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How Can You Measure Microbes? With PLFA Analysis

Category: Soil Health | No Comments

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soil lifeModern farmers and scientists have a pretty solid understanding of how to work with soil physics to grow a good crop. Our understanding of soil chemistry has stabilized over the centuries, and we’re good at identifying and providing the nutrients our crops need. Soil biology, however, has been a more difficult nut to crack, in part because the microbial life in soil is hard to measure.


What We Know & What We Don’t About Soil Composition

We farm the ground we have, not the ground we wish we had, and the only way to do this well is to understand what we have and how it is likely to respond to our management decisions. Knowing what we can expect from soils of different textures has been as straightforward as measuring soil texture and then observing how different soil textures produce different crops across generations. We have more control over soil chemistry, and by asking a lab to run extractions and titrations to tell us the current conditions of our soil, we can determine whether and how to adjust what’s available for our plants. Soil physics is a relatively stable knowledge base, and soil chemistry is generally well understood, but our knowledge in this area is still being refined.

Soil microbial life and soil microbial activity have no less importance in our crop outcomes. Microorganisms cycle nutrients, impact the composition of the plant community, regulate productivity, and decompose organic matter, but we have only begun to scratch the surface of how to measure them. Without the ability to measure soil microbes, we are unable to know whether we need to make changes to how we’re managing the soil and, if so, what changes to make.


Advances in Measuring Microbial Life

Several government agencies, including the US Department of Agriculture’s Natural Resources Conservation Service (NRCS), leapt into adoption of the Haney Soil Health Test. This included the Solvita CO2Burst test, which measures how much CO2 is produced in a soil sample over 24 hours. This basically tells you how many critters are breathing in your soil. The idea is that more breathing means more microbes, and more microbes are good. This isn’t wrong, but it is an oversimplification. The fact that something is breathing lets us know something is alive, but not what it is or how helpful or unhelpful it might be to our plants.

Scientists have attempted to culture soil microbes in lab environments to aid measurements but have so far been unsuccessful at culturing many of them. Examining microbial populations using ribosomal RNA analysis showed promise, but while this works for any one species, rRNA concentrations are not the same for all species, so this cannot be used for mixed communities like those we find in soils.

The PLFA (phospholipid fatty acid) analysis is a newer test that lets us notice the differences among different kinds of microbial life. Phospholipids are essential membrane components of all living cells, not in storage products or dead cells. Unlike rRNA, phospholipids make up a fairly constant percentage of the biomass of any organism. Testing from 1994 forward has shown that changes in the microbe community are reflected in changed PLFA analysis results. These data strongly suggest that PLFA analysis is the way we can get the fullest possible picture of a soil’s microbiome.

Soil scientists have developed a full enough understanding of many bacteria that we can recognize their PLFA signature and compare it against databases of whole-cell saponification fatty acid profiles for different pure cultures. We can also analyze a direct environmental sample to compare changes in a community over time.

When you get a PLFA analysis of soil, your report will include

  • Total living microbial biomass
  • A functional group diversity index
  • Total bacteria, including breakdowns of gram+ and gram- bacteria
  • Total fungi

You can compare your soil’s changes over time, monitor the fungi-to-bacteria ratio, and compile other useful metrics.

We are lucky to be farming at a time when technology is finally allowing us to measure processes where our forefathers had only been hoping for the best. As the PLFA test and others develop and are brought into widespread use, we will be able to manage the biology of a soil as well as we manage its chemistry and physics today.


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Written By

Allison Jonjak

Allison Jonjak

Precision Ag Analyst |

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