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Dear Subscribers,


Please see herebelow information from Davide Duthe of BIOPLANE on Scientists Unveil New 'Tree of Life'. 


Apologies for cross-posting.


Amir Kassam

Moderator

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---------- Forwarded message ----------
From: David Duthie <[log in to unmask]>
Date: Wed, Apr 13, 2016 at 1:39 AM
Subject: Scientists Unveil New ‘Tree of Life’
To: bioplan <[log in to unmask]>


Dear BIOPLANNERS,

For most of Life on Earth's approximately 3.5 billion year-old "life", there were only microbes, living and surviving in a very rough world before things calmed down enough to allow the emergence of eukaryotic life-forms and eventually multicellular life more familiar to us through the fossil record and the present day.

ALL life on Earth is still somehow connected to this origin through a chain of inheritance, when a chain breaks (no offspring), we lose a little piece of biodiversity history.

No visual image can possibly capture the immensity of all of these chains of inheritance - but many have tried, even before Charles Darwin's famous sketches (see link below).

This week, another attempt to capture the full scope and breadth of (genetic) biodiversity has been published and their tree is a bit of an eye-opener (see the figure in the links below)

Through a clever piece of "reverse engineering", the scientists have extracted genetic material (DNA) from a range of habitats and then re-assembled the DNA to identify specific sequences that represent different taxonomic groups.

Their surprising finding is that there is a huge microbial diversity out there of which we are hardly aware - somewhat similar to the dark internet, or offshore tax havens!

The abstract and link to the full paper is here:

Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., et al. (2016). A new view of the tree of life. Nature Microbiology, 16048. http://doi.org/10.1038/nmicrobiol.2016.48 (open access)

The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life’s diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

A good readable cover story by Carl Zimmer in the New York Time can be found at http://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html and pasted below.

It is worth going to the NYT article and/or the research article to see the "tree" itself - very different from the one which formed the only Figure in Darwin's "On the Origin of Species" - see https://upload.wikimedia.org/wikipedia/commons/4/4e/Darwins_tree_of_life_1859.png

What is remarkable about this research is that it reveals how little we still know about microbial diversity - and the potential applications of this diversity in the development of a more biodiversity-friendly human economy.

This "tree" follows hard on the heels of another remarkable publication last month from the J. Craig Venter Institute which announced the creation of a "minimal microbe" - a stripped-down version of a natural bacterium that has the fewest number of genes that still allow it to reproduce - under favourable laboratory conditions.

Again, what is remarkable about this research is that, for fully one-third of the essential genes, scientists have no clear knowledge of their function, opening up a whole new challenge for molecular biologists.

Again, the abstract and link to the the article is here:

Hutchison, C. A., Chuang, R.-Y., Noskov, V. N., Assad-Garcia, N., Deerinck, T. J., Ellisman, M. H., et al. (2016). Design and synthesis of a minimal bacterial genome. Science, 351(6280), 6253-6253. http://doi.org/10.1126/science.aad6253 (open access)

We used whole-genome design and complete chemical synthesis to minimize the 1079–kilobase pair synthetic genome of Mycoplasma mycoides JCVI-syn1.0. An initial design, based on collective knowledge of molecular biology combined with limited transposon mutagenesis data, failed to produce a viable cell. Improved transposon mutagenesis methods revealed a class of quasi-essential genes that are needed for robust growth, explaining the failure of our initial design. Three cycles of design, synthesis, and testing, with retention of quasi-essential genes, produced JCVI-syn3.0 (531 kilobase pairs, 473 genes), which has a genome smaller than that of any autonomously replicating cell found in nature. JCVI-syn3.0 retains almost all genes involved in the synthesis and processing of macromolecules. Unexpectedly, it also contains 149 genes with unknown biological functions. JCVI-syn3.0 is a versatile platform for investigating the core functions of life and for exploring whole-genome design. 

and a cover story has been pasted below the other news story.

We can rest assured that, no what future we chose to create for ourselves, microbial diversity will still be "little things that rule the world".

Best wishes

David Duthie

**************************

Scientists Unveil New ‘Tree of Life’

By CARL ZIMMER

APRIL 11, 2016


A team of scientists unveiled a new tree of life on Monday, a diagram outlining the evolution of all living things. The researchers found that bacteria make up most of life’s branches. And they found that much of that diversity has been waiting in plain sight to be discovered, dwelling in river mud and meadow soils.

