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Philippine Myxomycetes and Other Slime Molds*

*Statements must not be copied or used without permission from the author: Isidro A. T. Savillo

Current ecological observations and comments-

10/16/2016~~ Generally, there was no presence of myxomycetes (in its fruiting body forms) in several mangrove trees examined. These mangrove trees are characterized for being regularly subjected to flood- plains water (most likely a combination of marine and fresh) during high tides. The physical/chemical? structure of its bark and its regular exposure to the saltiness of the brackish water (especially during high tide) may not have allowed the myxomycetes to grow on the trunks of these mangrove trees. A report stated that Conocarpus erectus yielded numbers of myxomycetes (probably through sample analysis in the lab or actual growth observations for I have not read the whole paper) but I think the species examined if referring to actual observations of fruiting bodies may have lived not in the flood plains but in inland areas such as in this photo which shows that the myxomycetes observed may have encountered little disturbance. I also have not read about their sampling sites. I have not known where their actual sampling site in Brazil is located. Another species of Conocarpus typically grows inland.

*Mangrove growth of myxomycetes is dependent on the ecological characteristics of their (mangrove) stand.

3/25/2015~~ Included in my most current publication on incomplete ecological analysis/characterization of myxomycetes, I have this statement-
"Their abilities to form fructifications even their substrates are not dead plant materials could further be analyzed whether they have enough pre formed mRNA to represent proteins and other bypoducts or they have reserved foods for the development of matured  fructification bodies but how successful are the formation of spores? Can the spores germinate healthily and complete the complicated life cycle? It is believed that dead plant materials are the regular as well as natural substrates for myxomycetes, probably for an enzymatically induced extracellular digestion but until now no extensive enzym atic studies have been undertaken."

3/28/2015`` Here is my additional statement: The plasmodium seems to be the point of interest when it comes to food acquisition. If the plasmodium retains the amoeba's way of phagocytosis then any particular organic matter living or dead could be internalized and there will be enzymatic action in situ that could reduce them into digestible forms. But if the plasmodium follows the true fungal extracellular digestion then the enzymes are released outside along the way and food encountered will be digested and will be internalized. It is also possible that these work both ways  with the plasmodium.  Now with the fruting bodies, as explained  (as shown above) in my former statement regarding fructification in non living plant materials could be due to preformed mRNA but success here is a question compared to fructification in dead plant materials which we usually see where I think beside the preformed  mRNA if there is really a signal for this or it may be unnecessary, the fungal (re: fructification body) way of extracellular digestion can take over by releasing enzymes that could help them survive using dead plant materials as substrates. In this case myxomycetes is really a tug of war between protists and fungi and if these behaviors persist and exist it could even be advisable that it will have its own taxonomic world like lichens. I think lichens is now enjoying its realm independently (Kingdomless?) while myxomycetes is still being dissected up to where and until when?-

~contrasting between lichen and myxomycetes

 Lichens
individual alga(e) and fungi are in close association -> genetically, genes are not shared as one genome (e.g. an exception if DNA transfer ever exist ) but the products are  -> formation of peculiar,  specific spore bearing bodies.

 Myxomycetes
individual exhibits morphological/physiological framework of amoeba and fungus -> genetically, there is a fusion of both genomes (but not all components) or an evolution for both -> formation of peculiar, specific spore bearing bodies. 

