Frequently Asked Questions

About Biome Makers technology

Our analysis is based on 16S and ITS rRNA gene sequencing from soil samples. Using this information, we create a functional assessment of the soil, based on the relations of the microbial community for each specific site and crop.

Traditional soil analyses provide information about the physical properties (eg. texture) and the chemical properties of the soil, such as pH or the concentration of nutrients in the soil, but do not take soil microbiology into account.

Instead of measuring the amount of nutrients in the soil, BeCrop measures the microbial processes involved in nutrient cycling, such as those that fix carbon into the soil, or supply plants with available nutrient forms (eg. mineralization or solubilization) and those that immobilize nutrients back into forms not readily available for plants (immobilization, denitrification).

BeCrop Analysis

BeCrop provides growers with a tool to evaluate the effect of agricultural practices, and spot differences in productivity from different crops and parcels. It also evaluates the risk of plant diseases, which allows for more accurate IPM programs and product applications. Finally, it provides information about the impact of different product applications in the soil, and about which parcels might benefit the most from applications to boost the soil microbiota.


1.  Monitoring effect of new practices/applications on the biodiversity and functionality of the soil microbiome.

2. Short term monitoring of microbial carbon fixing pathways

3. Adjust pest management programs by knowing which soil-borne pathogens present and which ones are not at a certain point

4. Measure terroir differences between places. Microbiome as biomarker.

5. Find out whether nutrient deficiencies are caused by a lack of nutrient in the soil or by a low microbial capability to make nutrients available for plants (BeCrop+)


1.  Testing the effect of ag inputs in the soil microbiome

2. Testing how long certain biological products stay in the soil  

3. Justifying functional claims for bioactive products

4. Correlating yield (or other output) differences with specific functions in the soil

5. Bioactive Product Analysis

6. Justifying compositional claims of biological products

7. Describing the functional potential of a certain product

8. Confirming taxonomy and absolute quantification of microorganisms in biological products to manufacturers sourcing their inoculums externally

BeCrop does not measure the amount of nutrients, but the microbial processes involved in nutrient cycling, such as those that supply plants with available nutrient forms (eg. mineralization or solubilization) and those that immobilize nutrients back into forms not readily available for plants (immobilization).

We offer BeCrop +, which includes a physicochemical soil test performed by Waypoint Analytics, on top of the BeCrop functional analysis.

Have we looked at the differences between the same reports done with and without differencing dead/alive cells?

We have validated in our lab a protocol that uses propidium monoazide (PMA) to capture extracellular DNA, which we can perform previous to the DNA isolation step. The taxonomic annotation of species in low relative abundance is the most variable. Functional annotation, as well as ecological interactions among taxa that are also present in the BeCrop report, are less affected by remotion of extracellular DNA.

However, for biomarker discovery/diagnostics applications we are of the philosophy that all signals present in the soil, from dead and alive microorganisms, are relevant. Thus, our BeCrop reports are based on total DNA extraction and amplification. Samples are then compared to other samples derived from the same crop to normalize each of the markers into quintiles. So, we do not recommend removing extracellular DNA for BeCrop samples, given that interpretation is performed in the context of other samples for which we have performed total DNA extraction.

For self-contained R&D projects where samples are compared to one another, we can definitely implement the PMA protocol. Also, for our BeCrop Product report (absolute bacterial quantification of Ag-inputs) some of our clients request the removal of extracellular DNA for evaluating the viability of their products as well as their shelf life.

Yes, you can do so with a multivariable analysis

The metadata is crucial to map the allocations of samples to their blocks, define and draw comparisons between various blocks, as well as calculating weather and soil data.

Sampling & Shipping

Usually 4 to 6 weeks since sample arrival to the lab.

We provide sampling tubes with a sampling spoon to facilitate sampling. The amount of soil needed is about ¼ of the tube, the amount requested to be sent is 5gr. per sample. 


No special equipment is necessary, but it is recommended to use gloves and sanitize the trowel with ethanol and let it dry well before and in between samples.

Our samples are composite, meaning that each tube should contain subsamples from 3 to 12 locations in the block to study, in order to make the sample representative.

Our best resolution is around 1-2 acres, but in very uniform soils, the surface covered per sample can be increased without a significant loss of representativity. 

It is important that each sampling area has uniform soil characteristics (pH, texture) and management practices (fertilizer applications, irrigation, etc.)

The number of samples needed will depend on the questions you want to answer. This will be an asset prior to the sampling to make sure you will obtain the appropriate answers.

Do I need to ship the samples overnight?

Overnight shipping is not necessary. Ideally, samples should arrive at the lab before 72h from the time they were taken; however, we have not observed significant changes in the microbial communities for up to 15 days after sampling (at room temperature).

The storage and shipping guidelines

The soil microbiomes are sensitive, so here are some guidelines for storage and shipping:

– Soil samples can be long-term stored at -20 °C (-4 °F).

– Soil samples can be stored up to 3 days if refrigerated at 0-6 °C (32 48 °F).

– Ideally, soil samples should be shipped using 1-day shipping and no more than 5 days at room temperature in transit.


We recommend sampling at 6 inches deep, in order to get representation from the microbes in the topsoil and in the lower layers. Most pathogens and microbes involved with the nutrient cycling and supply of plant growth promoters are found in the rhizosphere, near the topsoil.

BeCrop report

Resistance is based on network properties of the microbial community, specifically co-occurrence/exclusion of pairs of microorganisms, and reflects the resilience of the network against external disruptions such as tillage or pesticide applications.
We have found that this metric correlates very well with management type in vineyards: conventionally managed ones tend to show very low to medium resistance, and vineyards under organic/biodynamic/regenerative practices show high to very high resistance. The pre-print version of the paper where we described this marker can be found here: Emergent properties in microbiome networks reveal the anthropogenic disturbance of farming practices in vineyard soil fungal communities.

Disease risk is calculated based on the abundance of the pathogens that cause the disease in the sample, as well as the ecological relationships of the pathogen with other microorganisms in the sample as measured by the resistance metric referred to above. Our disease database as well as the ecological relationships are crop-specific, and samples are compared to other samples of the same crop to normalize the risk into quintiles.