“It is a momentous discovery — an entire continent of life-forms,” said Eugene V. Koonin of the National Center for Biotechnology Information, who was not involved in the study.

The study was published in the journal Nature Microbiology.

In his 1859 book “On the Origin of Species,” Charles Darwin envisioned evolution like a branching tree. The “great Tree of Life,” he said, “fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”

Ever since, biologists have sought to draw the tree of life. The invention of DNA sequencing revolutionized that project, because scientists could find the relationship among species encoded in their genes.

In the 1970s, Carl Woese of the University of Illinois and his colleagues published the first “universal tree of life” based on this approach. They presented the tree as three great trunks.

Our own trunk, known as eukaryotes, includes animals, plants, fungi and protozoans. A second trunk included many familiar bacteria like Escherichia coli.

The third trunk that Woese and his colleagues identified included little-known microbes that live in extreme places like hot springs and oxygen-free wetlands. Woese and his colleagues called this third trunk Archaea.

Scientists who wanted to add new species to this tree of life have faced a daunting challenge: They do not know how to grow the vast majority of single-celled organisms in their laboratories.

A number of researchers have developed a way to get around that. They simply pull pieces of DNA out of the environment and piece them together.

In recent years, Jillian F. Banfield of the University of California, Berkeley and her colleagues have been gathering DNA from many environments, like California meadows and deep sea vents. They have been assembling the genomes of hundreds of new microbial species.

The scientists were so busy reconstructing the new genomes that they did not know how these species might fit on the tree of life. “We never really put the whole thing together,” Dr. Banfield said.

Recently, Dr. Banfield and her colleagues decided it was time to redraw the tree.

They selected more than 3,000 species to study, bringing together a representative sample of life’s diversity. “We wanted to be as comprehensive as possible,” said Laura A. Hug, an author of the new study and a biologist at the University of Waterloo in Canada.

The researchers studied DNA from 2,072 known species, along with the DNA from 1,011 species newly discovered by Dr. Banfield and her colleagues.

The scientists needed a supercomputer to evaluate a vast number of possible trees. Eventually, they found one best supported by the evidence.

It’s a humbling thing to behold. All the eukaryotes, from humans to flowers to amoebae, fit on a slender twig. The new study supported previous findings that eukaryotes and archaea are closely related. But overshadowing those lineages is a sprawling menagerie of bacteria.

Remarkably, the scientists didn’t have to go to extreme places to find many of their new lineages. “Meadow soil is one of the most microbially complex environments on the planet,” Dr. Hug said.

Another new feature of the tree is a single, large branch that splits off near the base. The bacteria in this group tend to be small in size and have a simple metabolism.

Dr. Banfield speculated that they got their start as simple life-forms in the first chapters in the history of life. They have stuck with that winning formula ever since.

“This is maybe an early evolving group,” Dr. Banfield said. “Their advantage is just being around for a really long time.”

Brian P. Hedlund, a microbiologist at the University of Nevada, Las Vegas who was not involved in the new study, said that one of the most striking results of the study was that the tree of life was dominated by species that scientists have never been able to see or grow in their labs. “Most of life is hiding under our noses,” he said.

Patrick Forterre, an evolutionary biologist at the Pasteur Institute in France, agreed that bacteria probably make up much of life’s diversity. But he had concerns about how Dr. Banfield and her colleague built their tree. He argued that genomes assembled from DNA fragments could actually be chimeras, made up of genes from different species. “It’s a real problem,” he said.

Dr. Banfield predicted that the bacterial branches of the tree of life may not change much in years to come. “We’re starting to see the same things over and over again,” she said.

Instead, Dr. Banfield said she expected new branches to be discovered for eukaryotes, especially for tiny species such as microscopic fungi. “That’s where I think the next big advance might be found,” Dr. Banfield said.

Dr. Hug disagreed that scientists were done with bacteria. “I’m less convinced we’re hitting a plateau,” she said. “There are a lot of environments still to survey.”