Taxonomy- Placing slime molds with the amoeboid protozoans (basing on the internal cytoplasmic flow)  would necessitate a question regarding fungal extracellular enzyme production. Are the myxamoeba or their plasmodium or their fruiting bodies capable of fungal type of extracellular enzymatic digestion? If the answer is yes, this is more of a fungal type of enzymatic characteristics a description that is centered in fungal like protists [Dictyostelium (sequenced for cellulase and its positive), Thraustochytrids (a chromist)] and this characteristic will bring them closer to the fungal group.  Do the common amoebas (and the rest of amoeboid protozoans except probably some slime molds now  grouped together with the amoebas) capable of producing extracellular enzymes? In fact in one paper, Protozoans that live inside a termite's body (?) could not even produce extracellular enzymes and would depend on the bacterial degraders to do so. In addition, the myxamoeba whether flaggelated or not represents gametes and not as "individual organisms**" which would be synonymous to fungal gametes, and even Dictyostelium displays  heterogeneity in its sexual thallus (e.g. homothallic) which is also fungal in character and Amoebas are individual organisms as well as apomictic slime molds (where there is meiosis arrest during spore formation) thus are not gametes but could reproduce asexually (binary fission) for no sexual reproduction was ever recorded about them. In case (rarely or has never occurred for apomictics is considered accidental rather than producing a permanent line) mating for the apomictics will occur for these diploid containing "gametes" to form a polyploid then this phenomenon will make it revert back to the common myxomycete life cycle or a part of it and depart from the asexual reproduction as mentioned previously for the Amoeba. But this time, a polyploid is produced for the final individual organism. Very surprising indeed.   Slime molds generally germinate from spores as haploids which is very much gametic rather than as individual organism especially that their goal is towards sexual reproduction. Once they are haploid regardless of years of  their existence or whether they undergo metamorphoses or not they are still in the gametic stage (e.g. Dictyostelium). A life cycle must only have one individual organism. If the myxameoba is your individual organism once it mates to become a zygote, there you produce another individual organism. It's like a bear metamorphosing into a bird which never occurs in any life cycle. By all means, identify which is your real individual organism in the stage(s) of the life cycle, for one as in this case, represents the gametes. I hope that by this taxonomic designation this would not lead to confusion especially upon unraveling the ecological, physiological and reproductive issues in the molecular and cellular levels pertaining to these organisms. How come that the fungal aspect is being missed out in this taxonomic strategy?
**being their last metamorphoses stage - they still have the fructification stage to be considered as an individual organism.

parallelism- (just examples irregardless of being diploid or not)

plasmodium -> fruiting body
mycelium-> fruiting body
basidiocarp-> fruiting body

sexual reproduction- 
fruiting body- myxamoeba- zygote (myxomycete)
fruiting body- gametes- zygote (chytrids); 
therefore it's not unusual.

mislabeling- gametes but not individual organisms

Synonymous to Amoeba is no other than the diploid plasmodium and the rest of the characteristics are fungal and these have to be included in whatever taxonomic title you have in mind. And the apomictics- but I hope this is occurring in nature and not as a result of a laboratory exposure.


3/30/2015~~ Towards Molecular Ecology- "Ecologically based observation of myxomycetes is not important unless in areas very uncommon e.g. marine but in the tropics this is a common spectacle for any amateur taxonomist.This does not need to be translated again and again. Laboratory analysis for the completion of a life cycle which is even a regular exercise in an undergrad lab  is not comparable for what is happening outside where these myxomycetes thrive. Which has more ecological trust- to find fruiting bodies in actual situations or gather dead plant materials and  stimulate it to produce the fruiting bodies in the lab?  In the latter the biotic materials used maybe due to accidents/contaminations and not their precise natural habitat. Lab. manipulation is good for taxonomic purposes but hopefully its structure(s), etc. is not modified for we all know that environmental factors especially artificial may have an epigenetic subjection. Regarding the gametic factor, fungi are sexually imbued on this and as this is meiotic in myxomycetes, the amoeboflagellates (or not necessarily flagellated ones) may assume that role. If it is mitotic then we have the deuteromycetes to compare only that the latter does not have the gametes. But gametes for a non sexual situation? Molecular Ecology is what is needed especially in some weird environmental- existing and persisting situations.This could give the audience a clear view of what is really actually happening and a much better way of relating especially if these results could be accurately duplicated."

