Chapter One

Useful charts for reference

1.1  Charles Darwin initially sketched his idea of a tree of life in a notebook sometime around July 1837 as illustrated above left. Above it, he scrawled “I think.”   That iconic image perfectly encapsulated Darwin’s big idea: that all living things share a common ancestor.

1.2  After 180 years of continuous, rancorous but fruitful debate, the tree of life been updated in 2016 by Laura A Hug, and  now  includes over 2 million species, as illustrated above right.  

1.3 Over time the tree has was developed into an overall scheme of all life forms based on their body plans or phyla – a phylogenic tree of life as shown below. This shows three great domains of life, beginning with the Prokaryotes, single celled organisms with no nucleus. These include the bacteria, and a little way up the evolutionary tree we can see where Cyanobacteria fit in. Whilst the domain of Archaea is represented in the lake, it is not so prominent. Next up are single celled organisms that have a nucleus, the Eukaryotes, which contain the more complex Algae. As can be seen from the tree, animals and plants, which comprise pretty much all the biological world we can see, are in fact just twigs at the tip of the tree of life.

1.4 More detail is given further below on the animals.  This shows where our Crustacea fit in – part of the Arthropod class, and the Rotifers even have their own class, at the same level as the Chordata, the class that contains most of the animals we can see!

1.5 We need a third, even more detailed,  view, specifically of the Chordata, to see where the fish and birds of the lake came from, and their relationship to mankind. The Actinopterygii are the class of ray finned fish to which the inhabitants of Lake Annecy belong.  As can be seen, these arose much earlier in evolution than the birds, and well before any of the mammals, let alone mankind.

1.6 Ever since Darwin, scientists have been adding names to the tree of life.  In 2016  one group compiled what they billed as a “comprehensive tree,” a garguantuan geneaology of some 2.3 million species that “encompasses all of life.’  We visible organisms are a small wedge on this chart. We’re latecomers to Earth’s story, and represent the smallest sliver of life’s diversity. Bacteria are the true lords of the world. They’ve been on the planet for billions of years and have irrevocably changed it, while diversifying into endless forms most wonderful and most beautiful. Many of these forms have never been seen, but we know they exist because of their genes. Using techniques that can extract DNA from environmental samples—scoops of mud or swabs of saliva—scientists have been able to piece together the full genomes of organisms whose existence is otherwise a mystery. And around half of these bacterial branches belong to a supergroup, which was discovered very recently and still lacks a formal name. Informally, it’s known as the Candidate Phyla Radiation. Within its lineages, evolution has gone to town, producing countless species that we’re almost completely ignorant about. With a single exception, they’ve never been isolated or grown in a lab. In fact, this supergroup and “other lineages that lack isolated representatives clearly comprise the majority of life’s current diversity,” wrote Hug and Banfield.

1.7 “This is humbling,” says Jonathan Eisen from the University of California, Davis, “because holy **#$@#!,  we know virtually nothing right now about the biology of most of the tree of life.”

1.8 Our ignorance is understandable. Ever since Antony van Leeuwenhoek became the first human to see bacteria in 1675, scientists have studied these organisms by growing them in beakers and Petri dishes. But most species simply won’t grow in a lab. This “uncultured majority” remained a mystery until the 1980s, when Norm Pace and others developed ways of sequencing microbial genes straight from environmental samples. From every organism in these samples, the team analyzed sixteen proteins that form part of the ribosome—a universal machine that’s found in all living things and that makes other proteins. Every organism has its own version of these proteins, and as new species diverge from each other, their versions become increasingly different. So by comparing these sixteen proteins, Hug and Banfield could work out how closely related their various microbes were, and draw their tree of life. Why does this matter? If needed, there’s one practical answer: almost all of our antibiotics come from the Actinobacteria, just one of the many branches that populate Hug and Banfield’s tree. Imagine what chemical and pharmaceutical riches lie in the other branches.

1.9 In the Autumn of 1946 Dr Servettaz set out on a seemingly impossible mission – to persuade his fellow citizens to support the most expensive, most complex and most long-term infrastructural investment in the history of their community, for a reason none of them yet understood. His strategy was simple and resolute. He would persuade people by science. Little by little, with facts, clarity, humour and patience, he would educate everyone and anyone he came across to understand the biology of the lake.   For only when they grasped the “Intimate life of the lake” as he would call it in his account of the story, would they give their support to this vital investment.

