scholarly journals Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors

2021 ◽  
Author(s):  
Harsh Maan ◽  
Jonathan Friedman ◽  
Ilana Kolodkin-Gal
Keyword(s):  
Growth Inhibition ◽  
Microbial Communities ◽  
Rapid Growth ◽  
Antibiotic Production ◽  
Fitness Cost ◽  
Systematic Evaluation ◽  
Defence Mechanisms ◽  
Ecological Concept ◽  
Common Strategy ◽  
Non Ribosomal Peptides

AbstractMicrobial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of all non-ribosomal peptides (NRP) produced by B. subtilis clade, we revealed that they acted either synergistically or additively to effectively eliminate phylogenetically distinct competitors. All four major NRP biosynthetic clusters were also imperative for the survival of B. subtilis in a complex community extracted from the rhizosphere. The production of NRP came with a fitness cost manifested in growth inhibition, rendering NRP synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, NRP production was only induced by the presence of peptidoglycan cue from a sensitive competitor. These results experimentally demonstrate a general ecological concept – closely related communities (“self”) are favoured during competition, due to compatibility in attack and defence mechanisms.

scholarly journals Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

2020 ◽  
Author(s):  
Dileep Kishore ◽  
Gabriel Birzu ◽  
Zhenjun Hu ◽  
Charles DeLisi ◽  
Kirill S. Korolev ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Systematic Evaluation ◽  
Sequencing Data ◽  
Systematic Analysis ◽  
16S Sequencing ◽  
Multiple Data Sets ◽  
And Function ◽  
And Control ◽  
Multiple Samples

AbstractMicrobes tend to organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, have the potential to reveal which microbes co-occur, providing a glimpse into the network of associations in these communities. The inference of networks from 16S data is prone to statistical artifacts. There are many tools for performing each step of the 16S analysis workflow, but the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and estimate steps that contribute most significantly to the variance. We further determine the tools and parameters that generate the most accurate and robust co-occurrence networks based on comparison with mock and synthetic datasets. Ultimately, we develop a standardized pipeline (available at https://github.com/segrelab/MiCoNE) that follows these default tools and parameters, but that can also help explore the outcome of any other combination of choices. We envisage that this pipeline could be used for integrating multiple data-sets, and for generating comparative analyses and consensus networks that can help understand and control microbial community assembly in different biomes.ImportanceTo understand and control the mechanisms that determine the structure and function of microbial communities, it is important to map the interrelationships between its constituent microbial species. The surge in the high-throughput sequencing of microbial communities has led to the creation of thousands of datasets containing information about microbial abundances. These abundances can be transformed into networks of co-occurrences across multiple samples, providing a glimpse into the structure of microbiomes. However, processing these datasets to obtain co-occurrence information relies on several complex steps, each of which involves multiple choices of tools and corresponding parameters. These multiple options pose questions about the accuracy and uniqueness of the inferred networks. In this study, we address this workflow and provide a systematic analysis of how these choices of tools and parameters affect the final network, and on how to select those that are most appropriate for a particular dataset.

scholarly journals Growth inhibition of Fusarium solani and F. oxysporum by Streptomyces sasae TG01, and its ability to solubilize insoluble phosphate

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
I Made Sudiana ◽  
ADELIA PUTRI ◽  
TOGA PANGIHOTAN NAPITUPULU ◽  
IDRIS ◽  
ISMU PURNANINGSIH ◽  
...  
Keyword(s):  
Growth Inhibition ◽  
Fusarium Solani ◽  
Antibiotic Production ◽  
Carbon Sources ◽  
Phytopathogenic Fungi ◽  
Major Constituent ◽  
Rrna Gene ◽  
Soluble Phosphate ◽  
Insoluble Phosphate ◽  
The 16S Rrna Gene

