DIP a bucket into the ocean anywhere and you can scoop up one of the great
mysteries of science. Within that modest-looking pail of water swarm millions of
bacteria and billions of viruses. Those microbes鈥攁nd their cousins spread
throughout the world鈥檚 oceans鈥攎ake up the bulk of the Earth鈥檚 biomass.
They form the all-important anchor at the base of the oceanic food chain, and
through photosynthesis they play a major role in the planet鈥檚 carbon cycle,
which will ultimately determine the extent of global warming.
Yet marine ecologists haven鈥檛 a clue what most of the microbes in the bucket
do for a living. They can measure what happens to the bucket鈥檚 contents as a
whole, but the details of what鈥檚 happening and how are still practically
unknown. They鈥檝e laboured to coax these enigmatic microbes into growing in the
lab, offering them tasty broth and a snug home, but the bugs usually die faster
than turtles from the pet store. In short, marine ecologists understand Earth鈥檚
biggest, most influential ecosystem about as well as most of us understand the
innards of our computers and TVs.
But marine scientists may now have an opportunity to figure out what鈥檚 going
on, and revolutionise our understanding of how the ocean functions. What is
finally allowing them to pry into the lives of oceanic bacteria is the infant
field of ecological genomics, a melding of traditional ecology and newfangled
genomic technology. Itself a brand-new discipline, genomics aims to identify the
functions of all an organism鈥檚 genes and learn how they collaborate to keep the
organism running. For ecologists, gene sequences and activity patterns can
reveal an organism鈥檚 metabolism and nutritional needs, and supply clues about
its role in the ecosystem and how it interacts with other species. 鈥淯ntil
recently, we鈥檝e only been able to study the microbes in the ocean almost as a
black box,鈥� says Sallie Chisholm, an oceanographer at the Massachusetts
Institute of Technology in Boston. 鈥淚t鈥檚 tremendously exciting to open the black
产辞虫.鈥�
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Just two decades ago, few researchers thought that black box held anything
much at all. After all, if you dribble some seawater in a Petri dish of agar,
only a few bacterial colonies will sprout. 快猫短视频s of the day interpreted the
scarcity of colonies to mean a scarcity of microbes in the ocean. But in
reality, the seas teem with bugs in unimagined numbers and variety. They just
don鈥檛 fancy laboratory hospitality. That became clear in the early 1980s, when
microbiologists began isolating and sequencing free-floating strands of
microbial DNA from seawater samples. Comparing these disembodied fragments with
DNA from known species revealed a wealth of previously unidentified microbes in
every marine habitat from shallows to abyss, from near-shore to mid-ocean, and
from tropics to poles (快猫短视频, 10 February 1996, p 26).
As the microbial family tree sprouted lush growth, the question of what these
droves of mystery bugs were doing became all the more tantalising. Marine
ecologists made some headway by focusing on the collective properties of
bacterial communities, measuring overall changes in carbon and nitrogen, biomass
and diversity. But no one could say what most of the species were up
to鈥攗ntil genomics came to the rescue.
One of the first researchers to make use of this new tool was Ed DeLong, a
microbial ecologist at the Monterey Bay Aquarium Research Institute in Moss
Landing, California. He and his colleagues fished a fairly long shard of
bacterial DNA鈥攁bout 130,000 nucleotide bases鈥攐ut of Monterey Bay.
The gene sequence identified the owner of the fragment as a common and
widespread bacterium that may make up 10 per cent of the microbes living near
the surface of temperate waters, but that had never been cultured or studied
closely.
To gain some insight into the bacterium鈥檚 lifestyle, DeLong and his
colleagues sequenced each gene they found and compared it with sequences filed
in public databases. Among the ordinary housekeeping genes, one sequence shone
out because it coded for the light-absorbing pigment rhodopsin鈥攕uggesting,
to everyone鈥檚 surprise, that this bacterium was photosynthesising
(快猫短视频, 23 September 2000, p 4).
鈥淭here鈥檚 no other way we could have learned about this process,鈥� says DeLong.
The study made a splash. 鈥淗ere鈥檚 an organism that is a ubiquitous component
of marine systems鈥攊t鈥檚 found everywhere at high abundance鈥攁nd we had
no idea that it uses light,鈥� says Craig Cary, a microbiologist at the University
of Delaware in Lewes. 鈥淭hat鈥檚 a profound discovery because it might alter how we
look at the carbon cycle.鈥� For instance, Cary says, working out how much carbon
these bacteria absorb might sharpen our understanding of global warming.
Hoping to duplicate their success, DeLong and his colleagues have already
started trawling for other large DNA fragments that can be analysed in a similar
way. Promising strands are being sent to microbial ecologist John Heidelberg and
his co-workers at The Institute for Genomic Research (TIGR) near Washington DC,
who are experts at high-speed sequencing. Heidelberg predicts that the team will
post the first fragment鈥檚 sequence on the Internet soon and will complete about
eight sequences a year.