1.10 This section is written in the spirit of Dr Servettaz, (although not as detailed as his account and including some more recent knowledge unavailable to him), enough to show the complexity and fragility of the lake’s web of life, and how the thoughtless discharge of human waste into that web of life was threatening to destroy it.

1.11 Forming a vision of the “intimate life of the lake” was difficult for his fellow citizens for three reasons. It was beneath the surface. It was invisible. And scientific descriptions just seemed to muddy the waters with extremely long names for extremely short organisms.

1.12 To assist understanding  the intimate life of the lake, some charts are included as a reference point when the text becomes too infuriating  to follow.  

1.13 To being with there are three extracts from the ‘tree of life’  to show how the organisms, discussed in this section,  fit into the chain of evolution.  The first is a big-picture phylogenic tree of life showing where Cyanobacteria and Algae fit in (to the Prokaryotes and Eukaryotes respectively). (The Archaea are not so dominant in Lake Annecy.) The next two tree diagrams focus on one of the twigs  of the phylogenic tree, the animals.  The scientific tree of life continues to evolve amidst continual debate, now particularly fervent with the introduction of DNA mapping.  In 2001, the majority of animals more complex than jellyfish and other Cnidarians were split by Nielsen into two groups, the Protostomes and Deuterostomes, as shown below. Protostomes are distinguished from Deuterostomes by their embryonic development.  In Deuterostomes, the first opening (the blastopore) becomes the anus, while in Protostomes, it becomes the mouth.  Protostomes account for the next batch of tiny lake-dwelling creatures discussed in this section, the rotifers, daphnia and copepods, while the Deuterosomes account for all the rest of the lake animals from fish, to birds, reptiles and us. 

1.14 Grouping of animals by Nielsen, 2001 

This shows the evolutionary origins from Protostomia of the dominant forms of microbial life in Lake Annecy,  the Rotifers, and the Crustaceans - Daphnia and Copepods, a large group within Arthropoda.

1.15 Neilsen tree of life for Deuterostomes

Including the remainder of animal life in Lake Annecy, fish (Actinopterygii), birds and reptiles (reptilia),  frogs (amphibia) and mammals (mammal) of Lake Annecy.

As can be seen from both these charts, the lake’s other inhabitants have a claim to their world far more long-standing than we.

1.16   Next is a sizing chart – since most of the life in the lake is invisible it helps to understand the relative sizes and complexity of the key tiny organisms showing where they fit into the lake.

1. 17 Finally, there is a simplified geological time scale showing where these organisms fit into the history of life on earth.

1.18 In addition, a couple of thoughts may be helpful at the outset.  First, the biology of the lake reflects the ancient history of life on earth and yields insights into the origins of life itself.  Some of the key inhabitants of the lake trace their origin back 3.8 billion years, and most of the key microbial inhabitants evolved not much more recently that 300 million years ago.  Since most of them have relatively short lives, from a few days to a few months, that makes for a lot of generations, in the billions. By comparison homo sapiens numbers around five thousand generations.  So although the lake itself was formed quite recently, around 60,000 years ago, the life in the lake is ancient, predating most of the animal and vegetable world we seen on land.

1.19   Second, is a simple analogy between the terrestrial life we can see and lake life we can’t see.  On land we can see simple forms of vegetation such as grass, more complex forms such as vegetables, the herbivores that graze on it them such as sheep, and the various carnivores that eat the herbivores such as wolves and humans.  In the lake the simplest form of vegetation is bacteria, and in particular one of the main protagonists in our story, Cyanobacteria.  More complex forms of vegetation are the various types of Algae including Diatoms,  Chrysophycees (Golden Algae) Chlorophycees (Green Algae) Cryptophycees, and Dinophycees.  Grazing on this food as well as particulate organic detritus, and dead bacteria, are the tiny herbivore crustacea, Daphnia, as well as the worm-like Rotifers.  These in turn are eaten by the bigger crustaceans, the Copepods, who in turn become food for the lake’s  fish:  Coregone, (Fera) Artic Char (Omble-chevalier), Trout (Truite), Perch (Perche), Roach (Gardon), Tench (Tanche) and Rudd (Rotengle)

Continue Reading  Chapter Two