Discovery of Microorganisms + Advice on Research Microscope

Do you have any microscopy questions, which you are afraid to ask? This is your place.
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Antartica
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Discovery of Microorganisms + Advice on Research Microscope

#1 Post by Antartica » Wed Mar 04, 2020 5:04 am

hello,

I am a complete beginner and know nothing of microscopy and microorganisms. However, it is a topic that greatly interests me. I was wondering, since very few of the worlds microbes have actually been discovered (by some estimates only 0.0002 percent), would it be possible for an amateur like me to discover new microbes? Specifically:

1) What microscope or equipment would I need to be able to discover new bacteria?
2) What microscope or equipment to discover new viruses?
3) Would I need to do DNA sequencing to validate the discovery? What is this process like and can it be done from home by sending to a lab?
4) How are new bacteria and viruses confirmed? Is it through research journals and papers? Or is there some other process by which new discoveries can be submitted for confirmation?

I'm really curious about how one would go about getting into microbe discovery (assuming its possible). I would imagine it is since scientists are frequently doing it, so why can't I? ;) I've always wanted to do asteroid/comet discovery, but I live in a city with a lot of light pollution, so microbes seem like another good option! :)
Last edited by Antartica on Mon Mar 09, 2020 4:08 am, edited 1 time in total.

Antartica
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Re: Discovery of Microorganisms

#2 Post by Antartica » Thu Mar 05, 2020 3:34 am

Can anyone help answer some of my questions?

wstenberg
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Re: Discovery of Microorganisms

#3 Post by wstenberg » Thu Mar 05, 2020 3:50 am

Ok, I'm not a microbiologist, but I have spent a few years working in a microbiology lab. So I'll jump in.

Agree that there are so many unknown bacteria. You could go out, grab a bucket of dirt out of your backyard, and find new organisms.

Most organisms are described by their biochemical actions, which means culturing them and seeing their response to various chemicals.

I would recommend a book "Field Guide to Bacteria" by Betsey Dexter Dyer. Gives a lot of hints for amateur microbiology. It's an enjoyable read.

Here's the Amazon link: https://www.amazon.com/Field-Guide-Bact ... 0801488540

Seems like viruses would be a lot more difficult. I don't know any amateur virologists!
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Scarodactyl
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Re: Discovery of Microorganisms

#4 Post by Scarodactyl » Thu Mar 05, 2020 5:04 am

You can't see viruses with a typical light microscope. They're just too small--the very largest ones are just slightly longer than the width of one wavelength of red light. I am not sure how viruses are typically discovered, but direct observation isn't the way.

Antartica
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Re: Discovery of Microorganisms

#5 Post by Antartica » Thu Mar 05, 2020 5:47 am

thank you wstenberg and scaro.

Anymore info from other users? With so many undiscovered microbes, there has to be a way for amateurs to make discoveries. If anyone else has any useful information, I would greatly appreciate it.

MicroBob
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Re: Discovery of Microorganisms

#6 Post by MicroBob » Thu Mar 05, 2020 8:09 am

Bacteria are seldomly worked on by amateur microscopists, but it is not impossible. The light microscope can only roughly discern bacteria: Dots- slashes, spirals. By staining the bacteria can be differentiated a bit more visually.
It is possible to culture bacteria on agar - plates. By working under a hard UV light the agar plate is kept bacteria free until the sample is added. From the agar plate on it becomes quite difficult.
I my eyes this is more "work" than "fun".

There is a book from former DDR, East Germany, that is said to cover this in a practical and amateur friendly way. I could try to get the title for you.

