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Mushrooms
Mushrooms for the collector is a potentially dangerous hobby.  However for those who just try to identify mushrooms, mushrooms have a powerful advantage over other plants.  Mushrooms especially those that occur on trees can be all year including the winter.  Identifying mushrooms is one way to lift the winter blues.  A fair warning: some mushrooms are rather difficult to identify, many require a microscope and some mushroom identification can defy even experts.  Good luck.

Mushrooms of Ontario and Eastern Canada Le grand livre des champignons du Québec et de l'est du Canada A Field Guide to Mushrooms Edible and Poisonous Mushrooms of Canada Mushrooms Demystified
Mushrooms of Ontario and Eastern Canada GB
If you read English this is the must have.  Gorgeous book filled with photographs of mushrooms.  
Le grand livre des champignons du Québec et de l'est du Canada Pub (English translation) Pub (French) GB
If you can read French this is the book to get.  It has the most species covered and is more local than the above book.
A Field Guide to Mushrooms GB
Edible and Poisonous Mushrooms of Canada GB
Older and out of print but has a good key.
Mushrooms Demystified GB
Combines a field guide with an easily digestible natural history of mushroom.  Not sure the scope of the book, may be all the US and Canada.

North American Boletes The Boletes of North America The Boleti of Northeastern North America Myxomycetes: A Handbook of Slimemolds Illustrated Guide to Common Slimemolds
North American Boletes GB
A guide to sponge mushrooms.
The Boleti of Northeastern North America GB
The Boletes of North America GB
The Boletes of Michigan Scan
Myxomycetes: A Handbook of Slimemolds GB Am
Slimemolds of the world, natural history, keys to orders, selected species covered.
Illustrated Guide to Common Slimemolds GB
Field Guide to North American Truffles The North America Species of Pholiota How to Know the Non-Gilled Fleshy Fungi Psilocybin Mushrooms of the World

Field Guide to North American Truffles GB
Ontario has very few truffle species.
Amanitas of North America
Amanitas are poisonous.
The North America Species of Pholiota GB
How to Know the Non-Gilled Fleshy Fungi GB
Psilocybin Mushrooms of the World GB
Psilocybin is a psychoactive ingredient in many mushroom species.  

Fungi of Elgin Country Mushrooms of the Great Lakes Region Mushrooms of the Boreal Forest Mushrooms of Northeastern North America How to Identify Mushrooms to Genus Series
Fungi of Elgin County
William G. Stewart, E. Stewart, I Carmichael 1999 softcover 21 p. (species list)
Mushrooms of the Great Lakes Region GB
Mushrooms of the Boreal Forest GB
Mushrooms of Northeastern North America GB
How to Identify Mushrooms to Genus Series GB

MushroomExpert.com
Keys to North American mushrooms and plenty of other information.
George Barron's Website on Fungi is done by the author of Mushrooms of Ontario and Eastern Canada and contains many pictures and much information that is not in his field guides.
American Mushrooms This website (done by the coauthor of Mushrooms of Northeastern North America) includes interesting mushroom trivia such as the coolest mushrooms, tiniest and smelliest.  
Fungi - The Fifth Kingdom Has many products available of interest.  It has a field guide that is both in book form and CD-ROM.  Many of the products are keys to specific groups of fungi.
Mycological Society of Toronto
North American Mycological Association

Lichens
Lichens are usually overlooked.  Yet they are diverse in appearance and look awesome under a hand lens.  If you want to really know your lichens you can do chemistry tests.

Lichens of the North Woods Lichens of North America Lichens of the Ottawa Region Lichens of Southern Ontario How to Know the Lichens
Lichens of the North Woods Pub GB
The must have book.  A beginner's guide.  It divides the lichens first by habitat (ground, rocks, and trees) and then by type (crustose, foliose, and fruiticose).  
Lichens of North America GB
A reference book, heavy but quite beautiful.  Covers far more local species than Lichens of the North Woods, and is handy in making sense of Lichens of the Ottawa Region.  This book has useful common names which can be transferred to the more scientific books below.
Lichens of the Ottawa Region >>
Many more species covered, especially the crustose which require a microscope.  The book is basically a key with a few black and white illustrations to help.  For those who really want to know their lichens.  
The Lichens of Southern Ontario >>
Probably similar in format to Lichens of the Ottawa Region.  Together these two books should cover most of Ontario's crustose lichens.
How to Know the Lichens GB
An older book with an illustrated key.  Covers macrolichens only.  All these books combined should cover all the macrolichens in Ontario although not necessarily all the microlichens (crustose).  Together these three technical books should cover most of Ontario's lichens.


Macrolichens of New England
Michigan Lichens
Lichens Above Treeline

The Macrolichens of New England Am
Michigan Lichens GB
Lichens above Treeline: A Hiker's Guide to Alpine Zone Lichens of the Northeastern United States Am

Identifying North American Lichens: A Guide to The Literature  For those most serious about lichens.
Identifying Mixed Hardwood Forest Lichens is an Ontario reference guide to common lichens
Lichens Home Page Photographic guide to lichens of North America
Annotated List of Lichens of the Macoun Club's nature study area
 
Bacteria
A Field Guide to Bacteria Guide to Microlife How to Know the Protozoa
A Field Guide to Bacteria GB
The only book that will help you identify major groups of bacteria in the field without a microscope.
Guide to Microlife GB
A field guide to bacteria seen under a microscope.
How to Know the Protozoa GB
A specific type of bateria is the protozoa.

Books to learn more about bacteria in general include A Field Guide to Germs, Human Wildlife: The Life That Lives on Us and Thieves, Deceivers, and Killers.

Microbiology: A Photographic Atlas for the Laboratory Exploring with the Microscope Using a Microscope: A Guide for Naturalists
Microbiology: A Photographic Atlas for the Laboratory GB
A microbiology textbook and altas that has gotten lots of good reviews on Amazon.
Exploring with the Microscope GB
Everything you need to know about microscopes.
Using the Microscope: A Guide for Naturalists GB

Tree Diseases of Ontario
Forest Area Disturbed by Tree Disease  Has a PDF "Tree Diseases of Ontario"