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Invisiblehermitic
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Book club: 21st Century Guidebook to Fungi
    #28289201 - 04/21/23 10:30 PM (9 months, 2 days ago)

Hey folks! I want to gain a deeper understanding of mycology as a whole (not just the parts needed for a successful cube or oyster grow), and I think reading through a mycology textbook might be a good way to do that.

I'm looking at 21st Century Guidebook to Fungi (website, pdf), and I was thinking folks here might be interested in a book club, where we read at a set schedule and discuss in a thread. Anyone interested? If so, say what kind of pace you'd be interested in. I think trying to do a chapter a week (ranging from ~20-50 pages, usually) would probably be reasonable.

Here's the table of contents (it's long, people are of course welcome to dip in and out as they find things interesting):

Code:

Part I Nature and origins of fungi
1 21st century fungal communities
1.1 What and where are fungi?
1.2 Soil, the essential terrestrial habitat
1.3 How much soil is there and where is it?
1.4 The nature of soil and who made it
1.5 Soil biota are extremely variedand numerous
1.6 Microbial diversity in soil
1.7 Microbial diversity in general
1.8 Geomycology
1.9 The origins of agriculture and ourdependence on fungi
1.10 References and further reading
2 Evolutionary origins
2.1 Life, the universe and everything
2.2 Planet Earth: your habitat
2.3 The Goldilocks planet
2.4 The tree of life has three domains
2.5 The Kingdom Fungi
2.6 The opisthokonts
2.7 Fossil fungi
2.8 The fungal phylogeny
2.9 References and further reading
3 Natural classification of fungi
3.1 The members of the Kingdom Fungi
3.2 The chytrids
3.3 More chytrids: the Neocallimastigomycota
3.4 Blastocladiomycota
3.5 Glomeromycota
3.6 The traditional Zygomycota
3.7 Ascomycota
3.8 Basidiomycota
3.9 The species concept in fungi
3.10 The untrue fungi
Water moulds
Slime moulds
3.11 Ecosystem mycology
Lichens
Endophytes
Epiphytes
3.12 References and further reading
Part II Fungal cell biology
4 Hyphal cell biology and growth on solid substrates
4.1 Mycelium: the hyphal mode of growth
4.2 Spore germination and dormancy
4.3 The fungal lifestyle: colony formation
4.4 Mycelium growth kinetics
4.5 Colony growth to maturity
4.6 Morphological differentiation of fungal colonies
4.7 Duplication cycle in moulds
4.8 Regulation of nuclear migration
4.9 Growth kinetics
4.10 Autotropic reactions
4.11 Hyphal branching
4.12 Septation
4.13 Ecological advantage of mycelial growth in colonising solid substrates
4.14 References and further reading
5 Fungal cell biology
5.1 Mechanisms of mycelial growth
5.2 The fungus as a model eukaryote
5.3 The essentials of cell structure
5.4 Subcellular components of eukaryotic cells: the nucleus
5.5 The nucleolus and nuclear import and export
5.6 Nuclear genetics
5.7 Mitotic nuclear division
5.8 Meiotic nuclear division
5.9 Translation of mRNA and protein sorting
5.10 The endomembrane systems
5.11 Cytoskeletal systems
5.12 Molecular motors
5.13 Plasma membrane and signalling pathways
5.14 Fungal cell wall
5.15 Cell biology of the hyphal apex
5.16 Hyphal fusions and mycelial interconnections
5.17 Cytokinesis and septation
5.18 Yeast-mycelial dimorphism
5.19 References and further reading
6 Structure and synthesis of fungal cell walls
6.1 The fungal wall as a working organelle
6.2 Fundamentals of wall structure and function
6.3 Fundamentals of wall architecture
6.4 The chitin component
6.5 The glucan component
6.6 The glycoprotein component
6.7 Wall synthesis and remodelling
6.8 On the far side
6.9 The fungal wall as a clinical target
6.10References and further reading
Part III Fungal genetics and diversity
7 From the haploid to the functional diploid: homokaryons, heterokaryons, dikaryons and compatibility
7.1 Compatibility and the individualistic mycelium
7.2 Formation of heterokaryons
7.3 Breakdown of a heterokaryon
7.4 The dikaryon
7.5 Vegetative compatibility
