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, 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 pinpoint variance 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. Lastly, it provides information about the impact of different product applications on the soil and which parcels might benefit the most from applications to boost soil microbiota.


1.  Monitors effects of new practices/applications on the biodiversity and functionality of the soil microbiome.

2. Short-term monitoring of microbial carbon fixing pathways.

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

4. Measures terroir differences between parcels/plots with the microbiome acting as a biomarker.

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


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

2. Tests how long certain biological products remain in the soil.  

3. Justifies functional claims of bioactive products.

4. Correlates yield or other output differences with specific functions in the soil.

5. Bioactive product analysis.

6. Justifies compositional claims of biological products.

7. Describes the functional potential of a certain product.

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

BeCrop does not measure the amount of nutrients, but it does quantify 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).

In addition to BeCrop, we also offer BeCrop+ which includes a physicochemical soil test performed by Waypoint Analytics as an add-on to the BeCrop functional analysis.

Has BeCrop compared the differences between two similar reports, one conducted with dead cells and the other conducted with living cells?

Our lab has validated a protocol that uses propidium monoazide (PMA) to capture extracellular DNA which we performed prior 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/diagnostic applications, we subscribe to the philosophy that all signals present in the soil, from both dead and living 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. Therefore, 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 side-by-side, 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 to evaluate the viability of their products as well as their shelf life.

Yes, that can be achieved with the utilization of a multivariable analysis.

The metadata is required to map the allocations of samples to their corresponding blocks, defining and drawing comparisons between various blocks as well as calculating weather and soil data.

Sampling & Shipping

Usually 4 to 6 weeks from the time the samples arrive at our lab.

We provide sampling tubes and a sampling spoon to facilitate soil collection. The amount of soil needed is approximately ¼ of the tube. The amount we request you send is 5gr.  per sample.

No special equipment is needed but we recommend you use gloves and sanitize the trowel with ethanol, allowing it to dry before and between sample collections.

Our samples are composite, which means that each tube should contain subsamples from 3 to 12 locations in the same block in order to make the sample truly representative for our study.

Optimal resolution is derived from 1-2 acres, but in 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 consistent management practices (fertilizer applications, irrigation, etc.).

The number of samples required depends on the specific questions you want answered. This will be assessed prior to the sampling to make sure you’re provided with the appropriate solutions.

Do I need to ship the samples overnight?

No, overnight shipping is not required. Ideally, samples should arrive at the lab within 72h from the time they are collected. However, we have not observed significant changes in the microbial communities for a period of up to 15 days after sampling (at room temperature).

Storage and shipping guidelines.

Given that soil microbiomes are sensitive, here are our recommended guidelines for proper storage and shipping:

– Soil samples can be stored long-term 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 with total transit time not to exceed more than 5 days at room temperature.

We recommend sampling at a depth of 6 inches to provide proper representation from the microbes located in both the topsoil and lower layers. Most pathogens and microbes involved with nutrient cycling and the 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’ve found that this metric correlates well with the type of  vineyard management:  i.e. conventionally managed vineyards tend to show low to medium resistance while vineyards utilizing organic/biodynamic/regenerative practices show high to very high resistance. The pre-print version of the paper where this marker is described can be found here: Emergent properties in microbiome networks reveal the anthropogenic disturbance of farming practices in vineyard soil fungal communities.

The level of disease risk is based on the abundance of pathogens that cause the disease to occur in the sample as well as the ecological relationships of the pathogen with other microorganisms as measured by the resistance metric referred to above. Both our disease database as well as the ecological relationships are crop-specific. Samples are compared to other samples of the same crop to normalize the risk into quintiles.