scholarly journals Metagenomic growth rate inferences of strains in situ

2020 ◽  
Vol 6 (17) ◽  
pp. eaaz2299
Author(s):  
Akintunde Emiola ◽  
Wei Zhou ◽  
Julia Oh
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
De Novo ◽  
Microbial Interactions ◽  
Strain Level ◽  
Disease Associations ◽  
Specific Growth Rates ◽  
Reference Strains

We developed a method for strain-level metagenomic estimation of growth rate (SMEG) for inferring growth rates of bacterial subspecies, or strains, from complex metagenomic samples. We applied our method, which is based on both reference strains and de novo approaches, to different gut metagenomic datasets, accurately identifying an outbreak-associated Escherichia coli strain and a previously unidentified association of an Akkermansia muciniphila strain in cancer immunotherapy responders. SMEG resolves strain-specific growth rates from mixtures of commensal or pathogenic strains to provide new insights into microbial interactions and disease associations at the strain level. SMEG is available for download at https://github.com/ohlab/SMEG.

scholarly journals Scaling of growth rate and mortality with size and its consequence on size spectra of natural microphytoplankton assemblages in the East China Sea

2013 ◽  
Vol 10 (8) ◽  
pp. 5267-5280 ◽  
Author(s):  
F. H. Chang ◽  
E. C. Marquis ◽  
C. W. Chang ◽  
G. C. Gong ◽  
C. H. Hsieh
Keyword(s):  
Growth Rate ◽  
Body Size ◽  
Growth Rates ◽  
Specific Growth ◽  
Size Structure ◽  
Scaling Exponent ◽  
The East China Sea ◽  
Size Category ◽  
Grazing Mortality ◽  
Specific Growth Rates

Abstract. Allometric scaling of body size versus growth rate and mortality has been suggested to be a universal macroecological pattern, as described by the metabolic theory of ecology (MTE). However, whether such scaling generally holds in natural assemblages remains debated. Here, we test the hypothesis that the size-specific growth rate and grazing mortality scale with the body size with an exponent of −1/4 after temperature correction, as MTE predicts. To do so, we couple a dilution experiment with the FlowCAM imaging system to obtain size-specific growth rates and grazing mortality of natural microphytoplankton assemblages in the East China Sea. This novel approach allows us to achieve highly resolved size-specific measurements that would be very difficult to obtain in traditional size-fractionated measurements using filters. Our results do not support the MTE prediction. On average, the size-specific growth rates and grazing mortality scale almost isometrically with body size (with scaling exponent ∼0.1). However, this finding contains high uncertainty, as the size-scaling exponent varies substantially among assemblages. The fact that size-scaling exponent varies among assemblages prompts us to further investigate how the variation of size-specific growth rate and grazing mortality can interact to determine the microphytoplankton size structure, described by normalized biomass size spectrum (NBSS), among assemblages. We test whether the variation of microphytoplankton NBSS slopes is determined by (1) differential grazing mortality of small versus large individuals, (2) differential growth rate of small versus large individuals, or (3) combinations of these scenarios. Our results indicate that the ratio of the grazing mortality of the large size category to that of the small size category best explains the variation of NBSS slopes across environments, suggesting that higher grazing mortality of large microphytoplankton may release the small phytoplankton from grazing, which in turn leads to a steeper NBSS slope. This study contributes to understanding the relative importance of bottom-up versus top-down control in shaping microphytoplankton size structure.

scholarly journals Effect of Specific Growth Rate on Fermentative Capacity of Baker’s Yeast

1998 ◽  
Vol 64 (11) ◽  
pp. 4226-4233 ◽  
Author(s):  
Pim Van Hoek ◽  
Johannes P. Van Dijken ◽  
Jack T. Pronk
Keyword(s):  
Growth Rate ◽  
Specific Growth Rate ◽  
Ethanol Production ◽  
Growth Rates ◽  
Specific Growth ◽  
Pyruvate Decarboxylase ◽  
Baker's Yeast ◽  
Fermentative Capacity ◽  
Yeast Biomass ◽  
Specific Growth Rates

