New Bacteria Groups, and Stunning Diversity,
Discovered Underground
Berkeley
Lab and UC Berkeley research also provides new clues about the roles of
subsurface microbes in globally important cycles
One of the most detailed genomic
studies of any ecosystem to date has revealed an underground world of stunning
microbial diversity, and added dozens of new branches to the tree of life.
Rifle ,
Colorado ,
where for the past several years scientists have conducted experiments designed
to stimulate populations of subterranean microbes that are naturally present in
very low numbers.
Berkeley
now dominates the tree of life as it does the periodic table,” Banfield says,
in a nod to the sixteen elements discovered at Berkeley Lab and UC Berkeley.
Berkeley
Lab and UC Berkeley research also provides new clues about the roles of
subsurface microbes in globally important cycles
One of the most detailed genomic
studies of any ecosystem to date has revealed an underground world of stunning
microbial diversity, and added dozens of new branches to the tree of life.
The bacterial bonanza comes from scientists who reconstructed
the genomes of more than 2,500 microbes from sediment and groundwater samples
collected at an aquifer in Colorado .
The effort was led by researchers from the Department of Energy’s Lawrence
Berkeley National Laboratory (Berkeley Lab) and UC Berkeley. DNA sequencing was
performed at the Joint Genome Institute, a DOE Office of Science User Facility.
As reported online October 24 in the journal Nature Communications, the
scientists netted genomes from 80 percent of all known bacterial phyla, a
remarkable degree of biological diversity at one location. They also discovered
47 new phylum-level bacterial groups, naming many of them after influential
microbiologists and other scientists. And they learned new insights about how
microbial communities work together to drive processes that are critical to the
planet’s climate and life everywhere, such as the carbon and nitrogen cycles.
These findings shed light on one of Earth’s most important and
least understood realms of life. The subterranean world hosts up to one-fifth
of all biomass, but it remains a mystery.
“We didn’t expect to find this incredible microbial diversity.
But then again, we know little about the roles of subsurface microbes in
biogeochemical processes, and more broadly, we don’t really know what’s down
there,” says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab’s
Climate & Ecosystem Sciences Division and a UC Berkeley professor in the
departments of Earth and Planetary Science, and Environmental Science, Policy,
and Management.
UC Berkeley’s Karthik Anantharaman, the first author of the
paper, adds, “To better understand what subsurface microbes are up to, our
approach is to access their entire genomes. This enabled us to discover a
greater interdependency among microbes than we’ve seen before.”
The research is part of a Berkeley Lab-led project called Watershed Function Scientific
Focus Area (formerly Sustainable Systems Scientific Focus Area 2.0).
The project is developing a predictive understanding of terrestrial
environments from the genome to the watershed scale. The field research
takes place at a research site near the town of
The scientists sent soil and water samples from these
experiments to the Joint Genome Institute for terabase-scale metagenomic
sequencing. This high-throughput method isolates and purifies DNA from
environmental samples, and then sequences one trillion base pairs of DNA at a
time. Next, the scientists used bioinformatics tools developed in Banfield’s
lab to analyze the data.
Their approach has redrawn the tree of life. Between the 47 new
bacterial groups reported in this work, and 35 new groups published last year (also found at the Rifle site),
Banfield’s team has doubled the number of known bacterial groups.
With discovery comes naming rights. The scientists named many of
the new bacteria groups after Berkeley Lab and UC Berkeley researchers. For example, there’s Candidatus Andersenbacteria, after
phylochip inventor Gary Andersen, and there’s Candidatus Doudnabacteria, after CRISPR genome-editing
pioneer Jennifer Doudna.
“
Another big outcome is a deeper understanding of the roles
subsurface microbes play in globally important carbon, hydrogen, nitrogen, and
sulfur cycles. This information will help to better represent these cycles in
predictive models such as climate simulations.
The scientists conducted metabolic analyses of 36 percent of the
organisms detected in the aquifer system. They focused on a phenomenon called
metabolic handoff, which essentially means one microbe’s waste is another
microbe’s food. It’s known from lab studies that handoffs are needed in certain
reactions, but these interconnected networks are widespread and vastly more
complex in the real world.
To understand why it’s important to represent metabolic handoffs
as accurately as possible in models, consider nitrate, a groundwater
contaminant from fertilizers. Subsurface microbes are the primary driver in
reducing nitrate to harmless nitrogen gas. There are four steps in this
denitrification process, and the third step creates nitrous oxide—one of the
most potent greenhouse gases. The process breaks down if microbes that carry
out the fourth step are inactive when a pulse of nitrate enters the system.
“If microbes aren’t there to accept the nitrous oxide handoff,
then the greenhouse gas escapes into the atmosphere,” says Anantharaman.
The scientists found the carbon, hydrogen, nitrogen, and sulfur
cycles are all driven by metabolic handoffs that require an unexpectedly high
degree of interdependence among microbes. The vast majority of microorganisms
can’t fully reduce a compound on their own. It takes a team. There are also
backup microbes ready to perform a handoff if first-string microbes are
unavailable.
“The combination of high microbial diversity and
interconnections through metabolic handoffs likely results in high ecosystem
resilience,” says Banfield.
http://newscenter.lbl.gov/2016/10/24/bacteria-underground/
[this link includes an excellent diagram of the many types of bacteria known to
exist underground]
No comments:
Post a Comment