The study of the composition and physiology of microbial communities and microorganisms in the environment and with each other.

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    Jay Siddharth replied

    Are you trying to do something on similar lines then MG-RAST might be what you are looking for http://cshprotocols.cshlp.org/content/2010/1/pdb.prot5368.abstract

    11 days ago
• Paul Waines

  Can FISH be used to assess bacterial viability within a mixed population, or does it need to be combined with another approach- if so, what?

  I am looking at not only using FISH to investigate the biofilm community in municipal drinking water systems, but also to assess the viability of the bacteria within pipe-associated biofilms. I haveI am looking at not only using FISH to investigate the biofilm community in municipal drinking water systems, but also to assess the viability of the bacteria within pipe-associated biofilms. I have used the Live/Dead kit before but wondered if FISH could be used in some way.

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    Jay Siddharth replied

    1)If you are trying to look at just live/dead in combination with universal probes to light up all bugs then I might suggest using a common gene product like from tca cycle as a fish probe target.1)If you are trying to look at just live/dead in combination with universal probes to light up all bugs then I might suggest using a common gene product like from tca cycle as a fish probe target. But it has the downside of ligting up a lot of bugs, so 2) if you want to look at specific subpopulation viablity, it would be better to target gene products specific from them and overlay with 338probes. With a decent confocal and about 4 cobitorial probes you can answer viablity of specific bugs within a biofilm. 3) As other learned members have pointed out, it all depends on what you are trying to ask scientifically and what answers would be of help.

    11 days ago

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    Roberto Anitori replied

    check out work done by people at Ames Research Center (NASA, Mountain View, CA). I think David Des Marais has done this

    13 days ago
• Srihari Gunji

  Is there any bacterial species in termite (white ant) producing cellulase?

  I am doing work on cellulase isolation from bacterial species and activity assay. If there is any bacteria in termite please share the details about that bacteria, isolation process of bacteria ?

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    Dr Neeraj --- replied

    You can contact Dr. Jaishree Paul <jpaul33@hotmail.com>, or Dr Shailendra Saxena <shailsaxena05@gmail.com> working at JNU, New Delhi. Both have worked on termite gut bacteria.

    16 days ago
• Ekrem Ayna

  What is the classical (non-molecular) method to quantify Nitrosomonas from earth sample without getting into HPLC and PCR, qPCR?

  I am looking for classical method/SOP (Standart Operation Protocol) to quantify this specific group Nitrosomonas. Any information would be greatly appreciated.

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    Ekrem Ayna replied

    Thanks for your excellent comment. I have searched for that article but i was shielded for inherent members from a similar field.

    Apr 14, 2012
• Pierre Joly

  Nitrates and Wavelength

  I'm currently trying to get the nitrates values of soil extracts by using a kit : Nitrates test Spectroquants (from Merck Chemicals). Here is the reference : 114773 Test Nitrates MéthodeI'm currently trying to get the nitrates values of soil extracts by using a kit : Nitrates test Spectroquants (from Merck Chemicals). Here is the reference : 114773 Test Nitrates Méthode photométrique 0.2 - 20.0 mg/l NO3-N 0.9 - 88.5 mg/l NO3- Spectroquant® The problem is that the protocol doesn't give any indication on the wavelength to use (clearly to buy their device with the methods inside). Can someone help me, it is a reaction in H2SO4, where NO3- ions form in benzoic acid a red compound?

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    Pierre Joly replied

    Thank you all ! Here is the answer (i got it from Merck chemicals) : 525 nm. It is nice to see so much people trying to help. I hope i will be able to give you help back in the future. Have a niceThank you all ! Here is the answer (i got it from Merck chemicals) : 525 nm. It is nice to see so much people trying to help. I hope i will be able to give you help back in the future. Have a nice day, Pierre

    Apr 12, 2012
• Sandhya Mishra

  Biomonitors of environmental contamination ?

  Is there any difference between biomonitors and bioindicators?

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    Kanagasabapathy Sivasubramanian replied

    Biomonitor and Bioindicator both name itself carry Bio means organism Monitor means Moniting the system, Indicator means Indicate about the system. Therefore organism that provides information onBiomonitor and Bioindicator both name itself carry Bio means organism Monitor means Moniting the system, Indicator means Indicate about the system. Therefore organism that provides information on the environment quality wher it is present is a "boimonitor" organism that indicates the presence of the pollutants is a "bioindicator".