4/01/2015~~ Regarding gametes... Let's go back to my previous statement (pasted here; taken from my Theoretical Biol. Web Page)-

Perpetuation of the Species is more important than Standard Reproduction.
The process of reproduction does not always follow the gender sensitivity rule.
As observed in various levels of organisms, gametes are also shed or released in 
unconscious situations but may have the goal towards successful fertilization.
Irregardless of what type of reproductive processes, evolution has patterned 
life to continue urgently the perpetuation of the species. Isidro Savillo* 3/12/2006 

Comment- therefore,  it doesn't matter having an amoeba like gamete.

01/17/2016- I have this mind for contrast ever since but have this opportunity to write - Human spermatozoa as  gametes also harbor nutrition just like the amoeboflagellates of myxomycetes. 

09/06/2014``Very unique indeed- an exception in the Myxomycete world----

 
 
 Do you think these "roots" are for anchor purposes only with no enzymatic activity going on?
 This is a species of Ceratiomyxa and if one looks closely, it has different internal structure compared to the common myxos (Stephenson, Steven and H. Stempen.1994. Myxomycetes: A Handbook of Slime Molds. Timber Press). It's molecular data is even different from the "true myxos" (Stephenson, Steven. 2014. personal communication). If its size could have been bigger and if does not exude an air of spores and does not appear cottony, it looks like a "Cladonia".-- I. Savillo



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5/ 2014``Celebrating the Dormancy [It is wrong to say death with the so many spores left behind] of this remarkable Stemonitis sp. Here is the subpage regarding this:

On Stemonitis sp. - Dormant for Years
Do you think the dormancy of Stemonitis may be due to the quality (quantity is not a question) of fructification bodies and spores? As far as to my observation, there was no alteration of the environment to where it was formerly sighted. Regeneration of the life cycle especially if robust ones is one aspect of myxomycete ecology that has to be looked into.
 
 
 
Nov. 24, 2011- News release- newly reported species- a Physarum whose plasmodiocarp have perpendicular marks before it "zips open" (lengthwise ) (like P. bivalve except for the perpendicular marks prior to opening), grows in a dead leaf; a Comatrichia sp. etc. with black "inky" in appearance stalk, grows in a dead stem...etc.

07/15/2008~NEW~Pls. visit the Myxomycetes in Panay Island (in progress)

*The Electronic Journal of Tropical Lichenology and Myxomycetology will soon be operational. Please visit this web site as frequently as possible. If you have any questions, please send an email to lichens_2001@yahoo.com. Thanks.


This Eumycetozoan Research Project web page is dedicated to the species of Myxomycetes and other eumycetozoans which are found in the Philippine archipelago and managed by Prof. Isidro T. Savillo. Taxonomic identification  and descriptions of their habitats will be posted in this webpage.

Prof. Isidro T. Savillo (use google's  internet explorer to search for this position):  is a Research Associate in the PBI (Planetary Biodiversity Inventory) Global Biodiversity of Eumycetozoan Project of  Dr. Steven Stephenson.   At present, Dr. Stephenson is a Research Professor and PBI Project Director in the Department of Biological Sciences, University of Arkansas in Fayetteville, Ark.

September 23, 2003:

Congratulations for the official approval of the project, PBI:Global Biodiversity of Eumycetozoans!!!*

* One of the Four Research Projects to first receive the prestigious Planetary Biodiversity Inventory (PBI) Award/Grant being funded by the National Science Foundation, and All Species Foundation.

PBI: Global Biodiversity of Eumycetozoans

European Mycological Association: Web Sites On Myxomycetes

Key to the Eumycetozoan (?) Genera of the Philippines...soon!



Web Page constructed/modified, respectively : July, 2003, May 25, 2005 and Dec. 24, 2006; July 12, 2015



   As part of my research abstract, Myxomycetes in Mangroves at the 2007 Society of Wetland Scientists International Conference at the Sacramento Convention Center, California.."...The ecological significance of myxomycetes in mangroves may never have been elucidated because if ever there are enzymatic studies they are maybe very much limited in publication and presentation", This will serve as an eye opener for budding young scientists to design and work out an experimental methodology to determine the enzymatic characteristics of myxomycetes which could clearly ascertain its ecological significance in nature. As what I further stated on plasmodial slime mold reproduction during my presentation, "The spore formation goes a long way compared to that of deuteromycetes" 
whereby this may serve as a barrier but I really don't think it will be for our young budding scientists. 

