Talk:Fungus/Archive 2

Yeast are animals, not fungi

I corrected it but it was reverted without discussion. Why?

• Because yeast are fungi. Abductive (reasoning) 06:13, 24 September 2009 (UTC)
• Yeast is not a distinct group of organisms, but is a life stage (i.e., growth habit) sometimes used by many different fungi. Cbrownhead (talk) 02:56, 18 November 2009 (UTC)

Mating in fungi

I recently came across Mating in fungi. I'm not sure if it covers the same things Fungus#Reproduction, but is it possible to merge it into that section if there is anything to merge? Squids'and'Chips 23:53, 11 April 2007 (UTC)

I prefer the idea of making Fungus#Reproduction an overview with a link for "See main article on Reproduction in Fungi (which I think is a better name for the article since it would allow both sexual and asexual reproduction to be covered). I won't change anything until others weigh in though. Jvbishop 13:56, 12 April 2007 (UTC)

Yes. "Reproduction" is better since "mating" presupposes male and female organisms whereas each fungal spore produced by a sporocarp is capable of merging with (nearly) every other spore produced by it. So we signify one from the other by using a positive (+) for the one we are looking at with a negative (-) symbol for all the other spores, cells or nuclei having "mate" potential. --Mycos (talk) 01:10, 19 February 2009 (UTC)

Fungus (2 votes) wins May-June Collab

Support:

1. Cas Liber 06:07, 10 January 2007 (UTC)
2. M&NCenarius 04:29, 16 January 2007 (UTC)

Comments:

• I forgot the original fungus article. As with Dinosaur, I guess there is a case to be made for this one as well to be first cab off the rank...Cas Liber 06:07, 10 January 2007 (UTC)
• "Fungus" actually was the target of an article improvement drive some months back, but which only yielded limited contributions. This article actually needs a lot of work and there are a lot of important topics that simply aren't covered. Check the "To Do" list and outline I've left on the talk page. Peter G Werner 22:28, 10 January 2007 (UTC)

Phylogeny and classification

Fifth line down on this Heading say "Cutting edge research" This is ambiguous and an opinion, not a concise fact. Lewis Haycraft 17:48, 5 June 2007 (EST) too lazy to mentally figure the UTC

The cladogram added, apart from the formatting problems, is problematical. Choanozoa appears not to be a clade (Cavalier-Smith doesn't mind paraphyletic taxa). The papers I've read suggests that there are five lineages involved here, icthyosporeans (mesomycetozoa, DRIPS), choanoflagellates, and three amoebiform groups, the nucleariid, capsosporid and ministeriid amoebas, these being respectively, IIRC, the sisters to fungi, mesomycetozoans and animals. I also wonder if there are statements in the text (e.g. presence of flagellae) applied to chytrids which should be applied to the three phyla into which they have been divided. Lavateraguy 19:11, 10 August 2007 (UTC)

Microsporidia

There ought to be something about microsporidia in the page. BTW, there's a newish paper on fungal classification, Hibbett et al, higher-level phylogenetic classification of the Fungi, Mycological Research 111: 509–547 (2007). Lavateraguy 20:31, 20 July 2007 (UTC)

We've applied the changes described in the paper, except the ones the authors weren't sure about. Microsporidia are still under Zygomycota here, although they're clearly not related to other members in the phylum. Everything in Zygomycota is really incertae sedis. Bendž|Ť 20:44, 20 July 2007 (UTC)

I didn't mean to suggest that Microsporidia should be included separately in the list of phyla/divisions. Whether Microsporidia is nested in Zygomycota remains, as far as I know, an open question. My point was intended to be that microsporidia are a distinctive, derived, group of fungi, and have as much right to a mention somewhere in the text as say lichens. Lavateraguy 19:11, 10 August 2007 (UTC)

Oh, and it seems to me that a category Microsporidia would be a good idea - so if microsporidians are excluded from Zygomycota youall only have to change the category, rather than all the microsporidia pages.

I've noticed inconsistencies with taxoboxes relating to microsporidia (and I've probably added to the problem myself); in particular with the ranks. The classification of microsporidia is uncertain enough that a "right" solution is not obviously to hand, but it would be nice if Wikipedia was at least consistent.

(Zyomycetes has Microsporidia as an order; Microsporidia has it as class.) Lavateraguy 21:17, 27 August 2007 (UTC)

Requested move

The following discussion is an archived discussion of the proposal. Please do not modify it. Subsequent comments should be made in a new section on the talk page. No further edits should be made to this section.

The result of the proposal was no consensus to move the page, per the discussion below. Dekimasuよ! 05:38, 19 December 2007 (UTC)

---

• Fungus → Fungi — The plural rather than singular form should be used as the article title — -- Alan Liefting-talk- 21:05, 16 December 2007 (UTC)

People, fungus do not grow in the Arctic!

Survey

Feel free to state your position on the renaming proposal by beginning a new line in this section with *'''Support''' or *'''Oppose''', then sign your comment with ~~~~. Since polling is not a substitute for discussion, please explain your reasons, taking into account Wikipedia's naming conventions.

• Oppose - we have bird, dinosaur, plant etc. why should this be different? cheers, Casliber (talk · contribs) 23:06, 16 December 2007 (UTC)

• Oppose - as already voiced by Casliber, most biology entries are singular, so there's no reason to change to the plural here. Thanks. Malljaja (talk) 23:44, 16 December 2007 (UTC)

• Oppose - other biological Kingdoms e.g. Animalia / Plantae similarly redirect to animal/plant, so no need for Fungi to be different. --Graminophile (talk) 01:38, 17 December 2007 (UTC)

• Oppose per above. Plant, animal, etc. are all singular and most encyclopedias don't pluralize such entries. Snocrates 04:09, 17 December 2007 (UTC)

• Oppose. I'm at a loss to think of any reason for this proposal, and none has been given. On the other hand, Wikipedia official policy at Wikipedia:Naming conventions#Prefer singular nouns reads In general only create page titles that are in the singular..., and none of the exceptions listed there seem to fit this case, nor do those mentioned at Wikipedia talk:Naming conventions/Archive 5#SOME article titles should be plural. Andrewa (talk) 16:35, 17 December 2007 (UTC)

• Oppose - Per Casliber. Stick to the singular, it makes more sense. Reginmund (talk) 22:41, 17 December 2007 (UTC)

Discussion

Any additional comments:

I'm not happy with the grammar of the first sentence though - "fungi are..." but surely "Fungi (Kingdom) is..." --Graminophile (talk) 01:41, 17 December 2007 (UTC)

The above discussion is preserved as an archive of the proposal. Please do not modify it. Subsequent comments should be made in a new section on this talk page. No further edits should be made to this section.

fungi do not devise

The article reads: Some fungi are predators of nematodes, which they capture using an array of devices such as constricting rings or adhesive nets.

Fungi do not use devices. Fungi use structures. Please correct. —Preceding unsigned comment added by 76.233.38.164 (talk) 00:24, 21 March 2008 (UTC)

Rather nit picky I'd day since most readers certainly understand what is ment. But go ahead anyway 76.233.38.164 if it hasn't been done already. J.H.McDonnell (talk) 01:58, 14 January 2010 (UTC)

Mycology journals

I've recently included three leading mycology research journals under the external links section. However, my additions got reverted here. I'm well aware that this section is often likely to balloon, but I feel that their inclusion is warranted here, since these are the top three mycological journals dealing with all aspects of the fungi. So I'm seeking some additional opinions as to whether their inclusion would be problematic or unjustified. Thanks! Malljaja (talk) 15:36, 2 August 2008 (UTC)

They are mycology journals, and would be better added there. --EncycloPetey (talk) 16:26, 2 August 2008 (UTC)

Alternative pronunciation of the plural.

/ˈfʌngaɪ/ is the typical pronunciation in the US. Please add alongside the UK /ˈfʌndʒaɪ/. See: http://dictionary.reference.com/browse/fungi --Evaniax (talk) 08:16, 9 November 2008 (UTC)

There are multiple pronunciations in both countries. That variation is handled at Wiktionary, not here on Wikipedia. --EncycloPetey (talk) 18:56, 11 November 2008 (UTC)

No, the variation is not even mentioned in Wiktionary. Many Wikipedia entries feature alternative pronunciations, see for example Xanthine. --Evaniax (talk) 01:39, 17 November 2008 (UTC)

But in that case it's the name of the article and there are two (and only two) pronunciation variants. In this case, the name of the article is 'Fungus, which has only one English pronunciation. You are correct that Wiktionary does not currently have the pronunciation information being discussed, but it is a Wiki. You can add it there. --EncycloPetey (talk) 18:51, 18 November 2008 (UTC)

/ˈfʌndʒaɪ/ is quite simply wrong. I don't know what sort of Latin you speak, but there is no case where a "g" is pronounced as /dʒ/. Latin does not even contain that phoneme. Now the article no longer includes the proper pronunciation, which is /ˈfʌngaɪ/. --70.131.246.208 (talk) 00:10, 18 March 2009 (UTC)

Except that "fungi" as used in the article is quite simply an English word, and need not be pronounced as it was in the Latin from which it was borrowed. Agathman (talk)

Are we not getting embroyled in the errelevant. It's realy mute whether to pronounce it fungi with a hard G as in go, or fungi with a soft G as in range. Stick with the science. J.H.McDonnell (talk) 02:05, 14 January 2010 (UTC)

Eumycota

Eumycota links here, but this article doesn't define the term. Shinobu (talk) 00:54, 27 December 2008 (UTC)

How do fungi benefit the environment?

--67.83.59.176 (talk) 01:00, 10 February 2009 (UTC) Cell walls of plants are made of cellulose and other large molecules. Animals are unable to digest cellulose. It's the major source of non-digestible fiber in our diets. Luckily fungi and other microorganisms are able to break down these compounds. If this were not the case then plant material, especially wood, would never rot and instead pile up, trapping high amounts of carbon and dropping the level of atmospheric carbon dioxide, seriously limiting future plant growth. Fungi are crucial recyclers! They release carbon, nitrogen and other needed nutrients for organisms and enrich the soil. But what about wood-eating termites and ruminants such as cows? Their guts contain specialized fungi and bacteria for plant digestion!

Mycorrhizae greatly increase a plant's uptake of nutrients, especially phosphorus and nitrogen, increase water uptake, and provide protection against soil pathogens. In exchange the fungi obtain sugars and other compounds. The vast majority of terrestrial plants, from oak trees to lawn grass and petunias, have mycorrhizal fungi helping them grow. Many plants utilize one kind of microscopic fungi within their roots (endomycorrhizae formed by zygomycetes). Most conifers and many hardwoods (e.g., birch, oak, aspen families) are partners with larger fungi which form fruitbodies or mushrooms. These ectomycorrhizae (meaning outside - fungus - roots) are formed by many basidiomycetes and certain ascomycetes. The sheathing fungus forms an interface between the root and the soil. Associations can be very specific. Certain Suillus grow only with white pine (five-needle pine) while other Suillus species associate with two-needle pines. Other fungi are not as choosy and may even form interconnections between different plant species. Recent studies show that net carbon flow can occur between two tree species (e.g., birch and spruce) via the mycorrhizal fungi. Roverous

Just out of curiosity...