    Mar 13, 2012
• Prasanna Kumar

  Marine Continental Slope Bacteria

  Recently I isolated a continental slope bacteria from Indian sediment sample in zobell marine agar. It may not be a specialized media but I do get 3 colonies looking same like fried hen egg, yellowRecently I isolated a continental slope bacteria from Indian sediment sample in zobell marine agar. It may not be a specialized media but I do get 3 colonies looking same like fried hen egg, yellow color in centre and white mucoid layer around it. Colonies were formed at 19 degree celcius, but still grow in room temperature but as pale creamy white colony. In zobell marine broth it forms thick mat in the surface of the broth which don't dissolve even after shaking. Can any one suggest what kinda bacteria this is? I do preparing for 16s sequencing. Has anyone had any such related experience with marine bacteria? I have plated this fellow in nutrient agar prepared in distilled water, and it still grows.... any suggestions?

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    Ruhi Rizvi replied

    I had worked with pectobacterium and the colony morphology described, revived memories from my old project :)

    Mar 3, 2012
• Hatairat Chaiprechapol

  How can I do with the microbial waste from plate count using membrane filter? The tests are running in the field.

  We (our labs) do the tests on the field with many samples up to 100 samples/day. The problem is we haven't Autoclave machine. what techniques can I do in the field with these waste?

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    Kevin McCabe replied

    If you have a heat source in the field, you could utilize a large pressure cooker as a substitute for an autoclave. They are basically the same thing. You would just need to test that the heat andIf you have a heat source in the field, you could utilize a large pressure cooker as a substitute for an autoclave. They are basically the same thing. You would just need to test that the heat and pressure of your chosen cooker and conditions are sufficient; something like these tests http://www.sterilizers.com/Indicator-Strips.html. A pretty good discussion of implementation can be found here: http://www.chaseunion.com/documents/safety/sterile1.htm

    Jan 19, 2012
• Ashish Srivastava

  In situ bioremediation of Pesticide contaminated soil

  Can you please suggest me any host bacteria to express the interested gene variants of haloalkane dehalogenase for insitu application into contaminated soil?

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    Mashood Ahmed replied

    Again as jay said, soil type and soil atmospheres are important before commenting

    Aug 23, 2011

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    Leah Tsuma replied

    Metagenomics....use 16S rRNA as suggested, but employ SSCP...checkout following publications: Schmalenberger et. al., 2001; Schmalenberger and Tebbe, 2003; Schwieger and Tebbe, 2003

    Jun 27, 2011
• Fernando Nieto

  Molecular taxonomy and phylogeny for microbes

  I am a novice to the use of bioinformatic and genomic tools. We have done a cloning of DNA extracted from soil and have sequenced the clones. How can we shift through the data beyond MegaBLAST. WeI am a novice to the use of bioinformatic and genomic tools. We have done a cloning of DNA extracted from soil and have sequenced the clones. How can we shift through the data beyond MegaBLAST. We have sequences for the 16S and 18S rDNA. Any help would be appreciated. thank you

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    Shivaji Sisinthy replied

    BLAST followed by Clustal and phylogenetic analysis would be the most appropriate.

    Jun 21, 2011
• VARSHA GOYAL

  Cellulose degrading microbes

  Can anybody tell me how to conform cellulose degrading microorganisms?

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    VARSHA GOYAL replied

    hello sir. wat r u doing. may i knw abt u.. and thanks for ur help sir . I will read these papers and do my experiments acoordingly . hopefully results will come.

    Jun 7, 2011
• Ajao Abdullahi

  Synergism

  Can anybody suggest protocols to study synergism among oil degrading bacteria?

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    Ajao Abdullahi replied

    Hi can anybody suggest protocol to study synergism among oil degrading bacteria.Thanks

    Apr 9, 2011
• Aparna Pandey

  Alginate Lyase

  Can anyone tell me under what condition is the enzyme alginate lyase induced?

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    Jay Siddharth replied

    Take a look at this paper: APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Volume 86, Number 2, 567-576, DOI: 10.1007/s00253-009-2278-z Analysis of extracellular alginate lyase and its gene from a marineTake a look at this paper: APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Volume 86, Number 2, 567-576, DOI: 10.1007/s00253-009-2278-z Analysis of extracellular alginate lyase and its gene from a marine bacterial strain, Pseudoalteromonas atlantica AR06 "The transcription of the alyA gene was induced by the presence of alginate in minimal medium, but its obvious induction was not observed in rich medium even in the presence of alginate."

    Apr 9, 2011