~4/08/2015- Problems with Molecular Taxonomy- (Pasted here from my Theoretical Biology Web Page- my statement:11/2013- Why loopholes in specific DNA Barcoding? Are there no more conserved specific DNA segment to identify species exactly? Are there no other besides stuffs with mito? Excuses..x2.)

Sometimes the conserved gene is there but the morphology is different or there is no exact gene but it has similar morphology to the rest that match exactly and this "stranger" now belongs to a "taxonomic orphan".  Unless there will be genes which the taxonomists can see and push it towards a different taxonomic direction but unfortunately morphologically there will be a big difference-  "When all the rest looks like Pinocchio, the new member in this group looks like Peter Pan" but accordingly  there are "similar molecules" to support it so it has to be.  How will the viewers satisfy themselves with this kaleidoscopic mixes of phenotypes and genotypes and which is not  and why not though it ought to be? After publishing a paper with this weight and later rectified because there is one which looks like or has a gene but it just can't belong or whatever new molecule has sprouted out evicting a member from the group, It is now  becoming an inconclusive journey. So is this the  style of intellectual endowment in the future to your learners/students?   A trial and error and an exclusivity plus an orphanage. Applying this taxonomic endeavor, maybe one day will decipher what human race is a direct descendant of the Sarawak chimpanzees.  I think the best way to do molecular taxonomy is to determine its evolutionary lineage (dormant or semi- dormant...etc.  conserved genes) because this is molecular taxonomy's goal but also include in the package the genes responsible for morphology (e.g. phenotype of common importance to 99.99% of the species).  We all know that the gene is plastic, and we are aware that the environment plays a role in gene expression thus we have the science of epigenetics, then do you think that a gene will be a permanent suitable marker for taxonomy?  Will it work for all? Please visit this forum for more info and click on these- 1 , 23 ,456 , 7, 8 and also follow this search for more related publications.

When it comes to molecular taxonomy inclusive to this is the famous DNA barcode, this ought to be the direction of taxonomic identification and this could be present in one individual organism being identified->

gene for family-> gene for species -> gene for a strain 

Can a DNA barcode produce a taxonomic ladder for easy comprehension and understanding? Or it will just be messy word puzzles of which fit or not? Remember we are talking science. Science is fixed.

I read a study about 3 @@@@bees that are very similar in looks thus there is no distinction but they are 3 different species... The questions are: Are you sure they belong to the same family? Did the same Family Gene sequence came out? Don't tell me that you have to rely to the traditional taxonomy to support your work now that you are engrossed with your DNA barcode.  Regarding the species gene- is that really the gene for the species or is that the strain representing 3 different kinds? Is that how easy to say species?  How sure are you? Is this universal for all species of @@@bees that you have in mind? How about if there is one which looks very similar to the three but it has own genetic identity? What will you do?  Of course look for other new DNA Barcodes  within or without  in mt  and some say they are gene segments but not bar codes they could just pin point  particular genes in the nucleus or chloroplast or even the plasmid/cosmid in the future. It looks like a game of finding similarities and differences  by chance without a referential root. But this could not stand on its own so they have to look for a species that has these new gene segments  and relate them evolutionarily to this species in question so at least  they were able to find its partner though they maybe morphologically similar the status is blurred. Why blurred- They didn't share the DNA barcode  of the majority of species which is suppose to be the DNA barcode for those species. This deviant species together with its newly found partner is a product of a DNA bar-coding based phylogeny, so a lot of genes are involved, not solely by a DNA barcode. Therefore the DNA barcode has looked for support to justify its usefulness. This is just to comply (getting into the loop) with the traditional taxonomy that morphologically similar organisms represents a species. But it is so funny to know that not a single barcode gene expresses a phenotype for a specific taxonomic i.d.  - a problem I see with Integrative Taxonomy. How about testing the other species for these new set of genes- are they not present in them too? If they are what's the use of making these two species (deviant and its partner) so inclusive. A paper needs through analysis before publishing. Otherwise this is just going around in circles, half- cooked and hanging. If a group of species are all positive for a barcode, can it establish a new family [bypassing the "family gene" and "gene(s) for the genera" or are there? ]?  I am not really sure but I think this is what happened to a group of fishes taken out from their previous family and assigned a different one. How powerful these barcodes are isn't it. As easy as that?  Then there is no need for a taxonomic ladder. It's the other way around, the species is now determining the broader titles of classification (a reversed taxonomic ladder).