A similar gene-by-gene approach is opening up the ecology of another
long-overlooked group of marine residents: viruses. Until about 10 years ago,
conventional wisdom held that there weren鈥檛 enough viruses in the ocean to
sneeze at. In fact, marine viruses turn out to be about 10 times as numerous as bacteria
(快猫短视频 supplement, 2 November 1996, p 8),
and much of their ecology remains a mystery. Marine ecologist Farooq Azam of the Scripps
Institution of Oceanography in La Jolla, California, his postdoc student Forest
Rohwer and their colleagues, have been delving into the lifestyles of marine
viruses by sequencing their genomes. In a study published last year, the team
reported that roseophages, which attack a common ocean bacterium known as
Roseobacter, have four genes for recycling their host鈥檚 phosphorus for use
in their own DNA. That the virus devotes four of its 30 genes to reclaiming
phosphorus suggests that this nutrient is vital鈥攁nd that its scarcity in
the ocean may limit viral growth, says Rohwer. This accords with experimental
results showing that adding phosphorus to seawater can trigger a viral
population explosion.
This is a good start, say microbial ecologists. But genomics makes possible a
deeper analysis that can reveal how an organism picks and chooses among its
genes to adapt to the particular environment in which it finds itself. For
example, Chisholm plans to use genomics to plumb the workings of the bacterium
Prochlorococcus, which accounts for up to 80 per cent of the
photosynthesis in tropical and subtropical oceans. A team from the US Department
of Energy has just completed the sequence of all the bacterium鈥檚 genes, around
1500 in total. Now, says Chisholm, 鈥淲e want to use the genome to let the
organism tell us what鈥檚 important to it in the environment.鈥�
Chisholm and her colleagues plan to construct a gene chip that will allow
them to monitor the activity of every one of Prochlorococcus鈥檚
thousands of genes at once. She intends to manipulate the bacterium鈥檚
surroundings in the lab鈥攃hanging temperature, light levels and the
availability of nutrients such as iron and nitrogen鈥攁nd let the chip tell
her which genes are activated under which conditions. Gene chips can also
profile samples collected in the wild, providing genomic snapshots of microbes
as they contend with the vagaries of their environment and revealing the genes
necessary for survival under natural conditions. Such genes may account for a
large share of the 鈥渕ystery genes鈥濃�攚ith no known function or similarity to
any gene known to science鈥攖hat have turned up in every genome sequenced to
date.
Eventually, scientists may be able to analyse whole ecosystems at the genomic
level. For example, says Chisholm, you can consider all the genes in an
ecosystem as a single genome, then compare different 鈥渆co-genomes鈥� to discern
rules for how ecosystems are put together. Is there a minimum set of genes
necessary for an ecosystem to exist? If there is a standard set of genetic
functions, are they parcelled out to different organisms in different
ecosystems? 鈥淭he idea is to see how these processes at the molecular level
manifest themselves as emergent properties of the ecosystem,鈥� she says.
But making sense of all that DNA won鈥檛 be easy. Seawater contains a mishmash
of DNA fragments that hail from all the various bacteria that are present. To
identify the owner of each fragment, microbiologists typically look for a gene
that codes for ribosomal RNA, a part of the cell鈥檚 protein-manufacturing
machinery. 快猫短视频s have sequenced this gene from many different organisms, so
it serves as a reliable molecular identity tag. DeLong鈥檚 study was so fruitful
because his fragment contained this tag, allowing him to finger the owner. The
catch is that most fragments lack the marker, making the task of matching
fragment to organism akin to reconstructing a document that has been
shredded.
Difficult, yes, but not impossible, says Claire Fraser, president of TIGR.
快猫短视频s there think they may be able to assemble all the fragments and
reconstruct the genomes of all or most of the organisms in a sample鈥攁
litre of seawater, say鈥攗sing the same 鈥渞andom shotgun sequencing鈥�
techniques that Celera Genomics used to piece together the human genome. The key
is a powerful computer program that scans the sequences of all the fragments
looking for areas of overlap, suggesting that two pieces belong together. TIGR鈥檚
scientists haven鈥檛 yet tried shotgun sequencing to assemble several genomes at
once, says Fraser, but the technique has successfully assembled a single genome
while ignoring fragments of a second genome in the sample.
Still, some scientists have reservations about whether the program can handle
the genetic diversity in a more complex mixture. Among the sceptics is
microbiologist Stephen Giovannoni of Oregon State University in Corvallis. He
believes we need to know much more about the variability within species before
we can be sure of coming up with the right solution鈥攆or example, five
slightly different sequences from the same species might look like five
different species to the computer.
And then there鈥檚 the question of money. Genomics is expensive, and scientists
fear a scarcity of funding may restrict their research. For example, the eight
fragments TIGR will process for DeLong each year will cost about $100,000
in total, says Heidelberg. It would cost anyone else many times more, because
TIGR already has the speedy sequencing machines and other equipment necessary
for such a study. And while the price of sequencing has plummeted and sequencing
power has soared over the past few years, scientists like Cary worry that the
trend won鈥檛 continue. The human genome project鈥攚ith its promise of huge
biomedical payoffs鈥攑owered these advances, he says. He鈥檚 concerned that
without that economic motivation, there won鈥檛 be any impetus to push the
technology into the realms of ecology.
Ecologists鈥� hopes may ride on whether environmental questions top the policy
agenda of funding bodies. 鈥淲ouldn鈥檛 it be wonderful,鈥� asks Cary, 鈥渢o be able to
understand our environment as well as we understand our own body?鈥