In the fall of 2010, Hoi-Ying Holman of the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) was approached by an international team researching a mysterious microbial community discovered deep in cold sulfur springs in southern Germany.
"They told me what they were doing and said, 'We know what you contributed to the oil-spill research,'" recalls Holman, who heads the Chemical Ecology group in Berkeley Lab's Earth Sciences Division. "They wondered if I could help them determine the biochemistry of their microbe samples."
Holman had co-authored a report in Science about bacteria in the Gulf of Mexico that thrived on the Deepwater Horizon oil plume. Using infrared spectromicroscopy at the Berkeley Synchrotron Infrared Structural Biology (BSISB) facility, which she directs at the Advanced Light Source (ALS), Holman helped determine how the novel bug obtained energy by eating the spilled crude. No stranger to subsurface bioscience, Holman would soon add a new actor to her cast of remarkable microbes.
Not extreme, but weird anyway
The name Archaea means "ancient things," but Archaea were recognized as a distinct domain of life less than forty years ago. First thought to be exclusively extremophiles – lovers of boiling hot springs, deep-sea black smokers, acid mine runoff, and other inhospitable environments – more and more archaea are found thriving in moderate and cold environments, almost always as minority members of much larger microbial communities.
A unique exception to this pattern was discovered less than 10 years ago in the Sippenauer Moor in Germany. In microbial mats in this cold sulfur spring's outflow, the SM1 Euryarchaeon lives in roughly equal abundance with bacteria in a community that forms symbiotic "strings of pearls": the archaea fill the "pearls" and filamentous bacteria cover the pearl surfaces and form strings between them. The two kinds of microbes were assumed to be syntrophic – dependent on each other for nourishment – but the biochemical details were a mystery.
Christine Moissl-Eichinger of the University of Regensburg was among the SM1 Euryarchaeon's discoverers. Before long what she calls "another amazing lifestyle" of the new archaeon emerged; biofilms that grew deep below the surface of another cold sulfur spring, the nearby Muehlbacher Schwefelquelle. Moissl-Eichinger and her team collected samples of the slime-like biofilm – which first seemed to be pure SM1 – on net traps underwater.
To augment their already extensive research, Moissl-Eichinger and Alexander Probst of her staff brought the Regensburg samples to Berkeley Lab, initially attracted by the PhyloChip, a DNA microarray invented by Berkeley Lab's Gary Andersen and Todd DeSantis and their colleagues. Because the PhyloChip probes for the 16S rRNA gene, found in all Bacteria and Archaea, it can quickly and accurately sort through all known species in a sample – including those, like SM1 and many other microorganisms, that can't be grown in culture.
Probst and DeSantis, both now with Second Genome, Inc., and Andersen were joined by Kasthuri Venkateswaran of the Jet Propulsion Laboratory, a member of NASA's Biotechnology and Planetary Protection Group. Probst wanted to know who was living where in the subsurface sulfur-spring samples; Venkateswaran's interest is understanding the role of Archaea in space and analogous sites. Although SM1 was by far the dominant species in the subsurface community, they found that small amounts of other archaea were present as well – and about five percent of the community consisted of bacteria.
Bring on the synchrotron
Led by Andersen, the PhyloChip's inventors had contributed to the oil-spill research, and their previous association with Holman brought her and her BSISB colleagues aboard the SM1 research team.
"Lots of biochemical techniques can tell you what's in a sample – lipids and carbohydrates, for example – but just because they're there doesn't mean they interact," says Holman's colleague Giovanni Birarda, a member of the BSISB staff. "Synchrotron radiation–based Fourier-transform infrared spectromicroscopy – SR-FTIR – takes images and spectra of the same sample, so you can map the chemical relationships by combining the images with spectra that identify where the archaea and bacteria are."
Holman says, "The main difference is in their membrane lipids. Bacterial membrane lipids consist of fatty acids with long alkylic chains" – functional groups of singly bonded carbon and hydrogen atoms – "which have only one to two terminal methyl groups," groups with one carbon and three hydrogen. "By contrast, archaeal membrane lipids generally consist of branched and saturated isoprenes" – a more complex common hydrocarbon – "and are relatively less alkylic but have more methyl groups."
By revealing the bright spectral signals of alkylic and methyl groups, together with sulfur functional groups, synchrotron FTIR unambiguously identified the sulfate-reducing metabolic activity of the bacteria within the SM1 samples. The archaeal cells themselves showed no such activity, leading the researchers to posit a thriving mutual metabolism of the archaea and bacteria.
In many cases, such syntrophy requires close physical association. Covering the surface of each SM1 cell the researchers found spines made of three protein strands, equipped with terminal hooks where the strands divided. Moissl-Eichinger named them hami, Latin for barbs or hooks. These "nano-grappling hooks" apparently hold the microbial partners together, working in synchronization. The major hami protein is unlike any known proteinaceous archaeal or bacterial filaments.
How SM1 Euryarchaea interact with their bacterial partners may be a model for understanding other syntrophic relations essential to the carbon and sulfur cycles on which Earth's life depends. So far found in just two sites in Germany, the species is the only example yet of an archaeon that dominates a biological ecosystem – but related species have been found in sulfur springs as far afield as Turkey and may be widespread.
DOE's Office of Science supported building and equipping the BSISB and also supports the ALS. For additional information, see below.
DOE/Lawrence Berkeley National Laboratory: http://www.lbl.gov
This press release was posted to serve as a topic for discussion. Please comment below. We try our best to only post press releases that are associated with peer reviewed scientific literature. Critical discussions of the research are appreciated. If you need help finding a link to the original article, please contact us on twitter or via e-mail.
Results of largest ever genetics study of a single population could also help refine dates for major events during human evolution Humans are evolving more rapidly than previously thought, according to the largest ever genetics study of a single population.
Latest genetic tests reveal another break in the male line, potentially undermining the legitimacy of the entire House of Plantagenet When scientists revealed last year that an adulterous affair had apparently broken the male line in Richard III’s family tree, they vowed to investigate further.
By 2016, Icelandic genetics company deCODE will have data on half the country's population. Releasing the data will be controversial, but could save lives
A clinical trial has shown that the drug aducanumab slows cognitive decline in people with Alzheimer's and reduces the amount of amyloid plaque in their brain
A leading researcher issues a call for pills that deliver a full course of treatment in one swallow.One of the world’s preëminent biomedical researchers is calling for a concerted effort by scientists to develop pills that would stay in the stomach or gut for weeks or months once swallowed, delivering one or more drugs continuously or over set intervals.
Two genes responsible for building up drug-resistance can easily be shared between a family of bacteria
When malaria parasites infect blood, they manufacture odor molecules that smell sweet to mosquitoes, scientists report. So how do these odors get from the bloodstream to the insects?
Researchers are developing new method of wireless deep brain stimulation.
Zoos belonging to World Association of Zoos and Aquariums filmed allowing shocking mistreatment of elephants, dolphins, lions, bears, penguins and whales
Owners of Highland Wildlife Park hope Victoria, 18, will get chummy with male Arktos during her stay in the Cairngorms