilms can withstand much higher antibiotic concentrations. To further elucidate biofilm behaviour, multispecies and pure culture biofilms were grown in a CO2 evolution measurement system (CEMS) that tracks whole-biofilm CO2 production non-destructively and in real-time. In addition, metagenomic analysis was performed on multispecies cultures to monitor community dynamics and the intrinsic potential in different physiological states. Multispecies biofilms grown in CEMS were exposed to aminoglycosides under various environmental conditions (e.g. nutrient and pH variations). Multispecies biofilms were most susceptible to high-dose streptomycin exposures when grown for less than 48 hours (young biofilm). However, carbon addition to the antibiotic medium decreased young biofilm susceptibility to streptomycin. Furthermore, young biofilms were susceptible to 4000 mg/1doses of streptomycin and gentamicin at pH6.0 and to 4000 mg/1 doses of streptomycin at pH 7.4. Biofilms were least susceptible to the aminoglycosides at neutral pH. Metagenomic analysis on the multispecies biofilms revealed the presence of aminoglycoside-modifying enzymes and that the cultures contained Pseudomonas aeruginosa and Stenotrophomonas maltophilia strains. The dominant strain in planktonic cultures was P.aeruginosa. However, in complex growth medium, S. maltophilia increased in proportion upon biofilm development and became the dominant species following a high-dose streptomycin exposure. The monitoring of biofilm metabolic responses revealed adding carbon to the antibiotic medium or exposing the biofilms to aminoglycosides at neutral pH reduces biofilm aminoglycoside susceptibility. In addition, metagenomic analysis uncovered community composition and genes that can play a role in biofilm survival to the antibiotics. However, even with the presence of antibiotic resistance genes, carbon and pH play an important role in biofilm survival to high-dose antibiotic exposures.

scholarly journals Scaling up biodiversity–ecosystem functioning relationships: the role of environmental heterogeneity in space and time

2021 ◽  
Vol 288 (1946) ◽  
pp. 20202779
Author(s):  
Patrick L. Thompson ◽  
Sonia Kéfi ◽  
Yuval R. Zelnik ◽  
Laura E. Dee ◽  
Shaopeng Wang ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Ecosystem Functioning ◽  
Environmental Heterogeneity ◽  
Community Dynamics ◽  
Formal Model ◽  
Spatial Scales ◽  
Scale Dependence ◽  
Space And Time ◽  
Number Of Species

The biodiversity and ecosystem functioning (BEF) relationship is expected to be scale-dependent. The autocorrelation of environmental heterogeneity is hypothesized to explain this scale dependence because it influences how quickly biodiversity accumulates over space or time. However, this link has yet to be demonstrated in a formal model. Here, we use a Lotka–Volterra competition model to simulate community dynamics when environmental conditions vary across either space or time. Species differ in their optimal environmental conditions, which results in turnover in community composition. We vary biodiversity by modelling communities with different sized regional species pools and ask how the amount of biomass per unit area depends on the number of species present, and the spatial or temporal scale at which it is measured. We find that more biodiversity is required to maintain functioning at larger temporal and spatial scales. The number of species required increases quickly when environmental autocorrelation is low, and slowly when autocorrelation is high. Both spatial and temporal environmental heterogeneity lead to scale dependence in BEF, but autocorrelation has larger impacts when environmental change is temporal. These findings show how the biodiversity required to maintain functioning is expected to increase over space and time.

The Ecotron: a controlled environmental facility for the investigation of population and ecosystem processes

1993 ◽  
Vol 341 (1296) ◽  
pp. 181-194 ◽  
Keyword(s):  
Environmental Conditions ◽  
Population Biology ◽  
Community Dynamics ◽  
Ecosystem Processes ◽  
Physical Factors ◽  
Physical Conditions ◽  
Secondary Consumers ◽  
Population And Community Dynamics ◽  
Radiation Sensors ◽  
Near Future

