Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review
Abstract
:1. Introduction
2. Improving Agricultural Soil Quality without Excessive Chemical Fertiliser Input
3. Disease-Suppressive Soils as Greener Alternatives against Biotic Stress
4. Development of Bioindicator in Environmental Biomonitoring
5. Summary and Future Outlooks
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Applications | Sample | Aims | Findings | Reference |
---|---|---|---|---|
Improving soil fertility | Paddy soil | Provide novel insights into the diversity of the soil community responsible for reductive nitrogen transformation (RNT). |
| [28] |
Agricultural soil vs. organic soil | Elucidate the microbial community structure and function in organic soil vs. agricultural land, which has undergone prolonged usage of chemical fertilisers, pesticides, and herbicides. |
| [29] | |
Subtropical natural grassland soils | Elucidate the soil microbial structure and function in response to short-term seasonal variations (cold vs. warm season). |
| [30] | |
Agriculture soil | Identify dominant species and major transcripts extracted from soil having a long history of chemical fertilisers and pesticide usage. |
| [31] | |
Crop stress management (disease) | Woody stems of grapevines | In planta profiling of putative virulence activities in the grapevine trunk disease (GTD) complex. |
| [32] |
Tomato and lettuce roots | Elucidate potential of microbial functional gene profiles and expression patterns as in vivo sensors of environmental stress affecting host and host-associated communities. |
| [33] | |
Rhizosphere soil | Provide insights into the functional profiles of the rhizosphere microbiome in response to soilborne pathogens (R. solani AG8) and identify the essential genes that play a significant role in disease suppression. |
| [20] | |
Leaves of healthy and infected basil plants | Develop a comprehensive pipeline to study the genes expressed in both the host plant (sweet basil) and its obligate downy mildew parasite (Peronospora belbahrii) without prior genomic information for either the plant host or the pathogen. |
| [34] |
Applications | Sample | Aims | Findings | Reference |
---|---|---|---|---|
Monitoring changes in the environment | River watersediments | Examine the connection between contaminant rates and transcription profiles of microbial genes and diversity |
| [92] |
River water sediments | Provide insights into microbial dynamics in freshwater hydrocarbon-rich environments |
| [93] | |
Mangrove’s microbiome | Analyse the local mangrove microbiome functionality and diversity |
| [94] | |
River watersediments | Identify the potential use of novel clusters of gene biomarkers to monitor aquatic health with regard to increasing hydrocarbon exposure |
| [95] | |
Seawater | Identify the potential use of genes pool in genosensing to indicate oil contamination in seawater |
| [96] | |
Coastal sediment | Outline the potential pathways involved in the production or degradation of nutrients regarding different levels of organic enrichment and metal contamination |
| [97] | |
Reducing negative impact on the environment | Cyanobacterial bloom (lake) | Provide an understanding of the roles and importance of cyanobacterial N2 fixation and phosphorous scavenging pathways during cyanobacterial blooms |
| [98] |
Flooded rice field soil | Clarify the impact of temperature on the structural and functional profiles of the anaerobic food web in rice field soil associated with methane production (mesophilic: 30 °C, thermophilic: 45 °C) |
| [99] | |
Activated sludge | Identify the diversity, abundance, and expression of antibiotic resistance gene (ARG) hosts in activated sludge in wastewater treatment plants |
| [100] | |
Seawater | Determine the mechanisms of natural oil-degrading bacteria in the presence of dispersants in the marine environment |
| [101] | |
Acid mine drainage | Provide insights into the role of iron-oxidising bacteria (Ferrovum sp.) in the bioremediation of arsenic |
| [56] | |
Bioleaching | Explain underlying mechanisms adapted by microbial communities (acidophilic strains) in bioleaching |
| [102] |
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Sharuddin, S.S.; Ramli, N.; Yusoff, M.Z.M.; Muhammad, N.A.N.; Ho, L.S.; Maeda, T. Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review. Int. J. Mol. Sci. 2022, 23, 3737. https://doi.org/10.3390/ijms23073737
Sharuddin SS, Ramli N, Yusoff MZM, Muhammad NAN, Ho LS, Maeda T. Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review. International Journal of Molecular Sciences. 2022; 23(7):3737. https://doi.org/10.3390/ijms23073737
Chicago/Turabian StyleSharuddin, Siti Suhailah, Norhayati Ramli, Mohd Zulkhairi Mohd Yusoff, Nor Azlan Nor Muhammad, Li Sim Ho, and Toshinari Maeda. 2022. "Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review" International Journal of Molecular Sciences 23, no. 7: 3737. https://doi.org/10.3390/ijms23073737