Bob

Hobbyst46
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Re: Discovery of Microorganisms

#7 Post by Hobbyst46 » Thu Mar 05, 2020 9:53 am

Antartica wrote:
Wed Mar 04, 2020 5:04 am
hello,

I am a complete beginner and know nothing of microscopy and microorganisms. However, it is a topic that greatly interests me. I was wondering, since very few of the worlds microbes have actually been discovered (by some estimates only 0.0002 percent), would it be possible for an amateur like me to discover new microbes? Specifically:

1) What microscope or equipment would I need to be able to discover new bacteria?
2) What microscope or equipment to discover new viruses?
3) Would I need to do DNA sequencing to validate the discovery? What is this process like and can it be done from home by sending to a lab?
4) How are new bacteria and viruses confirmed? Is it through research journals and papers? Or is there some other process by which new discoveries can be submitted for confirmation?

I'm really curious about how one would go about getting into microbe discovery (assuming its possible). I would imagine it is since scientists are frequently doing it, so why can't I? ;) I've always wanted to do asteroid/comet discovery, but I live in a city with a lot of light pollution, so microbes seem like another good option! :)
Here is the book I would read,as an introduction to the basic challenges of bacteriologists:
"Microbe Hunters" by Paul de Kruif.
Sold in Amazon and probably in most book stores for youngsters.
Although written for the youth, it is enjoyable at any age.
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Re: Discovery of Microorganisms

#8 Post by wstenberg » Thu Mar 05, 2020 2:48 pm

Here's a link to some helpful bacterial information from the UK microscopy site.

http://www.microscopy-uk.org.uk/mag/art ... teria.html

The methods useful for amateurs are liquid mixed cultures. Selective media and solid media like we use in the microbiology laboratory are more problematic for home use.

As mentioned, microscopy is not the sole diagnostic modality of new bacteria, but it is used as part of it.

When I used to work in the clinic, we would examine bacterial samples for motility. We would generally use darkfield, but I remember switching to phase contrast somewhere along the way. We would not identify be species, just by morphology, i.e., percentage of motile rods and spirochetes.

When doing this, would would occasionally see strange protozoa in human oral specimens. Things that were not identified in the books. We tried to record some of these (back in the day of VHS tapes), but mostly just a curiosity. Maybe they were just transient organisms that rode in on some food and found a new home in the mouth. But I think that at least some of them were new organisms, just waiting to be discovered. But they were not the focus of our observations, so we never spent much time them.
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Antartica
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Re: Discovery of Microorganisms

#9 Post by Antartica » Fri Mar 06, 2020 6:23 am

thanks for the added information. Yes, bacteria and virus are very small, and unfortunately most are out of reach of light microscopes. But with that being said, could someone suggest a sufficiently powerful microscope for someone like me that wants to dive into microbe discovery? I'm looking at a budget of max $700.

I would like to be able to see/discover things like this: https://www.cbc.ca/news/technology/anim ... -1.5478645

PeteM
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Re: Discovery of Microorganisms

#10 Post by PeteM » Fri Mar 06, 2020 6:55 am

The question of what microscopes to consider gets asked frequently, so you might want to start by searching some of the old threads here.

Your location is a factor. So, also, is how confident you might be in taking on tasks like cleaning and lubricating an older microscope.

$700 should could you an excellent used microscope and a satisfactory new one as well. You're hoping to push the limits of optical resolution, so gaining a bit of experience with a somewhat less expensive microscope might also be a good option.

Leitzcycler
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Re: Discovery of Microorganisms

#11 Post by Leitzcycler » Fri Mar 06, 2020 12:29 pm

Very interesting questions and I highly appreciate your ambitions! As I am molecular biologist and have long experience in gene cloning and have done some microbial identification too, let me present my point of view to some of your questions.

Fist of all, I would forget home lab-based virus research for now. Viruses need to be cultured in cells, which makes things difficult and quite expensive. There will be no realistic ways you could detect nor identify viruses at home.

For bacterial identification you need a microscope with 100x immersion oil objective. With your microscope and using different staining techniques you may see the shape and size of your bacteria as well as some chemical characteristics of e.g. bacterial cell wall. In microbiology books and internet you will find protocols. I think almost any microscope of good quality will be ok as you can't get any further with a light microscope.

