In the editorial of June 2006 Indian Journal of microbiology, Prof. Rup Lal laments, “We have a vast resource of diversified microorganisms that seem to possess unique characters and pathways that have evolved under diverse Indian climatic and environmental conditions. Unfortunately, we have not yet made a concerted effort to exploit this vast untapped resource.” In 1990 David Hawksworth estimated the number of fungi globally occurring based on the ratio of known species of plants to species of fungi in the well-studied regions. This ratio for various countries is: UK 1:6; USA 1:1; Finland 1:4; Switzerland 1:4. But, for India it is a measly 1:0.5. To verify thisand gauge how microbiology is faring, I tried contacting Microbial Cultures Centers in India, to learn by what numbers the microbial culture holdings have increased since some 10 years ago. Either there was no response or the data was ‘not available’. Had Hawksworth included data on the numbers of Bacteria and Archaea, the picture of microbial diversity in India would be still more dismal. Few will disagree with Rup Lal.Why is microbiology continuing to thrive elsewhere? Since new genera and species are regularly being discovered by workers, mostly in USA, Europe and Japan in unthought-of places and habitats. In countries which have built submersibles, microbiology is not only spread wide, it has also gone very deep. A perusal of some B.Sc. and M.Sc. microbiology syllabi reveals all the keywords, assuring that microbiology in India has a sound foundation. However, from several years of interviewing students seeking admission in Ph.D. research program and working with them, the impression is that microbiology is reduced to growing <italic>E. coli</italic> (culture obtained from abroad), transforming it with a cloning vector (also obtained from abroad), growing bacterial cells containing plasmid, isolating DNA, cutting the DNA and separating the DNA fragments by gel electrophoresis.If a nearly unanimous view exists, it is that a great many microorganisms remain to be discovered. It is believed that “The earth's biota was composed solely of bacteria for at least two-thirds of its total history. Many evolutionary innovations have been powered by changes in intracellular biochemistry rather than changes in the shape, size or the physical organization of the organism”. Yet microbiology, concerned with the study of the diversity of microbes and their biochemical activities using pure cultures, is now being given away in favour of metagenomics (<xref ref-type="bibr" rid="bib002">Handelsman 2004</xref>) - the direct extraction and cloning of DNA from unidentified mixtures (consortia) of microbial communities (for example, from soil, seawater, insect guts) collected from nature (<xref ref-type="bibr" rid="bib002">Handelsman 2004</xref>, <xref ref-type="bibr" rid="bib008">Tyson and Banfield 2006</xref>). I will not be surprised if some take a stand that in view of the emerging approach of metagenomics, the isolation and culture of microorganisms and knowledge of species’ adaptive characteristics are not necessary. Despite the success in cloning DNA from a metagenomic library and expression in <italic>E. coli</italic>, its expression in fungal host systems with their higher expression and secreting abilities is doubtful. In personal communication (10 August 2006), Prof. J. Handelsman tells me that “Heterologous gene expression with bacterial genes is poor, but getting better. The chances with fungi seem much worse”. It would therefore be premature to infer general applicability of metagenomic approach for obtaining economic-level expression of a <italic>majority</italic> of nonhomologous genes, i.e., expression of a portion of DNA isolated from a linkage group from an unidentified organism, from the cytoplasmic milieu in which it had evolved and adapted over millions of years, but now forcibly integrated into a genome in a foreign cytoplasm of an unrelated organism. It would be hasty to give-up the undiscovered species of microorganisms as ‘uncultivable’ without even a modicum of attempt to isolate and culture microorganisms from nature. For over a century, attempts to culture the rust fungi had been unsuccessful but recent advances have shown that such organisms may also be capable of saprophytic growth (<xref ref-type="bibr" rid="bib007">Staples 2000</xref>).A browsing of publications in international microbiology journals informs the significance of studying microbes in their natural habitats. Microbiologists are intrigued by the evolutionary improvisations in biochemistry of microbes found in habitats such as hot springs and composts (high-temperature environment), in Antarctica soils and lakes and deep oceans (low-temperature environment), in sulphur springs (acidic and hot), alkaline soils (high pH), mangrove ecosystem, coastal lagoons and saltems (saline environment), in oceans (low nutrient environment), in deserts (dry environment), and other materials such as slimy scum in flowing nullahs or inside the city water pipes, and the endophytes in plant tissues, or in the lakes - erstwhile with clear water, but ever so often turned into lakes of dead fishes (<xref ref-type="bibr" rid="bib005">Maheshwari, 2005a</xref>). The microorganisms inhabiting afore-mentioned habitats can be grouped under “extremophiles”. Research on extremophiles can be undertaken in nearby less-endowed institutions where such habitats are naturally present. The pioneering studies of Thomas Brock were done with only a couple of microscopes, thermistor probes, pH meter, balance, pressure cooker as autoclave, and a supply of simple glassware in a field laboratory in the volcanic areas of Yellowstone. He discovered bacteria growing in boiling water simply by suspending microscope slide from a fallen log of a tree into boiling pools and examining the slide at regular intervals. Where would molecular biology be today had Brock not discovered <italic>Thermus aquaticus —</italic> the source of <italic>Taq</italic> polymerase for the PCR amplification of minute DNA samples (Maheshwari 2005b). Therefore research on extremophiles would be one of the best ways to reach out and encourage young scientists. This is an area in which investigators have good chances of contributing new information and not feel frustrated.The major flaw in teaching of microbiology (and other sciences) is that facts, instead of observations and experiments, are emphasized (<xref ref-type="bibr" rid="bib006">Maheshwari 1995b</xref>). Words can not approximate the excitement felt in exploring biodiversity in places such as rain forests in Kerala, or mountains in the Himalayas — and in designing enrichment media, waiting in suspense for growth of unknown microorganisms, looking at their intricate morphology, finding some unusual behavior of their proteins and in discovering new genetic systems. Time is overdue for microbiologists in India to begin a concerted program of research on physiology, genetics, evolution and biochemistry and sequencing genomes of microbes representing the diversity of Indian climatic and environmental conditions. This would provide a means to compare genomes and determine whether a core genome is shared by all strains, and which is strain-specific, and lead to understanding of their metabolic pathways and exploitation (<xref ref-type="bibr" rid="bib001">Fraser-Liggett, 2005</xref>).</sec></body><back><ref-list><title>References

