Friday 7 October 2016


Q. What's the most abundant living thing on this our blue planet?

I recently read, through tears of frustration, Atlantic by Simon Winchester.  I found it worthy, erudite and informative . . . but scrappy and ultimately dissatisfying. But 430/490ths of the way through the book, he devotes a couple of pages to the - to me -wholly unexpected researches and calculations of Dr Penny Chisholm [R at the time when she made her remarkable discoveries] which sent me off down the rabbit-hole to fill in the details. I didn't go further than last year at the University of Illinois at Urbana-Champaign for a symposium Looking in the Right Direction: Carl Woese and the New Biology tribbing [bloboprev] UIUC's most famous scientific faculty member. Dr Chisholm led off the event with a stunning talk about her life on the ocean wave. If you can spell evolution, this is definitely worth the hour of your time (and stick around for the post-talk questions).

I spent 12 years of my life discovering genes in an immunology lab and being bemused by the instruments, experiments and mind-set of my immunology colleagues. Eventually I got to understand what they meant when they talked about CD4+CD8+ T-cells, CD4dims, side-scatter and gating. This is the language flow-cytometry, an instrument that immunologists use to characterise individual cells and count them under different experimental conditions. In 1985, Chisholm and her collaborator Rob Olson took one of these delicate monsters out into the wide Sargasso Sea and ran samples of salt water through it. They were looking for a blue-green alga BGA aka cyanobacteria called Synechococcus which had recently been discovered in marine samples. What they found as well was a smaller [0.6μm] amazingly abundant [105/ml] photosynthetic bacterium that eventual got the name Prochlorococcus marinus. Even if you only count the upper 200m of the oceans where sunlight penetrates there are a helluva a lot of mls of sea-water and the best estimate is that there are a Carl "Billions" Sagan number of Prochlorococcus - 3 billion billion billion = 1027 - out there; making them probably the most abundant species of which we know.

Math aside - there are lots of Prochlorococcus but they are very small and I think Homo sapiens has about the same biomass and rats Rattus norvegicus probably out-weigh us both.  Calculating the mass of all humanity is an exercise I do with my 1st Year Quant Methods. If we take the average weight (the clinically obese balanced by the starving infants) as 50kg and 7.4 billion of us in August 2016 [more today!] then there are 0.370 billion tonnes = 4 x 10tonnes available to carnivorous aliens from the Planet Zorg.  otoh, each Pcc weighs 2 x 10-19 tonnes and there are 3 x 1027 of them. So they tip the scales at 6 x 10tonnes. Not so tasty as humans and much harder to catch: got a sieve, Zorgistas?

Finding so many so tiny photosynthetic organisms in the ocean made us radically re-think our view of the carbon cycle, which up until then had been focused, with a sense of awe, on tropical rain-forest which includes some of the largest living things on the planet. The annual amount 5 Gtonnes of carbon fixed by Prochlorococcus is in the same ball-park as the excess 6 Gtonnes we are adding to the atmosphere by burning fossils fuels. Our carbon footprint is still increasing but the density of Prochlorococcus is remarkably stable year after year, despite doubling about once a day, so we must conclude that half of each day's reproductive bounty is promptly scarfed up by something else for dinner. As food, its carbon-based structures - protein, glucose and lipid - are quite quickly metabolised back into CO2 and so are unlikely to be a major player in locking up the carbon which we are hosing into the atmosphere as we drive to work and heat homes in ludicrously unsuitable living spaces like New England, the whole of Canada, Scandinavia, and much of Russia.

One of the things that makes Prochlorococcus suitable for a lifetime's scientific research is that some strains can be cultivated in the lab while they can also be studied in their natural environment. The first such tame strain was SS120 [Sargasso Sea 120m down]. By flipping focus between the data generated by these different approaches, Chisholm has built up a startling picture of this tiny organism's place in the wide wet world. Small as it is, they have discovered it shipping fluid-filled vesicles out from the surface membrane for purposes intriguing but not yet fully understood. These vesicles contain DNA, RNA and proteins and could be regarded as mobile workshops spreading out from the minuscule mother-ship. It seems that Prochlorococcus lives in a complex commensal relationship with other bacteria that have only a tenuous physical connexion - it's really dilute in the sea. These other bacteria are able to scavenge the limiting elements, mainly nitrogen, phosphorus and iron, in a marine environment. It's almost as if Prochlorococcus is paying its taxes in fixed carbon and receiving the key N, P, Fe building blocks for making more DNA and protein as it doubles its numbers every day.

And please, please be extremely skeptical of people, even 'scientists' who propose that, by seeding the ocean with iron or one of the other limiting elements we can boost the carbon-holding capacity of oceanic life. That reductionist single-factor analysis is likely mad bad and dangerous to implement because it will boost some unknown and unculturable microbes at the expense of others and upset the equilibrium of the n-dimensional [Fe, P, N, pH, salinity, conductivity, day-length, light intensity, depth, unknown-but-important-1, unmeasurable-but-important-2, intangible-but-vital-3 etc.] hyperspace that is an ecological niche. That niche is just one species characterised for what we can measure. But an ecosystem is an interlocked set of niches involving thousands of interacting and inter-dependent species. To the nearest whole number, the best estimate of how much we know about how an ecosystem works is . . . nothing.

A final word on genetic diversity. What they call Prochlorococcus marinus is a sort of universe in itself. Small cell has a small genome - 2,000 genes = about half that of E.coli - but the genetic complement = biochemical capability is wildly different between any tow randomly selected individuals from the "same species". When the US Dept Energy were planning to sequence the genome of Prochlorococcus marinus Chisholm insisted that they sequence two different genomes, to get a handle on 'allowable variability' in the species. Now there are 40 ecotypes fully sequenced. They all have a core genome of about 1,300 genes which make the proteins to do the 'housekeeping' tasks all living cells do every day. The rest - the flexi-genome - do different things, presumably related to the peculiar niche in which they serve/thrive. 200 m down is really different from 2 m down and the concentration of phosphorus is 10x different between the Atlantic and the Pacific.  If you sequence a genome and find nitrate reductase, then you know that bug will do well near an estuary where nitrate is flooding off the agricultural land upstream. With Prochlorococcus every time they sequence another isolate they find dozens or hundreds of new genes with novel functions. Collectively they have a "pan-genome" of 80,000 genes making them 4x more complex than, say, humans.

But then, my mentor Lynn Margulis [prev] often said that, given the astonishing diversity of life on Earth,  all mammals are 'essentially the same', each of these 5,000 furry lactating viviparous species are trifling variants on the same fundamental system. Molecular genetic comparisons have shown that there are several extra species of giraffe, rhinoceros and elephant and we now lose sleep over the likelihood that we cannot save them all from poaching and habitat destruction. On the Margulis 'essentially the same' argument we could lose all members of all three mammals and it will have less impact [biochemical, ecological, evolutionary] than the loss of a small fraction of the variants that are currently binned into species Prochlorococcus marinus. Bonnets off to Dr Chisholm for comtinuing to bowl this hoop along the road!

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