Are there plans in the short term to bring this article to FA-level? Other fungi have already been featured, and this one is the most important article in all of mycology. Leptictidium (mt) 20:49, 16 February 2009 (UTC)

Well, GA level in the short-term, FA-level will take a while (and input from others). Will post about plans and to-do list soon. Sasata (talk) 21:42, 16 February 2009 (UTC)

GA level should indeed be doable, and you're right it's the most important one. I've been working on this entry off and on over the last year or so, and I've seen it develop, but it's been slow in coming and can do with additional input. One recurring problem with this article has been frequent vandalism. It's under protection now, but this may affect its ratings. I look forward to the to-do list & other plans. Malljaja (talk) 21:52, 16 February 2009 (UTC)

Importance for humans

I feel the section "Importance for human use" should be moved below "Ecology" to make the article a little less anthropocentric. On the other hand I realise that the IFHU section is perhaps of greater interest to many readers. So I'm looking for some opinions re the structure of the entry. Thanks! Malljaja (talk) 19:16, 17 February 2009 (UTC)

I just restructured all the sections in the article in way that I think is more logical, including moving "Importance for Human Use" below "Ecology". In a sense, human uses of fungi are subset of ecological relationships, much like ant cultivation of fungi. Its just that from a human-centered point of view, that set of ecological relationships takes on a particular importance that elevates it to a topic in its own right. Peter G Werner (talk) 17:04, 18 February 2009 (UTC)

Hi Peter, thanks for re-arranging the entry including the IfHU section—I agree that this new organisation is more logical. Malljaja (talk) 18:13, 18 February 2009 (UTC)

The future of Fungus

It seems like there's agreement that this article—the most important of fungi articles—deserves to have some work done to help bring it up to featured quality. I'd like to start a to-do list to help organize that effort. I've read through the article a few times, and compared it to the Bacteria article, which is FA quality. If we make the assumption that the scope covered by both is roughly equivalent in breadth, then there's still at least another 20k that can be added to the length, and I believe ~100k is a good size to aim for. Ok, I'll toss out some ideas, please add to the list: Sasata (talk) 05:22, 22 February 2009 (UTC)

1. History section. Ideally, History of mycology will be a separate article that can be linked, but until then there should be at least a couple of paragraphs in here.
2. Put citation tags on anything that needs a source. Check all existing citations in the original sources, to confirm what's said in the article matches what's said in the source. When possible, primary sources should be swapped out for good secondary sources. All refs to go in proper citation templates with consistent formatting.
3. Pictures are needed in the characteristics, and diversity sections. With subject matter like this there's no reason for the article to not be lavishly illustrated with informative pictures.
4. In the reproduction section, the fungi on a Costan Rican fence post needs to be taken out and replaced with fungal life cycle diagram, preferably custom-made with a drawing program, in high-res professional quality (hey, shoot for the sky, right?).
5. Somewhere in this article there needs to be a picture/photo/electron micrograph of hyphae, and mycelia.
6. The cladogram needs some explanatory text. Or, perhaps it should be replaced with a phylogenetic tree?
7. Morphological and physiological features for substrate penetration - this heading has to be shortened.
8. Lichens needs far more recognition, and perhaps a pic or two (as does the Lichen article, but that's another story).
9. All redlinks removed/new articles created for them.

Sounds like a good start, though I wouldn't excise hsitory totally once a daughter article exists, there should still be a small summary. Casliber (talk · contribs) 06:22, 22 February 2009 (UTC)

Sounds very ambitious, but this entry really deserves to be bumped to the next level, and faint heart never wins fair content.

1. History section. I agree that there needs to be one, especially seeing that other major articles have one too. Not sure where to start though, as I'm no expert on this topic,

- I have a couple of books on the history of mycology in front of me, so I could take a stab at it. I've been meaning to start a History of mycology article as well, I think it could be fascinating if done properly. But I'm wondering if this is better suited for the mycology article? There's obvious overlap between this article and mycology and even mushroom, so I'm interested in hearing opinions on how to organize this. Sasata (talk) 20:29, 23 February 2009 (UTC)

I think the Fungus article should have a section on mycology, including a brief subsection on the history of mycology. The Mycology article (which is something else that needs work) could cover the topic in more detail. (I'm not sure if a separate History of mycology article is needed or whether it couldn't be covered in the context of the Mycology article.) BTW, which books on the history of mycology do you have? The two by Nicholas Money? How about EC Large's Advance of the Fungi? Peter G Werner (talk) 23:57, 23 February 2009 (UTC)

I have Money (2006), Ainsworth (1976), An Introduction to the History of Mycology, and Rogers (1977), Brief History of Mycology in North America. I'll add history stuff to the mycology article for now, from which can be reused in Fungi later. A breakout article will be easy enough to make later if the section threatens to become unwieldy. Sasata (talk) 00:49, 24 February 2009 (UTC)

That's great that you have the Ainsworth and Rogers books, because those are hard to come by. I have Advance of the Fungi, which is really a history of plant pathology, but those discoveries also represent milestones in the history of mycology, too. I'll contribute what I can from there, though I haven't read the whole thing (its kind of a long book). Money's Mr Bloomfield's Orchard is another good source. Peter G Werner (talk) 03:56, 24 February 2009 (UTC)

1. Put citation tags on anything that needs a source. This should be doable, but checking the existing ones will be somewhat daunting. I've inserted a number of references a while back, and will try to keep track should queries arise. I'm not sure what you mean by "primary sources should be swapped out for good secondary sources". Textbooks or reviews instead of research articles? I'm vigorously opposed to using such sources unless they're used to back up a broad statement or description, but I'm happy to go with any consensus when reached. References that are open access/open source content would be excellent as citations, since they do not require academic or paid access and therefore could verified by anybody. So I'd suggest swapping these in where possible.

- I was thinking mostly of here and here, where the use of secondary and tertiary sources are encouraged, and I'm thinking ahead to the FAC review. But any reference changes would be done incrementally on a case-by-case basis. Agree with using open access sources. I've got access to a good library and online academic databases, so I'll work on this part. Sasata (talk) 20:29, 23 February 2009 (UTC)

1. Pictures are needed in the characteristics, and diversity sections. I agree--I may have some, but have not navigated the "fair use" labyrinth yet.

I agree with all the other points. Malljaja (talk) 19:18, 23 February 2009 (UTC)

Thanks for bringing this up, Sasata, because I've been thinking about this article too and how it can be improved. The thing with "top level" articles like this is that they're really difficult to get into good shape simply because of the sheer breadth of the topic. Basically, you've got to condense a lot of information down to a concise article. Because of the breadth, I also don't think that the typical one-month article improvement drive is adequate for work on an article like this. My suggestion would be to have a number of AIDs for this, each one covering a particular section (and accompanying breakout article where necessary). An example would be have an AID for just the ecology section – which I can tell you right now is a subject big enough for its own article. So during the article improvement drive, we could get an "Ecology of Fungi" or "Fungal Ecology" article in the best shape possible, and as part of that put together a digest version that would be part of the Fungus article.

- That sounds like a plan that will produce a number of useful new fungi articles. Count me in! Sasata (talk) 20:29, 23 February 2009 (UTC)

Oh, and as for any microscopic pictures, I can supply these. Its actually something I'm working on right now.

Peter G Werner (talk) 19:42, 23 February 2009 (UTC)

- That's great, the article could really use some. Any opinions on the best representative life-cycle to use as a diagram in the Reproduction section? Sasata (talk) 20:29, 23 February 2009 (UTC)

Oh, that's a tough one. Even getting away from highly specialized life cycles like those of the rusts and yeasts, the general life cycles of chytrids, zygomycetes, and dikarya (ascos + basidios) are quite different. And its not really fair to say any one of those is more "representative". Peter G Werner (talk) 23:44, 23 February 2009 (UTC)

Agree. As a comparison, major depressive disorder took 5-6 months on an off, and lion and vampire also took several months IIRC. The other one was bird. I think it gets too fatiguing doing them all in one go. Casliber (talk · contribs) 20:03, 23 February 2009 (UTC)

Article structure : I like the proposed article structure given above in the "To Do" List, but I have made one change. It seems to me that the several sections on fungal reproduction warrant their own section and header, and I have so grouped them in the proposal. --EncycloPetey (talk) 05:40, 24 February 2009 (UTC)

I just updated this and changed it around some. In particular, I think "Ecology" and "Importance to humans" are large and distinct enough topics that they belong in their own sections rather than as part of "general features". The outline that I originally proposed was largely adapted from the Encyclopedia Britannica article on Fungi and may not be the best we can come up with. Still, I think we should at least aim to cover all of the topics the EB article covers. Peter G Werner (talk) 19:31, 24 February 2009 (UTC)

Cladogram

The cladogram needs updating based on papers on the subject from the last few years. The Neocallimastigomycota (a true mouthful) are pretty well established to be in a position sister to the Chytridiomycota, or even in the Chytridiomycota depending on how that's defined. The Zygomycota have now been broken out into several different clades of unclear relationship to one another, but its a group that's, in all likelihood, polyphyletic.

