scholarly journals Estimating the maximal growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns

2021 ◽  
Author(s):  
Jake L Weissman ◽  
Edward-Robert O Dimbo ◽  
Arianna I Krinos ◽  
Christopher Neely ◽  
Yuniba Yagues ◽  
...  
Keyword(s):  
Growth Rate ◽  
Water Column ◽  
Growth Rates ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Growth Potential ◽  
Maximal Growth ◽  
Culture Collections ◽  
Microbial Eukaryotes ◽  
Eukaryotic Microbes

Microbial eukaryotes are ubiquitous in the environment and play important roles in key ecosystem processes, including accounting for a significant portion of global primary production. Yet, our tools for assessing the functional capabilities of eukaryotic microbes in the environment are quite limited because many microbes have yet to be grown in culture. Maximum growth rate is a fundamental parameter of microbial lifestyle that reveals important information about an organism's functional role in a community. We developed and validated a genomic estimator of maximum growth rate for eukaryotic microbes, enabling the assessment of growth potential for both cultivated and yet-to-be-cultivated organisms. We produced a database of over 700 growth predictions from genomes, transcriptomes, and metagenome-assembled genomes, and found that closely related and/or functionally similar organisms tended to have similar maximal growth rates. By comparing the maximal growth rates of existing culture collections with environmentally-derived genomes we found that, unlike for prokaryotes, culture collections of microbial eukaryotes are only minimally biased in terms of growth potential. We then extended our tool to make community-wide estimates of growth potential from over 500 marine metagenomes, mapping growth potential across the global oceans. We found that prokaryotic and eukaryotic communities have highly correlated growth potentials near the ocean surface, but that this relationship disappears deeper in the water column. This suggests that fast growing eukaryotes and prokaryotes thrive under similar conditions at the ocean surface, but that there is a decoupling of these communities as resources become scarce deeper in the water column.

scholarly journals Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

2021 ◽  
Vol 118 (12) ◽  
pp. e2016810118
Author(s):  
Jake L. Weissman ◽  
Shengwei Hou ◽  
Jed A. Fuhrman
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Microbial Growth ◽  
Single Cells ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Growth Potential ◽  
Maximal Growth ◽  
Culture Collections ◽  
Maximal Growth Rate

Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity; extensions allow estimates from 16S rRNA sequences alone as well as weighted community estimates from metagenomes. We compared the growth rates of cultivated and uncultivated organisms to illustrate how culture collections are strongly biased toward organisms capable of rapid growth. Finally, we found that organisms naturally group into two growth classes and observed a bias in growth predictions for extremely slow-growing organisms. These observations ultimately led us to suggest evolutionary definitions of oligotrophy and copiotrophy based on the selective regime an organism occupies. We found that these growth classes are associated with distinct selective regimes and genomic functional potentials.

Reassessment of Maximum Growth Rates for C3 and C4 Crops

1978 ◽  
Vol 14 (1) ◽  
pp. 1-5 ◽  
Author(s):  
J. L. Monteith
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Growing Season ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Crop Growth ◽  
Close Inspection ◽  
Similar Difference ◽  
Photosynthetic Efficiencies

SUMMARYFigures for maximum crop growth rates, reviewed by Gifford (1974), suggest that the productivity of C3 and C4 species is almost indistinguishable. However, close inspection of these figures at source and correspondence with several authors revealed a number of errors. When all unreliable figures were discarded, the maximum growth rate for C3 stands fell in the range 34–39 g m−2 d−1 compared with 50–54 g m−2 d−1 for C4 stands. Maximum growth rates averaged over the whole growing season showed a similar difference: 13 g m−2 d−1 for C3 and 22 g m−2 d−1 for C4. These figures correspond to photosynthetic efficiencies of approximately 1·4 and 2·0%.

Kinetics And Morphology Of Homoepitaxial Cvd Growth On Diamond (100) And (111)

1995 ◽  
Vol 416 ◽  
Author(s):  
R. E. Rawles ◽  
W. G. Morris ◽  
M. P. D’Evelyn
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Chemical Vapor ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Arrhenius Behavior ◽  
Oriented Growth ◽  
Relative Growth Rates ◽  
Cvd Growth ◽  
Hot Filament