There are automatic mass spectrometer-based instruments in hospitals and diagnostic companies which are able to identify your microbe just in a few minutes. All you need is a single colony of a culture. The price is about 30 EUR per sample.

The other option is to extract DNA from your bacteria (you need a pure culture of course) and amplify a specific region of rRNA-coding sequence using PCR. After purification of the amplified product you get it sequenced. This specific DNA sequence is then compared to corresponding sequence libraries using online tools. The result you get is a DNA sequence homology comparison with information how identical your sequence is compared the most similar sequence in nucleotide sequence databases.

These methods will usually identify your sample at genus-level, in many cases at species level too. However, to identify a bacterial sample at species-level is not always easy at all. To make it more complicate, a single bacterial species can form multiple strains which have different metabolic characteristics e.g. related to their pathogenity. In this case there might be just a single nucletide difference between the genomes. If you try to publish a completely new species of bacteria, I think you should sequence the whole genome. However, this is not a difficult task nowadays.

DNA-based identification of bacteria as described above is quite straightforward process for an experienced molecular biologist in a lab. However, if you are planning to do it at home, it is quite a hard and lon-term project to establish the lab and put up the system, although not impossible. However, I would first recommend you to take part in some molecular biology course to see if you like the work or not. I think there are courses for amateurs nowadays. Or try to take part in a local universitys course for methods in molecular biology.

What comes to discovering something new in science: I think most important results have been found by accident. You would neet hard work and plenty of good luck to find something new. You may find a new species of bacteria, or you may spend twenty years in your lab without finding anything.

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Re: Discovery of Microorganisms

#12 Post by actinophrys » Fri Mar 06, 2020 7:13 pm

Just out of curiosity, any reason to single out bacteria? The case I know for sure of an amateur discovering a new species, albeit still to be described in full, is an amoeba found by Bruce Taylor. And for anyone here inclined to say "sure, but he's barely an amateur", I've also come relatively close: a ciliate that had been seen before, but only a few times decades prior in eastern Europe.

You can see that all the heavy work of redescribing it in detail, including DNA sequencing, was done by a professional protozoologist. But I still think that counts as contributing something to the field. And in such groups, with all the questions about flagship species and biogeography, I think there may be a lot of chances for a careful amateur to discover something useful even if it turns out not to be completely new.

Leitzcycler
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Re: Discovery of Microorganisms

#13 Post by Leitzcycler » Fri Mar 06, 2020 8:47 pm

It is possible to culture bacteria on agar - plates. By working under a hard UV light the agar plate is kept bacteria free until the sample is added. From the agar plate on it becomes quite difficult.
UV light is frequently used in laminar hoods to kill microbes: usually the UV light is on during night time when nobody is working there. The UV light is off during working time.
Working under UV light is dangerous for obvious reasons. Personally, I have doubts if UV lightning is necessary at all in most cases. However, I have never seen or even heard that culture plates are kept under UV light to keep them sterile. Usually plastic pre-sterilized petri dishes are used and culture medium is autoclaved, let to cool down about 40 - 50 C and then poured onto dishes. Dishes can be kept at +4 for several weeks. Before inoculating the microbe the dishes are let to dry (just to remove excess condensed water droplets) and get warmed in an incubator. You can handle the cultures and transfer microbes even in open air on an ordinary working bench if you are careful and the microbe is not an hazardous pathogen. You might get some fungus contamination on your plates during long-term storage. However, you must transfer your microbes to new culture from time to time anyway.

Making culture plates would be quite a simple task to do even at home. Sterile plastic dishes are quite expensive as you have to buy a package of huge number of them (like 1000 pcs). However, you can buy glass dishes and reuse them. They can be heat-sterilized at 150 C for 2h. For preparing culture medium you need a pressure cooker. At 118 C for 20 min will be fine. There are plenty of culture medium recipies available. The basic medium compositions are quite simple.