I'd work on this myself, but I really don't know how to work the Wikipedia tree template. Peter G Werner (talk) 04:55, 24 February 2009 (UTC)

If you can point me to a specific article and cladogram to refer to, I have experience doing Wikipedia trees (I did the one for the Plant article as well as those for the Magnoliidae and the Monocotyledons). While I know who some of the leading fungal authors are among the "Eumycota", I don't know which paper(s) to look into for the overall phylogeny of the basal taxa. --EncycloPetey (talk) 05:38, 24 February 2009 (UTC)

Looks like the Tree of Life site is a good bet. Sasata (talk) 05:55, 24 February 2009 (UTC)

If others agree with that cladogram, then I'll use that as my basis. The authors of that ToL page seem to be keeping it updated. --EncycloPetey (talk) 05:59, 24 February 2009 (UTC)

There's also more details and a diagram on page 515 of A higher-level phylogenetic classification of the Fungi, Mycological Research 111: 509–547 (2007), which was mentioned in discussion far above. Sasata (talk) 06:15, 24 February 2009 (UTC)

The TOL cladogram might be a good guide, though it seems to be manually drawn, representing a "consensus" tree based on several papers. I'm not sure why some of the branches are hatched (low bootstrap support?), and that there's a lone species (O. brassicacea) forming a single clade is a little unfortunate. Perhaps this could be somewhat simplified by focussing on the major clades. The Hibbett et al paper may indeed be a good source, as well as this one.Malljaja (talk) 15:00, 24 February 2009 (UTC)

The Hibbett, et al paper that Sasata just linked to is what I've been primarily going on. The TOL cladogram largely follows that, especially if you click on some of the specific branches and see that groups like the Neocallimastigomycota have, in fact, been put into the Chytridiomycota line. Where I do think TOL isn't quite reflecting the consensus of the papers that have been published in the last few years is its treatment of the Zygomycota, which it puts as a branch that "may not be monophyletic". That's an understatement – none of the papers I've seen published on the subject in the last few years support the monophyly of the Zygomycota. Generally speaking, the basal lineages of the fungi are not at all well worked out (low bootstrap/low Baysian posterior probability support), so most consensus diagrams show the groups immediately under the Kingdom Fungi as a "comb" phylogeny consisting of 1) the Microsporidia, 2) the Chytridiomycota (and allies), 3) Blastocladiomycota, 4) Zoopagomycotina, 5) Kickxellomycotina (called Harpellomycotina in a few older papers), 6) Entomophthoromycotina, 7) Mucormycotina (if the name "Zygomycota" is conserved, this group, or a larger clade containing it, would get that name), 8) Glomeromycota, and 9) Dikaryomycota (= Dikarya). The arrangement and relationship between these clades is still not understood, though there is a general sense that the Microsporidia and Chytridiomycota are more basal while the Glomeromycota and Dikaryomycota are more derived (and the two are likely sister taxa, though this hasn't been demonstrated conclusively). Peter G Werner (talk) 19:14, 24 February 2009 (UTC)

OK, this is all way over my head, so I will happily defer to those who know more :) Casliber (talk · contribs) 19:52, 24 February 2009 (UTC)

Here's another relatively recent paper on the basal relationships in the fungi: White MM, et al. (2006). Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98(6): 872–884. The phylogeny in this paper seems to be nicely resolved. Perhaps too well, and I'm not sure if the results of that paper have been generally accepted. Peter G Werner (talk) 22:53, 24 February 2009 (UTC)

Thanks for pointing that out, Peter—I've not directly compared the Hibbett paper and TOL cladogram. It's probably very worth noting somewhere that these trees are based on gene phylogenies, which like any method have some some drawbacks. For example, I've noticed (in Table 1 of the Hibbett paper) that there's a bit of a range of the genes that were used (mostly rRNA or structural genes), which is a possible caveat (aside from the choice of in silico analysis), but presumably the best there is right now—whole genome comparisons are probably in the works, but will not be available soon, I'd expect. Having said all this, what I like about the current cladogram is its relative simplicity (it would be nice though to include plants, oomycetes, and some myxomycetes if only to give the reader some feel for the taxonomic distances). So while acknowledging the complexity of these relationships, the group should be firmly held together, perhaps, if necessary, by leaving out some of the more "exotic" groups or names. Malljaja (talk) 20:05, 24 February 2009 (UTC)

OK, I've kind of figured out the format and here's what I'd like to go with:

Unikonta	Amoebozoa   Opisthokonta           Animalia Choanozoa Nucleariids   Fungi   Microsporidia Chytridiomycota Neocallimastigomycota (1) Blastocladiomycota Zoopagomycotina Kickxellomycotina Entomophthoromycotina Mucormycotina Glomeromycota   Dikarya   Ascomycota Basidiomycota

(1) Given phyllum status by Hibbett, et al (2006), but included in the Chytridiomycota by other authors.

I took out the italics, since those are only used with genus names. Also keep in mind that there isn't a consensus that the Unikonta are a real group.

Peter G Werner (talk) 22:11, 24 February 2009 (UTC)

Your tree omits the Neocallimastigomycota, which is included as a sister clade of the Chytridiomycota in the Hibbett (et al) paper. Is there a purpose in this omission, or merely an oversight? It might also be nice to add a parenthetical note about the estimated number of species after each fungal group name, since the average person will not know that the Ascomycota and Basidiomycota are the "typical" fungi most familiar to the layman. --EncycloPetey (talk) 04:32, 25 February 2009 (UTC)

Is there a way to equalise the branch lengths? In its current form it looks like a phylogram. Also, as per my comments above, would it be possible to include oomycetes and plants for comparison? I know this is picky, but while we're at it, we may do it right. Thanks! Malljaja (talk) 16:48, 25 February 2009 (UTC)

To the best of my knowledge, Template:Clade does not have any way of setting branch lengths. If anybody here is knowledgeable enough to fix this, have at it!

The basal phylogeny of eukaryotes is not at all well worked out, most notably because a truly rooted clade for the eukaryotes has never been produced. By a truly rooted clade, I mean one in which a group of prokaryotes is added as a sister group to the eukaryote tree to show which clades diverged early and which or more derived. (This has to do with the difficulty of using phylogenetic methods in general with prokaryotes due to the insane amount of horizontal gene transfer there. Also, its very hard to find analogous sequences in prokaryote and eukaryote genomes.) And, of course, if you can't root a clade, you can't really understand the nature of the relationships. For my part, I'm even reluctant to keep Unikonta in the above tree. There are several papers with phylogenies showing the Amoebazoa (true amoebas + slime molds) to be sister to the Ophistokonts, but I've seen at least one recent paper showing it to be quite distant. So there isn't really a consensus that the Unikonta are a real group.

Peter G Werner (talk) 17:46, 25 February 2009 (UTC)

Here's the consensus of fungal taxonomic structure according to the Baysian methods used in James, et al and White, et al:

Fungi	Dikarya Ascomycota Basidiomycota Glomeromycota "Zygomycota 1" Mucormycotina Mortierellales "Zygomycota 2" Kickxellomycotina Zoopagomycotina Entomophthoromycotina Basidiobolales Blastocladiomycota Chytridiomycota Neocallimastigomycota * Microsporidia

Peter G Werner (talk) 20:43, 25 February 2009 (UTC)

What of the two red links clades not present in the previous cladogram? Where would they fit in the Hibbett et al. classification? Also note: the first tree looks much better of the two when rendered on a Mac running Safari. The lower cladogram comes out looking like a horizontal line across the top to the Ascomycota, with a series of pendulous clades descending from the top line. The plant cladogram does the same thing, but I've not yet goten around to redoing it. --EncycloPetey (talk) 04:09, 26 February 2009 (UTC)

For Basidiobolales, I'll quote the abstract directly: Several genera of ‘basal’ Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. As for the Mortierellales, the Hibbett, et al paper puts those in Mucoromycotina, as does James, et al. The tree by White, et al found Mortierellales to be a sister group to the Mucoromycotina/Dikarya clade, so I placed it in an unresolved position in the consensus tree. Peter G Werner (talk) 04:22, 26 February 2009 (UTC)

I just looked at it in Safari and –wow– what a mess. That template really needs some work. Probably the best solution, once we agree on what the clades should look like, would be to simply create gif or jpeg images of the clades in Illustrator or a like drawing program, then upload those via Wikimedia commons. Peter G Werner (talk) 04:36, 26 February 2009 (UTC)

Update

I just put up this article for peer review, in the hopes of getting some new eyes on the subject, and helping move things along to eventual FA status. Have also started a bare-bones Mycology section, but it's not easy figuring out how to summarize 250 years of mycology in a paragraph or two. I'll continue slowly expanding it, but please feel free to add, subtract, revert, etc. Sasata (talk) 07:18, 26 April 2009 (UTC)

Anyone have strong feelings about using either British or American spellings? If there's no objections here in a week I'll go through and make it all consistently American. Sasata (talk) 17:59, 27 April 2009 (UTC)

American spelling is probably the way to go, seeing that most changes to entries of this general topic are Brit-->Amer, probably because of the larger US readership. Malljaja (talk) 18:10, 27 April 2009 (UTC)

Characteristics section

I see the "characteristics" section as the core of what should be the new "distinguishing taxonomic features" section proposed in the to-do list. The current section needs references, of course. The part with similarities to other groups works okay, but the "other features" section is a bit vague. This should be the "distinguishing" features that make them fungi. Then perhaps this section should also include the phyla of fungi and their distinguishing features as well? Agathman (talk) 02:02, 30 April 2009 (UTC)

I believe renaming the "Characteristics" section to "Distinguishing features" could do the trick. ("Distinguishing taxonomic features" would be a little misplaced here, since fungal taxonomy is covered further down.) Re references, there is already a tag at the end of the lead sentence for this section, and several of these aspects are covered in more detail in other sections of the entry. Distinguishing features of the phyla are given under "Taxonomic groups"--several of those have been delineated based on molecular data, so including this here would not be very meaningful. This small section provides a pointed overview of what is a very large and diverse group of organisms. Malljaja (talk) 15:59, 30 April 2009 (UTC)

Regarding the external link for 'fungiphoto'

The editors who have either modified or removed this external link have drawn an incorrect conclusion related to my having included it here (original inclusion diff → http://en.wikipedia.org/w/index.php?title=Fungus&diff=286112337&oldid=286015569). Removal under #4 of Wikipedia:External_links#Links_normally_to_be_avoided is incorrect as I am not affiliated with this site nor do I have a vested interest in the site's promotion. I included it as having been highlighted as being of high quality by a biotechnology trade magazine in a column that has been maintained for many years, and documented this through citation. This inclusion is no different in principle (though very different in kind) from the acceptance of recognized reviewers ratings and commentary in articles about motion pictures. I just wanted to set the record straight so that there was no lingering thought that I was trying to spam this article. With the explanation provided above, I will leave you to consider maintaining exclusion of the link or re-introducing it and will not myself take further editorial action in this regard. --User:Ceyockey (talk to me) 02:04, 30 April 2009 (UTC)

No malicious intent was assumed... although the link has nice high quality photos, the site's purpose is largely to promote the sale of "TAYLOR'S DVDs, BOOKS, POSTERS, and other items", and so doesn't fit with wiki's external link guidelines. Sasata (talk) 05:17, 1 May 2009 (UTC)

Looking at the site I also believe that the inclusion of this link violates wiki criteria—it's clearly a commercial website. Malljaja (talk) 17:36, 1 May 2009 (UTC)

Psilocybes

I reverted the recent good faith edits putting mention of Psilocybin mushrooms in the "medicinal use" section. I think that placement is a stretch, other than the recent use of psilocybin to relieve cluster headaches, they aren't typically known as being "medicinal". As the article is becoming so large, it's best to make cautious, prudent choices about what to put in. The picture of the dried cubes was too much, that section already has two pictures that are a bit unwieldy, and need some tweaking with respect to image placement. Talk page discussion about extra material to include, or about shifting around information currently there is certainly welcome. Sasata (talk) 04:33, 12 May 2009 (UTC)

