GroEL-proteotyping of bacterial communities by tandem mass spectrometry DOI Creative Commons
Simon Klaes, Shobhit Madan, Darja Deobald

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 3, 2023

Abstract Profiling bacterial populations in mixed communities is a common task microbiology. 16 S rRNA-based sequencing widely accepted and functional approach but relies on amplification primers cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping an effective alternative for taxonomically profiling microorganisms. We suggest that targeted approaches can complement traditional population analyses. Therefore, we describe to assess community compositions at the family level using taxonomic marker protein GroEL, which ubiquitously found bacteria, except few obligate intracellular species. refer our method as GroEL-proteotyping. GroEL-proteotyping based high-resolution tandem of GroEL peptides identification GroEL-derived taxa via Galaxy workflow subsequent Python-based analysis script. Its advantage it be performed with curated extendable sample-independent database pre-separated by SDS-PAGE reduce sample complexity, improving while simultaneously decreasing instrument time. was validated employing comprehensive raw data set obtained through metaproteome from synthetic microbial well real human gut samples. Our show enables fast straightforward highly abundant reasonable resolution.

Language: Английский

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems DOI Creative Commons
Bouchra Benmrid, Cherki Ghoulam,

Youssef Zeroual

et al.

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Oct. 6, 2023

Abstract Ensuring plant resilience to drought and phosphorus (P) stresses is crucial support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth stress tolerance. Intercropping systems also offer through facilitative interactions, improving in water- P-deficient soils. Application of microbial consortia can boost the intercropping, although questions remain about establishment, persistence, legacy effects within resident soil microbiomes. Understanding microbe- plant-microbe dynamics drought-prone soils key. This review highlights beneficial rhizobacterial consortia-based inoculants legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development P-solubilizing drought-adapted consortia, identifies research gaps crop-microbe interactions.

Language: Английский

Citations

24
Phytoremediation: Harnessing plant power and innovative technologies for effective soil remediation DOI Creative Commons
Malika Oubohssaine,

Ikram Dahmani

Plant Stress, Journal Year: 2024, Volume and Issue: 14, P. 100578 - 100578

Published: Aug. 27, 2024

Language: Английский

Citations

7
Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production DOI Creative Commons
Anna M. Timofeeva,

Maria R. Galyamova,

Sergey E. Sedykh

et al.

Microorganisms, Journal Year: 2023, Volume and Issue: 11(12), P. 2864 - 2864

Published: Nov. 26, 2023

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia believed to be the most promising form of these bacteria. However, designing and modeling bacterial achieve desired phenotypic outcomes plants is challenging. This review aims address this challenge by exploring key antimicrobial interactions. Special attention given approaches developing soil plant consortia. Additionally, advanced omics-based methods analyzed that allow microbiomes characterized, providing an understanding molecular functional aspects microbial communities. A comprehensive discussion explores utilization preparations biofertilizers agricultural applications, focusing on intricate design synthetic with preparations. Overall, provides valuable insights strategies intentionally enhance growth development.

Language: Английский

Citations

16
Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods DOI
Blake J. Rasor,

Payal Chirania,

Grant A. Rybnicky

et al.

ACS Synthetic Biology, Journal Year: 2023, Volume and Issue: 12(2), P. 405 - 418

Published: Jan. 26, 2023

Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these is optimization extract preparation methods. However, applied nature optimizations often limits investigation complex themselves, which contain thousands proteins reaction networks hundreds metabolites. Here, we sought uncover black box metabolites Escherichia coli cell-free reactions based on different We assess changes transcription translation activity σ70 promoters prepared acetate or glutamate buffer common post-lysis processing steps a runoff incubation dialysis. then utilize proteomic metabolomic analyses potential mechanisms behind highlighting impact cold shock-like role composition.

Language: Английский

Citations

13
Characterization and environmental applications of soil biofilms: a review DOI
Guoliang Wang, Li Tian, Qixing Zhou

et al.