You spread your microbe sample onto the culture medium using a sterile platinum loop (or a toothpick, long coctail pics are even better if you don't have a platinum loop in your kitchen) or alternatively you spread a diluted sample onto the plate using a flame-sterilized glass rod triangle. After incubation will get colonies of pure microbes. Then you just spread onto objective slide, dry, stain and observe under microscope.

And about amateurs and professionals: I don't even see any point to make such categories. I would say I am a professional molecular biologist. However, I consider myself to be more like an amateur in microscopy. I am here to learn things. There are huge number of professional research scientists using microscopes for their research. And yet many of them actually know very little about microscopes and microscoping compared to forum members here.

It doesn't matter so much which background you have. However, according to my experience making science is not fast and easy. Most people don't understand the amount of dissapointments and frustration you have to tolerate.

Antartica
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Re: Discovery of Microorganisms

#14 Post by Antartica » Sat Mar 07, 2020 4:37 am

Thanks Leitzcycler! That was exactly the type of information I needed. You've given me so much to think about. For starters, now I know to look for a microscope with a 100x immersion oil objective.

And I'm not solely focused on bacteria. I would like to discover ANYTHING new, as long as it's a microbe. And the thing is, there are billions of undiscovered ones, so I feel its an area ripe for exploration!
There are automatic mass spectrometer-based instruments in hospitals and diagnostic companies which are able to identify your microbe just in a few minutes. All you need is a single colony of a culture. The price is about 30 EUR per sample.
Can you provide some links to these resources? I would like to start investigation local sources if possible. I'm in southern california if that helps.
The other option is to extract DNA from your bacteria (you need a pure culture of course) and amplify a specific region of rRNA-coding sequence using PCR. After purification of the amplified product you get it sequenced. This specific DNA sequence is then compared to corresponding sequence libraries using online tools. The result you get is a DNA sequence homology comparison with information how identical your sequence is compared the most similar sequence in nucleotide sequence databases.

These methods will usually identify your sample at genus-level, in many cases at species level too. However, to identify a bacterial sample at species-level is not always easy at all. To make it more complicate, a single bacterial species can form multiple strains which have different metabolic characteristics e.g. related to their pathogenity. In this case there might be just a single nucletide difference between the genomes. If you try to publish a completely new species of bacteria, I think you should sequence the whole genome. However, this is not a difficult task nowadays.
Yes, I have read that DNA is the most common way to determine a new species. For example if you read the Journal paper that made this recent amazing discovery about the first known microbe that does not need Oxygen to live: https://sci-hub.tw/https://doi.org/10.1 ... 1909907117
it looks like they did genome and mitochondrial DNA analysis to confirm the results. Is there a database or website that is searchable by DNA to determine if it is a new species? How do microbiologist search across ALL microbes to claim a new organism?

Lastly, the above Journal Paper mentioned that they used a "Leica DMR compound fluorescence microscope at 630× and 1,000× magnification." Does anyone have an estimate of how much such a microscope would cost? Does it include an immersion oil objective? Or is fluorescence a different type of microscop?

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Re: Discovery of Microorganisms

#15 Post by PeteM » Sat Mar 07, 2020 6:20 am

Leica DMR with fluorescence and a 63x plan fluor or plan apo might be around $3000 used if you're a bit patient.

Your budget can let you view all sorts of amazing protozoa and the outlines of most bacteria. You just won't be likely able to prove you're the first to see one, however unique it might seem.

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Re: Discovery of Microorganisms

#16 Post by Leitzcycler » Sat Mar 07, 2020 8:23 pm

I would like to discover ANYTHING new, as long as it's a microbe.
Well… microbes are an enormously large group of organisms including bacteria, fungi and protozoan. Each group has its own field (or fields) of research. Years of experience is needed to be able to identify even the common species. My modest experience is limited only to bacteria and fungi. From my point of view, they are more “easy” to identify because of the methods based on DNA analysis. There are no such comprehensive sequence databases for other microbes. I think their identification is more based on morphology, which needs very deep experience and is very professional field indeed.