ABSTRACT The specific growth rate is a key control parameter in the industrial production of baker’s yeast. Nevertheless, quantitative data describing its effect on fermentative capacity are not available from the literature. In this study, the effect of the specific growth rate on the physiology and fermentative capacity of an industrialSaccharomyces cerevisiae strain in aerobic, glucose-limited chemostat cultures was investigated. At specific growth rates (dilution rates, D) below 0.28 h−1, glucose metabolism was fully respiratory. Above this dilution rate, respirofermentative metabolism set in, with ethanol production rates of up to 14 mmol of ethanol · g of biomass−1 · h−1at D = 0.40 h−1. A substantial fermentative capacity (assayed offline as ethanol production rate under anaerobic conditions) was found in cultures in which no ethanol was detectable (D < 0.28 h−1). This fermentative capacity increased with increasing dilution rates, from 10.0 mmol of ethanol · g of dry yeast biomass−1 · h−1 at D= 0.025 h−1 to 20.5 mmol of ethanol · g of dry yeast biomass−1 · h−1 atD = 0.28 h−1. At even higher dilution rates, the fermentative capacity showed only a small further increase, up to 22.0 mmol of ethanol · g of dry yeast biomass−1 · h−1 at D= 0.40 h−1. The activities of all glycolytic enzymes, pyruvate decarboxylase, and alcohol dehydrogenase were determined in cell extracts. Only the in vitro activities of pyruvate decarboxylase and phosphofructokinase showed a clear positive correlation with fermentative capacity. These enzymes are interesting targets for overexpression in attempts to improve the fermentative capacity of aerobic cultures grown at low specific growth rates.

The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei

Microbiology ◽  
2005 ◽  
Vol 151 (1) ◽  
pp. 135-143 ◽  
Author(s):  
Tiina M. Pakula ◽  
Katri Salonen ◽  
Jaana Uusitalo ◽  
Merja Penttilä
Keyword(s):  
Growth Rate ◽  
Protein Synthesis ◽  
Specific Growth Rate ◽  
Trichoderma Reesei ◽  
Growth Rates ◽  
Protein Production ◽  
Specific Growth ◽  
Synthesis Rate ◽  
Specific Rate ◽  
Specific Growth Rates

Trichoderma reesei was cultivated in chemostat cultures on lactose-containing medium. The cultures were characterized for growth, consumption of the carbon source and protein production. Secreted proteins were produced most efficiently at low specific growth rates, 0·022–0·033 h−1, the highest specific rate of total protein production being 4·1 mg g−1 h−1 at the specific growth rate 0·031 h−1. At low specific growth rates, up to 29 % of the proteins produced were extracellular, in comparison to only 6–8 % at high specific growth rates, 0·045–0·066 h−1. To analyse protein synthesis and secretion in more detail, metabolic labelling of proteins was applied to analyse production of the major secreted protein, cellobiohydrolase I (CBHI, Cel7A). Intracellular and extracellular labelled CBHI was quantified and analysed for pI isoforms in two-dimensional gels, and the synthesis and secretion rates of the molecule were determined. Both the specific rates of CBHI synthesis and secretion were highest at low specific growth rates, the optimum being at 0·031 h−1. However, at low specific growth rates the secretion rate/synthesis rate ratio was significantly lower than that at high specific growth rates, indicating that at low growth rates the capacity of cells to transport the protein becomes limiting. In accordance with the high level of protein production and limitation in the secretory capacity, the transcript levels of the unfolded protein response (UPR) target genes pdi1 and bip1 as well as the gene encoding the UPR transcription factor hac1 were induced.

Morphogenetic expression of Arthrobacter globiformis 425 in continuous culture with carbon or biotin limitation

1978 ◽  
Vol 24 (1) ◽  
pp. 28-30 ◽  
Author(s):  
Adrian P. Wills ◽  
E. C. S. Chan
Keyword(s):  
Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
Normal Growth ◽  
Arthrobacter Globiformis ◽  
Glucose Limitation ◽  
Abnormal Morphology ◽  
Chemostat Cultures ◽  
Specific Growth Rates ◽  
Biotin Limitation

When deprived of biotin, Arthrobacter globiformis 425 exhibits abnormal morphology (large, branched forms of variable size) and a retardation of its normal growth rate. In chemostat cultures, when cells were grown under glucose limitation, the morphology was normal (coccoids or rods) at specific growth rates between 0.05 and 0.125 h−1 (doubling times between 14 and 5.5 h, respectively) at 25 °C. The coccoid-to-rod morphogenesis occurs at a specific growth rate of 0.11 h−1. At the same specific growth rates and temperature, but under biotin limitation, abnormal morphology was observed.

