scholarly journals Leave or Stay: Simulating Motility and Fitness of Microorganisms in Dynamic Aquatic Ecosystems

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1019
Author(s):  
Alexandra Klimenko ◽  
Yury Matushkin ◽  
Nikolay Kolchanov ◽  
Sergey Lashin
Keyword(s):  
Nutrient Availability ◽  
Aquatic Ecosystems ◽  
Nutrient Concentration ◽  
Microbial Population ◽  
Microbial Populations ◽  
Nutrient Source ◽  
Energetic Costs ◽  
Agent Based ◽  
Adaptation Factor ◽  
Settler Population

Motility is a key adaptation factor in scarce marine environments inhabited by bacteria. The question of how a capacity for adaptive migrations influences the success of a microbial population in various conditions is a challenge addressed in this study. We employed the agent-based model of competition of motile and sedentary microbial populations in a confined aquatic environment supplied with a periodic batch nutrient source to assess the fitness of both. Such factors as nutrient concentration in a batch, batch period, mortality type and energetic costs of migration were considered to determine the conditions favouring different strategies: Nomad of a motile population and Settler of a sedentary one. The modelling results demonstrate that dynamic and nutrient-scarce environments favour motile populations, whereas nutrient-rich and stagnant environments promote sedentary microorganisms. Energetic costs of migration determine whether or not the Nomad strategy of the motile population is successful, though it also depends on such conditions as nutrient availability. Even without penalties for migration, under certain conditions, the sedentary Settler population dominates in the ecosystem. It is achieved by decreasing the local nutrient availability near the nutrient source, as motile populations relying on a local optimizing strategy tend to follow benign conditions and fail, enduring stress associated with crossing the valleys of suboptimal nutrient availability.

scholarly journals Linking Toluene Degradation with Specific Microbial Populations in Soil

1999 ◽  
Vol 65 (12) ◽  
pp. 5403-5408 ◽  
Author(s):  
Jessica R. Hanson ◽  
Jennifer L. Macalady ◽  
David Harris ◽  
Kate M. Scow
Keyword(s):  
Microbial Community ◽  
Microbial Population ◽  
Phospholipid Fatty Acid ◽  
Microbial Populations ◽  
Complex Environments ◽  
Toluene Degradation ◽  
Effective Technique ◽  
Soil Microbial ◽  
Isotope Tracer ◽  
Plfa Analysis

ABSTRACT Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil.

Performance differences in Pinus radiata progeny with differing site nutrient availability

2004 ◽  
Vol 34 (12) ◽  
pp. 2410-2423 ◽  
Author(s):  
S D Carson ◽  
M F Skinner ◽  
A T Lowe ◽  
M O Kimberley
Keyword(s):  
Nutrient Availability ◽  
Pinus Radiata ◽  
Nutrient Concentration ◽  
Radiata Pine ◽  
Substantial Improvement ◽  
Treatment Combination ◽  
Control Seed ◽  
Foliar Nutrient ◽  
Selection For ◽  
Selection Of

Two intensive harvesting trials with contrasting nutrient capital were examined for genetic × environment interactions to age 5 years after planting. Treatments included differences in removal of organic matter and in site preparation and weed control, with each treatment having both fertilized and nonfertilized plots. Three harvest treatments (both fertilized and nonfertilized) were common to both sites, with two additional treatments at one site. There were four replicate plots of each treatment combination at each site, with two trees from each of three control seed lots and 47 open-pollinated families chosen to represent the range of performance for growth planted in each plot. Large differences among sites and among treatments in both growth and foliar nutrient concentration were observed. Genetic × site interactions and genetic × treatment within site interactions were seldom significant. Significant interactions did not appear to be related to changes in rankings of families, but rather to the differences in variance among families in different treatments. This study suggests that selection of specific radiata pine (Pinus radiata D. Don) families for better growth performance on nutrient-deficient sites in New Zealand would not result in substantial improvement over selection for growth on all sites disregarding nutrient availability.

scholarly journals Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Ganesh Babu Malli Mohan ◽  
Ceth W. Parker ◽  
Camilla Urbaniak ◽  
Nitin K. Singh ◽  
Anthony Hood ◽  
...  
Keyword(s):  
16S Rrna ◽  
Metal Surfaces ◽  
Microbial Population ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Particle Board ◽  
Shotgun Metagenomics ◽  
Glass Surfaces ◽  
Glass Metal

ABSTRACT Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance. IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.

scholarly journals A Review on Anaerobic Co-Digestion with a Focus on the Microbial Populations and the Effect of Multi-Stage Digester Configuration

Energies ◽  
2019 ◽  
Vol 12 (6) ◽  
pp. 1106 ◽  
Author(s):  
Anahita Rabii ◽  
Saad Aldin ◽  
Yaser Dahman ◽  
Elsayed Elbeshbishy
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Population ◽  
System Stability ◽  
Microbial Consortia ◽  
Microbial Populations ◽  
Stage Versus ◽  
Two Stage ◽  
Waste Sludge ◽  
Multi Stage ◽  
Mode A

