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‫بسم ال الرحمن الرحيم‬

 The Importance of Microbial
        Biodiversity

             Nura A. Abboud
 M.Sc Desert Studies  Molecular Microbiology
The Jordanian Society for Microbial Biodiversity

     Biodiversity International Day  RSCN
                  May 22th 2012
The Jordanian Society for
   Microbial Biodiversity

                 2006
         Back to Green Jordan
Reports (microbiology, water management
          (,environmental policy
                2011217
http://home.fnal.gov/~carrigan/pillars/Tree_of_life.htm
: The Prokaryote

  • First Earth inhibitor
 • Anaerobic
 • Harsh conditions
 • Photosynthesis
 • New ecosystem
50 - 90%
                                                            of all
                                                          biomass
                                                          on Earth
                                                              is
                                                          microbial
http://home.fnal.gov/~carrigan/pillars/Tree_of_life.htm
   Everywhere!

Harmful
Benign /beneficial...




Necessary for all ecosystems
•Soil is a
diverse
habitat:
Bacteria
, fungi,
archaea,
protozoa
& algae.
Importance of soil
   microbes

oBiological Engine of the Earth

o Maintaining soil functions
Nutrient cycles:
 Nitrogen (N),Carbon (C),
Phosphorus (P), Sulfur (S)
http://en.wikipedia.org/wiki/Nitrogen_fixation
X
Agricultural Applications
     ‫أهمية مايكروبات التربة‬
Pharmaceutical Applications




Antibiotics
Actinomycetes          Streptomycin
Bacterocins
•Bacteria & Archaea

•Water purification
•Food preservations
•Veterinary Medicine
•Agricultural Applications
•Health Applications : Human ,
plants & Animals
Medical Laboratories

Lab and
diagnostics
reagents
Industrial Applications
   Industrial bacterial
    enzymes :Lipase ,
    amylase
 Instead of
  synthetic chemicals.

   Ex: to enhance
    detergents
Food industries:
  Whole   cells
  Amino   Acids

  Vitamins
Biogas and Energy production


             +
             =
   Viruses generates electricity




Luminescence bacteria lighting your
house



                                    Bacterial
                                     DNA
 Bacteria & Glue



 Medical ,dental & Engineering
 applications
Clostridium sporogenes
         Vs
       cancer
Biodiversity
 Greatest   Earth treasures
 Microorganisms: most
 diverse & abundant
 1-5%

 Huge   Impact on our life
Research lab   DNA based methods for
               characterizing microbial
                    :communities
                16r DNA Gene library

                               Bacterial
                                DNA
 Pl c t
   as or
    ve
     m
       id




     D NA
PCR : 16S rRNA-gene
amplification




     TRFLP
2 3 4 5 6 7   1
Halobacterium
   salinarum
?What do HS do
:Astrobiology
Representatives of
life in the universe


                  ?
? What can HS do
?What do HS do

 Biological  treatment tool
    :highly saline industrial waste
    effluents
   (Dong-Jin Ha et al – 2006(
?What do HS do

• Photobioreactor:
• HS + solar = energy (H
  gas)
• Daily Human consumption
•   (Zabut et al 2006)
CBD 1993
My Hypothesis:

  Jordan has highly diverse
community of microorganisms
My recommendations:

• Full survey : microbial biodiversity
in Jordan

• Genetic bank

• Microorganisms & overgrazing …etc
Long term
 To gain a better understanding of the
 ecology of important microorganisms in the
 environment
Questions we ask
•Which bacteria are present
in a soil sample?
•How many different types?
•Which bacteria are active
and growing?
•What is the role of bacteria
in the context of their
environment?
•How can we apply this
The only
barrier is our
faith in what
   we have
! Thank you