My advice is that you hold your horses a while and first learn how to find, culture, isolate, stain and observe microbes using a microscope. After getting the basic knowledge and lab practice you can then focus into some specific question in the field.

For selecting microscope, please read very comprehensive discussions in this forum about this subject. I think you should get a very good microscope spending no more than about 500USD. Fluorescence microscope is used in cell biology to localize different structures or molecules in cells. Usually it is based on fluorochrome-coupled antibody which specifically binds to some proteins or gene expression studies using a recombinant green fluorescent protein. Using these methods is very expensive and you don’t need a fluorescence microscope for microbe identification.

It is hard to advice you from the other side of the globe about your local resources as you should be able to find them in the net as easily as I do. However, this seems to have very wide selection of services and also has offices all around USA including southern California.
https://www.emsl.com/Services.aspx?acti ... tegoryID=5

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Re: Discovery of Microorganisms

#17 Post by Leitzcycler » Sat Mar 07, 2020 9:09 pm

Here is an example to show you how it goes. You have isolated a pure bacterial culture. On culture plate, the bacterial colony is deep yellow. Under microscope the bacteria look quite big and they form very regular groups of four, eight and so on. This sample has been stained with toluidine blue, which is like a universal stain. By using more specific staining methods (such as Gram staining) you can in many cases further focus your identification to some group of bacteria. Anyway, already this information (color, cell size and form, formation of regular groups of cells) would tell to an experienced observer which bacterium it might be. However, to be sure we also isolated the genomic DNA and amplified a part of ribosomal RNA-coding region. The sequence is as follows:

GATTACCATCGGCGCAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTAGGGAAGAAGCGAAAGTGACGGTACCTGCAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGTCGTGAAAGTCCGGGGCTTAACCCCGGATCTGCGGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACAGGATTAGAAACCCCTGTAGTCCA

Now you go to this address: https://blast.ncbi.nlm.nih.gov/Blast.cg ... lastSearch
You then copy-paste the sequence into the first open box under “Enter Query Sequence”. Then press “BLAST” in the end of the page. Wait until you get your results. The most identical sequences from the database appears first. Now which species you bacteria most probably is?

This is, however, very easy and clear example. The sequences may be very similar between different species. I am not familiar with the process needed to validate a new species. I assume there must be anomaly compared to existing species, but how much I don’t know.
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Antartica
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Re: Discovery of Microorganisms + Advice on Research Microscope

#18 Post by Antartica » Mon Mar 09, 2020 4:26 am

Okay guys, I spent all weekend obsessively reading everything I could regarding microscopes and which type/model to get.

I've decided to purchase a research microscope. However, I don't have $3000-5000 right now to buy it outright. So I'm looking to purchase something that I can grow, modify, and add to over time. That means a modular microscopy platform. Based on my research, right now I'm leaning towards Olympus, Nikon, or Zeiss.

My requirements are:
1) Trinocular compound. I want to take photos and videos so this is a must.
2) LED illumination
3) The ability to add DIC, Phase Contrast, and Fluorescence
4) Dplan or Splan apo optics? Unsure about this one
5) Intuitive software for viewing results on computer

Right now I can push my budget to max $800-900. Of course I realize that I can't get all of the above at that price. For now I guess a quality brightfield microscope. But I want a solid model that I can upgrade over time to piece together a sophisticated and advanced research microscope. Can someone recommend me some good models in my price range that meet these conditions. My main concern is that I want the hardware options to be readily available so that when the time comes, I can find them easily and continue upgrading my microscope.

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Re: Discovery of Microorganisms + Advice on Research Microscope

#19 Post by PeteM » Mon Mar 09, 2020 4:34 am

An Olympus BH2/BHS series or Nikon Labophot or Optiphot would be good choices. Both Olympus and Nikon were sold in such large quantities that upgrades (used and somewhat affordable) will be available. I'm sure someone else will chime in for Zeiss - I'd just put it a tiny step behind. However if you find a Zeiss Standard complete with a trinocular head, phase contrast etc. -- it's a fine choice.