7.6 Biology of incompatibility systems
7.7 Gene segregation during the mitotic division cycle
7.8 Parasexual cycle
7.9 Cytoplasmic segregations: mitochondria, plasmids, viruses and prions
7.10 References and further reading
8 Sexual reproduction: the basis of diversity and taxonomy
8.1 The process of sexual reproduction
8.2 Mating in budding yeast
8.3 Mating type switching in budding yeast
8.4 Mating types of Neurospora
8.5 Mating types in Basidiomycota
8.6 Biology of mating type factors
8.7 References and further reading
9 Continuing the diversity theme: cell and tissue differentiation
9.1 What is diversity?
9.2 Mycelial differentiation
9.3 Making spores
9.4 Aspergillus conidiophores
9.5 Conidiation in Neurospora crassa
9.6 Conidiomata
9.7 Linear structures: strands, cords, rhizomorphs and stipes
9.8 Globose structures: sclerotia, stromata, ascomata and basidiomata
9.9 References and further reading
Part IV Biochemistry and developmental biology of fungi
10 Fungi in ecosystems
10.1 Contributions of fungi to ecosystems
10.2 Breakdown of polysaccharide: cellulose
10.3 Breakdown of polysaccharide: hemicellulose
10.4 Breakdown of polysaccharide: pectins
10.5 Breakdown of polysaccharide: chitin
10.6 Breakdown of polysaccharide: starch and glycogen
10.7 Lignin degradation
10.8 Digestion of protein
10.9 Lipases and esterases
10.10 Phosphatases and sulfatases
10.11 The flow of nutrients: transport and translocation
10.12 Primary (intermediary) metabolism
10.13 Secondary metabolites, including commercial products like statins and strobilurins
10.14 References and further reading
11 Exploiting fungi for food
11.1 Fungi as food
11.2 Fungi in food webs
11.3 Wild harvests: commercial mushroom picking
11.4 Cells and mycelium as human food
11.5 Fermented foods
11.6 Industrial cultivation methods
11.7 Gardening insects and fungi
11.8 Development of a fungal fruit body
11.9 References and further reading
12 Development and morphogenesis
12.1 Development and morphogenesis
12.2 The formal terminology of developmental biology
12.3 The observational and experimental basis of fungal developmental biology
12.4 Ten ways to make a mushroom
12.5 Competence and regional patterning
12.6 The Coprinopsis fruit body: making hymenia
12.7 Coprinopsis and Volvariella making gills (not forgetting how polypores make tubes)
12.8 The Coprinopsis fruit body: making stems
12.9 Coordination of cell inflation throughout the maturing fruit body
12.10 Mushroom mechanics
12.11 Metabolic regulation in relation to morphogenesis
12.12 Developmental commitment
12.13 Comparisons with other tissues and other organisms
12.14 Classic genetic approaches to study development and the impact of genomic data mining
12.15 Degeneration, senescence and death
12.16 Basic principles of fungal developmental biology
12.17 References and further reading
Part V Fungi as saprotrophs, symbionts and pathogens
13 Ecosystem mycology: saprotrophs, and mutualisms between plants and fungi
13.1 Ecosystem mycology
13.2 Fungi as recyclers and saprotrophs
13.3 Make the earth move
13.4 Fungal toxins: food contamination and deterioration (including mention of statins and strobilurins)
13.5 Decay of structural timber in dwellings
13.6 Using fungi to remediate toxic and recalcitrant wastes
13.7 Release of chlorohydrocarbons into the atmosphere by wood-decay fungi
13.8 Introduction to mycorrhizas
13.9 Types of mycorrhiza
13.10 Arbuscular (AM) endomycorrhizas
13.11 Ericoid endomycorrhizas
13.12 Arbutoid endomycorrhizas
13.13 Monotropoid endomycorrhizas
13.14 Orchidaceous endomycorrhizas
13.15 Ectomycorrhizas
13.16 Ectendomycorrhizas
13.17 The effects of mycorrhizas and their commercial applications and the impact of environmental and climate changes
Other benefits of mycorrhizal associations
Structure and change of natural communities
The impact of climate change
Commercial applications of mycorrhizas
13.18 Introduction to lichens
13.19 Introduction to endophytes
13.20 Epiphytes
13.21 References and further reading
14 Fungi as pathogens of plants