Abstract. Sudiana A, Putri A, Napitupulu TP, Purnaningsih I, Idris, Kanti A. 2020. Growth inhibition of Fusarium solani and F. oxysporum by Streptomyces sasae TG01, and its ability to solubilize insoluble phosphate. Biodiversitas 21: 429-435. Actinomycetes have been widely explored for new antibiotic production, but not many studies explore its abilities to inhibit the growth of phytopathogenic fungi and solubilize insoluble phosphate hence stimulate the growth of plants. We isolated Actinomycetes from the soil. Based on morphology, physiology, and 16S rDNA analyses, the isolate is closely related to Streptomyces sasae. The strain was able to inhibit the growth of phytopathogenic fungi Fusarium solani, and Fusarium oxysporum. S. sasae produced secondary metabolites 2-methyl-1,3-dioxolane as the major constituent. The strain assimilated variable carbon sources include L-arabinose, D-fructose, D-glucose, D-mannitol, Lactose, raffinose, L-rhamnose, and sucrose. The strain grew at pH 6.0 to 8.0, and at salinity (1-3%). Their growth was affected by the salinity level. The strain solubilized Ca-P at 1-3% salinity, but their ability to solubilize phosphate was influenced by salinity. The strain was also able to solubilize rock phosphate. Their ability to solubilize less soluble phosphate and inhibit the growth of F. solani and F. oxysporum may imply that this strain is potential for biocontrol agents. The 16S rRNA gene was submitted to DDBJ with the entry number 5df623c1a3c8820021322a36.TG01, and the accession number is LC514451.

scholarly journals Effects of Bacterial Antibiotic Production on Rhizosphere Microbial Communities from a Culture-Independent Perspective

1998 ◽  
Vol 64 (12) ◽  
pp. 5020-5022 ◽  
Author(s):  
Eduardo A. Robleto ◽  
James Borneman ◽  
Eric W. Triplett
Keyword(s):  
Phaseolus Vulgaris ◽  
Microbial Communities ◽  
Antibiotic Production ◽  
Intergenic Spacer ◽  
Rhizobium Etli ◽  
Apparent Effect ◽  
Ribosomal Intergenic Spacer ◽  
Culture Independent

ABSTRACT The effects of antibiotic production on rhizosphere microbial communities of field-grown Phaseolus vulgaris were assessed by using ribosomal intergenic spacer analysis. Inoculum strains ofRhizobium etli CE3 differing only in trifolitoxin production were used. Trifolitoxin production dramatically reduced the diversity of trifolitoxin-sensitive members of the α subdivision of the class Proteobacteria with little apparent effect on most microbes.

scholarly journals Improving CoQ10 productivity by strengthening glucose transmembrane of Rhodobacter sphaeroides

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuying Yang ◽  
Lu Li ◽  
Haoyu Sun ◽  
Zhen Li ◽  
Zhengliang Qi ◽  
...  
Keyword(s):  
Glucose Metabolism ◽  
Growth Inhibition ◽  
Rhodobacter Sphaeroides ◽  
Bacterial Growth ◽  
Rapid Growth ◽  
Biomass Yield ◽  
Phosphotransferase System ◽  
Maximum Biomass ◽  
Bacterial Growth Inhibition

Abstract Background Several Rhodobacter sphaeroides have been widely applied in commercial CoQ10 production, but they have poor glucose use. Strategies for enhancing glucose use have been widely exploited in R. sphaeroides. Nevertheless, little research has focused on the role of glucose transmembrane in the improvement of production. Results There are two potential glucose transmembrane pathways in R. sphaeroides ATCC 17023: the fructose specific-phosphotransferase system (PTSFru, fruAB) and non-PTS that relied on glucokinase (glk). fruAB mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase (12–24 h) and promotion since 36 h. Glucose metabolism showed a corresponding change in characteristic vs. the growth. For ΔfruAΔfruB, maximum biomass (Biomax) was increased by 44.39% and the CoQ10 content was 27.08% more than that of the WT. glk mutation caused a significant decrease in growth and glucose metabolism. Over-expressing a galactose:H+ symporter (galP) in the ΔfruAΔfruB relieved the inhibition and enhanced the growth further. Finally, a mutant with rapid growth and high CoQ10 titer was constructed (ΔfruAΔfruB/tac::galPOP) using several glucose metabolism modifications and was verified by fermentation in 1 L fermenters. Conclusions The PTSFru mutation revealed two effects on bacterial growth: inhibition at the early cultivation phase and promotion later. Additionally, biomass yield to glucose (Yb/glc) and CoQ10 synthesis can be promoted using fruAB mutation, and glk plays a key role in glucose metabolism. Strengthening glucose transmembrane via non-PTS improves the productivity of CoQ10 fermentation.

