Exploration of soil operative resistance factors: modulators of plant ecophysiological responses DOI
Sankalp Misra

DELETED, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 18, 2024

The increasing intensity of environmental stresses presents significant challenges to modern agriculture. assorted group all stress-related genes and mechanisms carried out by various soil-inhabiting microorganisms could readily contribute resistance in crop plants represented as soil factors (SRFs). It is essential have a profound knowledge the SRFs their interaction with current basic develop appropriate strategies that effectively improve plant growth. Modern microbiological research dedicated understanding relationship between organization gene function involved processes. A fraction scientific community primarily engaged developing culture-independent techniques substantial (99%) portion still not cultivable laboratory conditions. However, exploitation are commencement. metagenomic method has proven be strong methodological tool for microbiome SRF analysis. obtaining detail any particular can completely characterize intricacy metagenomes interpret meaningful conclusions about native microbial communities challenging. This review provides an overview methods employed gain insights into specific microbiomes confer abiotic biotic on crops.

Language: Английский

Semisynthetic simulation for microbiome data analysis DOI Creative Commons
Kris Sankaran, Saritha Kodikara, Jingyi Jessica Li

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 26(1)

Published: Nov. 22, 2024

Abstract High-throughput sequencing data lie at the heart of modern microbiome research. Effective analysis these requires careful preprocessing, modeling, and interpretation to detect subtle signals avoid spurious associations. In this review, we discuss how simulation can serve as a sandbox test candidate approaches, creating setting that mimics real while providing ground truth. This is particularly valuable for power analysis, methods benchmarking, reliability analysis. We explain probability, multivariate regression concepts behind simulators different implementations make trade-offs between generality, faithfulness, controllability. Recognizing all only approximate reality, review evaluate accurately they reflect key properties. also present case studies demonstrating value in differential abundance testing, dimensionality reduction, network integration. Code examples available an online tutorial (https://go.wisc.edu/8994yz) be easily adapted new problem settings.

Language: Английский

Citations

0
Exploration of soil operative resistance factors: modulators of plant ecophysiological responses DOI
Sankalp Misra

DELETED, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 18, 2024

The increasing intensity of environmental stresses presents significant challenges to modern agriculture. assorted group all stress-related genes and mechanisms carried out by various soil-inhabiting microorganisms could readily contribute resistance in crop plants represented as soil factors (SRFs). It is essential have a profound knowledge the SRFs their interaction with current basic develop appropriate strategies that effectively improve plant growth. Modern microbiological research dedicated understanding relationship between organization gene function involved processes. A fraction scientific community primarily engaged developing culture-independent techniques substantial (99%) portion still not cultivable laboratory conditions. However, exploitation are commencement. metagenomic method has proven be strong methodological tool for microbiome SRF analysis. obtaining detail any particular can completely characterize intricacy metagenomes interpret meaningful conclusions about native microbial communities challenging. This review provides an overview methods employed gain insights into specific microbiomes confer abiotic biotic on crops.

Language: Английский

Citations

0