Environmental Chemistry Letters, Journal Year: 2024, Volume and Issue: 22(4), P. 1989 - 2011

Published: April 8, 2024

Language: Английский

Citations

4
Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology DOI Creative Commons
Muneer Ahmad Malla, Faiz Ahmad Ansari, Faizal Bux

et al.

Environmental Research, Journal Year: 2024, Volume and Issue: 259, P. 119439 - 119439

Published: June 18, 2024

Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly entail huge energy carbon consumption greenhouse gas emissions. Owing to their unique ability capturing resource recovery, microalgae-microbiome based a potential approach widely used for carbon-neutral treatment. Microalgae-bacteria synergy (i.e., functionally beneficial microbial synthetic communities) performs better enhances carbon-sequestration nutrient recovery from plants. This review presents comprehensive information regarding as sustainable agent discusses synergistic approaches effective removal. Moreover, this discusses, role omics-biology Insilco in unravelling understanding algae-microbe synergism response toward Finally, it various microbiome engineering developing microalgae-bacteria partners sequestration wastewater, summarizes future research perspectives on bioremediation.

Language: Английский

Citations

4
Hot viewpoint on how soil texture, soil nutrient availability, and root exudates interact to shape microbial dynamics and plant health DOI

A. A. Adeniji,

Jingxuan Huang,

Shidong Li

et al.

Plant and Soil, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 28, 2024

Language: Английский

Citations

4
Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition DOI Creative Commons
Jia Wang, Manasa R. Appidi,

Leah H. Burdick

et al.

mSystems, Journal Year: 2024, Volume and Issue: 9(4)

Published: March 12, 2024

Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated formation bacterial under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized in nutrient-rich environments, without metabolic interdependency growth, still not fully disclosed. In this study, three strains isolated from

Language: Английский

Citations

3
Critical steps in an environmental metaproteomics workflow DOI Creative Commons
Daniel J. Nebauer, Leanne A. Pearson, Brett A. Neilan

et al.

Environmental Microbiology, Journal Year: 2024, Volume and Issue: 26(5)

Published: May 1, 2024

Abstract Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As still maturing, it lacks consistent workflows, making challenging for non‐expert researchers to navigate. This review aims introduce workflow environmental metaproteomics. It outlines standard practices sample collection, processing, analysis, offers strategies overcome unique challenges presented by common matrices such as soil, freshwater, marine environments, biofilms, sludge, symbionts. The also highlights bottlenecks in data analysis are specific samples suggestions obtain high‐quality datasets. includes recent benchmarking studies descriptions software packages specifically built analysis. article written without assuming reader's familiarity with single‐organism proteomic accessible those new proteomics or mass spectrometry general. primer improve accessibility this exciting technology empower tackle ambitious research questions. While primarily resource field, should be useful established looking streamline troubleshoot their experiments.

Language: Английский

Citations

3
Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants DOI

Neemisha,

Arun Kumar, Poonam Sharma

et al.

Journal of Applied Microbiology, Journal Year: 2022, Volume and Issue: 133(5), P. 2694 - 2716

Published: June 3, 2022

Plant rhizo-microbiome comprises complex microbial communities that colonize at the interphase of plant roots and soil. growth-promoting rhizobacteria (PGPR) in rhizosphere provide important ecosystem services ranging from release essential nutrients for enhancing soil quality improving health to imparting protection plants against rising biotic abiotic stresses. Hence, PGPR serve as restoring agents rejuvenate mediate fitness facet changing climate. Though it is evident nutrient availability managed through inter-linked mechanisms, how expedite these processes remain less recognized. Promising results inoculation on growth are continually reported controlled environmental conditions, however, their field application often fails due competition with native microbiota low colonization efficiency roots. The development highly efficient smart bacterial synthetic by integrating ecological genetic features provides better opportunities successful inoculant formulations. This review an overview interplay between disease suppression governed followed role developing inoculants. Moreover, outlook beneficial activities modifying characteristics sustainably boost agroecosystem functioning also provided.

Language: Английский

Citations

11