I suppose we can leave the image out of the article for now, but psilocybin mushrooms do have traditional medical uses among many indigenous peoples of latin america. In fact in many communities it is an integral tool of healing, administered by a shaman (notably among the Mazatec). Since there is mention of fungi use in chinese traditional medicine and other asian traditions, I don't see why psilocybin could not be included here. The section isn't just about its medicinal uses in the West in treating conditions like cluster headache or late stage cancer mood alleviation, it's also about medicinal uses worldwide.....so it does fit much better in the "medicinal use" section than the "Other" section. Zachorious (talk) 10:59, 12 May 2009 (UTC)

I find this addition problematic, which has mainly to do with the recreational use of psilocybin as a hallucinogen—a cursory look at Pubmed shows that most studies deal with the various and often problematic effects of this monoamine on cognition and behaviour. Moreover, shamanism (a highly overused and therefore meaningless term) is not the same as a medical profession that adheres to standardized practices, such as TCM or Western medicine. I also question the assertion that its use by indigenous people is a tool for healing; rather its use is probably more akin to our visits of pubs and bars. If in doubt leave it out, and there's too much doubt here in my opinion. Malljaja (talk) 14:32, 12 May 2009 (UTC)

(edit conflict) There are several dozen fungi that qualify as "medicinal" (or perhaps several hundred, depending how you define the criteria for inclusion), however, this is an overview article, and to prevent issues of undue weight, only those widely-known and most representative examples should be included in the category. If we include the psilocybes, what's to stop the next person from coming along, and justifiably adding Jelly fungus, or Honey mushrooms, Chaga, Wood Ear, etc. – all of which have more documented history of medicinal use. Also, there's the issue of putting too mush emphasis on "mushrooms" in this article, and forgetting about the other, less visible "fungi". The sentence you want to include could more justifiably go into a similar section in the mushroom article (which is far less developed, and could certainly use some attention), and could definitely go into the new medicinal mushrooms article. Sasata (talk) 14:53, 12 May 2009 (UTC)

Antibiotics

I think it is important to explain why fungi produce antibiotics—they don't do this for our benefit. Fungi have to compete with ubiquitous bacteria for nutrients. As an aside, it might interesting to point out that resistance to antibiotics seen in many bacterial species pre-dates the antibiotic era of medicine. Graham Colm ^Talk 20:33, 26 July 2009 (UTC)

I agree with you to some extent. Though on reflection this is bit of a can of worms, and it goes beyond the scope of this entry, since fungi are not the only organisms that make antibiotics—it properly belongs into the Antibiotics article (which still needs some development and fixing). There may be more to it than a simple role in microbial defence; one notion now holds that antibiotics can also function in quorum sensing, and there are some strong arguments for this. So in short, I do not think that we should attempt to elaborate too much on this here unless there's something peculiar about a particular fungal antibiotic that is not found in others. Malljaja (talk) 23:24, 26 July 2009 (UTC)

I'm with Graham on this one. I'm glad there's now a specific subsection on antibiotics, but at the moment I think it should have a little less about the antibiotics themselves and a little more about why fungi make them, ie focus more on the aspects of antibiotics that are especially relevant to fungi. I think a single sentence mentioning both competition with other microbes and quorum sensing would be ideal, including any necessary caveats. I definitely support mentioning quorum sensing – that seems like just the kind of up-to-date and relevant information Wikipedia can provide that might be missing from students' old textbooks. Interesting to established biologists, too. Adrian J. Hunter^{(talk•contribs)} 15:46, 27 July 2009 (UTC)

Thanks for both your comments. I agree that it's an important aspect also relevant to this new section, and I've now added a sentence detailing the role of antibiotics in nature as both defensive molecules and quorum-sensing agents. Let me know what you think. Thanks again. Malljaja (talk) 17:15, 27 July 2009 (UTC)

Comments from Cryptic C62

Here are some comments on the article's prose:

