Earth Biogenome project is a novel initiative from 24 scientists who recently wrote a paper to propose massive international collaboration for ‘sequencing life for future of life’. They believe that “Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms.”
This team then presents “a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalogue, and characterise the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years.” The team is confident that the “the outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services.” About the hurdles that the project faces, the team mentions: “data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol.” Their paper describes “the far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.”
The question is what happened to the unique and unanimous resolution of Goa assembly to undertake an All Taxa Biodiversity Inventory (ATBI) of the state to map and catalogue every species within Goa? There is huge emotional investment in macrospecies (tigers, turtles, birds, snakes, frogs) but the importance of microbial diversity is less understood and gets ignored. For example 25 soil types were identified by National Bureau of Soil Survey and Land Use Planning, Nagpur when they completed the soil diversity survey of Goa in 1995 for a ‘Soil Atlas’. Now what is the magnitude of microbial diversity of these 25 soil types? Microbial community occurs in different horizons of the soil and even deeper.
So what do we really lose when soil erosion takes place from any of these soil types? Some of these local soil types are spread over a few hundred hectares and could be very rare due to local geology and weathering processes. My PhD student Sonashia Velho-Pereira now in London, UK extensively worked since 2006 on a group of ecologically and chemically very creative microbial group called ‘Actinobacteria’ (formerly Actinomycetes). Her entire PhD viva voce can be viewed here (https://www.youtube.com/watch?v=7Zvhp4eyqhc and some of our educational videos on actinobacteria are available here: https://www.youtube.com/watch?v=NYHLycu0iIw and https://www.youtube.com/watch?v=l7iwrj3p2l4). We developed many novel techniques to study these industrially useful filamentous bacteria.
During course of her work she had to study numerous types of soil samples. We found antibiotic resistant bacteria in some soil samples raising serious questions about consequences of disturbing such soils and bringing these soil particles in contact with human or animals. But we were really surprised to get a highly creative strain of Actinobacteria later identified by DNA sequencing as ‘Streptomyces parvulus” in pristine soil of Canacona, at a location few hundred metres from Talpona estuary and the Arabian sea. Microbial communities including actinobacteria survive in rocks and soil for millions of years and play an important part in biogeochemical cycling. Streptomyces is largest genus of actinobacteria with about 600 unique species. Annually 100 thousand tons of antibiotics are produced and those sourced from Streptomyces strains account for 80 per cent of them.
Most of these strains are found in the soil so we were not surprised that the Canacona strain of ‘Strepetomyces parvulus’ produced a powerful antibiotic. Sonashia characterised its bench top production (preprint here: https://www.biorxiv.org/content/early/2016/06/23/060392) and identified it as Streptolydigin, a non ribosomal peptide antibiotics which inhibits many gram positive bacteria. Now what’s so special about an already known antibiotic? It was the strain found in Goa which was telling us its own evolutionary history possibly from an original marine environment.
Previously all that we knew was that S parvulus strains found elsewhere in world produce – Actinomycin D also known as Dactinomycin, a well known anti cancer drug. But Goa strain was a different chemotype. It yielded an antibiotic. That means other strains found elsewhere in world were not expressing their antibiotic genes. The most important finding was that the antibiotic produced from this strain proved much more powerful in inhibiting a human pathogen – the dreaded Staphylococcus bacteria as compared to more than 30 commercially available antibiotics which we tested in lab. It meant that the Canacona strain of Streptomyces parvulus was more creative than other Streptolydigin producer strains.
This discovery showed us that we can’t dismiss soils of Goa (and rest of India) as just ordinary soils but need to consider these as nationally valuable microhabitats yielding antibiotic producing strains. In the frenzy of development, soils get disturbed, eroded and there is no knowledge about loss of microbial diversity from mining, quarrying, road construction, hill cutting and similar activities. By now it’s impossible to estimate how many chemically creative strains of actinobacteria we might have lost from Goa and the world denied the discovery of powerful novel antibiotics. If he were to be alive, Goa’s most famous Microbiologist Froilano De Mello would have pitied us for our ignorance.