********************

Synthetic microbe lives with fewer than 500 genes

By Robert F. ServiceMar. 24, 2016 , 2:00 PM

When it comes to genome size, a rare Japanese flower, called Paris japonica, is the current heavyweight champ, with 50 times more DNA than humans. At the other end of the scale, there’s now a new lightweight record-holder growing in petri dishes in California. This week in 
Science, researchers led by genome sequencing pioneer Craig Venter report engineering a bacterium to have the smallest genome—and the fewest genes—of any freely living organism, smaller than the flower’s by a factor of 282,000. Known as Syn 3.0, the new organism has a genome whittled down to the bare essentials needed to survive and reproduce, just 473 genes. “It’s a tour de force,” says George Church, a synthetic biologist at Harvard University.

The microbe’s streamlined genetic structure excites evolutionary biologists and biotechnologists, who anticipate adding genes back to it one by one to study their effects. “It’s an important step to creating a living cell where the genome is fully 
defined,” says synthetic biologist Chris Voigt of the Massachusetts Institute of Technology in Cambridge. But Voigt and others note that this complete definition remains a ways off, because the function of 149 of Syn 3.0’s genes—roughly one-third—
remains unknown. Investigators’ first task is to probe the roles of those genes, which promise new insights into the basic biology of life.

As Syn 3.0’s name suggests, it’s not the first synthetic life made by Venter, who heads the J. Craig Venter Institute (JCVI) and is a founder of Synthetic Genomics, a biotech company, both in San Diego, California. In 2010, Venter’s team reported that they had synthesized the sole chromosome of Mycoplasma mycoides—a bacterium with a relatively small genome—and transplanted it into a separate mycoplasma called M. capricolum, from which they had previously extracted the DNA. After several false starts, they showed that the synthetic microbe booted up and synthesized proteins normally made by M. mycoides rather than M. capricolum (Science, 21 May 2010, 
p. 958). Still, other than adding a bit of watermark DNA, the researchers left the genetic material in their initial synthetic organism, Syn 1.0, unchanged from 
the parent.

In their current work, Venter, along with project leader Clyde Hutchison at JCVI, set out to determine the minimal set of genes needed for life by stripping nonessential genes from Syn 1.0. They initially formed two teams, each with the same task: using all available genomic knowledge to design a bacterial chromosome with the hypothetical minimum genome. Both proposals were then synthesized and transplanted into 
M. capricolum to see whether either would produce a viable organism.

“The big news is we failed,” Venter says. “I was surprised.” Neither chromosome produced a living microbe. It’s clear, Venter says, that “our current knowledge of bio
logy is not sufficient to sit down and design a living organism and build it.”

Venter and his colleagues had better success with trial and error. They divided Syn 1.0’s genome, with its 901 genes, into eight sections. To the beginning and end of each section they added identical DNA tags that made the pieces easy to reassemble. That allowed them to treat the sections as independent modules, removing each one in turn, deleting chunks of DNA, then reassembling the full genome and reinserting it into M. capricolum to see whether it produced a living cell. If the altered genome wasn’t viable, they knew they had cut out an essential gene that had to be restored. The researchers also assessed the necessity of numerous genes in the microbe by inserting foreign genetic material, called transposons, to disrupt their function.

All this enabled them to systematically whittle away genes that either had nonessential functions or duplicated the function of another gene. In the end, Venter says, his team built, designed, and tested “multiple hundreds” of constructs before settling on Syn 3.0, with a genome about half the size of Syn 1.0’s. (Syn 2.0 was an intermediate stage in this process, the first microbe with a genome smaller than that of M. genitalium, which with 525 genes has the fewest of any free-living natural organism.)

Once the whittling was complete, the researchers reordered the remaining genes, aligning ones that work in common pathways. The procedure tidied up the genome much as a computer compresses and re
organizes files on its hard drive to save disk space. This will likely make life much easier for synthetic biologists who will experiment with Syn 3.0 in the future, Voigt says.

With a total of 531,000 bases, the new organism’s genome isn’t much smaller than that of M. genitalium, with 600,000 bases. But M. genitalium grows so slowly that a population of cells can take weeks to double. Syn 3.0, by contrast, has a doubling time of 3 hours, suggesting that it thrives with its slimmed down genome. “We’re not saying this is the ultimate minimum genome,” 
Venter says. For now, however, Syn 3.0 reigns as the world’s new lightweight champ.

  • DOI: 10.1126/science.aaf4038
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