Resolved issues

"Sexual and asexual reproduction of fungi is commonly via spores" Commonly what? This sentence needs a verb before "via". I changed this to, "Fungi reproduce sexually or asexually via spores". Malljaja (talk) 16:29, 28 July 2009 (UTC) "Some have lost the ability to form reproductive structures, and propagate solely by vegetative growth." Suggest adding "fungi" after "some". The previous sentence introduced several new terms, so it might not be immediately clear to the reader what "some" refers to. Done. Malljaja (talk) 16:29, 28 July 2009 (UTC) "Yeasts, molds, and mushrooms are examples of fungi." This is written somewhat informally. Suggested rewrite: "Common examples of fungi include yeasts, molds, and mushrooms" or some such. Rephrased this to "Examples of fungi include yeasts, molds, and mushrooms".Malljaja (talk) 16:29, 28 July 2009 (UTC) "Occurring worldwide, most fungi are invisible to the naked eye." The use of "occurring" implies that a fungus is an event. Suggest changing to "Abundant", as this also ties the two clauses together nicely. Also, why are they invisible? The sentence which follows this one doesn't really clarify the issue. Changed to, "Abundant worldwide, most fungi are invisible to the naked eye because of the very small size of their vegetative structures." Does this improve clarity? Malljaja (talk) 16:29, 28 July 2009 (UTC) Indeed it does! Struck. --Cryptic C62 · Talk 15:37, 30 July 2009 (UTC) "They perform an essential role in ecosystems in decomposing organic matter" As this is written, it implies that entire ecosystems exist in dead bodies. Suggest removing "in ecosystems in". "and are indispensable in nutrient cycling and exchange." The use of "indispensable" is unencyclopedic and promotes a pro-fungus POV, if such a thing exists. I changed this sentence to, "They perform an essential role in decomposing organic matter in ecosystems and have fundamental roles in nutrient cycling and exchange." I agree that "indispensable" is strong word and have removed it, the overall literature makes a strong case for the fundamental role of fungi in these processes. Many thanks for your suggestions! Malljaja (talk) 16:29, 28 July 2009 (UTC) Does "in decomposing organic matter" mean that their essential role is the decomposition of organic matter? Or does it mean that their essential role, which is not mentioned, is performed inside decomposing organic matter? I think "in ecosystems" should be removed unless some sort of descriptor is added: "in various land-based ecosystems" or some such. This now reads, "They perform an essential role in the decomposition of organic matter". Malljaja (talk) 16:57, 30 July 2009 (UTC) "More recently, fungi have been used as sources for various enzymes important in industry and used in detergents" Somewhat ambiguous. Are fungi used in industrial enzymes and detergents? Or are fungal enzymes used in industry and detergents? I agree that the meaning of this sentence is a bit opaque; the latter is correct, so I rephrased this to "Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially and in detergents". Malljaja (talk) 16:57, 30 July 2009 (UTC) "Losses due to fungal diseases of crops" It's unclear what is being lost here. Suggest moving "crops" closer to the beginning of the sentence: "The loss of crops due to fungal diseases" That was my sloppy wording—changed as suggested. Malljaja (talk) 16:57, 30 July 2009 (UTC) "The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies and life cycle strategies, and morphologies ranging from amoeba-like protists and single-celled aquatic chytrids to large mushrooms." Are ecologies and life cycle strategies distinct items in this list? If so, suggest replacing the first "and" with a comma. If not, suggest removing "and life cycle strategies". I also recommend removing one of the first two morphology examples to make the comparison clearer and the sentence shorter. They're distinct terms, so I inserted comma and removed "amoeba-like protists". Many thanks for your comments! Malljaja (talk) 16:57, 30 July 2009 (UTC) "For a long time" A very vague and unencyclopedic phrase. Ask an astronomer and a five-year-old what this means and you'll get two very different answers! Changed this to "Before the introduction of molecular methods for phylogenetic analysis, taxonomists considered fungi to be members of the Plant Kingdom, based largely on similarities in lifestyle:"Malljaja (talk) 20:47, 30 July 2009 (UTC) "based largely on similarities in lifestyle" Is "lifestyle" the correct word here? I'm not that familiar with biology, but I've only seen "lifestyle" used to refer to the activities of humans. Yes, "lifestyle" is a word quite commonly used by biologists (see, e.g., here). Malljaja (talk) 20:47, 30 July 2009 (UTC) "including mannitol and other sugar alcohols, trehalose and glycogen" Are mannitol, trehalose and glycogen all examples of sugar alcohols? Or is just mannitol a sugar alcohol? If the latter, I suggest removing "mannitol and other" to make a more cohesive list. I've rephrased this sentence to "Fungi have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols (e.g., mannitol), disaccharides, (e.g., trehalose), and polysaccharides (e.g., glycogen, which is also found in animals).", which I think makes the whole sentence a bit more cohesive. Malljaja (talk) 20:47, 30 July 2009 (UTC) "and extend at their tips that each contain an organized assembly of vesicles" Uh... what? "This apical growth form is shared with the structurally similar oomycetes" If the growth is shared with oomycetes, why is it listed under Unique features? I've moved this sentence to the "Shared features section" and reworded it to, "Fungi typically grow as hyphae, which may have multiple nuclei within each hyphal compartment, and extend at their tips; each growing hyphal tip contains an organized assembly of vesicles, called Spitzenkörper." I hope this makes it clearer what the relationship between hyphae and the Spitzenkörper is. Malljaja (talk) 20:47, 30 July 2009 (UTC) "The fungal cell wall contains glucans and chitin; the former compounds are also found in plants and the latter in the exoskeleton of arthropods." Again, as this is written, it implies that this feature is not unique to fungi. The uniqueness refers to the combination of glucan and chitin in the cell wall, so to highlight this, I've changed this to, "The fungal cell wall is composed of glucans and chitin; while the former compounds are also found in plants and the latter in the exoskeleton of arthropods, fungi are the only organisms that combine these two structural molecules in their cell wall." Malljaja (talk) 20:47, 30 July 2009 (UTC) "To overcome these limitations, some fungi, such as Armillaria, form rhizomorphs or mycelial cords" It was not until I searched "rhizomorphs" that it became clear that the term is synonymous with "mycelial cords". I suggest either making it clearer that they are the same or simply dropping one and keeping whichever is more prominently used in the literature. Done! Malljaja (talk) 16:34, 17 August 2009 (UTC) "Characteristics shared with plants include a similar pathway in the biosynthesis of large organic molecules with important roles in cellular development and for defense, called terpenes." After rereading this sentence multiple times, it isn't clear if terpenes are involved in biosynthesis of large organic molecules and cellular development / defense, or if terpenes are involved in biosynthesis of organic molecules which are themselves related to cellular development / defense. The latter interpretation seems more logical, but if that is the case, why does this introductory sentence on terpenes complicate itself by introducing seemingly unnecessary information on organic molecules? This sentence has been greatly simplified, by omitting inessential info.Malljaja (talk) 16:34, 17 August 2009 (UTC) "However, the biochemical pathways for the synthesis of similar or even identical compounds often differ markedly between fungi and plants, which is shown by studies that have demonstrated that the fungal and plant enzymes for making these compounds differ strongly in their sequence and other characteristics, indicating that they have evolved separately in fungi and plants." This is a very long sentence. Consider slicing it into smaller sentences for better readability. Done. Malljaja (talk) 16:34, 17 August 2009 (UTC) "More than 60 species display the phenomenon of bioluminescence of mycelia or fruiting bodies." This seems like a bit of a non sequitor for this paragraph. Perhaps it would be better placed in the Diversity section? Now it reads "In common with some plant and animal species" to highlight the fact that it is a shared characteristic, and I now moved it to the appropriate section. Malljaja (talk) 16:34, 17 August 2009 (UTC) "In mycology, species have historically been distinguished using a variety of species concepts." The meaning of "species concepts" is not clear. If it is a commonly-used taxonomy phrase, suggest finding something to link it to. I agree. I've changed this to "In mycology, species have historically been distinguished by a variety of methods and concepts." This now segues into the different methods of classification. Malljaja (talk) 18:07, 17 August 2009 (UTC) "such as the chytrid fungus Batrachochytrium dendrobatidis, which has been responsible for a worldwide decline in amphibian populations." Suggest making it clearer here why it is responsible for the decline. Consider replacing "which" with "whose parasitic behavior" or some such. Included "parasite" in its description; the wikilinked entry for this species is fairly extensive, so to avoid content inflation, I kept this short here. Malljaja (talk) 18:07, 17 August 2009 (UTC) "Other examples include fungi living in hydrothermal areas of the ocean." Other examples of fungi, aquatic fungi, or parasitic fungi? Reworded to " Other examples of aquatic fungi include those living in hydrothermal areas." 18:07, 17 August 2009 (UTC) "but the true dimension of global fungal diversity is not well understood." I don't think "dimension" is the best word here. How about "extent"? "Dimension" conveys a meaning that seems more appropriate here than "extent"—the term needs to encompass both number of species as well as their diversity in lifestyles, morphologies, occurrences, etc. Arguably a matter of debate—I'll leave it as is for now, pending further input. Malljaja (talk) 18:07, 17 August 2009 (UTC) Ordinarily, yes, "dimension" implies diversity whereas "extent" simply implies number. However, be sure to read the entire sentence we're discussing: "but the true dimension/extent of global fungal diversity is not well understood". Regardless of the word choice, diversity is mentioned. Here's an alternative arrangement that I think works well: "but the global diversity of the fungus kingdom is not fully understood." or some such. --Cryptic C62 · Talk 02:05, 19 August 2009 (UTC) Sounds good to me. It's now: "...but the global biodiversity of the fungus kingdom is not fully understood." Sasata (talk) 02:49, 19 August 2009 (UTC) "Hyphae can be septate, i.e., divided into compartments separated by cross walls (septa), each compartment containing one or more nuclei, or can be coenocytic, i.e., lacking hyphal compartmentalization." I suggest rearranging this sentence to put both "septate" and "coenocytic" at the beginning: "Hyphae can be either septate or enocytic: septate hyphae are divided into comparments separated by cross walls (septa), with each compartment containing one or more nuclei; coenocytic hyphae are not compartmentalied." Also, what does "cross walls" mean? Done. I've also defined the term cross wall in the context of hyphae. Malljaja (talk) 15:13, 23 August 2009 (UTC) "Many species have developed specialized hyphal structures for nutrient uptake from living hosts" Many coenocytic species? Or just many species? If the latter, suggest splitting off into a separate paragraph to avoid confusion. The latter is true; split para as suggested. Malljaja (talk) 20:54, 25 August 2009 (UTC) "examples include haustoria in plant parasites of most phyla" It isn't clear what "most phyla" refers to. Most fungal phyla? Most plant phyla? Fungal phyla, so I've added this here. Thanks! Malljaja (talk) 20:54, 25 August 2009 (UTC) "examples include haustoria in plant parasites of most fungal phyla" Hmm. After taking a second look, this implies that there are plant species that are members of fungal phyla. Perhaps something like "examples include haustoria in most parasitic fungal phyla" or some such. I agree this sounds ambiguous. I changed this to "examples include haustoria in plant-parasitic species of most fungal phyla" Malljaja (talk) 14:18, 31 August 2009 (UTC) "Although fungi are part of the opisthokont clade" Most people will not be familiar with "clade", but wikilinking two consecutive terms is also confusing. Suggest rewording to either remove "clade" or to separate it from "opisthokont" so it can be wikilinked. I removed clade. I also removed the hyphen in "evolutionarily related", as per WP:MoS. Malljaja (talk) 14:18, 31 August 2009 (UTC) "Septa have pores, such as the dolipore septa in the basidiomycetes that allow cytoplasm, organelles, and sometimes nuclei to pass through." The relationship between these technical terms is not clear. Is a basidiomycete a structure of hyphae, or is it an organism? It is a member of the Basidiomycota, so I've added a parenthetical statement clarifying this. Malljaja (talk) 20:54, 25 August 2009 (UTC) Honestly, I really don't think this sentence benefits from being so specific. Suggested simplification: "Some septa have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through." These pores are unique structures and mentioning them in passing does not do them justice, so I would like to retain the doliporus as an example; I've reworded this as "Septa have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through; an example is the dolipore septum in the fungi of the phylum Basidiomycota." How about "Some septa, such as those of the basidiomycota phylum, have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through." ? I feel that the current wording expresses the relationship between septa and pores (with the doliporus example) very well, and our suggestion would water it down in my opinion—feel free to insert your version if this is a sticking point for you. Malljaja (talk) 16:15, 7 September 2009 (UTC) "Fungal mycelia can become visible macroscopically, for example, as concentric rings on various surfaces, such as damp walls, and on other substrates, such as spoilt food, and are commonly and generically called mold (British spelling, mould)" This is a rather long sentence. I suggest cutting it up. I also suggest removing the parenthetical comment at the end, as it doesn't really seem necessary. Shortened and rephrased to "Fungal mycelia can become visible macroscopically, for example, on various surfaces and substrates, such as damp walls and on spoilt food, where they are commonly called mold (British spelling, mould). I think this small exposé on mold justifies the parenthetical comment, if only to prevent periodical edits aimed at favouring (or favoring) one form of spelling over the other. Malljaja (talk) 14:18, 31 August 2009 (UTC) "can become visible macroscopically" just sounds like an overly technical way of saying that fungi can be seen. Any way to dejargonize this phrase? Also, I have removed the parenthetical comment. If British/American edit warring becomes a problem, the correct solution would be to post {{American English}} on the talk page, not to add an awkward unorthodox unnecessary parenthetical comment. --Cryptic C62 · Talk 21:29, 5 September 2009 (UTC) Changed to "can become visible to the naked eye." Hmmm, if there's an orthodoxy to be followed here, I wasn't aware of it. I think this statement would have also helped the reader, some of whom may not be aware of the difference in spelling. Malljaja (talk) 16:15, 7 September 2009 (UTC) "Some individual fungal colonies can grow to a very large size and mass, in some cases reaching extraordinary dimensions and ages" Redundant and overly excited. Suggest condensing to mention size, mass, and age only once each. Shortened to "Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of..." The physical dimensions of this fungal specimen are indeed impressive, making it one of the largest organisms on Earth. Something to be mildly excited about, hence use of the the superlative "extraordinary". Malljaja (talk) 16:15, 7 September 2009 (UTC) "exhibiting characteristic macroscopic growth shapes and colors" What does "characteristic" refer to here? "Characteristic" is indeed a vague term here. It referred to these shapes and colors as features that may be useful in the identification of fungal groups or species. So I've modified this to "These colonies can exhibit growth shapes and colors (due to spores or pigmentation) that can be used as diagnostic features in the identification of species or groups." The sentence could be further simplified by removing the parenthetical "(due to spores or pigmentation)", but I leave it in for now, pending further input. Malljaja (talk) 16:15, 7 September 2009 (UTC) "Diagnostic" is a medical term, and I have never heard it used in taxonomy. It's also a bit wordy. Suggested rewrite: "The shapes and colors of these colonies can help identify species and groups." or some such. No, "diagnosis" is quite commonly used also in biological contexts, including taxonomy (see, e.g., definition here here). Malljaja (talk) 22:23, 14 September 2009 (UTC) "In the ascomycetes, a specialized structure important in sexual reproduction is the apothecium" Are ascomycetes a group of fungi that have specialized structures called apotheciums? Or are ascomycetes specialized structures which contain apotheciums? It's the former, so I rephrased this to "The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a cup-shaped structure that..." Thanks! Malljaja (talk) 16:15, 7 September 2009 (UTC) Definitely better. Are any of the structures mentioned in this sentence fruiting bodies? If so, it would be useful to specify which ones. If not, it is unclear how this sentence relates to the one that follows it. They are fruiting bodies, so I've recast this to, "The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a cup-shaped fruiting body that holds the hymenium, a layer of tissue containing the spore-bearing cells. The fruiting bodies of the basidiomycetes and some ascomycetes can sometimes grow very large, and many are well-known as mushrooms."Malljaja (talk) 22:23, 14 September 2009 (UTC) "The fruiting bodies of the basidiomycetes and some ascomycetes can sometimes grow very large, and are well-known as mushrooms." From this sentence, it is not entirely clear whether all mushrooms are basidiomycete/ascomycete fruiting bodies. I've included "many" in the above sentence, indicating that not all fruiting bodies are mushrooms.Malljaja (talk) 22:23, 14 September 2009 (UTC) "The growth of fungi as filamentous hyphae" The word "filamentous" is used several times through this article without being linked or elaborated upon. I've elaborated this to, "The growth of fungi as hyphae, which are long and elongated (filamentous) structures, on or in solid substrates or as single cells in aquatic environments..." Malljaja (talk) 22:23, 14 September 2009 (UTC) Added in proof: I've just moved this definition to the "Characteristics" section. Malljaja (talk) 22:29, 14 September 2009 (UTC) "uses a similar structure to penetrate the eggs of plant-parasitic nematodes" I think the inclusion of "plant-parasitic" here may be confusing for some because the previous sentence discussed plant-parasitic fungi. At the very best it is a superfluous detail, so I suggest removing it. Perhaps it should be replaced with "some". "While the vast majority of filamentous fungi grow in a polar or directional fashion by extension at the tip of the hypha" It is unclear what the distinction is between "polar" and "directional" growth. Does "polar" imply circularity as in a polar coordinate system, or something more akin to chemical polarity? Does "directional" mean linear? Also in consideration to the two comments below, I've recast and split this sentence to define the term "polar" (growth into one direction), explain "intercalary", and limit confusion by re-arranging the partial sentence in question. 18:29, 30 September 2009 (UTC) "intercalary extension as in the case of some endophytic fungi" Intercalary extension should be explained or wikilinked. I'm not sure where it should be linked to; intercalation seems totally unrelated. See above. Malljaja (talk) 18:29, 30 September 2009 (UTC) "While the vast majority of filamentous fungi grow in a polar or directional fashion by extension at the tip of the hypha, intercalary extension as in the case of some endophytic fungi, or by volume expansion during the development of mushroom stipes and other large organs are alternative forms of growth." I had to reread this multiple times before I realized that the first item on the list is the norm and the other two are the exception. At first I thought that all three were "alternative forms of growth" and that something was missing. To avoid this confusion, I suggest removing the second comma and placing "alternative forms of growth" immediately after the first comma. Done.Malljaja (talk) 18:29, 30 September 2009 (UTC) "as seen and independently evolved in animals and plants" Not a very natural phrasing. Suggest rewriting to: "a feature which evolved independently in animals and plants" or some such. Done. Malljaja (talk) 18:29, 30 September 2009 (UTC) "Fungi have evolved a remarkable metabolic versatility" Very excited! How about "Fungi have evolved a very versatile metabolism" instead? I've changed this to "high degree of metabolic versatility", as "very versatile metabolism" would suggest that all fungi possess one single type of versatile metabolism. Malljaja (talk) 20:35, 5 October 2009 (UTC) "This process might bear similarity to CO2 fixation via anaplerotic reactions using visible light, but instead utilizing ionizing radiation as a source of energy" It isn't clear if this is also speculative or if it means "These things might appear similar to someone with zero knowledge of either process..." :P You're right. It's indeed rather speculative and the sentence now states this with a recent review by the same authors as a reference. Malljaja (talk) 20:35, 5 October 2009 (UTC) "reflecting the heterogeneity in lifestyles" Heterogeneity is not a word that I would expect all readers to be familiar with. I'm not even sure what it means in this context. Changed this to "differences in lifestyles". Malljaja (talk) 20:35, 5 October 2009 (UTC) "It is estimated that a third of all fungi use more than one type of reproduction" Is it correct to say that fungi "use" different types of reproduction? I would think "undergo" would be a better word choice. Re-worded to "It is estimated that a third of all fungi reproduce by different modes of propagation; for example, reproduction may occur in two well-differentiated stages within the life cycle of a species, the teleomorph and the anamorph." This hopefully also clears up your next query. Malljaja (talk) 20:35, 5 October 2009 (UTC) "frequently in two well-differentiated life cycle stages (the teleomorph and the anamorph)." It isn't clear whether this means that (a) in these two stages, fungi reproduce frequently, or (b) the multiplicity of reproduction types is often made possible by the differentiation of the life cycle stages. I suspect it is the latter. "Environmental conditions trigger genetically determined developmental programs" Is "programs" an appropriate word here? It is a jargony word used by those studying the genetics and biochemistry of development, so I've now changed this to the more readily understandable "developmental states". Malljaja (talk) 20:35, 5 October 2009 (UTC) "These structures aid both reproduction and efficient dispersal of spores or spore-containing propagules" A reader (such as myself) might assume that the dispersal of spores is considered a method of reproduction, thus making the phrase "both reproduction and efficient dispersal of spores" seem redundant. Perhaps there is some way to specify exactly what "reproduction" refers to here. Fixed, by stating how these structures help in reproduction and dispersal. Malljaja (talk) 20:35, 5 October 2009 (UTC)

