Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review
While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ a...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/7/3737 |
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| author | Siti Suhailah Sharuddin Norhayati Ramli Mohd Zulkhairi Mohd Yusoff Nor Azlan Nor Muhammad Li Sim Ho Toshinari Maeda |
| author_facet | Siti Suhailah Sharuddin Norhayati Ramli Mohd Zulkhairi Mohd Yusoff Nor Azlan Nor Muhammad Li Sim Ho Toshinari Maeda |
| author_sort | Siti Suhailah Sharuddin |
| collection | DOAJ |
| description | While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment. |
| first_indexed | 2024-03-09T11:46:36Z |
| format | Article |
| id | doaj.art-83e654429cb2485f92ca7f28a97c5b4a |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T11:46:36Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-83e654429cb2485f92ca7f28a97c5b4a2023-11-30T23:21:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01237373710.3390/ijms23073737Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A ReviewSiti Suhailah Sharuddin0Norhayati Ramli1Mohd Zulkhairi Mohd Yusoff2Nor Azlan Nor Muhammad3Li Sim Ho4Toshinari Maeda5Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, MalaysiaDepartment of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, MalaysiaDepartment of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, MalaysiaInstitute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, MalaysiaSime Darby Plantation Technology Centre Sdn Bhd, Sime Darby Plantation, Serdang 43400, Selangor, MalaysiaDepartment of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu, Kitakyushu 808-0196, JapanWhile chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.https://www.mdpi.com/1422-0067/23/7/3737metatranscriptomicspollutionenvironmental sustainabilityproductive agriculturebioindicator |
| spellingShingle | Siti Suhailah Sharuddin Norhayati Ramli Mohd Zulkhairi Mohd Yusoff Nor Azlan Nor Muhammad Li Sim Ho Toshinari Maeda Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review International Journal of Molecular Sciences metatranscriptomics pollution environmental sustainability productive agriculture bioindicator |
| title | Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review |
| title_full | Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review |
| title_fullStr | Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review |
| title_full_unstemmed | Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review |
| title_short | Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review |
| title_sort | advancement of metatranscriptomics towards productive agriculture and sustainable environment a review |
| topic | metatranscriptomics pollution environmental sustainability productive agriculture bioindicator |
| url | https://www.mdpi.com/1422-0067/23/7/3737 |
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