Questions ?
References
1) L.Prescott, J. Harely, D.Klein, Microbiology, fifth edition, McGraw-Hill Higher Education
2) Mar. 2007 www.webdomino1.oecd.org/comnet/agr/soil_ero_bio.nsf/viewHtml/index/$FILE/Winding.PDF>
3)Apr2007<http://webdomino1.oecd.org/comnet/agr/soil_ero_bio.nsf/viewHtml/index/$FILE/Winding.PDF >.
4) Www.fuhrmanlab.usc.edu." Fuhrman Lab. University of southern California. Mar. 2007.
5) Mary Anderson Home Page. Department of microbial ecology research group. 10 Apr. 2007
<http://www.ucd.ie/indmicro/mary/technique.html>.
6) Crecchio, C, A Gelsomino, R Ambrosoli, J Minati, and P Ruggiero. "Soil Biology &Biochemistry." Elsevier.
2004 <www.elsevier.com>.
7) Jones, Cm, and Je. Thies. "Soil Microbial Community Analysis Using Two-Dimensional Polyacrylamide Gel
Electrophoresis of the Bacterial Ribosomal Internal Transcribed Spacer Regions." Pubmed. 29 Apr. 2007
<http://www.ncbi.nlm.nih.gov >.
8) Bohme, Livia, and Frank Bohme. European Journal of Soil. 2006 <www.sciencedirect.com>.
9) Paul, E., and F. Clark. Soil Microbiology and Biochemistry. 2nd ed. Academic P.
10) "RFLP." U.S Food & Drug Administration. 9 Apr. 2007 <www.cfsan.fda.gov>.
11) Campbell, N., and J. Reece. Biology. 6th ed. Benjamin Cummings.
12) Polymerase Chain Reaction." Wikipedia. 6 Dec. 2005 <www.wikipedia.org>.
13) Shivaji S. Microbial biodiversity: Shotgun libraries to metagenome. Indian J Med Microbial 2001; 19:171-171
14) What is Microbiology.” Department of Molecular Biosciences-the University of Kansas. Mar. 2007
<http://www2.ku.edu>.
15) 16S RRNA: the Diagnostic Gene." Mar. 2007 <http://pilbara.mq.edu.au/wiki/16S_rRNA>.
16) Experiment 9: Microbial Biodiversity." Mar. 2007
www.plantpath.wisc.edu/fac/joh/Exp9DiversityStudentGuide.htm>.
17) Mar. 2007 <www2.for.nau.edu/courses/pzf/Aronson_RestEco1993.pdf>.
18) "Microbiology and Molecular Biology Reviews." Mar. 2007 <http://mmbr.highwire.org/>.
19) Biodiversity of Soil Microbial Communities in Agricultural Systems." Mar. 2007 <http://www.springerlink.com>.
20) Mar. 2007 <http://www.hcs.harvard.edu/~hsr/pdfswinter2003/cook26- 28.pdf>.
21) Mar. 2007 http://www.cook.rutgers.edu/~dbm/forneypitfalls.pdf
22) Mar. 2007 http://www.blackwell-synergy.com/doi/abs/10.1111/j.1574-6941.2006.00134.x
23) 21 Mar. 2007 www.Montana.Edu.
24) Jensen, D.b., M. Torn, and J. Harte. "In Our Own Hands: a Strategy for Conserving Biological Diversity in
California," 1990:" 22 Mar. 2007 <www.ceres.ca.gov>.
25) Mar. 2007 <http://www.unu.edu/env/plec/cbd/Montreal/papers/Scherr.pdf>.
26) Mar. 2007 <www.microbes.org/biodiversity.asp>.
27) Microb Zoo." Mar. 2007 <http://commtechlab.msu.edu/sites/dlc-me/zoo/>.
28) SPECIAL SECTION: MICROBIAL DIVERSITY." Department of Microbiology, Maharshi Dayanand Saraswati
University, Ajmer 305 009, India. Mar. 2007 <http://www.iisc.ernet.in/~currsci/jul102005/91.pdf>.
29) Tree of Life Project." Mar. 2007 <http://tolweb.org/tree/phylogeny.html>.