I'd drop the LED requirement. You don't need it. It won't come in a system research scope in your price range. And it could always be done as a retrofit later.

The DPlan and Splan designations are for Olympus BH2/BHS series scopes. DPlan is very good. SPlan a bonus if you happen to find a scope with them. The Nikon equivalents are E Plan and the CFN series with (like SPlans) slightly higher numerical apertures in most magnifications.

If you want phase contrast, look for a scope with it. Should be possible, if patient, within your price range.

For Olympus, make sure the power and supply are OK. $100+ fix if not. For Nikon check the fine focus gear. $50 or so part to fix. For Zeiss, make sure none of the optics are delaminated.

Software will be 3rd party.

I'll repeat that your location (I'm assuming not Antartica) is a factor in which models will be widely and affordably available.

Good luck.

Tom Jones
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Re: Discovery of Microorganisms + Advice on Research Microscope

#20 Post by Tom Jones » Tue Mar 10, 2020 3:15 am

To insert a little reality here, while you might, eventually find something new, it is extremely unlikely. :?

In order to find something new, you must generally be able to identify all of the currently known organisms of the type you are studying. Why? Unless you can identify potentially each piece of hay, the needle will never reveal itself. The quantity of hay is beyond astounding, and after you sort through it all, you will need to compare your potential needle to everything it resembles that has already been identified, and rule them out. That is an extremely complicated and expensive process not at all suited to amateur enterprise. :cry:

I would suggest you go ahead and buy a nice microscope to play with, such as the BH-2/BHS that PeteM suggests. Look for organisms you can visually identify - pond life is a great place to start - and find things new to you, science be damned. While maybe not as rewarding as finding an organism new to science, it should be very rewarding to you. Study them. Photograph them. Maybe learn to culture them. It can keep you busy the rest of your life, and is far, far cheaper than a specific attempt to find a new species. Besides, you might accidentally find something new anyway! :o

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Re: Discovery of Microorganisms + Advice on Research Microscope

#21 Post by BramHuntingNematodes » Tue Mar 10, 2020 3:25 am

Identifying and monitoring local wildlife species IS science.
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Antartica
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Re: Discovery of Microorganisms + Advice on Research Microscope

#22 Post by Antartica » Tue Mar 10, 2020 4:52 am

PeteM wrote:
Mon Mar 09, 2020 4:34 am
An Olympus BH2/BHS series or Nikon Labophot or Optiphot would be good choices. Both Olympus and Nikon were sold in such large quantities that upgrades (used and somewhat affordable) will be available. I'm sure someone else will chime in for Zeiss - I'd just put it a tiny step behind. However if you find a Zeiss Standard complete with a trinocular head, phase contrast etc. -- it's a fine choice.

I'd drop the LED requirement. You don't need it. It won't come in a system research scope in your price range. And it could always be done as a retrofit later.

The DPlan and Splan designations are for Olympus BH2/BHS series scopes. DPlan is very good. SPlan a bonus if you happen to find a scope with them. The Nikon equivalents are E Plan and the CFN series with (like SPlans) slightly higher numerical apertures in most magnifications.

If you want phase contrast, look for a scope with it. Should be possible, if patient, within your price range.

For Olympus, make sure the power and supply are OK. $100+ fix if not. For Nikon check the fine focus gear. $50 or so part to fix. For Zeiss, make sure none of the optics are delaminated.

Software will be 3rd party.

I'll repeat that your location (I'm assuming not Antartica) is a factor in which models will be widely and affordably available.