• I think that the Characteristics information should be organized primarily by kingdom, not by similarity/uniqueness. This would make it easier to write paragraphs. For example, there would be a plant paragraph (or several) which discusses both similarities and differences between fungi and plants.

  That's a good suggestion—seeing that this a more drastic change, I'll wait for additional input/opinions before looking at re-organizing this. Thanks! Malljaja (talk) 20:47, 30 July 2009 (UTC)

  Sounds good to me, I think the information would be better organized that way. Plus, it would get rid of the bullets, and perhaps allow for the addition of a left-aligned image. Sasata (talk) 05:42, 3 August 2009 (UTC)

  After some discussion, both Sasata and I felt that the current format is preferable over one that splits characteristics by kingdom. The present structure is more condensed than one that would list characteristics strictly by kingdoms; eg, bioluminescence occurs in several kingdoms, as does biosynthesis of lysine via the aa pathway, and so this would introduce a fair amount of unnecessary repetition. Malljaja (talk) 16:34, 17 August 2009 (UTC)

  Fair enough, struck. I'll keep the suggestion outside the collapse box in case anyone else has any input on the matter. --Cryptic C62 · Talk 17:30, 17 August 2009 (UTC)

• "new tips typically form by branching from sub-apical hyphal locations or occasionally by bifurcation (forking) of growing tips." This sentence is too technical for me to understand it, nor can I tell what the difference between those two growth methods.

  You hit on an important point. The anatomy of hyphae may need a schematic drawing of its main features. I believe this would be appropriate for the Hypha entry–there's no such schematic at Commons, so I'll see whether I can come up with such a drawing (although my artistic skills are a little limited). I've now recast the sentence trying to rid it off technical lingo–is the new description more comprehensible now? Malljaja (talk) 15:13, 23 August 2009 (UTC)

  I still don't really understand the difference between branching and forking, something that I think would be best fixed by some sort of diagram. --Cryptic C62 · Talk 19:04, 25 August 2009 (UTC)

• "A few species seem to be able to utilize the pigment melanin" Wishy washy. Can they utilize melanin or not? If it's speculative/new research, try either making it clearer that it's not definitive or simply deleting it until it is more certain.

  This work, while intriguing, is still rather fresh, and hasn't been replicated by other researchers. So there's the potential of undue weight and it certainly has the whiff of speculation still, even if there are some data showing an effect of radiation on growth of fungal isolates that have melanin. So I've recast the sentence, describing more directly the finding and its limitations. Hopefully, if a significant contribution of this "radiotrophic" energy pathway can be further demonstrated, there's more to fill in. With the current rush for all kinds of "alternative" energy, there should be more research into this underway as we speak. Malljaja (talk) 20:35, 5 October 2009 (UTC)

  Much better. However: "The authors speculate that this process..." The meaning of "the authors" is unclear because the paragraph does not mention who they are or what they wrote.

• Perhaps the Asexual reproduction section could be expanded by adding some notable examples of Deuteromycota.
• "Sexual reproduction with meiosis exists in all fungal phyla (with the exception of the Glomeromycota)" I don't understand why Glomeromycota isn't mentioned in Asexual reproduction and Deuteromycota isn't mentioned here.

More to come. --Cryptic C62 · Talk 15:44, 28 July 2009 (UTC)

So... it's been a while since any changes have been made to this section. Did you guys forget that this was here, or do you just plan on taking a look after Awadewit is done with their review? --Cryptic C62 · Talk 12:40, 13 August 2009 (UTC)

Hello Cryptic. Sorry for the lack of detailed responses to your suggestions and comments. Sasata is currently on a brief wiki leave, and I've been snowed under with work and family obligations over the past few days. I believe several of your suggestions have been already incorporated. The one issue that we still have to iron out is the "Characteristics" section—after some deliberation, taking into account the content and considerable amount of work that has gone into it, both Sasata and I agree that it may be best to retain the current format. I'll get back to you on this, once I find the time, ie. this weekend or thereafter. Many thanks again for your comments and your patience. Malljaja (talk) 14:36, 13 August 2009 (UTC)

No worries, mate. Just drop a note here when you're ready to continue. --Cryptic C62 · Talk 18:53, 13 August 2009 (UTC)

Medicinal fungi

This section has been clearly improved by my last edit. But it is being reverted to make it a "good article" status. Ironic...Jatlas (talk) 00:28, 1 August 2009 (UTC)

Thanks for coming to the talk page! What changes do you think are necessary? Sasata (talk) 00:39, 1 August 2009 (UTC)

The version that I put up, before it was quickly removed, was clearly better than what is up right now. This section is currently on the verge of being poorly written IMO. Please switch it back, or let me know if I can make the change without it being reverted. Thanks! Jatlas2 (talk) 18:10, 20 August 2009 (UTC)

Let's compare:

Before: Research has identified compounds produced by these fungi that have inhibitory biological effects against viruses and cancer cells. Specific metabolites with biological or antimicrobial activities, such as polysaccharide-K, ergotamine, and β-lactam antibiotics, are routinely used in clinical medicine.

After: Research has identified compounds produced by these fungi that have inhibitory biological effects against high blood sugar, viruses and cancer cells. Specific fungal metabolites with biological or antimicrobial activities, such as lovastatin, polysaccharide-K, ergotamine, and β-lactam antibiotics, are routinely used in clinical medicine.

Remember, the medicinal mushrooms section is a subsection in the main section called "Human use". The problem with the high blood pressure claim is, on top of the fact that 5 five citations to support a single point is rather excessive, the references all involve primary pre-clinical research studies on rodents. Here's a reminder quote by jfdwolff from your blanked talk page: "When selecting references, "more" is not always better. In medical and pharmacology articles we have agreed on a hierarchy in sources. Have a look at WP:MEDRS and see if you agree with its premises. Generally, avoid discussing treatments still in pre-clinical, phase I or phase II development. The vast majority of these never reach clinical application, and their mention is just a distraction."

If you could find a suitable secondary source that summarizes clinical research with humans that shows the hypoglycemic effects of mushroom extracts, we could use that here. Regarding the inclusion of lovastatin, can you confirm that source 10 says or implies "...routinely used in clinical medicine"? Sasata (talk) 19:04, 20 August 2009 (UTC)

Accessibility review

Here are some concerns that I have with accessibility for the lay reader. They are listed by section. I have tried to articulate my concerns as clearly as possible, but I may not have done so - it is difficult to explain one's confusion! Please ask me questions to clarify my confusion so that we can effectively reword the article, if possible.