30) Mark Osborn, A., Edward R. B. Moore, and Kenneth N. Timmis. "An Evaluation of Terminal-Restriction
Fragment Length Polymorphism (T-RFLP) Analysis for the Study of Microbial Community Structure and
Dynamics." Mar. 2007 <www.blackwell-synergy.com>.
31) SPECIAL: BIODIVERSITY FOR FOOD AND AGRICULTURE." Mar. 2007 <www.fao.org/>.
32) What is an Aridic Soil?" Soil Arid Regions of the United States and Israel. Mar. 2007
<http://ag.arizona.edu/OALS/soils/aridsoils.html>.
33) The International Arid Lands Consortuim. Mar. 2007 <http://ag.arizona.edu/OALS/IALC/Home.html>.
34) IUCN the World Conservation Union. Mar. 2007 <http://www.iucn.org/themes/pbia/wl/docs/biodiversity/sbstta4/dry.pdf>.
35) Office of Science-Department of Energy. Mar. 2007 <www.eurekalert.org/features/doe/2001-06/danl-md061402.php>.
36) Microbial Diversity: Let's Tell It How It Is." Mar. 2007 <http://www.ncbi.nlm.nih.gov/books/bv.fcgi?
Rid=coffeebrk.chapter.622>.
37) The Search for Microbial Biodiversity." The Woodrow Wilson Foundation Leadership Programme for Teachers. Mar. 2007
<http://www.woodrow.org/teachers/bi/1999/projects/group8/sediment1.html>.
38) E. Marquis, Robert. "Bacteria" Encarta-Msn. 30 Apr. 2007 <www.encarta.msn.com>.
39) M. Awramik, Stanley, and Robert E. Riding. Microbial Sediments. google. 30 Apr. 2007 <www.google.jo>.
40) "The Microbial Community of the Soil Ecosystem." university college cork. 30 Apr. 2007 <www.ucc.ie>.
41) "TAE." IBI. 1 May 2007 <www.sheltonscientific.com>.
 42) El-Hage Scialabba, Nadia. "ORGANIC AGRICULTURE AND SOIL BIODIVERSITY." 1 May 2007
<www.fao.org/organicag/doc/soil_biodiversity.htm>.
 43) "What the Heck is PCR?" 13 May 2007 <http://www.hepatitis-c.de/pcr.htm>.
 44) "PCR (Polymerase Chain Reaction)." 13 May 2007 <http://lifesciences.asu.edu/resources/mamajis/pcr/pcr.html>.
 45) "Protocol for PCR with Taq DNA Polymerase." 13 May 2007
<http://www.fermentas.com/techinfo/pcr/dnaamplprotocol.htm>.
46) http://biosci.usc.edu/courses/2002-fall/documents/bisc300-lab_Hi-Lo_DNA_Marker.jpg
Agarose Gel Electrophoresis of DNA." 13 May 2007 ) "47
>.<http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/gels/agardna.html
>.May 2007 <http://www.bionewsonline.com/g/what_is_pcr.htm) 48
Microbial Diversity and Function in Soil." May 2007 ) " 49
>. <http://cropandsoil.oregonstate.edu/classes/CSS645/notes/Overview/CurOpinMicro_02-0240.pdf
May 2007 <http://216.109.125.130/search/cache? P=soil+microbiology+ARDRA &ei=UTF-8&Fr=yfp-t- ) 50 
>. 501&u=plato.acadiau.ca/isme/Symposium16/muyzer. PDF&w= soil+microbiology+ardra&d=OOk7gurnOqj8&icp=1&.intl=us
/http://gizfactory.com/article/philips-develops-micro-organisms-based-bio---light
-http://www.msnbc.msn.com/id/12389963/ns/technology_and_science-science/t/bacteria-make-worlds-strongest
http://www.dailymail.co.uk/health/article-2033871/Soil-bacteria-clostridium-sporogenes-new-weapon-cancer-fight.html