ABSTRACTGrowth rates for homoepitaxy of diamond (100) and (111) by hot-filament chemical vapor deposition were measured via in situ Fizeau interferometry and the surface morphologies were subsequently characterized by atomic force microscopy (AFM). (100)-oriented growth from 0.5% CH4 in H2 exhibited pure Arrhenius behavior, with an activation energy of 17±1 kcal/mol, up to a substrate temperature of 1100°C. Addition of oxygen to the feed gas resulted in an increased growth rate below 900°C, a maximum growth rate between 900 and 1000°C, and etching (of diamond) above 1050 - 1100°C. However, the presence of oxygen apparently had less effect on the surface morphology than did the (100)-to-(111) growth rate parameter α, determined directly from the relative growth rates of (100) and (111) substrates mounted side by side. During homoepitaxial growth from 0.5% CH4 in H2 at 875°C of ca. 1-micron-thick films,α = was 2.2 without oxygen and 1.3 for growth with 0.14% O2. The (100) film grown with α = 2.2 was quite smooth, while that with α = 1.3 was covered by numerous hillocks and penetration twins. AFM analysis revealed surprisingly little difference between the (111) films despite the considerable difference in α. Implications of these results for the growth mechanism are discussed.

Growth Rate Responses of Lotic Periphytic Diatoms to Experimental Phosphorus Enrichment: The Influence of Temperature and Light

1988 ◽  
Vol 45 (2) ◽  
pp. 261-270 ◽  
Author(s):  
Max L. Bothwell
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Phosphorus Enrichment ◽  
Enrichment Experiments ◽  
Community Growth ◽  
Specific Growth Rates ◽  
The Relationship ◽  
River Water Temperature

Phosphate enrichment experiments were conducted year-round at the experimental troughs research apparatus (EXTRA) on the South Thompson River in British Columbia to determine the relationship between external concentration of orthophosphate and the growth rates of lotic periphytic diatom communities. Growth rate saturation always occurred at a phosphate concentration of approximately 0.3–0.6 μg P∙L−1. The maximum growth rate (μmax-P) with phosphorus enrichment varied seasonally with temperature. The relative specific growth rates (μ:μmax-P) as a function of external phosphate were constant. Seasonal changes in solar insolation (PAR) had no effect on the autotrophic community growth rates in unamended river water. Temperature exerted the most dominant influence on phosphorus-replete growth rates.

Shoot and leaf growth in Fraxinuspennsylvanica and its relation to crown location and pruning

1994 ◽  
Vol 24 (10) ◽  
pp. 1997-2005 ◽  
Author(s):  
W.R. Remphrey ◽  
C.G. Davidson
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Leaf Growth ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Logistic Growth ◽  
Parameter Estimates ◽  
Regression Equations ◽  
Green Ash ◽  
Growth Duration

Elongation of shoots in various crown locations, and of individual internodes and leaves of the leading shoot, were recorded at 2-day intervals throughout the 1991 growing season in four clones of Fraxinuspennsylvanica var. subintegerrima (Vahl) Fern. (green ash). Other trees were disbudded and pruned to a single leader. Using a logistic growth function, nonlinear regression equations were generated and parameter estimates were used to determine maximum growth rates. Terminal leading shoots had a longer growth duration and a greater maximum growth rate than lateral shoots. The pruning treatment resulted in larger shoots, which grew 2–3 weeks longer and had a higher maximum growth rate. Leaf emergence occurred at regular intervals but the rate of emergence varied among clones. Leaf maximum growth rates were not significantly different among clones. Leaf size declined acropetally whereas internode length increased and then decreased. The longest leaves and internodes had the highest maximum growth rates. The size and maximum growth rates of putative preformed leaves were larger than putative neoformed leaves. As a shoot expanded, growth of one internode tended to cease during the linear phase of growth of its associated leaf and that of the succeeding internode.

Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach

Microbiology ◽  
2004 ◽  
Vol 150 (5) ◽  
pp. 1413-1426 ◽  
Author(s):  
Robert A. Cox
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Mycobacterium Tuberculosis ◽  
Growth Rates ◽  
Specific Growth ◽  
Streptomyces Coelicolor ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
E Coli ◽  
Specific Growth Rates

Further understanding of the physiological states of Mycobacterium tuberculosis and other mycobacteria was sought through comparisons with the genomic properties and macromolecular compositions of Streptomyces coelicolor A3(2), grown at 30 °C, and Escherichia coli B/r, grown at 37 °C. A frame of reference was established based on quantitative relationships observed between specific growth rates (μ) of cells and their macromolecular compositions. The concept of a schematic cell based on transcription/translation coupling, average genes and average proteins was developed to provide an instantaneous view of macromolecular synthesis carried out by cells growing at their maximum rate. It was inferred that the ultra-fast growth of E. coli results from its ability to increase the average number of rRNA (rrn) operons per cell through polyploidy, thereby increasing its capacity for ribosome synthesis. The maximum growth rate of E. coli was deduced to be limited by the rate of uptake and consumption of nutrients providing energy. Three characteristic properties of S. coelicolor A3(2) growing optimally (μ=0·30 h−1) were identified. First, the rate of DNA replication was found to approach the rate reported for E. coli (μ=1·73 h−1); secondly, all rrn operons were calculated to be fully engaged in precursor-rRNA synthesis; thirdly, compared with E. coli, protein synthesis was found to depend on higher concentrations of ribosomes and lower concentrations of aminoacyl-tRNA and EF-Tu. An equation was derived for E. coli B/r relating μ to the number of rrn operons per genome. Values of μ=0·69 h−1 and μ=1·00 h−1 were obtained respectively for cells with one or two rrn operons per genome. Using the author's equation relating the number of rrn operons per genome to maximum growth rate, it is expected that M. tuberculosis with one rrn operon should be capable of growing much faster than it actually does. Therefore, it is suggested that the high number of insertion sequences in this species attenuates growth rate to still lower values.

