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Published June 23, 2023 | Version v3
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Composite sampling method for soil microbiome and microbial abundance analysis

  • 1. Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore - 575018, India

Description

Composite sampling is a statistical technique that involves collecting and analyzing composite samples, which are formed by combining individual samples from multiple sources (Lancaster and Keller-mcnulty, 1998). In the present article, an overview of composite sampling methods has been described, which is a very useful method for the analysis of microbial abundance and core microbiomes from various environments (Fig. 1). This is an advantageous method compared to traditional sampling methods. It highlights the potential benefits of composite sampling in terms of cost reduction, time efficiency, and increased precision in estimation. Moreover, composite sampling enables the collection and analysis of a representative sample of a larger population. For instance, in coastal areas, composite sampling may involve collecting a number of smaller samples from different locations within the study area and then combining them to form a single composite sample. This composite sample can then be analyzed to determine the overall characteristics of the population. It is a useful tool for studying the characteristics of populations in coastal areas and can help reduce the cost and complexity of collecting and analyzing large numbers of individual samples over the huge geography of the country. Soil, sand, beach samples, sediment and rock samples can be collected through this method. All collected samples must be stored and transported to the laboratory under cooling conditions in dry ice for further downstream processing. When samples arrive at the laboratory, all samples must be cleaned to remove debris, litter, stones, roots of plants, hair, and remnants of animal origin. Cleaned samples can be used for measurement of moisture content and pH of the sample using standard protocols. One gram of the sample was suspended in sterile deionized water (5 mL) and vortexed for 5 minutes. The suspended sample was allowed to settle for 2–3 minutes at 25 °C. HiIndicator pH paper (LA310, HiMedia Laboratories) can be used to measure the pH of each sample of water. The pH of sample can be confirmed using Benchtop pH Meters ( Thermo Scientific™ Orion™ Versa Star Pro™) as per manufacturer instructions. Hence, this article serves as a valuable resource for researchers and practitioners interested in understanding and applying composite sampling methods. It provides a comprehensive overview and covers various aspects of the design, estimation, and implementation of composite sampling techniques required for soil microbiome and microbial abundance analysis.

 

Legend to figure:

Figure 1. Composite sampling method: 1) Select a plot of fixed size, preferably 15 m2. All flags figure and mark sampling points from x1, x2, x3, x4, and x5. 2) Insert the sampler as indicated by putting even pressure on both sides of the sampler. The sampler was removed, and a 10-cm soil layer was drawn from the window of the sampler. 3) Mix soil evenly and collect a minimum of 500 g to 2 kg for further downstream processing, depending on use. For microbial analysis, such as isolation and next-generation sequencing, a maximum of 10 g of soil is sufficient. 4-6) Extract soil from double-distilled water, filter, and measure the pH of the soil.

 

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References

  • Lancaster, V. A., & Keller-mcnulty, S. (1998). A Review of Composite Sampling Methods. Journal of the American Statistical Association, 93(443), 1216–1230. doi: 10.1080/01621459.1998.10473781