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  • 1. ‫بسم ال الرحمن الرحيم‬ The Importance of Microbial Biodiversity Nura A. Abboud M.Sc Desert Studies Molecular Microbiology The Jordanian Society for Microbial Biodiversity Biodiversity International Day RSCN May 22th 2012
  • 2. The Jordanian Society for Microbial Biodiversity 2006 Back to Green Jordan Reports (microbiology, water management (,environmental policy 2011217
  • 3.
  • 4.
  • 6. : The Prokaryote • First Earth inhibitor • Anaerobic • Harsh conditions • Photosynthesis • New ecosystem
  • 7. 50 - 90% of all biomass on Earth is microbial http://home.fnal.gov/~carrigan/pillars/Tree_of_life.htm
  • 8.
  • 9. Everywhere! Harmful
  • 11. •Soil is a diverse habitat: Bacteria , fungi, archaea, protozoa & algae.
  • 12. Importance of soil microbes oBiological Engine of the Earth o Maintaining soil functions Nutrient cycles: Nitrogen (N),Carbon (C), Phosphorus (P), Sulfur (S)
  • 14. X
  • 15. Agricultural Applications ‫أهمية مايكروبات التربة‬
  • 17. Bacterocins •Bacteria & Archaea •Water purification •Food preservations •Veterinary Medicine •Agricultural Applications •Health Applications : Human , plants & Animals
  • 19. Industrial Applications  Industrial bacterial enzymes :Lipase , amylase  Instead of synthetic chemicals.  Ex: to enhance detergents
  • 20. Food industries:  Whole cells  Amino Acids  Vitamins
  • 21. Biogas and Energy production + =
  • 22. Viruses generates electricity Luminescence bacteria lighting your house Bacterial DNA
  • 23.  Bacteria & Glue  Medical ,dental & Engineering applications
  • 25.
  • 26.
  • 27. Biodiversity  Greatest Earth treasures  Microorganisms: most diverse & abundant  1-5%  Huge Impact on our life
  • 28.
  • 29. Research lab DNA based methods for characterizing microbial :communities 16r DNA Gene library Bacterial DNA Pl c t as or ve m id D NA
  • 30. PCR : 16S rRNA-gene amplification TRFLP
  • 31. 2 3 4 5 6 7 1
  • 32. Halobacterium salinarum
  • 33. ?What do HS do :Astrobiology Representatives of life in the universe ?
  • 34. ? What can HS do
  • 35. ?What do HS do  Biological treatment tool :highly saline industrial waste effluents  (Dong-Jin Ha et al – 2006(
  • 36. ?What do HS do • Photobioreactor: • HS + solar = energy (H gas) • Daily Human consumption • (Zabut et al 2006)
  • 38. My Hypothesis: Jordan has highly diverse community of microorganisms
  • 39. My recommendations: • Full survey : microbial biodiversity in Jordan • Genetic bank • Microorganisms & overgrazing …etc
  • 40. Long term To gain a better understanding of the ecology of important microorganisms in the environment Questions we ask •Which bacteria are present in a soil sample? •How many different types? •Which bacteria are active and growing? •What is the role of bacteria in the context of their environment? •How can we apply this
  • 41. The only barrier is our faith in what we have
  • 42.
  • 43.
  • 45. References 1) L.Prescott, J. Harely, D.Klein, Microbiology, fifth edition, McGraw-Hill Higher Education 2) Mar. 2007 www.webdomino1.oecd.org/comnet/agr/soil_ero_bio.nsf/viewHtml/index/$FILE/Winding.PDF> 3)Apr2007<http://webdomino1.oecd.org/comnet/agr/soil_ero_bio.nsf/viewHtml/index/$FILE/Winding.PDF >. 4) Www.fuhrmanlab.usc.edu." Fuhrman Lab. University of southern California. Mar. 2007. 5) Mary Anderson Home Page. Department of microbial ecology research group. 10 Apr. 2007 <http://www.ucd.ie/indmicro/mary/technique.html>. 6) Crecchio, C, A Gelsomino, R Ambrosoli, J Minati, and P Ruggiero. "Soil Biology &Biochemistry." Elsevier. 2004 <www.elsevier.com>. 7) Jones, Cm, and Je. Thies. "Soil Microbial Community Analysis Using Two-Dimensional Polyacrylamide Gel Electrophoresis of the Bacterial Ribosomal Internal Transcribed Spacer Regions." Pubmed. 29 Apr. 2007 <http://www.ncbi.nlm.nih.gov >. 8) Bohme, Livia, and Frank Bohme. European Journal of Soil. 2006 <www.sciencedirect.com>. 9) Paul, E., and F. Clark. Soil Microbiology and Biochemistry. 2nd ed. Academic P. 10) "RFLP." U.S Food & Drug Administration. 9 Apr. 2007 <www.cfsan.fda.gov>. 11) Campbell, N., and J. Reece. Biology. 6th ed. Benjamin Cummings. 12) Polymerase Chain Reaction." Wikipedia. 6 Dec. 2005 <www.wikipedia.org>. 13) Shivaji S. Microbial biodiversity: Shotgun libraries to metagenome. Indian J Med Microbial 2001; 19:171-171 14) What is Microbiology.” Department of Molecular Biosciences-the University of Kansas. Mar. 2007 <http://www2.ku.edu>. 15) 16S RRNA: the Diagnostic Gene." Mar. 2007 <http://pilbara.mq.edu.au/wiki/16S_rRNA>. 16) Experiment 9: Microbial Biodiversity." Mar. 2007 www.plantpath.wisc.edu/fac/joh/Exp9DiversityStudentGuide.htm>. 17) Mar. 2007 <www2.for.nau.edu/courses/pzf/Aronson_RestEco1993.pdf>.
