Current Challenges and Pitfalls in Soil Metagenomics

TY - JOUR

T1 - Current Challenges and Pitfalls in Soil Metagenomics

AU - Leite, Marcio F.A.

AU - van den Broek, Sarah W.E.B.

AU - Kuramae, Eiko E.

N1 - 7468, ME

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - data-sharing guidelines

KW - metagenomics

KW - microbial ecology

KW - soil physicochemical properties

KW - untreated controls

U2 - 10.3390/microorganisms10101900

DO - 10.3390/microorganisms10101900

M3 - Article

AN - SCOPUS:85140981361

SN - 2076-2607

VL - 10

JO - Microorganisms

JF - Microorganisms

IS - 10

M1 - 1900

ER -