14.1 Fungal diseases and loss of world agricultural production
14.2 A few examples of headline crop diseases
14.3 The rice blast fungus Magnaporthe grisea (Ascomycota)
14.4 Armillaria (Basidiomycota)
14.5 Pathogens that produce haustoria (Ascomycota and Basidiomycota)
14.6 Cercospora (Ascomycota)
14.7 Ophiostoma (Ceratocystis) novo-ulmi (Dutch elm disease or DED) (Ascomycota)
14.8 Black stem rust (Puccinia graminis f. sp. tritici) threatens global wheat harvest
14.9 Plant disease basics: the disease triangle
14.10 Necrotrophic and biotrophic pathogens of plants
14.11 The effects of pathogens on their hosts
14.12 How pathogens attack plants
14.13 Host penetration through stomatal openings
14.14 Direct penetration of the host cell wall
14.15 Enzymatic penetration of the host
14.16 Preformed and induced defence mechanisms in plants
14.17 Genetic variation in pathogens and their hosts: co-evolution of disease systems
14.18References and further reading
15 Fungi as symbionts and predators of animals
15.1 Fungal co-operative ventures
15.2 Ant agriculture
15.3 Termite gardeners of Africa
15.4 Agriculture in beetles
15.5 Anaerobic fungi and the rise of the ruminants
15.6 Nematode-trapping fungi
15.7 References and further reading
16 Fungi as pathogens of animals, including humans
16.1 Pathogens of insects
16.2 Microsporidia
16.3 Trichomycetes
16.4 Laboulbeniales
16.5 Entomogenous fungi
16.6 Biological control of arthropod pests
16.7 Cutaneous chytridiomycosis: an emerging infectious disease of amphibians
16.8 Aspergillosis disease of coral
16.9 Mycoses: the fungus diseases of humans
16.10 Clinical groupings for human fungal infections
16.11 Fungi within the home and their effects on health: allergens and toxins
16.12 Comparison of animal and plant pathogens and the essentials of epidemiology
16.13 Mycoparasitic and fungicolous fungi
16.14 References and further reading
Part VI Fungal biotechnology and bioinformatics
17 Whole organism biotechnology
17.1 Fungal fermentations in submerged liquid cultures
17.2 Culturing fungi
17.3 Oxygen demand and supply
17.4 Fermenter engineering
17.5 Fungal growth in liquid cultures
17.6 Fermenter growth kinetics
17.7 Growth yield
17.8 Stationary phase
17.9 Growth as pellets
17.10 Beyond the batch culture
17.11 Chemostats and turbidostats
17.12 Uses of submerged fermentations
17.13 Alcoholic fermentations
17.14 Citric acid biotechnology
17.15 Penicillin and other pharmaceuticals
17.16 Enzymes for fabric conditioning and processing, and food processing
17.17 Steroids and use of fungi to make chemical transformations
17.18 The QuornTM fermentation and evolution in fermenters
17.19 Production of spores and other inocula
17.20 Natural digestive fermentations in herbivores
17.21 Solid state fermentations
17.22 Digestion of lignocellulosic residues
17.23 Bread: the other side of the alcoholic fermentation equation
17.24 Cheese and salami manufacture
17.25 Soy sauce, tempeh and other food products
17.26 References and further reading
18 Molecular biotechnology
18.1 Antifungal agents that target the membrane
18.2 Antifungal agents that target the wall
18.3 Clinical control of systemic mycoses at the start of the 21st century: azoles, polyenes and combinatorial therapy
18.4 Agricultural mycocides at the start of the twenty-first century: strobilurins
18.5 Understanding fungal genetic structure
18.6 Sequencing fungal genomes
18.7 Annotating the genome
18.8 Fungal genomes and their comparison
18.9 Manipulating genomes: targeted gene disruption, transformation and vectors
18.10 Fungi as cell factories producing heterologous proteins
18.11 Recombinant protein production by filamentous fungi
18.12 Bioinformatics in mycology: manipulating very large data sets
18.13 Genomic data mining supports the notion that there are different developmental control mechanisms in fungi, animals and plants
18.14 Effects of climate change on fungi revealed by analysis of large survey data sets
18.15 Cyber fungi: mathematical modelling and computer simulation of hyphal growth



