Octillions of microbes in the seas: Ocean microbes show incredible genetic diversity

The smallest, most abundant marine microbe, Prochlorococcus,is a photosynthetic bacterial species essential to the marine ecosystem.

It’s estimated that billions of the single-celled creatures live in the oceans, forming the center of the marine food web.

They occupy a range of ecological niches based on temperature, light, water chemistry and interactions with other species.

But the diversity within this single species remains a puzzle.

To probe this question, scientists at the Massachusetts Institute of Technology (MIT) recently performed a cell-by-cell genomic analysis of a wild population of Prochlorococcus living in a milliliter of ocean water–less than a quarter of a teaspoon–and found hundreds of distinct genetic subpopulations.

Each subpopulation in those few drops of water is characterized by a set of core gene alleles linked to a few associated flexible genes–a combination the scientists call the “genomic backbone.”

This backbone gives the subpopulation a finely tuned ability to fill a particular ecological niche.

Diversity also exists within backbone subpopulations; most individual cells in the samples carried at least one set of flexible genes not found in any other cell in its subpopulation.

A report on the research by Sallie Chisholm and Nadav Kashtan at MIT, along with co-authors, appears in this week’s issue of the journal Science.

The National Science Foundation (NSF), through its Divisions of Environmental Biology and Ocean Sciences, supported the research.

“In this extraordinary finding on the power of natural selection, the scientists have discovered a mosaic of genetically distinct populations of one of the most abundant organisms on Earth,” says George Gilchrist, program director in NSF’s Division of Environmental Biology.

“In spite of the constant mixing of the oceans,” Gilchrist says, “variations in light, temperature and chemistry create unique habitats that evolution has filled with an enormous diversity of populations over millions of years.”

Adds David Garrison, program director in NSF’s Division of Ocean Sciences, “The results will change the way marine ecologists think about how planktonic microbes and, in turn, planktonic communities may respond to climate and environmental change.”

The scientists estimate that the subpopulations diverged at least a few million years ago.

The backbone is an older, more slowly evolving, component of the genome, while the flexible genes reside in areas of the genome where gene exchange is relatively frequent, facilitating more rapid evolution.

The study also revealed that the relative abundance of the backbone subpopulations changes with the seasons at the study site near Bermuda, adding strength to the argument that each subpopulation is finely tuned for optimal growth under different conditions.

“The sheer enormity of diversity that must be in the octillionProchlorococcus cells living in the seas is daunting to consider,” Chisholm says. “It creates a robust and stable population in the face of environmental instability.”

Ocean turbulence also plays a role in the evolution and diversity of Prochlorococcus.

A fluid mechanics model predicts that in typical ocean flow, just-divided daughter cells drift rapidly, placing them centimeters apart from one another in minutes, tens of meters apart in an hour, and kilometers apart in a week’s time.

“The interesting question is, ‘Why does such a diverse set of subpopulations exist?'” Kashtan says.

“The huge population size of Prochlorococcus suggests that this remarkable diversity and the way it is organized is not random, but is a masterpiece product of natural selection.”

Chisholm and Kashtan say the evolutionary and ecological distinction among the subpopulations is probably common in other wild, free-living (not attached to particles or other organisms) bacteria species with large populations and highly mixed habitats.

Other co-authors of the paper are Sara Roggensack, Sébastien Rodrigue, Jessie Thompson, Steven Biller, Allison Coe, Huiming Ding, Roman Stocker and Michael Follows of MIT; Pekka Marttinen of the Helsinki Institute for Information Technology; Rex Malmstrom of the U.S. Department of Energy Joint Genome Institute and Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences.

The NSF Center for Microbial Oceanography, U.S. Department of Energy Genomics Science Program and the Gordon and Betty Moore Foundation Marine Microbiology Initiative also supported the work.