Recent studies have shown that anaerobic co-digestion (AnCoD) is superior to conventional anaerobic digestion (AD). The benefits of enhanced bioenergy production and solids reduction using co-substrates have attracted researchers to study the co-digestion technology and to better understand the effect of multi substrates on digester performance. This review will discuss the results of such studies with the main focus on: (1) generally the advantages of co-digestion over mono-digestion in terms of system stability, bioenergy, and solids reduction; (2) microbial consortia diversity and their synergistic impact on biogas improvement; (3) the effect of digester mode, i.e., multi-stage versus single stage digestion on AnCoD. It is essential to note that the studies reported improvement in the synergy and diverse microbial consortia when using co-digestion technologies, in addition to higher biomethane yield when using two-stage mode. A good example would be the co-digestion of biodiesel waste and glycerin with municipal waste sludge in a two-stage reactor resulting in 100% increase of biogas and 120% increase in the methane content of the produced biogas with microbial population dominated by Methanosaeta and Methanomicrobium.

scholarly journals Molecular Analysis of Surfactant-Driven Microbial Population Shifts in Hydrocarbon-Contaminated Soil

2000 ◽  
Vol 66 (7) ◽  
pp. 2959-2964 ◽  
Author(s):  
Gregory M. Colores ◽  
Richard E. Macur ◽  
David M. Ward ◽  
William P. Inskeep
Keyword(s):  
Gel Electrophoresis ◽  
Microbial Population ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Populations ◽  
Alcohol Ethoxylate ◽  
Rrna Gene ◽  
Mineralization Kinetics ◽  
Gradient Gel Electrophoresis ◽  
The Impact ◽  
Parallel Cultivation

ABSTRACT We analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. A mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. Witconol SN70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (CMC) in soil (CMC′) (determined to be 13 mg g−1). Addition of the surfactant at a concentration below the CMC′ (2 mg g−1) did not affect the mineralization rates of either hydrocarbon. However, when surfactant was added at a concentration approaching the CMC′ (10 mg g−1), hexadecane mineralization was delayed and phenanthrene mineralization was completely inhibited. Addition of surfactant at concentrations above the CMC′ (40 mg g−1) completely inhibited mineralization of both phenanthrene and hexadecane. Denaturing gradient gel electrophoresis of 16S rRNA gene segments showed that hydrocarbon amendment stimulatedRhodococcus and Nocardia populations that were displaced by Pseudomonas and Alcaligenespopulations at elevated surfactant levels. Parallel cultivation studies revealed that the Rhodococcus population can utilize hexadecane and that the Pseudomonas andAlcaligenes populations can utilize both Witconol SN70 and hexadecane for growth. The results suggest that surfactant applications necessary to achieve the CMC alter the microbial populations responsible for hydrocarbon mineralization.

Soil bulk density effects on soil microbial populations and enzyme activities during the growth of maize (Zea mays L.) planted in large pots under field exposure

2002 ◽  
Vol 82 (2) ◽  
pp. 147-154 ◽  
Author(s):  
C. H. Li ◽  
B. L. Ma ◽  
T. Q. Zhang
Keyword(s):  
Zea Mays ◽  
Bulk Density ◽  
Enzyme Activities ◽  
Soil Compaction ◽  
Microbial Population ◽  
Soil Bulk Density ◽  
Microbial Populations ◽  
Growth Stages ◽  
Soil Microbial ◽  
Plant Growth Stages

Soil compaction associated with inappropriate maneuvering of field equipment, and/or modern cropping system negatively affect soil physical properties, and thus, may limit microbial activities and biochemical processes, which are important to nutrient bioavailability. An experiment was carried out using the pot-culture technique to determine the effect of bulk density on soil microbial populations and enzyme activities in an Eutric Cambisol sandy loam soil (United Nations’ classification) planted with maize (Zea mays L.) in the Experimental Farm of Henan Agricultural University, Henan, China (34°49′N, 113°40′E). Numbers of bacteria, fungi, and actinomycetes and the enzyme activities of invertase, polyphenol oxidase, catalase, urease, protease, and phosphatase were determined at various stages during the plant growing season. Microbial numbers were negatively and linearly related to soil bulk density. With increases in soil bulk density from 1.00 to 1.60 Mg m-3, total numbers of bacteria, fungi and actinomycetes declined by 26-39%. The strongest correlations between the soil microbial population and bulk density occurred at the plant growth stages of the 6 fully expanded leaf (V6) and anthesis (R1), with R2 > 0.90 (P< 0.01) for all three microorganism categories. Increasing soil bulk density was related quadratically to the activities of soil invertase and polyphenol oxidase, protease and catalase. It appears that the greatest activities of most soil enzymes occurred at a bulk density of 1.0 to 1.3 Mg m-3, which are optimum for most field crops. The plant growth stages also had an important impact on soil enzyme activities and microbial populations, with strong positive associations between soil microorganisms and enzyme activities with crop growth. Key words: Maize, soil enzymes, microbial population, soil compaction, bulk density, Zea mays

scholarly journals Redox regime shifts in microbially mediated biogeochemical cycles