Good luck.
Thank you Pete! Because of your detailed post, I have started my search for an Olympus BH2/BHS! Excited to jump into this hobby and find some new organisms! I'll be checking ebay regularly to see if I can snag a good one. Btw, I'm in Southern California :)

Leitzcycler
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Re: Discovery of Microorganisms + Advice on Research Microscope

#23 Post by Leitzcycler » Tue Mar 10, 2020 6:21 am

Have you done your home work and identified the bacterium I gave you?

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Re: Discovery of Microorganisms + Advice on Research Microscope

#24 Post by MichaelG. » Tue Mar 10, 2020 8:07 am

Leitzcycler wrote:
Tue Mar 10, 2020 6:21 am
Have you done your home work and identified the bacterium I gave you?
I have been following this discussion with ‘detached interest’ ...
What you are doing is way out of my league, but it is astonishing [in a very good way] to see that BLAST search facility freely available on-line.

With thanks and great respect
MichaelG.
Too many 'projects'

Leitzcycler
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Re: Discovery of Microorganisms + Advice on Research Microscope

#25 Post by Leitzcycler » Tue Mar 10, 2020 10:44 am

Blast is a program for sequence comparison and there are also other programs as well as many other websites for database search. Most are readily available for the scientific community.

One possibility for bacterium and to some extent fungal identification which can be done at home is API-tests. They are based on metabolic profiling of microbes. Originally (decades ago) all this was done by preparing the reagents in the lab and performing the reactions in individual test tubes. All this can be done in a single API test strip having dried reagents in the bottom of the reaction chambers ready for rehydration. I think this is a bit old-fashioned method today as metabolic profiling is usually done by automatic instruments. I have done this through only a couple of times in the mid 90s when I studied some microbiology courses. However I remember it was a quite nice experience. The absolute prerequisite is that your microbe culture is totally clean containing only one microbe species. Usually Gram-staining and microscoping is starting point for the whole identification process.

I think even API tests, how simple they are, are rather expensive. I would guess 20 EUR per one test strip or something like that. A couple of links to API, it seems there are many videos in youtube.
https://www.biomerieux-usa.com/clinical/api
https://www.youtube.com/watch?v=ekRPD-eojd4

And finally, I want to emphasize that whatever identification method you will use, you probably end up to the same conclusion with more rare microbe species: this seems to be something like that, but is it really that one or something different?

Antartica
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Re: Discovery of Microorganisms + Advice on Research Microscope

#26 Post by Antartica » Wed Mar 11, 2020 12:53 am

Leitzcycler wrote:
Tue Mar 10, 2020 6:21 am
Have you done your home work and identified the bacterium I gave you?
Yes I did. I do see that it is hard to identify new organisms. The sequence you gave me looks like Micrococcus luteus. That would be my guess :) But I'm determined to discover something new, so I'm not going to give up!

Could anyone comment on this listing: https://www.ebay.com/itm/OLYMPUS-BH2-TR ... Sw7t9eVZoD

Is the price high? What would be a reasonable amount to pay for it? The listing says it has no filter holder for the light source. How much is that?

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Re: Discovery of Microorganisms + Advice on Research Microscope

#27 Post by Tom Jones » Wed Mar 11, 2020 3:22 am

Could anyone comment on this listing: https://www.ebay.com/itm/OLYMPUS-BH2-TR ... Sw7t9eVZoD
With four DPlans and a trinoc head, and free shipping, it looks like a pretty good price to me, and I have a BHS. Importantly, the seller says it's tested, works fine, and backs it up by accepting returns up to 30 days.

I doubt you'll do much better. If you don't like it for some reason you can send it back for the cost of shipping.

gastrotrichman
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Re: Discovery of Microorganisms + Advice on Research Microscope

#28 Post by gastrotrichman » Wed Mar 11, 2020 5:44 am

"Microorganism" is a very broad term. If a light microscope is to be your primary tool, you'll probably want to consider algae, protozoans, the many, many microscopic invertebrates, and perhaps even microscopic parasites. I would avoid bacteria and viruses because their generally small size limits the value of light microscopy in studying them.