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Invisiblejack_straw2208
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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28289228 - 04/21/23 11:11 PM (9 months, 1 day ago)

I am just a little wary of the site


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Invisiblehermitic
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Re: Book club: 21st Century Guidebook to Fungi [Re: jack_straw2208]
    #28289238 - 04/21/23 11:28 PM (9 months, 1 day ago)

The library.lol link is Library Genesis, which is generally quite trusted as far as these things go. You can of course find it elsewhere/on your own if you'd prefer.


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InvisibleChRnZN
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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28289598 - 04/22/23 09:10 AM (9 months, 1 day ago)

Ha, Library Genesis is an illegal site but it survives (like the pirate bay) because it hides its stolen content behind a hundred different layers of code and proxies. Not that its really "bad" to post links to that kind of thing on the shroomery, its just not a great idea because your post links your profile to an illegal site. Libgen is certainly "trusted" by thieves, but not by your average mushroom enthusiast who usually gets his cultivation guides and mycological literature from more common sources like the bookstore or a site that's actually legal in another country. Just a matter of culture.


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Invisiblejack_straw2208
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Re: Book club: 21st Century Guidebook to Fungi [Re: ChRnZN]
    #28290065 - 04/22/23 03:35 PM (9 months, 1 day ago)

Thank you for chiming in.


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OfflineBirdsOnTrees
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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28291240 - 04/23/23 10:26 AM (9 months, 12 hours ago)

I think this is a great idea and I would be super down to participate in something like this. I just started reading Mushroom Biology: Concise Basics and Current Developments by Miles and Chang (like 1 chapter in), and am loving it, but I am down to switch to another text and also to have a group of people to chat with about what we're learning. Keep me posted please!


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Edited by BirdsOnTrees (04/23/23 11:39 AM)


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Offlinewanderingpsilocybe
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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28294131 - 04/25/23 02:25 AM (8 months, 29 days ago)

Thanks so much for the suggestion I’ve been trying to fill the gap in my knowledge from being a dedicated enthusiast to actual knowing more details about fungi and their processes biologically/chemically. I started it tonight am taking notes. Got up to section 1.8 today trying to do 1/2-1 section a day.


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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28295962 - 04/26/23 09:11 AM (8 months, 28 days ago)

Lead the way!


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Invisiblehermitic
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Re: Book club: 21st Century Guidebook to Fungi [Re: Shu]
    #28296488 - 04/26/23 05:11 PM (8 months, 28 days ago)

Ok, sounds like there are enough people interested to go ahead with this!

Let's start out at one chapter per week, starting with Chapter 1 (today — May 3rd). Please post any notes, things you found interesting, questions, etc in this thread.

Looking forward to going through it with everyone!


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OfflineBirdsOnTrees
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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28296518 - 04/26/23 05:31 PM (8 months, 28 days ago)

I've got finals this week, so I might be lagging behind just a little bit, but I'll get started this weekend. I'm fairly studious so I'll likely be able to keep up but there's a chance I'll be a bit behind.

Excited to learn with all'ya'all :boombox2:


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Invisiblehermitic
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Re: Book club: 21st Century Guidebook to Fungi [Re: BirdsOnTrees]
    #28296891 - 04/26/23 09:23 PM (8 months, 28 days ago)

And, here are my notes:

  • first eukaryotes were "fungal in nature"
  • 95% of all terrestrial plants depend on mycorrhizal fungi
  • less than 1% of the known species of fungi have been found in marine habitats
  • soil air always has a relative humidity near 100%
  • 20,000 kilometres of hyphae per square metre of agricultural soil
  • ~1.5 million species of fungi on Earth, only 98,000 of which have been isolated or described
  • fungi are involved in geological transformation of soil
  • many fungi can grow oligotrophically — thriving in environments with few food sources by scavenging nutrients from air and rainwater


“We have been dependent on fungi since we became human.”