This paper reports on aspects of the design and philosophy of the Ecotron, an integrated series of 16 controlled environmental chambers at the NERC Centre for Population Biology. The Ecotron serves as an experimental means for analysing population and community dynamics and ecosystem processes under controlled physical conditions. Within the chambers, terrestrial experimental communities are assembled into foodwebs of desired complexity from a pool of species selected for their preadaptations to the physical conditions of the Ecotron. These species include decomposers (earthworms, snails, microarthropods and microbes), primary producers (16 species of plants), primary consumers (four species of herbivorous arthropods), and secondary consumers (four species of parasitoids). The design of the Ecotron is unique in several aspects with respect to its blend of biology and technology. It supports small, dynam ic communities of up to 30 plant and metazoan species, thereby making it among the more biologically complex controlled environmental systems currently in use. Its architecture permits replication and variation of spatial scale in experimental design. Its artificial climate simulates natural environmental conditions within chambers allowing experimental control over light, water, temperature, humidity, and in the near future CO 2 and UV-B radiation. Sensors monitor both macro- and micro-environmental conditions of a number of physical factors within the chambers. Preliminary experiments show the Ecotron to be an excellent facility for long-term population and community-level experiments. We discuss the results of one of these early experiments and briefly consider ongoing and future experiments.

scholarly journals Oxidative stress antagonizes fluoroquinolone drug sensitivity via the SoxR-SUF Fe-S cluster homeostatic axis

PLoS Genetics ◽  
2020 ◽  
Vol 16 (11) ◽  
pp. e1009198
Author(s):  
Audrey Gerstel ◽  
Jordi Zamarreño Beas ◽  
Yohann Duverger ◽  
Emmanuelle Bouveret ◽  
Frédéric Barras ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Environmental Conditions ◽  
Drug Sensitivity ◽  
Efflux Pump ◽  
Cell Metabolism ◽  
Drug Efflux ◽  
Phenazine Methosulfate ◽  
Phenotypic Analysis ◽  
Antibiotic Resistance Profile ◽  
Drug Efflux Pump

The level of antibiotic resistance exhibited by bacteria can vary as a function of environmental conditions. Here, we report that phenazine-methosulfate (PMS), a redox-cycling compound (RCC) enhances resistance to fluoroquinolone (FQ) norfloxacin. Genetic analysis showed that E. coli adapts to PMS stress by making Fe-S clusters with the SUF machinery instead of the ISC one. Based upon phenotypic analysis of soxR, acrA, and micF mutants, we showed that PMS antagonizes fluoroquinolone toxicity by SoxR-mediated up-regulation of the AcrAB drug efflux pump. Subsequently, we showed that despite the fact that SoxR could receive its cluster from either ISC or SUF, only SUF is able to sustain efficient SoxR maturation under exposure to prolonged PMS period or high PMS concentrations. This study furthers the idea that Fe-S cluster homeostasis acts as a sensor of environmental conditions, and because its broad influence on cell metabolism, modifies the antibiotic resistance profile of E. coli.

scholarly journals Long-Term Patterns of Amphibian Diversity, Abundance and Nutrient Export from Small, Isolated Wetlands

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 598
Author(s):  
Carla L. Atkinson ◽  
Daniel D. Knapp ◽  
Lora L. Smith
Keyword(s):  
Life History ◽  
Environmental Conditions ◽  
Life History Traits ◽  
Community Dynamics ◽  
Animal Movement ◽  
Nutrient Content ◽  
Environmental Data ◽  
Spatial And Temporal Variability ◽  
Isolated Wetlands

Seasonally inundated wetlands contribute to biodiversity support and ecosystem function at the landscape scale. These temporally dynamic ecosystems contain unique assemblages of animals adapted to cyclically wet–dry habitats. As a result of the high variation in environmental conditions, wetlands serve as hotspots for animal movement and potentially hotspots of biogeochemical activity and migratory transport of nutrient subsidies. Most amphibians are semi-aquatic and migrate between isolated wetlands and the surrounding terrestrial system to complete their life cycle, with rainfall and other environmental factors affecting the timing and magnitude of wetland export of juveniles. Here we used a long-term drift fence study coupled with system-specific nutrient content data of amphibians from two small wetlands in southeastern Georgia, USA. We couple environmental data with count data of juveniles exiting wetlands to explore the controls of amphibian diversity, production and export and the amphibian life-history traits associated with export over varying environmental conditions. Our results highlight the high degree of spatial and temporal variability in amphibian flux with hydroperiod length and temperature driving community composition and overall biomass and nutrient fluxes. Additionally, specific life-history traits, such as development time and body size, were associated with longer hydroperiods. Our findings underscore the key role of small, isolated wetlands and their hydroperiod characteristics in maintaining amphibian productivity and community dynamics.

scholarly journals State of the California Current 2019–2020: Back to the Future With Marine Heatwaves?