Partitioning of CO2 Incorporation Among Planktonic Microbial Guilds and Estimation of In Situ Specific Growth Rates

2005 ◽  
Vol 50 (2) ◽  
pp. 230-241 ◽  
Author(s):  
Josefina García-Cantizano ◽  
Emilio O. Casamayor ◽  
Josep M. Gasol ◽  
Ricardo Guerrero ◽  
Carlos Pedrós-Alió
Keyword(s):  
Growth Rates ◽  
Specific Growth ◽  
Specific Growth Rates

scholarly journals Picoplankton Diel Variability and Estimated Growth Rates in Epipelagic and Mesopelagic Waters of the Central Red Sea

2021 ◽  
Vol 8 ◽  
Author(s):  
Najwa Al-Otaibi ◽  
Francisca C. García ◽  
Xosé Anxelu G. Morán
Keyword(s):  
Cell Size ◽  
Red Sea ◽  
Growth Rates ◽  
Specific Growth ◽  
Nucleic Acid Content ◽  
Autotrophic Picoplankton ◽  
Heterotrophic Prokaryotes ◽  
Diel Variability ◽  
Specific Growth Rates

The diel variability of the abundance and cell size of picoplanktonic groups in the central Red Sea was monitored every 2 h in situ on 4 occasions (once per season) from 2015 to 2016. We distinguished Prochlorococcus, low (LF-Syn) and high (HF-Syn) fluorescence Synechococcus, small (Speuk) and large (Lpeuk) picoeukaryotes and two groups of heterotrophic prokaryotes of low (LNA) and high (HNA) nucleic acid content. The diel variability in abundance was less marked than in cell size and more apparent in autotrophs than heterotrophs. Specific growth rates were estimated by an empirical relationship from measurements obtained in bottle incubations of surface and deep samples collected in the winter compared with in situ variations in cell size over 24 h. Autotrophic picoplankton groups generally grew faster (0.23–0.77 d–1) than heterotrophic prokaryotes (0.12–0.50 d–1). Surface to 100 m depth-weighted specific growth rates displayed a clear seasonal pattern for Prochlorococcus, with maxima in winter (0.77 ± 0.07 d–1) and minima in fall (0.52 ± 0.07 d–1). The two groups of Synechococcus peaked in spring, with slightly higher growth rates of LF-Syn (0.57 ± 0.04 d–1) than HF-Syn (0.43 ± 0.04 d–1). Speuk and Lpeuk showed different seasonal patterns, with lower values of the former (0.27 ± 0.02 and 0.37 ± 0.04 d–1, respectively). HNA consistently outgrew LNA heterotrophic prokaryotes, with a higher growth in the epipelagic (0–200 m, 0.36 ± 0.03 d–1) than in the mesopelagic (200–700 m, 0.26 ± 0.03 d–1), while no differences were found for LNA cells (0.19 ± 0.03 d–1 and 0.17 ± 0.02 d–1, respectively). With all data pooled, the mean diel abundances of autotrophic picoplankton in the upper epipelagic and of HNA cells in the epipelagic and mesopelagic layers were significantly correlated with the specific growth rates estimated from cell size variations. Our high-resolution sampling dataset suggests that changes in growth rates underlie the noticeable seasonality of picoplankton recently described in these tropical waters.

Examining the influence of substrates and temperature on maximum specific growth rate of denitrifiers

2006 ◽  
Vol 54 (8) ◽  
pp. 155-162 ◽  
Author(s):  
Y. Mokhayeri ◽  
A. Nichols ◽  
S. Murthy ◽  
R. Riffat ◽  
P. Dold ◽  
...  
Keyword(s):  
Growth Rate ◽  
Specific Growth Rate ◽  
Growth Rates ◽  
Specific Growth ◽  
Treatment Plant ◽  
Capacity Utilization ◽  
Maximum Specific Growth Rate ◽  
Corn Syrup ◽  
Plant Uses ◽  
Specific Growth Rates

Facilities across North America are designing plants to meet stringent limits of technology (LOT) treatment for nitrogen removal (3–5 mg/L total effluent nitrogen). The anoxic capacity requirements for meeting LOT treatment are dependent on the growth rates of the denitrifying organisms. The Blue Plains Advanced Wastewater Treatment Plant (AWTP) is one of many facilities in the Chesapeake Bay region that is evaluating its ability to meet LOT treatment capability. The plant uses methanol as an external carbon source in a post-denitrification process. The process is very sensitive to denitrification in the winter. One approach to improve anoxic capacity utilization is to use an alternative substrate for denitrification in the winter to promote the growth of organisms that denitrify at higher rates. The aim of this study was to evaluate denitrification maximum specific growth rates for three substrates, acetate, corn syrup and methanol, at two temperatures (13 °C and 19 °C). These temperatures approximately reflect the minimum monthly and average annual wastewater temperature at the Blue Plains AWTP. The results suggest that the maximum specific growth rate (μmax) for corn syrup (1.3 d−1) and acetate (1.2 d−1) are higher than that for methanol (0.5 d−1) at low temperature of 13 °C. A similar trend was observed at 19 °C.

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