Current Challenges and Pitfalls in Soil Metagenomics
Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicoche...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-09-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/10/1900 |
| _version_ | 1797471145291677696 |
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| author | Marcio F. A. Leite Sarah W. E. B. van den Broek Eiko E. Kuramae |
| author_facet | Marcio F. A. Leite Sarah W. E. B. van den Broek Eiko E. Kuramae |
| author_sort | Marcio F. A. Leite |
| collection | DOAJ |
| description | Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility. |
| first_indexed | 2024-03-09T19:45:18Z |
| format | Article |
| id | doaj.art-5211d698174e4df4be24f64d54bf0d87 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T19:45:18Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-5211d698174e4df4be24f64d54bf0d872023-11-24T01:25:05ZengMDPI AGMicroorganisms2076-26072022-09-011010190010.3390/microorganisms10101900Current Challenges and Pitfalls in Soil MetagenomicsMarcio F. A. Leite0Sarah W. E. B. van den Broek1Eiko E. Kuramae2Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The NetherlandsDepartment of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The NetherlandsDepartment of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The NetherlandsSoil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.https://www.mdpi.com/2076-2607/10/10/1900soil physicochemical propertiesmicrobial ecologymetagenomicsuntreated controlsdata-sharing guidelines |
| spellingShingle | Marcio F. A. Leite Sarah W. E. B. van den Broek Eiko E. Kuramae Current Challenges and Pitfalls in Soil Metagenomics Microorganisms soil physicochemical properties microbial ecology metagenomics untreated controls data-sharing guidelines |
| title | Current Challenges and Pitfalls in Soil Metagenomics |
| title_full | Current Challenges and Pitfalls in Soil Metagenomics |
| title_fullStr | Current Challenges and Pitfalls in Soil Metagenomics |
| title_full_unstemmed | Current Challenges and Pitfalls in Soil Metagenomics |
| title_short | Current Challenges and Pitfalls in Soil Metagenomics |
| title_sort | current challenges and pitfalls in soil metagenomics |
| topic | soil physicochemical properties microbial ecology metagenomics untreated controls data-sharing guidelines |
| url | https://www.mdpi.com/2076-2607/10/10/1900 |
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