Overall — mostly background info, but some interesting stuff in here. Looking forward to chapter two.


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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28298544 - 04/28/23 07:46 AM (8 months, 26 days ago)

I'll use these posts to record my notes as I go...
Chapter 1, 4/28
  • As it stands, the Earth does not have enough land for all inhabitants to enjoy an affluent diet as that is presently defined
    -=- I had no idea there was simply not enough arable land on earth for everyone to have an american diet

  • 4x10^10 cells/g soil (dry weight); but the viable count was 4x10^6 colony-forming units/g soil.  There may be several reasons for it, including fastidious growth requirements of presently unknown nature, and our current inability to break the dormancy of many of the living cells that can be detected.
    -=- only 1% of the organisms in soil are cultivable! There is a huge reservoir life about which we know little or nothing

  • If you subtract the 98 000 described species from the estimated total 1.5 million species of fungi on Earth, you might well ask: ‘Where are the other 1.402 million undescribed fungi?’
    -=- I've noticed several undue conclusions and hyperbole. I suppose they're meant to stimulate the imagination but at this rate it's going to become tiresome quickly.

  • desert varnish...chemical interactions of exopolysaccharide with mineral substrates
    -=- I always thought that patina was just oxides, huh! Biofilm.

  • There is increasing evidence that fungi are important components of rock-inhabiting microbial communities with significant roles in mineral dissolution and secondary mineral formation.
    -=- I guess I'll start adding the rock dust to to the heap before composting rather than after

    Chapter 2, 5/9

  • the Earth is comfortably located in what astronomers have called the ‘Goldilocks orbit'
    -=-should read "Goldilocks Zone", there are many Goldilocks orbits

  • the iron Theia contained slurped into the Earth’s liquid iron core, and rocky debris
    from the impact exploded into orbit around the Earth

  • You will appreciate that if Earth’s orbit was very slightly closer to the Sun, let’s say by about one Earth radius, surface temperatures would be intolerably high all the time.
    -=-The earth's radius is 4000 miles while the orbital radius is about 93 million miles. The southern summer is 1.3 million mile closer to the sun than the northern summer.  Their statement goes beyond hyperbole, it's just wrong.

  • Although SSU rRNA genes satisfy these criteria, it is important not to allow phylogenetic trees based on a single gene to dominate evolutionary and systematic conclusions. Instead, account needs to be taken of phylogenetic trees based on a range of conserved molecules with a judgement being made about the weight to be given to the different lines of evidence so obtained.
    Table 2.1 Ribosomal rRNA sequences used to identify and classify fungi

  • They concluded that the ‘greening of Earth’ started about 850 million years
    ago in coastal regions and resulted in an extensive spread of photosynthetic microbes (as ‘an explosion of photosynthesising communities on late Precambrian land surfaces’). They suggest that by 1000 million years ago this ‘greening’ was sufficient to increase atmospheric oxygen,
    -=-retrocausality?



Edited by Shu (05/10/23 11:09 AM)


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Re: Book club: 21st Century Guidebook to Fungi [Re: Shu]
    #28302248 - 05/01/23 01:30 PM (8 months, 23 days ago)

Hey friends, here are some notes of mine from reading the first chapter:

- molecular phylogenetics places animals and fungi together at the root of evolutionary trees with the first eukaryotes being “fungal in nature”
   
- A subsistence diet requires about 180 kg of grain per person per year, which requires on average 0.045 hectares of land, but an affluent meat diet requires at least 4x more grain (=0.18 hectares)
   
- Soil has solid, liquid and gaseous phases integrated together.
   
- Elements most commonly found in soil minerals are silicon, oxygen and aluminum
   
- Grasslands and forests form different soils, with there being more rapid nutrient recycling in grasslands
   
- Hummus is slowly decomposing organic material
   
- Soil air has more CO2, but less O2 than open atmosphere
   
- 20k kilometers of hyphae per square meter
   
- Ecosystem diversity is measured by range of processes, complexity of interactions, and # of trophic levels.
   