Review by Awadewit

Characteristics both fungi and plants are mainly sessile, and have similarities in general morphology and growth habitat - Although I happen to know the word "sessile", this is not a commonly known world. What do you think about replacing it with "immobile" and linking to "sessile"? Done. Malljaja (talk) 22:12, 2 August 2009 (UTC) DNA with noncoding regions called introns, sterol-containing membranes, and ribosomes of the 80S type. - This is a lot of detail - I was lost after the introns. I am unsure if this has to be reworded - is the essential part of this bullet point "Fungi are eukaryotic, containing membrane-bound nuclei with chromosomes"? If so, the details are probably irrelevant to someone like me. If however, they are essential, perhaps they should be explained a bit more. I've re-arranged this sentence—one could argue for removing these characteristics entirely, since they are what define eukaryotes. I left them in for now, but wouldn't oppose a removal for brevity.Malljaja (talk) 22:12, 2 August 2009 (UTC) Fungi lack chloroplasts and are heterotrophic organisms, requiring preformed organic compounds as energy sources and also as carbon skeletons for organic synthesis. - While this sentence is generally comprehensible, I'm wondering if there is a way to word it that makes it less work to get through. This is the second section of the article, so, as a reader, I'm not going to want to read each sentence twice or three times. :) Yes, I agree, so I deleted "and also as carbon skeletons for organic synthesis". Malljaja (talk) 22:12, 2 August 2009 (UTC) With euglenoids and bacteria: Higher fungi, euglenoids, and some bacteria biosynthesize the amino acid L-lysine via the α-aminoadipate pathway - This is one of those details that I just take as lost to someone like me, as I don't really know anything about specific amino acids. If it is important, a new wording should be found. This is indeed important, at least to some biochemists and taxonomists, so I rephrased this sentence. Is the new version more accessible now? Malljaja (talk) 22:12, 2 August 2009 (UTC) Yes, and how little it took! Awadewit (talk) 14:57, 4 August 2009 (UTC) Fungi typically grow as hyphae, which may have multiple nuclei within each hyphal compartment,[12] and extend at their tips; each growing hyphal tip contains an organized assembly of vesicles, called Spitzenkörper.[15] This apical growth form is shared with the structurally similar oomycetes[16] and is in contrast with other filamentous organisms, like filamentous green algae, which grow by repeated cell divisions within a chain of cells (intercalary growth). - I think the structure of the organism can be described better - what is a hyphae, a hyphal compartment, a vesicle, "apical growth"? The comparison with the oomycetes does not help me out. Would a diagram help out here? I tried my hand at rephrasing and re-ordering this, and included a short description of what a hypha is; I hope it's a little less cluttered and easier to follow now. Malljaja (talk) 22:12, 2 August 2009 (UTC) There are a lot of parentheses there. Let me see if I can come up with something more elegant later tonight. Awadewit (talk) 14:57, 4 August 2009 (UTC) Suggestion: Fungi typically grow in groups of elongated, tubular, thread-like cells called hyphae, which may contain multiple nuclei and extend at their tips. Each tip contains sets of organized vesicles called Spitzenkörper, cellular structures consisting of proteins, lipids, and other larger organic molecules. Both fungi and oomycetes grow as filamentous hyphal cells. In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells. Awadewit (talk) 00:11, 6 August 2009 (UTC) Sounds good to me, have now replaced with your version. The net result is that Spitzenkörper is better explained, and the unnecessary parenthetical mention of intercalary growth is left out, which makes the sentence more comprehensible to the neophyte. Sasata (talk) 05:51, 6 August 2009 (UTC) Unlike many plants, most fungi lack an efficient vascular system, such as xylem or phloem for long-distance transport of water and nutrients. Some, such as Armillaria, form rhizomorphs or mycelial cords,[21] resembling and functionally related to, but morphologically distinct from plant roots. - I get the idea here, but notice that there are four new terms in this one sentence. If there is a way to reduce this, that would be helpful. Done, also in response to a comment by another reviewer. Malljaja (talk) 22:12, 2 August 2009 (UTC) Characteristics shared with plants include a similar pathway in the biosynthesis of terpenes using mevalonic acid and pyrophosphate as biochemical precursors;[22] plants however use an additional terpene biosynthesis pathway in the chloroplasts that is apparently absent in fungi. - I don't understand this - does it mean that the fungi use the acid and pyro-stuff to start a chemical reaction of the resin/oil stuff? Note that this sentence follows the one above and also introduces a slew of technical terms. Readers will very quickly tire of clicking, I assure you (even if they bother to in the first place). I commiserate—descriptions of biochemical pathways are often quite inscrutable, even to those who work in the field. But this pathway is of interest to those trying to understand the evolution of plant and fungal biochemical pathways. My first attempt at disentangling this and making it more decipherable prompted more criticism by another reviewer, so I changed it yet again—please have a look and comment in case it is still too obtuse. Malljaja (talk) 22:12, 2 August 2009 (UTC) I think we can do better. I'll return to this one tonight as well. Awadewit (talk) 15:03, 4 August 2009 (UTC) Suggestion: Characteristics shared with plants also include a biosynthesis pathway for producing terpenes that uses mevalonic acid and pyrophosphate as catalysts. However, plants have an additional terpene pathway in their chloroplasts, a structure fungi do not possess. Awadewit (talk) 00:22, 6 August 2009 (UTC) Added your suggested sentence with some modifications: "Characteristics shared with plants also include a biosynthetic pathway for producing terpenes that uses mevalonic acid and pyrophosphate as chemical building blocks. However, plants have an additional terpene pathway in their chloroplasts, a structure fungi do not possess." Changed catalysts (incorrect term here) to "chemical building blocks" and piped the link to Precursor (chemistry). Sasata (talk) 05:51, 6 August 2009 (UTC) Similar to plants, fungi produce a plethora of secondary metabolites functioning as defensive compounds or for niche adaptation; however, genes, genomic organization, and biochemical pathways for the synthesis of similar or even identical compounds often differ markedly between fungi and plants. - Could you give an example of the niche adaptation? How do the genes, etc. "differ markedly" between fungi and plants? You've raised a very good point and I changed this as you suggested, pointing out how differences between plant and fungal enzymes are evaluated. Thanks! Malljaja (talk) 22:12, 2 August 2009 (UTC) Diversity Until recently, species were characterized based mainly on morphological characteristics, such as the size and shape of spores or fruiting structures, as well as biochemical and physiological characteristics, and biological species concepts. - The examples in the first part of this sentence were good - could the other categories be given them as well? Sadly, most people learn by example. :) I'm afraid I don't quite follow what you're asking here, do you mean to give examples of biochemical and physiological characteristics and biological species concepts? Sasata (talk) 05:37, 3 August 2009 (UTC) Yes, exactly. Awadewit (talk) 15:03, 4 August 2009 (UTC) Ok how's this: "In mycology, species have historically been distinguished using a variety of species concepts. Classification based on morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy.[35] Species may also be distinguished by their biochemical and physiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction to chemical tests. The biological species concept discriminates species based on their ability to mate." Wonderful! Awadewit (talk) 22:03, 6 August 2009 (UTC) I'll just keep adding by section. Awadewit (talk) 17:42, 2 August 2009 (UTC) Morphology Although fungi are part of the opisthokont clade, all phyla except for the chytrids have lost their posterior flagella - This is a rather startling beginning to a section - it seems to be a very specific claim about evolutionary development. Could you add a sentence explaining why this information is significant and prepare the reader for the topic of the section in general? Now that you point it out, I agree, it's a jarring start. Have moved the first two sentences down to the end, so the section starts out talking about hyphae. Sasata (talk) 05:32, 3 August 2009 (UTC) Most fungi grow as thread-like filamentous microscopic structures called hyphae- This is a good description of the hyphae - could we use it earlier in the article, say the first time the term appears? In a previous section (Characteristics) it says "Fungi typically grow as hyphae, which are elongated, tubular (filamentous) cells, which may contain multiple nuclei and extend at their tips; ..." This section states "Most fungi grow as thread-like filamentous microscopic structures called hyphae, which are between 2–10 µm in diameter and up to several centimeters in length, and which collectively form the mycelium." In my opinion, there's only a little bit of information overlap between the two statements; perhaps this slight repetition can be justified by its fundamental importance? Sasata (talk) 05:32, 3 August 2009 (UTC) Was "filamentous" recently added to the "Characteristics" description? That and "thread-like" really helped me understand the hyphae. Awadewit (talk) 15:03, 4 August 2009 (UTC) Hyphae can be septate, i.e., divided into compartments separated by a septum, each compartment containing one or more nuclei, or can be coenocytic, i.e., lacking hyphal compartmentalization - Could this description of the hyphal compartments be adapted for the "Characteristics" section? One problem we are encountering here is that later sections of the article explain terms used earlier. We need to fix that. Although hyphae are discussed twice, I think the focus is separate in the two sections: "Characteristics" discusses hyphae as a growth form, "Morphology/Microscopic structures" discusses the structural and functional characteristics of hyphae. Am not convinced these separate discussions need to combined to avoid having to talk about hyphae twice. Thoughts Malljaja? Sasata (talk) 05:32, 3 August 2009 (UTC) I agree that there's some overlap so I changed the sentence in the "Microscopic structures" section to, "Most fungi form hyphae, which are thread-like structures that are between 2–10 µm in diameter and up to several centimeters in length, and which collectively form the mycelium." As mentioned in the above comment, the hypha is the defining growth form of fungi, so some overlap is justified here to drive this home—one might argue that "thread-like structures" could be removed, since hyphae are already described as "elongated and tubular" in the "Characteristics" section, but I left it in for now as a refresher. Malljaja (talk) 13:59, 3 August 2009 (UTC) Let's work on getting the first description of hyphae crystal clear. Awadewit (talk) 00:24, 6 August 2009 (UTC) Specialized structures important in sexual reproduction are the apothecia, perithecia, and cleistothecia in the ascomycetes - I would suggest describing what these structures do rather than just linking to them. Actually, I've removed perithecia, and cleistothecia, as they are merely different forms of apothecia and introduce unwarranted detail and complexity to this sentence. The term apothecia is now explained. Sasata (talk) 05:32, 3 August 2009 (UTC) Reproduction In sexually reproducing fungi, compatible individuals may combine by fusing together their hyphae by anastomosis—a process required for the initiation of the sexual cycle. - As anastomosis seems to be an important process, perhaps we could describe it? The lead of the article says "a network of streams that both branch out and reconnect" - is that a fair description? In glomeromycetes (formerly zygomycetes), haploid hyphae of two individuals fuse, forming a gametangia, which develops into a zygospore. - I would suggest defining "gametangia" and "zygospore" as they seem to be terms specific to fungi. These mechanisms include, for example, forcible discharge of ascospores enabled by the structure of the ascus and accumulation of osmolytes in the fluids of the ascus that lead to explosive discharge of the ascospores into the air - This is a little bit hard to follow - again, it is the build up of terms. Must we use all of them here? This section reworked. How does it sound now? Sasata (talk) 21:49, 2 August 2009 (UTC) I'm not sure that just adding a parenthetical makes it easier - is it possible to explain this without so many of the terms that will be new to a reader unfamiliar with fungus? Awadewit (talk) 23:53, 5 August 2009 (UTC) Try now: "For example, the structure of the spore-bearing cells in some ascomycete species is such that the buildup of substances affecting cell volume and fluid balance enables the explosive discharge of spores into the air." I think that is better. Awadewit (talk) 22:03, 6 August 2009 (UTC) Adding more. Awadewit (talk) 18:12, 2 August 2009 (UTC) Evolution I'm wondering if a timeline could be made for this section. Do you mean something like the {{Include timeline}} template? I'll see if I can figure out how to use it. Sasata (talk) 21:49, 2 August 2009 (UTC) That's exactly it. Awadewit (talk) 23:59, 5 August 2009 (UTC) Taxonomy The major phyla (sometimes called divisions) of fungi have been classified based mainly on the characteristics of their sexual reproductive structures. Currently, seven phyla are proposed: - I would suggest listing all seven terms right after the colon. Since there are no bullets, the colon seems like a mistake. The bullets were there, but removed as a MOS violation... so have now listed all seven as you suggested. Not sure whether to link the seven phyla right away in the mini-list, or wait until the words appear in their respective paragraphs so they are surrounded with more context. Suggestions? Sasata (talk) 04:20, 3 August 2009 (UTC) I like linking later, as the article currently has it, since the link is then in context, as you say. Awadewit (talk) 23:59, 5 August 2009 (UTC) Phylogenetic analysis has demonstrated conclusively that the Microsporidia, unicellular parasites of animals and protists, are fairly recent and highly derived endobiotic fungi, - As "endobiotic" seems like a crucial term here, I think explaining it in the article would be a good idea. The very short Wikipedia article says "A type of creature which lives in another's tissue" - is that a fair description? Have defined parenthetically: "Phylogenetic analysis has demonstrated conclusively that the Microsporidia, unicellular parasites of animals and protists, are fairly recent and highly derived endobiotic fungi (living within the tissue of another species),..." Sasata (talk) 04:20, 3 August 2009 (UTC) The blastocladiomycetes are fungi that are saprotrophs and parasites of all eukaryotic groups - As "saprotrophs" seems to be an important part of the description of this group, I think we should describe what it is in this article. Could we say that this means that they eat decomposing material? Also defined parenthetically now: "The blastocladiomycetes are fungi that are saprotrophs (feeding on dead organic matter)..." As an aside, how do you feel about these parenthetical definitions? Are they clumsy? Should one try harder to smoothly incorporate definitions into the prose without making it too obvious? Sasata (talk) 04:20, 3 August 2009 (UTC) I do feel that they are rather clumsy. Some I have marked above as overpowering the text, but a few scattered ones are fine. Of course, ideally we would not have any - everything would flow smoothly without any side comments. :) Awadewit (talk) 23:59, 5 August 2009 (UTC) Now: "The blastocladiomycetes are saprotrophs, feeding on dead organic matter, and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids, which mostly exhibit zygotic meiosis, the blastocladiomycetes undergo sporic meiosis." Better? Sasata (talk) 05:51, 6 August 2009 (UTC) Yes. Awadewit (talk) 22:03, 6 August 2009 (UTC) Members of the Glomeromycota form arbuscular mycorrhizae with higher plants. - I'm not really sure what this structure is. As it is a key component of the group's definition, I think we should explain it. "... form arbuscular mycorrhizae, a form of symbiosis where fungal hyphae invade plant root cells and both species benefit from the resulting increased supply of nutrients." Sasata (talk) 04:20, 3 August 2009 (UTC) Oh, it is not a structure. Oops. Thanks! Awadewit (talk) 23:59, 5 August 2009 (UTC) Because of similarities in morphology and lifestyle, the slime molds (myxomycetes) and water molds (oomycetes) were formerly classified in the kingdom Fungi. Unlike true fungi, however, the cell walls of these organisms contain cellulose and lack chitin. Slime molds are unikonts like fungi, but are grouped in the Amoebozoa. Water molds are diploid bikonts, grouped in the Chromalveolate kingdom. Neither water molds nor slime molds are closely related to the true fungi, and, therefore, taxonomists no longer group them in the kingdom Fungi. Nonetheless, studies of the oomycetes and myxomycetes are still often included in mycology textbooks and primary research literature. - Side note: This paragraph needs a citation. Done. Sasata (talk) 04:20, 3 August 2009 (UTC) Ok, this section has been revised. Good points, all. Sasata (talk) 21:07, 2 August 2009 (UTC) Progressing. Awadewit (talk) 18:59, 2 August 2009 (UTC) Ecology As decomposers, they play an essential role in nutrient cycling, especially as saprotrophs and symbionts, degrading organic matter to inorganic molecules, which can then re-enter anabolic metabolic pathways in plants or other organisms. - This is a helpful description of saprotroph - perhaps we could add it into the article the first time the term appears? It's not really a description of saprotroph, just a reference to the fact that saprotrophic behavior leads to nutrient recycling. The first mention of saprotroph in the above section has a parenthetical definition of the term: "The blastocladiomycetes are fungi that are saprotrophs (feeding on dead organic matter)..." Sasata (talk) 04:20, 3 August 2009 (UTC) Now that the parenthetical has been added, this is a moot point. !!!! Human use Certain mushrooms enjoy usage as therapeutics in traditional and folk medicines, such as Traditional Chinese medicine. Most notable species include those of the genus Agaricus,[163][164] Ganoderma,[165] and Cordyceps,[166] which are used in the treatment of several diseases - This is vague - can we add some details? Have removed "which are used in the treatment of several diseases", as this is discussed with specific examples further down. Sasata (talk) 04:20, 3 August 2009 (UTC) Well-known types of fungi are the edible and the poisonous mushrooms. Many species are commercially raised, but others must be harvested from the wild. Agaricus bisporus, sold as button mushrooms when small or Portobello mushrooms when larger, is a commonly-eaten species, used in salads, soups, and many other dishes. Many Asian fungi are commercially grown and have increased in popularity in the West. They are often available fresh in grocery stores and markets, including straw mushrooms (Volvariella volvacea), oyster mushrooms (Pleurotus ostreatus), shiitakes (Lentinula edodes), and enokitake (Flammulina spp.). - Side note: this paragraph needs citation(s). Done. Sasata (talk) 04:20, 3 August 2009 (UTC) There are many more mushroom species that are harvested from the wild for personal consumption or commercial sale. Milk mushrooms, morels, chanterelles, truffles, black trumpets, and porcini mushrooms (Boletus edulis) (also known as king boletes) demand a high price on the market. They are often used in gourmet dishes. - Side note: this paragraph needs a citation. Reffed. Sasata (talk) 04:20, 3 August 2009 (UTC) Mycology Mycology is the branch of biology concerned with the systematic study of fungi, including their genetic and biochemical properties, their taxonomy, and their use to humans as a source of medicine, food, and entheogens - Instead of the word "entheogens", could we just say "psychotropic substances used for religious purposes" and link to "entheogen"? Done as suggested. Sasata (talk) 04:20, 3 August 2009 (UTC) Done! I'll revisit in the coming days. Awadewit (talk) 22:46, 2 August 2009 (UTC) I will try to get back to this tonight or tomorrow - thanks for all of the improvements! Awadewit (talk) 14:58, 4 August 2009 (UTC) Sorry I didn't get back to this last night - RL stuff. Awadewit (talk) 00:01, 6 August 2009 (UTC)