IJM

Indian Journal of Microbiology

0046-8991

The Association of Microbiologists of India

ijm-46-3-016

NEWS AND VIEWS

The plight and resurrection of microbiology in India

Maheshwari

Formerly, Department of Biochemistry, Indian Institute of Science, Bangalore 560012

*E-mail: ramesh.maheshwari@gmail.com

92006

463283284

In the editorial of June 2006 Indian Journal of microbiology, Prof. Rup Lal laments, “We have a vast resource of diversified microorganisms that seem to possess unique characters and pathways that have evolved under diverse Indian climatic and environmental conditions. Unfortunately, we have not yet made a concerted effort to exploit this vast untapped resource.” In 1990 David Hawksworth estimated the number of fungi globally occurring based on the ratio of known species of plants to species of fungi in the well-studied regions. This ratio for various countries is: UK 1:6; USA 1:1; Finland 1:4; Switzerland 1:4. But, for India it is a measly 1:0.5. To verify thisand gauge how microbiology is faring, I tried contacting Microbial Cultures Centers in India, to learn by what numbers the microbial culture holdings have increased since some 10 years ago. Either there was no response or the data was ‘not available’. Had Hawksworth included data on the numbers of Bacteria and Archaea, the picture of microbial diversity in India would be still more dismal. Few will disagree with Rup Lal.Why is microbiology continuing to thrive elsewhere? Since new genera and species are regularly being discovered by workers, mostly in USA, Europe and Japan in unthought-of places and habitats. In countries which have built submersibles, microbiology is not only spread wide, it has also gone very deep. A perusal of some B.Sc. and M.Sc. microbiology syllabi reveals all the keywords, assuring that microbiology in India has a sound foundation. However, from several years of interviewing students seeking admission in Ph.D. research program and working with them, the impression is that microbiology is reduced to growing <italic>E. coli</italic> (culture obtained from abroad), transforming it with a cloning vector (also obtained from abroad), growing bacterial cells containing plasmid, isolating DNA, cutting the DNA and separating the DNA fragments by gel electrophoresis.If a nearly unanimous view exists, it is that a great many microorganisms remain to be discovered. It is believed that “The earth's biota was composed solely of bacteria for at least two-thirds of its total history. Many evolutionary innovations have been powered by changes in intracellular biochemistry rather than changes in the shape, size or the physical organization of the organism”. Yet microbiology, concerned with the study of the diversity of microbes and their biochemical activities using pure cultures, is now being given away in favour of metagenomics (<xref ref-type="bibr" rid="bib002">Handelsman 2004</xref>) - the direct extraction and cloning of DNA from unidentified mixtures (consortia) of microbial communities (for example, from soil, seawater, insect guts) collected from nature (<xref ref-type="bibr" rid="bib002">Handelsman 2004</xref>, <xref ref-type="bibr" rid="bib008">Tyson and Banfield 2006</xref>). I will not be surprised if some take a stand that in view of the emerging approach of metagenomics, the isolation and culture of microorganisms and knowledge of species’ adaptive characteristics are not necessary. Despite the success in cloning DNA from a metagenomic library and expression in <italic>E. coli</italic>, its expression in fungal host systems with their higher expression and secreting abilities is doubtful. In personal communication (10 August 2006), Prof. J. Handelsman tells me that “Heterologous gene expression with bacterial genes is poor, but getting better. The chances with fungi seem much worse”. It would therefore be premature to infer general applicability of metagenomic approach for obtaining economic-level expression of a <italic>majority</italic> of nonhomologous genes, i.e., expression of a portion of DNA isolated from a linkage group from an unidentified organism, from the cytoplasmic milieu in which it had evolved and adapted over millions of years, but now forcibly integrated into a genome in a foreign cytoplasm of an