I would not use "plagues"; cases can be found, but it is not usual. If the problem is an animal (usually an insect) the word "pest" is used; if it is fungi or bacteria, the usual word is "diseases". Since you say that it includes fungi, "diseases should be included.

Here are two good sources, one British, one American:

"Pests and diseases
Use the pest and disease factsheets to diagnose the problems with your plants and follow the recommended solutions to treat them."
http://www.bbc.co.uk/gardening/advice/pests_and_diseases/

"Purdue Plant and Pest Diagnostic Laboratory"
http://www.ppdl.purdue.edu/PPDL/index.html

"Less-than-ideal weather conditions across the U.S. this spring raise concerns about the potential for early-season pests and diseases in corn"
http://cornandsoybeandigest.com/cooler-wet-spring-raises-con...

"pest
a destructive insect or other animal that attacks crops, food, livestock, etc.."
http://oxforddictionaries.com/definition/pest?region=us&q=pe...

You can say just "early" instead of "early-season", but the latter is more common and I would recommend using it.

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Note added at 6 hrs (2012-02-29 18:34:36 GMT)
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PS. Thanks and acknowledgements to Ana for a very important intervention in the discussion!