2015 ◽  
Vol 12 (12) ◽  
pp. 3713-3724 ◽  
Author(s):  
T. Bush ◽  
I. B. Butler ◽  
A. Free ◽  
R. J. Allen
Keyword(s):  
Population Dynamics ◽  
Environmental Change ◽  
Microbial Population ◽  
Biogeochemical Cycles ◽  
Sulfur Cycle ◽  
Regime Shifts ◽  
Microbial Populations ◽  
Iron Cycling ◽  
Biogeochemical Models ◽  
Microbial Population Dynamics

Abstract. Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

In‐situ apparent conductivity measurements and microbial population distribution at a hydrocarbon‐contaminated site

Geophysics ◽  
2004 ◽  
Vol 69 (1) ◽  
pp. 56-63 ◽  
Author(s):  
Estella A. Atekwana ◽  
D. Dale Werkema ◽  
Joseph W. Duris ◽  
Silvia Rossbach ◽  
Eliot A. Atekwana ◽  
...  
Keyword(s):  
Microbial Degradation ◽  
Microbial Population ◽  
Population Distribution ◽  
Microbial Populations ◽  
Contaminated Site ◽  
Most Probable Number ◽  
Bulk Conductivity ◽  
Probable Number ◽  
A Site

We investigated the bulk electrical conductivity and microbial population distribution in sediments at a site contaminated with light nonaqueous‐phase liquid (LNAPL). The bulk conductivity was measured using in‐situ vertical resistivity probes; the most probable number method was used to characterize the spatial distribution of aerobic heterotrophic and oil‐degrading microbial populations. The purpose of this study was to assess if high conductivity observed at aged LNAPL‐impacted sites may be related to microbial degradation of LNAPL. The results show higher bulk conductivity coincident with LNAPL‐impacted zones, in contrast to geoelectrical models that predict lower conductivity in such zones. The highest bulk conductivity was observed to be associated with zones impacted by residual and free LNAPL. Data from bacteria enumeration from sediments close to the resistivity probes show that oil‐degrading microbes make up a larger percentage (5–55%) of the heterotrophic microbial community at depths coincident with the higher conductivity compared to ∼5% at the uncontaminated location. The coincidence of a higher percentage of oil‐degrading microbial populations in zones of higher bulk conductivity suggests that the higher conductivity in these zones may result from increased fluid conductivity related to microbial degradation of LNAPL, consistent with geochemical studies that suggest that intrinsic biodegradation is occurring at the site. The findings from this study point to the fact that biogeochemical processes accompanying biodegradation of contaminants can potentially alter geoelectrical properties of the subsurface impacted media.

scholarly journals Redox regime shifts in microbially-mediated biogeochemical cycles

2015 ◽  
Vol 12 (4) ◽  
pp. 3283-3314
Author(s):  
T. Bush ◽  
I. B. Butler ◽  
A. Free ◽  
R. J. Allen
Keyword(s):  
Population Dynamics ◽  
Environmental Change ◽  
Microbial Population ◽  
Biogeochemical Cycles ◽  
Regime Shifts ◽  
Microbial Populations ◽  
Iron Cycling ◽  
Biogeochemical Models ◽  
Microbial Population Dynamics ◽  
Parameter Ranges

Abstract. Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the sulfur and nitrogen cycles in the present-day natural environment, and may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

scholarly journals The interplay of phenotypic variability and fitness in finite microbial populations

2020 ◽  
Vol 17 (166) ◽  
pp. 20190827 ◽  
Author(s):  
Ethan Levien ◽  
Jane Kondev ◽  
Ariel Amir
Keyword(s):  
Growth Rate ◽  
Exponential Growth ◽  
Finite Population ◽  
Microbial Population ◽  
Phenotypic Variability ◽  
Growth Conditions ◽  
Microbial Populations ◽  
Steady State Distribution ◽  
State Distribution ◽  
History Of

In isogenic microbial populations, phenotypic variability is generated by a combination of stochastic mechanisms, such as gene expression, and deterministic factors, such as asymmetric segregation of cell volume. Here we address the question: how does phenotypic variability of a microbial population affect its fitness? While this question has previously been studied for exponentially growing populations, the situation when the population size is kept fixed has received much less attention, despite its relevance to many natural scenarios. We show that the outcome of competition between multiple microbial species can be determined from the distribution of phenotypes in the culture using a generalization of the well-known Euler–Lotka equation, which relates the steady-state distribution of phenotypes to the population growth rate. We derive a generalization of the Euler–Lotka equation for finite cultures, which relates the distribution of phenotypes among cells in the culture to the exponential growth rate. Our analysis reveals that in order to predict fitness from phenotypes, it is important to understand how distributions of phenotypes obtained from different subsets of the genealogical history of a population are related. To this end, we derive a mapping between the various ways of sampling phenotypes in a finite population and show how to obtain the equivalent distributions from an exponentially growing culture. Finally, we use this mapping to show that species with higher growth rates in exponential growth conditions will have a competitive advantage in the finite culture.

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