Microbiology of sourdough yeast (#7)

This adds how sourdough yeast works. It goes into detail
on the microbiology looking at how the yeast lives in
the environment

book/basics/how-sourdough-works.tex

@@ -194,6 +194,122 @@ Would you like to reduce the amount of gluten in your
 final bread? These are all factors you can influence
 by adjusting the speed of fermentation.
 
-
 \section{Yeast}
+
+Yeasts are single celled microorganisms that are part of
+the fungus kingdom. Yeast spores that are hundreds
+of million years old have been identified by scientists.
+There is a wide variety of species and so far around 1500
+different species have been recognized. Yeasts are not creating
+a mycelium network like mold does for instance
+\cite{molecular+mechanisms+yeast}.
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=1.0\textwidth]{saccharomyces-cerevisiae-microscope}
+  \caption{Saccharomyces cerevisiae: Brewer's yeast under the microscope}
+  \label{saccharomyces-cerevisiae-microscope}
+\end{figure}
+
+
+Yeasts are saprotrophic fungi. This means they are not
+producing their own food. They rely on external food sources
+which they decompose and break down. For yeasts
+carbohydrates and broken down to carbon dioxide and
+alcohols. The products of this fermentation process
+have been used for thousands of years when making
+bread or alcoholic beverages. Yeasts can grow
+in both aerobic and anaerobic conditions. When oxygen
+is present the yeast almost completely produces
+carbon dioxide and water. When no oxygen is present
+the yeast starts switches its metabolism. The
+yeast starts to produce alcoholic compounds \cite{effects+oxygen+yeast+growth}.
+The temperatures at which the yeast grows vary. Some
+yeasts such as {\it Leucosporidium frigidum} grows
+best at temperatures between -2°C up to 20°C. Other
+yeast grows better at higher temperatures. The warmer
+it is the faster the yeast's metabolism works. The yeast
+that you cultivate in your sourdough starter works best
+at the temperatures where the grain was grown and at
+the point when it was harvested. So if you are from a 
+cooler place and cultivate a sourdough starter from
+a nordic rye variety, then chances are your yeast
+prefers this colder environment. As an example
+beer makers discovered that a beneficial yeast lives
+in the cold caves around the city of Pilsen, Czech Republic.
+This yeast has produced excellent tasting beers at
+lower temperatures. Varieties of these strains
+are now used to make popular lager beers.
+
+Yeasts in general are very common in the environment.
+They can be found on cereal grains, fruits, other plants
+in the soil and also in your gut. Very little is known
+about the ecology of why yeasts we use for baking
+are cultivating the leaves of the plants. The plants
+are protected via the cell walls and hardly any
+fungi and other bacteria can penetrate. Some fungi and
+bacteria are producing enzymes that are able
+to break down the cell walls and infect the plant.
+There are fungi and bacteria that live within the plant
+without causing any distress. These are known as {\it endophytes}.
+They are not damaging the plant per se. In fact they are
+living in a symbiotic relationship with the host. They
+help the plant to protect itself from additional pathogens
+that might enter through the leaves of the plant. They
+help with water stress, heat stress and nutrient availability. 
+In exchange for the service they receive carbon for energy
+from the plant host. They are not always strictly mutualistic though.
+Sometimes under stress conditions they can become pathogens
+on their own \cite{endophytes+in+plants} and decay begin
+decaying the plant.
+
+The yeasts we use for baking are
+living as as epiphytes on the plant. Compared to
+the previously mentioned endophytes they are not
+breaching the walls of the cells. Most of them
+receive nutrients from rain water, the air or other animals.
+These sources also include honeydew produced
+by aphids. Pollen that lands on the leaf's surface
+is an additional source of food. Interestingly
+though when you remove that external food source,
+you still find a large variety of epiphytic fungi
+and bacteria on the plant's surface. The food
+for them is coming directly from the plant it seems.
+Some research has shown that the plants are
+on purpose releasing some compounds such as sugars,
+organic acids, amino acids, some methanol and various
+salts via the surface. These nutrients would
+then attract the epiphytes to live on the surface.
+The plants benefit from enhanced protection against
+mold and other pathogens. It is in the best interest
+of the epiphytes to keep the plants alive
+as long as possible \cite{leaf+surface+sugars+epiphytes}.
+More and more research is conducted on using yeasts
+as a biocontrol agents to protect plants. These bio-agents
+would be food-safe as yeasts are generally considered save.
+The yeasts would start to grow on the leaves on the plant
+and essentially shield the plants from other molds. This
+could be a game changer for wineyeards suffering from mildew.
+This could also be helpful to shield the plant against the
+psychoactive ergot fungus. The ergot fungus likes to grow
+in more humid colder environments and poses a huge
+problem to rye farmers. The fungus parasites the plant
+and infects it. Consumption of ergot is not recommended
+as it is highly toxic to the liver. That's why lawmakers
+have recently reduced the amount of allowed ergot contamination
+in rye flour. Another interesting experiment from Italian scientists
+visualized how important yeasts could be when protecting
+plants. They added tiny incisions into some of the grapes.
+They would then infect some of the damaged surfaces with
+mold. The other wounds they infected with some of the 150
+different wild yeast strains isolated from the leaves plus
+the mold. When mixing the mold with the yeast the grape
+sustained no significant damage \cite{yeasts+biocontrol+agent}.
+In another experiment however scientists have shown
+how the brewer's yeast became an aggressive pathogen to wine plants.
+Initially the yeast lived in symbiosis with the plant. After the grapevine
+sustained damages the yeast became opportunistic and started to
+attack the plant event producing hyphae to deeply
+penetrate the plants tissue.
+
 \section{Bacteria}

