On various occasions I was receiving soil or sending soil by messenger service company (UPS, DHL) to and from other countries and there was no need for any additional documents apart from the description in the messenger company forms, but it was all within the EU countries. I do not know how would it work for the shipment from outside EU.

Soil from outside of the EU will be a subject to restrictions imposed on the import. In the UK one needs to carry a soil license to import any non-EU soil samples. You have to check the German regulations.

You should check the German regulation on this subject. If it is a university, in this case the university must have permit or licence for importing soil and/or similar matterials. When you enter  germany you must declare the situation to the custom.

You will need to get quarantine clearance from both the countries.  At the least German regulations must be strictly followed to take soil samples there. 

Usually an official letter from the sending institution (in English should do most times) should be sufficient, stating that the samples are used for research only, are sterile in terms of pathogens and contain no substances affecting environmental health. We do it all the time without any problems.

agree with the above. Be careful to make sure that you include a copy of any authorisation with the sample as well asin person if you are travelling by air for example. I send a lot to japan, and they must have the strictest import conditions, as things need to be triple bagged, with licences attached in a very specific way. In terms of posting, I have sent soils in air-dry form across Europe without a licence, just stating that it is sterile soil for laboratory comparisons,but for fresh soils, you ought to make sure you folow the conditions, otherwise you might get into some trouble, especially with the current climate of infectious soil and plant diseases being spread.