# Sustainable Agriculture

## Sustainable Agriculture

**sustainable agriculture**, a system of [farming](https://www.britannica.com/topic/agriculture) that strives to provide the resources necessary for present human populations while conserving the planet’s ability to sustain future generations.

### Remarks

- One of the main goal of modern farming
- Essential for addressing the world's most pressing challenges:
  - climate change & environmental degradation [@singh2024], [@filho2023]
  - food security [@hunter2017]
- UN Sustainable Development Goals 2 and 13: Zero Hunger; Climate Action

## Plant Diseases

Plant diseases refer to a series of abnormal physiological processes caused by the infection of plants by various pathogens, such as fungi, bacteria, and viruses, resulting in the retardation of plant growth and development, a decrease in yield and quality, and even death in severe cases

### Remarks

- Pose a serious threat to agricultural production and food security:
  - Annual loss of crop yield due to plant diseases is estimated to be more than 30% globally [@savaryGlobalBurdenPathogens2019]
  - Reduce the quality and value of agricultural products [@vurroEmergingInfectiousDiseases2010]
  - Can produce toxin in some cases [@wuMeasuringEconomicImpacts2007]

## Chemical (Synthetic) Pesticides

- [@chaudhary2024]:

  - negative effects on soil biodiversity

  - constant use has led to irremediable damages to nature.

- discouraged & disallowed by the EU [@2009]

## Biological Control Agents (BCAs)
- Bacteria, fungi, and viruses that exhibit mechanisms to protect plant
- Merits [@glare2019]:
	- Decomposability: no compromise on groundwater, soil, and air qualities
	- Less likely to persist in agricultural goods, further prioritizing their use in agriculture

### Remarks
- Emerged as a solution to reduce dependence on pesticides [@villavicencio-vasquez2025]
- Usually seen as the most effective method for managing diseases in the ways that is environment-friendly, cost-effective, and less toxic, promoting sustainable agriculture [@lahlali2022]

# Pseudomonas Spp. 
## Pseudomonas spp.

Pseudomonads are Gram-negative, rod-shaped, non-endosporeforming plant-associated bacteria and belong to the Proteobacteria group.

### Remarks

- Gathered attention due to several attributes: [@yangGreenGuardiansBiocontrol2025]
  - thrive in diverse environmental conditions, adaptable to various agricultural settings
  - production of an array of bioactive antimicrobial metabolites (AMs)
    - exhibit potent antifungal and antibacterial properties but also enhance plant resilience against pathogens.
    - stimulate plant growth by promoting root development and nutrient uptake.

## Current Landscape
[@yangGreenGuardiansBiocontrol2025]
- Identity of key biocontrol metabolites
  - & Their biosynthetic gene clusters
- Some regulatory elements

## Knowledge Gap

- In regulatory network
  - Post-transcriptional & Translational [@heeb2004]
  - Environmental [@buch2023]
- Lab-rhizosphere inconsistency [@alattas2024]
- Field-based validation
- Finding/Identifying new AMs

# Proposal
## Aim

<!-- > **While the genetic capacity of biocontrol Pseudomonas spp. for metabolite production is increasingly well-characterized through genomics, the dynamic regulatory logic governing when, where, and how these metabolites are produced in ecologically relevant contexts (rhizosphere colonization, pathogen encounter, host immune signaling) remains poorly understood. Integrated multi-omics approaches — combining transcriptomics, proteomics, and metabolomics in time-resolved and spatially resolved experimental designs — are needed to bridge the gap between the known biosynthetic potential encoded in Pseudomonas genomes and the actual regulatory programs that determine biocontrol efficacy under field conditions.**  -->
- Schadt et al., “An Integrated Metagenomic, Metabolomic and Transcriptomic Survey of Populus across Genotypes and Environments.”

- [@schadtIntegratedMetagenomicMetabolomic2024] combined metagenomics (318 metagenomes), plant transcriptomics (98 transcriptomes), metabolomics (314 profiles), and soil chemistry/activity measurements across 27 tree genotypes grown in two different field environments.
	- > "molecular-level events to system-level properties and their environmental influences."

## Data Collection
- Established:
  - Genomics
    - [dedicated site](https://pseudomonas.com/)
  - Transcriptomics
  - Proteomic
- Problematic:
  - Metabolomics 
  - Environmental data 

### Metabolomics & Environmental Data 
- Pseudomonas Aeruginosa is the only species with dedicated database (PAMD)
- Data for others are scattered across literature 
- Available through National Microbiome Data Collective

## Data Harmonization/Normalization

<!-- From fields as varied as socio-economics to ecology7 and the ‘Internet of Things’, data scientists report the lack of big data itself is a major bottleneck in using big data tools. Increasingly, data scientists must first sort through heterogeneous, incongruent, and fragmented datasets before any analyses can be conducted” (Cheng et al., “A General Primer for Data Harmonization.”) -->

### Cross-study

[@villalba2023]

### Multi-omics correction

[@choi2026]

## Integration

Schadt et al., “An Integrated Metagenomic, Metabolomic and Transcriptomic Survey of Populus across Genotypes and Environments.” Li et al., “Profiling Soil–Plant–Microbial Communities.”

# Summary
## Summary

# Extra

## How did we get here?