I think a key to success as a serious amateur student of microorganisms is specialization. Focus on a genus or perhaps family, but take your time making that decision … look at lots of critters before deciding how to specialize.

A second key to success is gathering all the relevant literature. This means literature that is published in technical journals that generally are not to be found in public libraries. There may be websites by experts who keep up with the literature and post citations as new works are published. Such citations will lead you to the published papers. Some public libraries have excellent interlibrary loan services that can be used to borrow or obtain copies of publications. Some universities will permit access by non-students to their holdings. Papers have literature cited sections that will lead you to additional relevant papers. Keeping up with the literature is an ongoing and sometimes onerous task. Keeping your choice of critters narrow can ease the literature-gathering task. You need to read and understand all the relevant literature to fully understand and appreciate the critters you study.

The journals to which you might submit a manuscript will have instructions to authors. The publication process is demanding. You may want to study critters without publishing the results. There is nothing wrong with that approach. Some skilled scientists carry on research to satisfy their own curiosity, and never intend to publish the results.
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Leitzcycler
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Re: Discovery of Microorganisms + Advice on Research Microscope

#29 Post by Leitzcycler » Wed Mar 11, 2020 12:26 pm

Well done with luteus! My point is that it is essential to understand the basics of the identification process before you are able to find something new. And it is also vital to understand what Tom Jones very nicely clarified to see the real perspective. However, “determined” and “not giving up” are also very good characteristics for a scientist. A very good starting point as well.

I would like to set a question this way: Let’s assume you will find a novel and previously unknown microbe species. Now, then what? Is it interesting? Is it ecologically important? Or does it produce some new antibiotics or some other valuable biochemical? Is it a pathogen? Finding and characterization of a novel species is valuable as such of course. However, what scientists mainly aim at is to produce new information. So how about broaden the perspective a little and putting the question the other way: could you study some previously known microbe to find something new? Many microbe species, though they are known, are not so well characterized. This way you would already have some solid ground under your feet. Yet you could be able to find something new information and that process could be even more rewarding than finding a previously unknown species. Or you might eventyally find a new species as a fortunate by-product of this research.

For publication searches this is the main source scientists use: https://www.ncbi.nlm.nih.gov/pubmed
However, this database is mainly for biomedical and life science resource and there may be some zoology journals which are not indexed there. The other very useful site is this: https://www.researchgate.net/ and maybe also this: https://www.academia.edu/

Many articles are not open access but you may write to the corresponding author and ask a copy. This can be done either sending email to corresponding author or sending a request in researchgatenet where you may find some articles being available anyway. University libraries should be able to give you temporary password for their internet access so you can download articles there.

As you read articles, you will see that most of them have at least three to five authors. We are not living the days of Barbara McClintock any more and publishing a research article usually needs co-operation of several people with different backgrounds and areas of expertise. Again, this is to bring some reality: even experienced scientists with a wide network of co-operation and institutional support have difficulties to get their results published. However, I know cases of a single author publication and it is always possible to do research for hobby without publishing. Sadly, any research, no matter how well it is done, is not scientifically valid before it has been published.

About the microscope: I have very little experience with Olympus and never used this model. As far as I understand it looks very nice and it is well presented in Ebay which suggests that the seller has inspected it carefully. Probably a good choice.

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Re: Discovery of Microorganisms + Advice on Research Microscope

#30 Post by Antartica » Fri Mar 13, 2020 4:39 am

Thanks again Leitzcycler!

You've given me so much good information. I have a very good idea of what I need to do now be successful. It's going to take a lot of work, but I have the passion and energy to do it.

I had one more question regarding this microscope: https://www.ebay.com/itm/OLYMPUS-BH2-TR ... Sw7t9eVZoD

The listing says there is no filter holder for the light source.

1) Is that a big deal? What exactly does the filter holder for light source do?
2) How much would it cost to replace it?
3) I can't find it on ebay. Are filter holders for the light source available? Where to get them?

thanks

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