3 thoughts on “Octillions of microbes in the seas: Ocean microbes show incredible genetic diversity

  1. When I had used the words at my comment above `learned(genetically programmed- in other words `coded` ) to be in maximum flexibility to adapt as quickly as possibly to the sudden change in order to survive the –genes /DNA- RNA – of organisms genetic program – ;
    What I really meant is the intrinsic molecular characteristics of DNA and RNA molecules (Genetic code carriers) during Molecular Code Duplication processes and the molecular act of creation of their next generation of life forms ; that the – random change in genetic “code in maximum possible diversity” – which STARTS at the point of code duplication process .
    Simply the process of ` code duplication ` is not perfect by its very molecular –DNA`s or RNA`s structural nature – , for all and every member of that species , there has been and will be always errors or error making members of that species – letters or words and even whole sentences and paragraphs – so to speak – as Base pairs of the DNA and RNA codes are reshaped and reorganized at the duplication process – the brand new code in a given molecular duplication process is completely different from the parental `original` code in certain extent – the character and the importance and the necessary amount of that code change is always balanced with ` whether that random code change at the one end of the spectrum has any immediate life threatening characteristic for the next generation in other words if it is a -lethal code change- or non lethal one by simply increasing the diversity of that species as the end result . Higher more complex life forms the the errors in duplication process for the next generation is increased all the way up to % 100 -guaranteed – in each and every member of that species in some part of the original genetic code they carry –in other words more the total number of base pairs in the DNA code like 3 billions of base pairs we human species has – almost % 100 assured that there will be lots of error(s ) copying that 3 billion( 9 zeros behind) base pairs of codes for the next generation . Of course every member of that species makes the error in duplication at the different part of their individual genetic code . “Nobody is perfect “ is the most valid term here for all life forms indeed ..
    In this process of Diversification of new code (Genetically different life forms) generation ; vast environmental factors –radiation ,chemical and physical(temperature , light etc. ) – of course plays large role – make no mistake here – there is no anticipation or prediction of helpful beneficial use of that newly created code for that particular species in the future life whatsoever ; but the only real GAIN IS THE DIVERSITY VARIABILITY of INDIVIDUAL MEMBERS and THE FLEXIBILITY of that species – as a whole species – when taken together , for potential and intrinsically unknown/unknowable rainy days –bottle necks- ahead – the only purpose is to maintain maximum Diversification (variability)of the species no matter what , at all costs ( lethal metabolic changes ,defects and malformations all very costly individual member changes are all included at the one end of the spectrum ) – in this error making process of genetic code – at the creation of next generation of that species . Of course higher life forms with evolved individual multiple separate and different `chromosomes` `chromatids` like different volumes and chapters of different books and subjects of the library play their own new –additional – `tricks` so to speak , for increase their diversity of next generations during duplication process –like inversions,duplications, cross overs and so many many more – all of which is to ensure `DIVERSIFICATION` of that species to the maximum extent .

  2. Re : “The interesting question is, ‘Why does such a diverse set of subpopulations exist?’” Kashtan says.” .
    The answer is ; since the Big Bang 13,8 billion years ago , nothing has been –constant at all- everything first of course the non living matter and than the living matter ; has been and will be changing constantly and evolving into different forms and structures and compositions , mixing combinations with ever `changing time .
    And only living beings can survive by their genetic diversity and their ability to be as flexible as possible to the sudden environmental change as possible – those unfortunate genetic life forms not diverse enough that can NOT do that sudden adjustment are simply had perished long time ago and never to be seen in live form again – only the ones(species) who can maintain diversity and flexibility to change remained so far . Environmental change can be very sudden and –un expected – no warning has been the rule most of the time with repeated mass extinctions as this planet had seen many of them one after another .
    So `being in a maximum possible genetic diversity at all times and to be ready for any which way and shape possible to a sudden unexpected change all the way to the far extremes ` is the name of the game called `survival` and to be `fit` at all times as a species .
    Those species or strains or subpopulations that can not somehow handle and maintain that required diversity as efficiently and flexibly as needed ; are doomed to be extinct in a very short notice ; it has been just a matter of time . And this fact has been the reality of our planet over and over again during 3,5 billion years of earth`s evolutionary history of life forms . Without diversity of subpopulations the survival is not possible in this ever changing world of ours , todays observed diversity is the end result of billions of years of learned(genetically programmed- in other words `coded` ) to be in maximum flexibility to adapt as quickly as possibly to the sudden change in order to survive and the –genes /DNA- RNA – of organisms genetic program – in a very unforgivable hard way – by extinction- that is .

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