2021 ◽  
Vol 8 ◽  
Author(s):  
Edward D. Weber ◽  
Toby D. Auth ◽  
Simone Baumann-Pickering ◽  
Timothy R. Baumgartner ◽  
Eric P. Bjorkstedt ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Community Dynamics ◽  
Coastal Upwelling ◽  
Juvenile Fish ◽  
California Current ◽  
Trophic Levels ◽  
Warm Water ◽  
Seabird Species ◽  
Cool Water ◽  
The North

The California Current System (CCS) has experienced large fluctuations in environmental conditions in recent years that have dramatically affected the biological community. Here we synthesize remotely sensed, hydrographic, and biological survey data from throughout the CCS in 2019–2020 to evaluate how recent changes in environmental conditions have affected community dynamics at multiple trophic levels. A marine heatwave formed in the north Pacific in 2019 and reached the second greatest area ever recorded by the end of summer 2020. However, high atmospheric pressure in early 2020 drove relatively strong Ekman-driven coastal upwelling in the northern portion of the CCS and warm temperature anomalies remained far offshore. Upwelling and cooler temperatures in the northern CCS created relatively productive conditions in which the biomass of lipid-rich copepod species increased, adult krill size increased, and several seabird species experienced positive reproductive success. Despite these conditions, the composition of the fish community in the northern CCS remained a mixture of both warm- and cool-water-associated species. In the southern CCS, ocean temperatures remained above average for the seventh consecutive year. Abundances of juvenile fish species associated with productive conditions were relatively low, and the ichthyoplankton community was dominated by a mixture of oceanic warm-water and cosmopolitan species. Seabird species associated with warm water also occurred at greater densities than cool-water species in the southern CCS. The population of northern anchovy, which has been resurgent since 2017, continued to provide an important forage base for piscivorous fishes, offshore colonies of seabirds, and marine mammals throughout the CCS. Coastal upwelling in the north, and a longer-term trend in warming in the south, appeared to be controlling the community to a much greater extent than the marine heatwave itself.

scholarly journals TEMPERATURE AND NUTRIENT CONDITIONS MODIFY THE EFFECTS OF PHENOLOGICAL SHIFTS IN PREDATOR-PREY COMMUNITIES

2021 ◽  
Author(s):  
Volker H.W. Rudolf
Keyword(s):  
Climate Change ◽  
Environmental Conditions ◽  
Community Dynamics ◽  
Arrival Time ◽  
Environmental Context ◽  
Nutrient Addition ◽  
Predator Prey ◽  
Early Arrival ◽  
Phenological Shifts ◽  
Predation Rates

While there is mounting evidence indicating that the relative timing of predator and prey phenologies shapes the outcome of trophic interactions, we still lack a comprehensive understanding of how important the environmental context (e.g. abiotic conditions) is for shaping this relationship. Environmental conditions not only frequently drive shifts in phenologies, but they can also affect the very same processes that mediate the effects of phenological shifts on species interactions. Thus, identifying how environmental conditions shape the effects of phenological shifts is key to predict community dynamics across a heterogenous landscape and how they will change with ongoing climate change in the future. Here I tested how environmental conditions shape effects of phenological shifts by experimentally manipulating temperature, nutrient availability, and relative phenologies in two predator-prey freshwater systems (mole salamander- bronze frog vs dragonfly larvae-leopard frog). This allowed me to (1) isolate the effect of phenological shifts and different environmental conditions, (2) determine how they interact, and (3) how consistent these patterns are across different species and environments. I found that delaying prey arrival dramatically increased predation rates, but these effects were contingent on environmental conditions and predator system. While both nutrient addition and warming significantly enhanced the effect of arrival time, their effect was qualitatively different: Nutrient addition enhanced the positive effect of early arrival while warming enhanced the negative effect of arriving late. Predator responses varied qualitatively across predator-prey systems. Only in the system with strong gape-limitation were predators (salamanders) significantly affected by prey arrival time and this effect varied with environmental context. Correlations between predator and prey demographic rates suggest that this was driven by shifts in initial predator-prey size ratios and a positive feedback between size-specific predation rates and predator growth rates. These results highlight the importance of accounting for temporal and spatial correlation of local environmental conditions and gape-limitation in predator-prey systems when predicting the effects of phenological shifts and climate change on predator-prey systems.

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