book/intro/foreword.tex

@@ -1,2 +1,2 @@
 Hopefully one day there is going to be an awesome foreword
-by another break baker!
+by another bread baker!

book/references.bib

@@ -136,3 +136,53 @@
   year      = {2006},
   page      = {254}
 }
+
+@article{molecular+mechanisms+yeast,
+  author    = {Jure Piskur et al.},
+  title     = {Molecular Mechanisms in Yeast Carbon Metabolism},
+  year      = {2014},
+  page      = {98}
+}
+
+@article{effects+oxygen+yeast+growth,
+  author    = {Hiroshi Kuriyama et al.},
+  title     = {Effects of oxygen supply on yeast growth and metabolism in continuous fermentation},
+  year      = {1993},
+  journal   = {Journal of Fermentation and Bioengineering},
+  publisher = {Elsevier},
+  volume    = {75,5},
+  pages     = {364--367}
+}
+
+@article{endophytes+in+plants,
+  author    = {Matsumoto H et al.},
+  title     = {Bacterial seed endophyte shapes disease resistance in rice},
+  year      = {2021},
+  journal   = {Nature Plants},
+  volume    = {7},
+  pages     = {60--72}
+}
+
+@article{leaf+surface+sugars+epiphytes,
+  author    = {Julien Mercier},
+  title     = {Role of Leaf Surface Sugars in Colonization of Plants by Bacterial Epiphytes},
+  year      = {2000},
+  journal   = {Applied and Environmental Microbiology},
+  volume    = {66,1}
+}
+
+@article{yeasts+biocontrol+agent,
+  author    = {Gianluca Bleve et al.},
+  title     = {Isolation of epiphytic yeasts with potential for biocontrol of Aspergillus carbonarius and A. niger on grape},
+  year      = {2006},
+  journal   = {International Journal of Food Microbiology},
+  volume    = {108,2}
+}
+
+@article{saccharomyces+cerevisiae+pathogen,
+  author    = {Sabine Gognies et al.},
+  title     = {Saccharomyces cerevisiae, a potential pathogen towards grapevine, Vitis vinifera},
+  year      = {2001},
+  journal   = {FEMS Microbiology Ecology},
+  volume    = {37,2}
+}