  • 46. 18) "Microbiology and Molecular Biology Reviews." Mar. 2007 <http://mmbr.highwire.org/>. 19) Biodiversity of Soil Microbial Communities in Agricultural Systems." Mar. 2007 <http://www.springerlink.com>. 20) Mar. 2007 <http://www.hcs.harvard.edu/~hsr/pdfswinter2003/cook26- 28.pdf>. 21) Mar. 2007 http://www.cook.rutgers.edu/~dbm/forneypitfalls.pdf 22) Mar. 2007 http://www.blackwell-synergy.com/doi/abs/10.1111/j.1574-6941.2006.00134.x 23) 21 Mar. 2007 www.Montana.Edu. 24) Jensen, D.b., M. Torn, and J. Harte. "In Our Own Hands: a Strategy for Conserving Biological Diversity in California," 1990:" 22 Mar. 2007 <www.ceres.ca.gov>. 25) Mar. 2007 <http://www.unu.edu/env/plec/cbd/Montreal/papers/Scherr.pdf>. 26) Mar. 2007 <www.microbes.org/biodiversity.asp>. 27) Microb Zoo." Mar. 2007 <http://commtechlab.msu.edu/sites/dlc-me/zoo/>. 28) SPECIAL SECTION: MICROBIAL DIVERSITY." Department of Microbiology, Maharshi Dayanand Saraswati University, Ajmer 305 009, India. Mar. 2007 <http://www.iisc.ernet.in/~currsci/jul102005/91.pdf>. 29) Tree of Life Project." Mar. 2007 <http://tolweb.org/tree/phylogeny.html>. 30) Mark Osborn, A., Edward R. B. Moore, and Kenneth N. Timmis. "An Evaluation of Terminal-Restriction Fragment Length Polymorphism (T-RFLP) Analysis for the Study of Microbial Community Structure and Dynamics." Mar. 2007 <www.blackwell-synergy.com>. 31) SPECIAL: BIODIVERSITY FOR FOOD AND AGRICULTURE." Mar. 2007 <www.fao.org/>. 32) What is an Aridic Soil?" Soil Arid Regions of the United States and Israel. Mar. 2007 <http://ag.arizona.edu/OALS/soils/aridsoils.html>. 33) The International Arid Lands Consortuim. Mar. 2007 <http://ag.arizona.edu/OALS/IALC/Home.html>. 34) IUCN the World Conservation Union. Mar. 2007 <http://www.iucn.org/themes/pbia/wl/docs/biodiversity/sbstta4/dry.pdf>.
  • 47. 35) Office of Science-Department of Energy. Mar. 2007 <www.eurekalert.org/features/doe/2001-06/danl-md061402.php>. 36) Microbial Diversity: Let's Tell It How It Is." Mar. 2007 <http://www.ncbi.nlm.nih.gov/books/bv.fcgi? Rid=coffeebrk.chapter.622>. 37) The Search for Microbial Biodiversity." The Woodrow Wilson Foundation Leadership Programme for Teachers. Mar. 2007 <http://www.woodrow.org/teachers/bi/1999/projects/group8/sediment1.html>. 38) E. Marquis, Robert. "Bacteria" Encarta-Msn. 30 Apr. 2007 <www.encarta.msn.com>. 39) M. Awramik, Stanley, and Robert E. Riding. Microbial Sediments. google. 30 Apr. 2007 <www.google.jo>. 40) "The Microbial Community of the Soil Ecosystem." university college cork. 30 Apr. 2007 <www.ucc.ie>. 41) "TAE." IBI. 1 May 2007 <www.sheltonscientific.com>.  42) El-Hage Scialabba, Nadia. "ORGANIC AGRICULTURE AND SOIL BIODIVERSITY." 1 May 2007 <www.fao.org/organicag/doc/soil_biodiversity.htm>.  43) "What the Heck is PCR?" 13 May 2007 <http://www.hepatitis-c.de/pcr.htm>.  44) "PCR (Polymerase Chain Reaction)." 13 May 2007 <http://lifesciences.asu.edu/resources/mamajis/pcr/pcr.html>.  45) "Protocol for PCR with Taq DNA Polymerase." 13 May 2007 <http://www.fermentas.com/techinfo/pcr/dnaamplprotocol.htm>. 46) http://biosci.usc.edu/courses/2002-fall/documents/bisc300-lab_Hi-Lo_DNA_Marker.jpg Agarose Gel Electrophoresis of DNA." 13 May 2007 ) "47 >.<http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/gels/agardna.html >.May 2007 <http://www.bionewsonline.com/g/what_is_pcr.htm) 48 Microbial Diversity and Function in Soil." May 2007 ) " 49 >. <http://cropandsoil.oregonstate.edu/classes/CSS645/notes/Overview/CurOpinMicro_02-0240.pdf May 2007 <http://216.109.125.130/search/cache? P=soil+microbiology+ARDRA &ei=UTF-8&Fr=yfp-t- ) 50  >. 501&u=plato.acadiau.ca/isme/Symposium16/muyzer. PDF&w= soil+microbiology+ardra&d=OOk7gurnOqj8&icp=1&.intl=us /http://gizfactory.com/article/philips-develops-micro-organisms-based-bio---light -http://www.msnbc.msn.com/id/12389963/ns/technology_and_science-science/t/bacteria-make-worlds-strongest http://www.dailymail.co.uk/health/article-2033871/Soil-bacteria-clostridium-sporogenes-new-weapon-cancer-fight.html