- Less than 1% of fungal organisms can be cultivated and characterized as live cultures
   
- Estimated 1.5 million species of fungi on earth with only 98,000 isolated and described
   
- many fungi are oligotrophic, meaning they thrive in low resource and nutrient environments


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Re: Book club: 21st Century Guidebook to Fungi [Re: hermitic]
    #28304778 - 05/03/23 11:06 AM (8 months, 21 days ago)

Hey guys here are my chapter notes transcribed sorry for being late I hand write mine in a notebook bc it helps me retain info better

1.1
-Fungi are not bacteria they're eukaryotes (organisms whose cells have a nucleus)

1.2
-Overwhelming amount of fungi has soil habitat vs 1%< marine habitat
-all life is dependent on existence of soil

1.3
-Only 7.5% of earth is terrestrial suitable for agriculture the other 5% of terrestrial is poor quality/rocky

1.4
-Soil is part of the earth's surface that is composed of fragmented rock and humus (dark organic matter in soil formed by decomposition of organic material)
-most common elements in soil minerals: Silicon, Aluminum,
-When Soil is moved down: leeching effect of rain water. Wind, Water and Ice: <- ->
-Climate is most important soil forming factor ie. Temp, rainfall, living organisms + vegetation (effects run off, erosion, organic matter deposited on surface, soil microbial nutrients) = faster chemical processes
-Humus is the main carbon reservoir in the biosphere
-Organic soil is dominated by organic matter vs mineral wetlands where production of organic materials by plants exceed rate of decomposition = peat formation

-Soil is made up of Solid, Liquid and Gaseous phases

-Solid-> mineral + organic matter
-minerals can be primary (cooled from a molten mass and chemically unchanged from the day they’re created) or secondary (formed by chemical modification–precipitation, recrystallization, of chems released by weathering of parental rocks)

Liquid-> 'soil solution' from which plants/organisms take up nutrients + -water

-Gas-> soil atmosphere supplying oxygen to plant roots & other organisms for respiration

-Rocks: Igneous (from magma) Sedimentary (cemented accumulations of minerals (limestone, sandstone, quartzite, shale)) Metamorphic (started as one rock and became another (slate hardened shale marble, hardened limestone))

-Weathering -> processes that cause rocks and minerals to disintegrate into smaller parts -> loose unconsolidated weathering is soil
-Physical: main force is expansion of water when frozen
-Chemical: warm/moist climates & most important
->Oxidation & Reduction (gain/loss of Oxygen)
->Carbonation (dissolution of minerals in H2O made acidic by CO2)
->Hydrolysis (who water splits into H and OH- and one or
            more particle participates directly)
->Hydration (when water is incorporated into crystal structure of a mineral, changing the properties of that mineral)

-Space btw soil particles = “Pore Space” which contains air + water
-Soil Air: more CO2, less O2 than open air b/c organisms in soil consume O2/Produce CO2, soil has relative humidity of 100%
-Soil Solution: contains soluble salt, organic solutes and some colloids, soil water controlled by pore size/influenced by proportion of coarse materials like can and fine minerals like clay
-Small Pores = more water/water retention
-Large Pores=water escape by drainage or evaporation
-Soil is a dynamic matrix of organic and mineral constituents enclosing a network of pores and voids.

1.5
-

1.6
-

1.7

-Micro Organisms exist I basically every place on earth–temperature is maybe the only limit on where they can/cant exist
-Mycologist eat there are 1.5mil fungi species/only 98k have been isolated
-Fungi communities are very diverse metabolically, physiologically and taxonomically

1.8
-Geomycology : fungal involvement in geological transformations that produce & modify soils
-Fungi is involved in biogeochemical xformations large and small
-In/Organic xformations element cycling
-rock/mineral xformations
-bioweathering
-mineral formation
-fungal clay interactions
-metal/fungal interactions
-The Fungal form is ideal for soil but pore network determines how mycelia grown through soil as well as the distribution of water + spatial distributions of nutrients crucial to fungal activity and development (my favorite part)
-Many fungi can grow oligiotrophically ie. Thrive in environs low on food sources
-Scavenge nutrients from air and rain water which allows them to survive on stone  surfaces

1.9
Great tables

Fin


Edited by wanderingpsilocybe (05/03/23 11:07 AM)


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