unrelated organism. It would be hasty to give-up the undiscovered species of microorganisms as ‘uncultivable’ without even a modicum of attempt to isolate and culture microorganisms from nature. For over a century, attempts to culture the rust fungi had been unsuccessful but recent advances have shown that such organisms may also be capable of saprophytic growth (<xref ref-type="bibr" rid="bib007">Staples 2000</xref>).A browsing of publications in international microbiology journals informs the significance of studying microbes in their natural habitats. Microbiologists are intrigued by the evolutionary improvisations in biochemistry of microbes found in habitats such as hot springs and composts (high-temperature environment), in Antarctica soils and lakes and deep oceans (low-temperature environment), in sulphur springs (acidic and hot), alkaline soils (high pH), mangrove ecosystem, coastal lagoons and saltems (saline environment), in oceans (low nutrient environment), in deserts (dry environment), and other materials such as slimy scum in flowing nullahs or inside the city water pipes, and the endophytes in plant tissues, or in the lakes - erstwhile with clear water, but ever so often turned into lakes of dead fishes (<xref ref-type="bibr" rid="bib005">Maheshwari, 2005a</xref>). The microorganisms inhabiting afore-mentioned habitats can be grouped under “extremophiles”. Research on extremophiles can be undertaken in nearby less-endowed institutions where such habitats are naturally present. The pioneering studies of Thomas Brock were done with only a couple of microscopes, thermistor probes, pH meter, balance, pressure cooker as autoclave, and a supply of simple glassware in a field laboratory in the volcanic areas of Yellowstone. He discovered bacteria growing in boiling water simply by suspending microscope slide from a fallen log of a tree into boiling pools and examining the slide at regular intervals. Where would molecular biology be today had Brock not discovered <italic>Thermus aquaticus —</italic> the source of <italic>Taq</italic> polymerase for the PCR amplification of minute DNA samples (Maheshwari 2005b). Therefore research on extremophiles would be one of the best ways to reach out and encourage young scientists. This is an area in which investigators have good chances of contributing new information and not feel frustrated.The major flaw in teaching of microbiology (and other sciences) is that facts, instead of observations and experiments, are emphasized (<xref ref-type="bibr" rid="bib006">Maheshwari 1995b</xref>). Words can not approximate the excitement felt in exploring biodiversity in places such as rain forests in Kerala, or mountains in the Himalayas — and in designing enrichment media, waiting in suspense for growth of unknown microorganisms, looking at their intricate morphology, finding some unusual behavior of their proteins and in discovering new genetic systems. Time is overdue for microbiologists in India to begin a concerted program of research on physiology, genetics, evolution and biochemistry and sequencing genomes of microbes representing the diversity of Indian climatic and environmental conditions. This would provide a means to compare genomes and determine whether a core genome is shared by all strains, and which is strain-specific, and lead to understanding of their metabolic pathways and exploitation (<xref ref-type="bibr" rid="bib001">Fraser-Liggett, 2005</xref>).</sec></body><back><ref-list><title>References1Fraser-Ligget

C M

(2005). Insights on biology and evolution from microbial genome sequencing. Genome Research15: 1603–1610.2Handelsman

(2004). Metagenomics: application of genomics to uncultured microorganisms; Microbiol. Mol. Biol. Revs. 68: 699–685.3Hawksworth

D L

(1990). The fungal dimension of biodiversity. Mycol. Res. 95: 641–655.4Maheshwari

(1995). Whither microbiology? Curr. Sci. 69: 401–406.5Maheshwari

(2005a). Fish death in lakes. Curr. Sci. 88: 1719–1721.6Maheshwari

(2005b). Life at high temperatures. Resonance10: 23–36.7Staples

R C

(2000). Research on the rust fungi during the twentieth century. Annu. Rev. Phytopathol. 38: 49–69.8Tyson

G W

Banfield

J F

(2006). Cultivating the uncultivated: a community genomics perspective. Trends Microbiol. 13: 411–416.