There are several methods to investigate the inner or outer part of aggregates.

As Thiele-Bruhn mentioned, the aggregates can be peeled using a blade (Chenu et al., 2001). However, it is difficult to work on small aggregates sizes. You can also use a device like a grater that peel the surface of the aggregates, and is less painful than peeling with scalpel (sorry, I can’t find a reference for it).

Other studies used washing steps to collect microorganisms on the surface of aggregates coupled with centrifugation (Ranjard et al., 1997, 2000; Chenu et al., 2001), The problem with such method, is that the use of water is likely to affect the activity of your community and subsequently your results (Bach and Hofmockel, 2014). To reduce the effect of water, you have to use water at 4 degrees and work quickly. However, the advantage of this method is that you can use it for small aggregates and larger amount of soil that peeling.

Finally, UV-light has been used to sterilise the surface of aggregates, to target specifically the microorganisms in the inner part of aggregates (Mummey and Stahl, 2004). The inconvenience with this method is that you can’t work on the outer aggregates only, but either inner or whole aggregates.

Hope that help,

Aimeric

References:

Chenu, C., Hassink, J., Bloem, J., 2001. Short-term changes in the spatial distribution of microorganisms in soil aggregates as affected by glucose addition. Biol. Fertil. Soils 34, 349–356. doi:10.1007/s003740100419

Mummey, D.L., Stahl, P.D., 2004. Analysis of Soil Whole- and Inner-Microaggregate Bacterial Communities. Microb. Ecol. 48, 41–50. doi:10.1007/s00248-003-1000-4

Ranjard, L., Poly, F., Combrisson, J., Richaume, A., Gourbière, F., Thioulouse, J., Nazaret, S., 2000. Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microb. Ecol. 39, 263–272. doi:10.1007/s002480000032

Ranjard, L., Richaume, A., Jocteur-Monrozier, L., Nazaret, S., 1997. Response of soil bacteria to Hg(II) in relation to soil characteristics and cell location. FEMS Microbiol. Ecol. 24, 321–331. doi:10.1111/j.1574-6941.1997.tb00449.x

Hi, I don't know.

You will have to separate the outer shell and the inner core of teh  aggregates.

Either you peel the aggregates using a scalpell or you scrape out the core by cutting the aggregate first into to halves and then scraping them out with a small spatula.

This is easiest done when you use macroaggregates and becomes more challenging the smaller the aggregates are.

In preliminary experiments you should test which soil misture is best for that purpose (depends on soil properties) but usually field moist status is preferred.

To not mix core and shell material we discarded material from the transitional area between shell and core.

Thank you! Could you give me link on a refference on this method? Although I guess it is very hard to work with 1-2 mm aggregate.

thanks

Interesting idea and useful method. Thank you guys!

Sorry, I don't have a reference with a detailed method description on hand. We used an in-house method. A very brief and rough description has been published in "Reichel R., Patzelt D., Barleben C., Rosendahl I., Ellerbrock R.H., Thiele-Bruhn S. (2014) Soil microbial community responses to sulfadiazine-contaminated manure in different soil microhabitats. Applied Soil Ecology 80, 15–25."

But the method is really not complicate.

Regards

Thank you we gona try.

There are several methods to investigate the inner or outer part of aggregates.

As Thiele-Bruhn mentioned, the aggregates can be peeled using a blade (Chenu et al., 2001). However, it is difficult to work on small aggregates sizes. You can also use a device like a grater that peel the surface of the aggregates, and is less painful than peeling with scalpel (sorry, I can’t find a reference for it).

Other studies used washing steps to collect microorganisms on the surface of aggregates coupled with centrifugation (Ranjard et al., 1997, 2000; Chenu et al., 2001), The problem with such method, is that the use of water is likely to affect the activity of your community and subsequently your results (Bach and Hofmockel, 2014). To reduce the effect of water, you have to use water at 4 degrees and work quickly. However, the advantage of this method is that you can use it for small aggregates and larger amount of soil that peeling.

Finally, UV-light has been used to sterilise the surface of aggregates, to target specifically the microorganisms in the inner part of aggregates (Mummey and Stahl, 2004). The inconvenience with this method is that you can’t work on the outer aggregates only, but either inner or whole aggregates.

Hope that help,

Aimeric

References:

Chenu, C., Hassink, J., Bloem, J., 2001. Short-term changes in the spatial distribution of microorganisms in soil aggregates as affected by glucose addition. Biol. Fertil. Soils 34, 349–356. doi:10.1007/s003740100419

Mummey, D.L., Stahl, P.D., 2004. Analysis of Soil Whole- and Inner-Microaggregate Bacterial Communities. Microb. Ecol. 48, 41–50. doi:10.1007/s00248-003-1000-4

Ranjard, L., Poly, F., Combrisson, J., Richaume, A., Gourbière, F., Thioulouse, J., Nazaret, S., 2000. Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA). Microb. Ecol. 39, 263–272. doi:10.1007/s002480000032

Ranjard, L., Richaume, A., Jocteur-Monrozier, L., Nazaret, S., 1997. Response of soil bacteria to Hg(II) in relation to soil characteristics and cell location. FEMS Microbiol. Ecol. 24, 321–331. doi:10.1111/j.1574-6941.1997.tb00449.x

Thank you, Aimeric.

I agree with the suggestions given above. I would just like to add that you do not want to use water to separate your aggregates of different sizes. Water based separation is obviously the easiest esp when you are working with small aggregates. But the rewetting and drying will very likely change the enzyme activity, and microbial community composition and abundance significantly, etc and your data will really not be useful. We recently reviewed the effect of rewetting and drying during routine soil lab analyses and the findings are pretty serious ... these procedures introduce a lot of bias and/or errors to experimental results. see the attached file

Article How air-drying and rewetting modify soil organic matter char...