On Integrative Taxonomy- I would suggest that there will something in common in both and that's the gene. So there is a phenotype gene  and a DNA Barcode. If the phenotype gene is there and it is expressed and the DNA Barcode is also there and this happens to a number of look- a- like individuals (this is what the phenotype gene(s) codes for) therefore they may then be considered as belonging to the same species- thumbs up for Integ. Tax.  In case both genes (DNA Barcode and the phenotype) are present but the phenotype gene is not expressed  or not expressed properly then it is time to snoop into the epigene. It could be a loitering gene waiting to clasp that segment or a neighboring gene, etc.  for a change of phenotype. Therefore, instead of a new species which is usually the goal later is to assign it to a new family, it becomes a strain or a variety and remains with the genus/family. But if the DNA barcode is nowhere to be seen then it transits to the orphanage. First the DNA barcode used has to be determined as a universal one before something new will be assigned. This need for a pondering of the minds because  I  don't think  epigene works  here (absence or different DNA Barcode segment)  but it could be a mutation or what! In case more than one phenotype genes were identified and these are all present  regardless of the absence of the specific barcode this could be assigned as a subfamily rather a different one. Phenotype gene is now powerful and points for Traditional Taxonomy.  This time a high tech lab is needed for Integrative Taxonomy.

I haven't explored these DNA barcodes in medicine of course we are after genes which cause disease.  These are not disease genes because these are short segments which can be useful to taxonomic med. as they claimed. We will see the progress of these taxonomic tags if they can cure a disease directly and instantly provide a solution.

*May 17, 2016- This is the day where we had experienced rain after a hot but more or less windy weeks of the year... GPS loc... ? Nevertheless, I do have a biological perspective about homosexuality though I have been giving some hints about this in my other statements. But to make this clear and not as what some social scientists? say that this is an abnormality, I would rather say  that this is an error (in case of humans) probably evolutionary in the earnest goal of the human organism in the perpetuation of its species. Unfortunately the Homo sapiens is now overpopulated with both sexes represented. To look  at the lower forms (e.g. shell species) of organisms or even complicated ones (e.g. fishes), they have the capacity to change sex organs so change of gametes to successfully perpetuate their species. Unfortunately, this is not possible naturally in humans. I had a discussion of this in my past publication (at Biologybrowser). 

10/21/2017~~  To The Level of a species.... I encountered two papers ( e.g. one in fishes but I haven't read about it yet and the other is on lichens affecting a collection) that give some sparks that taxonomy must not be dependent to molecular identification for I think in spite of similarities in CO1 (though I haven't investigated whether they did this) there are differences in chemical morphology or structural morphology, etc. and may instigate separation into different species. Look into the revision of one lichen family, one species represented by 2 samples may share similar COI (but this COI already has discrepancies as I mentioned above) but the other sample is different in terms of chemical morphology and was funneled to a new species.  Genetically speaking, this has "jumped over" the strain or variety (of a species) identification. What do you think if there will be a revision of these types in Eumycetozoans? 
 

Sometimes, it is worthwhile to be a writer; and the same time taking the task of a scientist * and to be a  scholarly search item.

*In Bing.com  the region has to be set in U.S. English, India, U.K., Canada English