On the asymptotic behaviour of sample spacings

1981 ◽  
Vol 90 (2) ◽  
pp. 293-303 ◽  
Author(s):  
John Hawkes
Keyword(s):  
Growth Rate ◽  
Asymptotic Behaviour ◽  
Growth Rates ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Unit Interval ◽  
Sample Spacing ◽  
Image Position ◽  
Almost All ◽  
Sample Spacings

SummarySuppose that we are given a random sample of size n chosen according to the uniform distribution on the unit interval. Let Zn(x) = Zn(x, ω) be the length of the unique left-closed and right-open sample spacing that contains x. The purpose of this paper is to examine the almost sure, and exceptional, growth rates of the process {Zn}. The typical maximum growth rate and the growth rate of the maximum can be of quite different orders of magnitude as is shown by the following two results.Theorem 2. With probability one we havefor almost all x.Theorem 3. With probability one we have

scholarly journals Intrinsic thermoacoustic modes and their interplay with acoustic modes in a Rijke burner

2018 ◽  
Vol 10 (4) ◽  
pp. 315-325 ◽  
Author(s):  
N Hosseini ◽  
VN Kornilov ◽  
I Lopez Arteaga ◽  
W Polifke ◽  
OJ Teerling ◽  
...  
Keyword(s):  
Growth Rate ◽  
Time Delay ◽  
Growth Rates ◽  
Acoustic Waves ◽  
Time Delays ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Reflection Coefficients ◽  
Thermoacoustic Instabilities ◽  
Acoustic Modes

The interplays between acoustic and intrinsic modes in a model of a Rijke burner are revealed and their influence on the prediction of thermoacoustic instabilities is demonstrated. To this end, the system is examined for a range of time delays, temperature ratios and reflection coefficients as adjustable parameters. A linear acoustic network model is used and all modes with frequency below the cut-on frequency for non-planar acoustic waves are considered. The results show that when reflection coefficients are reduced, the presence of a pure ITA mode limits the reduction in the growth rate that usually results from a reduction of the reflection coefficients. In certain conditions, the growth rates can even increase by decreasing reflections. As the time delay of the flame and thus the ITA frequency decreases, the acoustic modes couple to and subsequently decouple from the pure ITA modes. These effects cause the maximum growth rate to alternate between the modes. This investigation draws a broad picture of acoustic and intrinsic modes, which is crucial to accurate prediction and interpretation of thermoacoustic instabilities.

scholarly journals Growth rate and haploidization of Aspergillus niger on medium containing p-fluorophenylalanine

1968 ◽  
Vol 12 (3) ◽  
pp. 305-315 ◽  
Author(s):  
Pol Lhoas
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Growth Curves ◽  
Dry Weight ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Complete Medium ◽  
Acid Analogue ◽  
Mean Size ◽  
The Mean

1. The comparison of the dry weight of thin layer haploid and diploid colonies of A. niger on complete medium and complete medium supplemented with p-fluoro-phenylalanine led to the conclusion that there is a difference in growth rates of hyphae under these different conditions.2. The growth curves of the same strains on both media were established. On complete medium, haploids and diploid show a growth rate increasing linearly for about 20 h after germination and reaching a maximum which is then maintained. On p-fluorophenylalanine, the haploids show a similar curve, although the maximum growth rate reached and maintained is about half that on complete medium; for the diploid, however, the maximum is less than the corresponding one in the haploid and, once this maximum has been reached, the growth rate goes down linearly to a very low value which is then maintained.3. The cytological study of the hyphal tip cell showed, in the presence of the amino acid analogue, a reduction of the mean size of the diploid nuclei together with an increase of the number of nuclear fragments. This explains the growth rates observed and is accepted as a confirmation that p-fluorophenylalanine, by its action on the mitosis, favours chromosome losses which lead finally to the production of haploid nuclei.

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