scholarly journals Counteraction of antibiotic production and degradation stabilizes microbial communities

Nature ◽  
2015 ◽  
Vol 521 (7553) ◽  
pp. 516-519 ◽  
Author(s):  
Eric D. Kelsic ◽  
Jeffrey Zhao ◽  
Kalin Vetsigian ◽  
Roy Kishony
Keyword(s):  
Microbial Communities ◽  
Antibiotic Production

scholarly journals Rapid Growth Inhibition of Avena Coleoptile Segments by Abscisic Acid

1973 ◽  
Vol 51 (1) ◽  
pp. 93-96 ◽  
Author(s):  
Marilyn M. Rehm ◽  
Morris G. Cline
Keyword(s):  
Abscisic Acid ◽  
Growth Inhibition ◽  
Rapid Growth ◽  
Avena Coleoptile

Preliminary DoE Analysis and Control of Mapping Procedure for a Turbocharger on an Engine Gas-Stand

2016 ◽  
Author(s):  
Calogero Avola ◽  
Pavlos Dimitriou ◽  
Richard Burke ◽  
Colin Copeland
Keyword(s):  
Diesel Engine ◽  
Mass Flow ◽  
Pressure Ratio ◽  
Direct Consequence ◽  
Systematic Evaluation ◽  
System Modelling ◽  
Mapping Procedure ◽  
Powertrain System ◽  
Common Strategy ◽  
Extensive Test

The use of turbochargers on both gasoline and diesel engines is started to become a common strategy to comply with stringent limits on CO2. The main action towards lowering fuel consumption of powertrains is achieved by reduction of engine size and number of cylinders, annexed to the lower friction. However, this is directly linked to the worsening of deliverable output power under the natural aspirated configuration. Therefore, turbocharging is often adopted to overcome this problem where useful energy contained in the exhaust gasses is used to increase the air density at the intake. The increase in power from a natural aspirated configuration is a direct consequence of higher fuel quantity to be injected. In order to pursue a systematic evaluation of the powertrain system, engine, turbochargers and auxiliary components are included into 1D models. Several conditions can be simulated without the need of an extensive test plan. In 1D software like Ricardo Wave, turbochargers performance are imposed as input. These are previously measured in appropriate turbocharger gas-stand where hot or cold air is blown through the turbine while load on compressor is controlled by adjusting a back pressure valve. Compressor and turbine maps are generated for constant speed lines which are corrected for total temperature. Pressure ratio, mass flow and isentropic efficiency are also monitored as parameters to characterize performance maps of turbomachinery. In gas-stands, steady flow conditions are imposed at compressor and turbine. However, in turbocharged engines, pulsating flows induced by the engine valvetrain disturb continuously turbocharger conditions during the engine cycle. In fact, the effects that the conditions of the engine air-path could have on the turbocharger operations are excluded from the system modelling. In this study, an appropriate engine gas-stand has been developed in order to improve the accuracy on estimating the turbine extraction power in 1D powertrain simulations. In addition, future analyses on turbocharger transient operations could be investigated. The compressor outlet has been disconnected from the 2.2L Diesel engine intake so that the load on turbocharger and engine can be independently controlled. In order to extend the engine capability in delivering mass flow and pressure at the turbine inlet, an external boost rig has been installed with the capability to control pressure, mass flow and temperature at the engine intake. In a first instance, a 1D model of the system including turbomachinery, Diesel engine and boost rig has been developed using the commercial platform Ricardo Wave. In this way, a preliminary DoE study of the entire system has been performed in order to evaluate the effects of parameters and actuators on the turbocharger operations. Additionally, the control of the rig has been tested by confirming the previous DoE study. Approaches to create turbochargers maps are shown. Last section of the paper focuses on turbine pulsations and the interpretation of efficiency calculated in experiments and simulations.

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