Conservation Section

I think it's necessary for this article to include a Conservation section. I realized that not much information is known about the Fungus kingdom's status, due to the fact that numerous species of fungus are microscropic as well as that they are only visible through their fruiting bodies. But I think it still should be added to increase the coverage of this article. I'll be willing to help on this section, if agreed. KnowledgeRequire (talk) 20:28, 10 August 2009 (UTC)

I've done a draft for the Conservation of fungus. Any additional information can be added, perhaps a copyedit can be performed before publishing. KnowledgeRequire (talk) 21:18, 10 August 2009 (UTC)

This article deserves a much better Introduction Picture IMO

Jatlas2 (talk) 18:06, 20 August 2009 (UTC)

"Better" in what way? Do you have some suggestions? Sasata (talk) 15:17, 21 August 2009 (UTC)

I do... I think one image (like most pages) would be much better than jamming a few together (of these, one is a bad quality image of moldy break and another is a blurry black and white microscope picture). Also it is impossible for me to edit this page... I am done trying! Goodluck all! Jatlas (talk) 22:41, 26 August 2009 (UTC)

The existing collage isn't perfect, but I think it's a great way to illustrate the diversity of the fungal kingdom in one picture. Any suggestions for a specific picture that might do a better job? Sasata (talk) 20:47, 3 September 2009 (UTC)

Sorry I didn't get back to you earlier... Still just putting my thoughts out there, but the picture is much too cluttered. 5 pictures, with an evolution table, a long caption describing the pictures with links, and information about fossils... I would take out the evolutionary table because it would be a great stand alone image in this article in the "evolution" section. Along with the image could go the fossil description. From there, I would use two images combined. A better mushroom image and a colorful microscopic image of fungi.Jatlas (talk) 23:06, 9 September 2009 (UTC) As far as specific pictures go, it is easy to find great high quality mushroom pictures like (Xerocomus chrysenteron 7840.jpg). It is more difficult to find fungi pictures under a microscope or pictures of fungi which do not show the fruiting body. Here is a neat picture of yeast that has color (Hefezellen.jpg), and this image (Leaves fungus bosnia.jpg) is better than that grainy image of mold on bread.Jatlas (talk) 23:41, 9 September 2009 (UTC)

Fruiting and the lead

I found this sentence misleading so I removed it from the lead:

Fungi reproduce via spores, which are often produced on specialized structures or in fruiting bodies, such as the head of a mushroom, though some microscopic species are capable of reproducing asexually through budding, such as yeast.

The problem was that not all fungi produce spores, and this sentence didn't make it clear whether budding is in addition to or an alternative to spore production. In any case, budding is not the only form of asexual reproduction.

I'm also not sure about this sentence:

They may become noticeable when fruiting, either as mushrooms or molds.

Plenty of noticeable molds (eg Aspergillus niger) don't have a known sexual cycle so cannot be said to "fruit", if I understand that term correctly. I'm not sure where to go from here – some mention of fruiting, spore production, and asexuaul forms of reproduction (budding, division, vegetative mycelial propagation) seems appropriate in the lead, but it's too late at night for me to think now >_< Adrian J. Hunter^{(talk•contribs)} 14:47, 28 August 2009 (UTC)

external links

I think that the following link from the external links should be deleted http://www.mycolog.com/fifthtoc.html

The Fifth Kingdom] – Online textbook

It is not an online textbook, but part of a CD-ROM based textbook that is for sale on the site, so most of the text is missing from this free/advertising version. I'm just posting this here because I don't know if it's a good idea to just delete it myself.

Lars ˝˝˝˝ —Preceding unsigned comment added by Larsuld (talk • contribs) 16:51, 3 September 2009 (UTC)

Thanks, I've removed it. –xeno^talk 16:55, 3 September 2009 (UTC)