Crystalline nanotube-forming bacteria help crumble mountains in a tropical rainforest

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Mineral weathering, the slow crumbling, dissolving, and chemical transformation of solid bedrock into smaller fragments and clays, replenishes Earth’s surface with the raw materials needed to make soil and the elements needed to support life.  In the Luquillo mountains of Puerto Rico, hot rain beats incessantly onto the ground and seeps deep into the earth, creating cracks and fissures in solid rock. While a warm, wet climate, frequent hurricanes and mudslides that shake up the landscape all contribute to the rapid weathering of these tropical mountains, a recently published study indicates crystal-forming bacteria may also be important contributors to the most rapid chemical weathering rates recorded on the planet.

Luquillo rainforest in northeast Puerto Rico- a steep, mountainous, tropical forest that has been the site of extensive ecological research for decades

Luquillo rainforest in northeast Puerto Rico- a steep, mountainous, tropical forest that has been the site of extensive ecological research for decades

Historically, scientists have studied weathering as an abiotic (i.e., non-living) process. However, there is growing evidence that living organisms, from bacteria and fungal mycelia  to treescan actively participate in the replenishment of fresh rock material to the soil. In the mid 1980’s, scientists studying geothermal sediments from Yellowstone found the some of the first evidence of biological weathering when they discovered iron-silicate minerals in association with bacterial remains. These bacterial cell fragments, the scientists hypothesized, can act as mineral “nucleation” sites – surfaces to which minerals can condense and grow. If you’ve ever made rock candy, you’ve formed sugar crystals by this same nucleation process.

Snow crystals vizualized by a scanning electron microscope. Like other types of crysals, the formation of snow crystals is promoted by nucleates- things for ice to condense and grow onto. Credit:  Agricultural Research Service, United States Department of Agriculture

Snow crystals vizualized by a scanning electron microscope. Like other types of crysals, the formation of snow crystals is promoted by nucleates- things for ice to condense and grow onto. Credit: Agricultural Research Service, United States Department of Agriculture

Why is crystal nucleation important in weathering? As primary minerals, the stuff coming directly out of rocks, are broken down, they can undergo a series of chemical transformations into a variety of secondary minerals. Many of these secondary minerals, including clays, become important raw materials for the formation of new soils.

Which brings us back to Luquillo. Here, Earth scientists from many different fields- geology, ecology, atmospheric chemistry, and hydrology to name a few, are attempting to build a holistic picture of the processes that shape landscapes. For nearly a decade, a team of scientists now affiliated with the Luquillo Critical Zone Observatory have been drilling holes in the ground to study what makes the rocks crumble. Deep holes. Mineral weathering is so rapid in these mountains that they must drill through five or even ten meters of saprolite- soft, mineral rich material, no longer solid rock but not quite soil yet- before hitting bedrock. What have they found? For one, there are more bacteria living near bedrock– at that contact zone between hard rock and soft saprolite, where weathering is actively occurring-  than higher up. Roughly a hundred times more. This led researchers to ask a simple question- if bacteria are concentrated at the so-called “weathering front”, are they just passive bystanders, or do they have an important role to play in the transformation of rock into soil?

To answer this question, a research team led by Dr. Susan Brantely, a geochemist at Penn State University, drilled several holes to bedrock, collected samples from the contact zone between saprolite and rock, and used high-resolution scanning electron and transmission electron microscopy (SEM and TEM) to investigate the structure and composition of actively weathering minerals. While SEM provides information on the 3-d structure of an object, the higher resolution TEM technique can provide information on crystal bonding structure and help determine the elemental composition of a sample.

Their findings? In most of the samples, the scientists identified halloysite, a secondary mineral that forms long, tube-like crystals. Halloysite is a natural weathering product in young soils and its presence was not entirely surprising.The really exciting part came when they identified small round and rod-shaped cells buried amidst the so-called “crystalline nanotubes”. Bacteria, sheathed in crystals.  Moreover, all of the bacterial cells observed were intact, suggesting that being coated in crystals does not damage these hardy bacteria. The presence of living bacteria within secondary minerals also implicitly suggests longevity:  halloysite crystals can take weeks or months to form.

Scanning electron microscopy image (50,000x) showing a coccus-shaped bacteria surrounded by halloysite nanotubes

Scanning electron microscopy image (50,000x) showing a coccus-shaped bacteria surrounded by halloysite nanotubes. Credit: Minyard et al. 2011.

That bacteria can serve as condensation nuclei for secondary minerals in Luquillo has important ecological implications. For instance, in this  study, halloysite minerals often occurred in higher densities around bacteria than inorganic surfaces. This may be an indication that some bacteria are evolved to be highly efficient nucleating agents. These mineral-formers may have  structures attached to their cell membranes which have a high affinity for particular mineral elements, such as silica.

Scanning electron microscope images of bacteria associated with secondary minerals nearly five meters deep in Luquillo saprolite. From Minyard et al. 2011.

Scanning electron microscope images of bacteria associated with secondary minerals nearly five meters deep in Luquillo saprolite. Credit: Minyard et al. 2011.

Bacteria that serve as mineral nucleation sites may also be able to influence mineral chemistry. Other researchers have found that sulfur, considered to be an “impurity” is more concentrated in halloysite when bacteria are present. Iron, another common impurity in halloysite, was found in many of the samples in this study. The presence of iron could indicate the crystal-forming bacteria are iron oxidizers, organisms that use iron for fuel instead of carbon. Perhaps serving as mineral nucleation sites allows these bacteria to access iron they need for energy.

Scanning electron microscope image of iron oxidizing bacteraia Acidovorax sp. BoFeN1, encrusted in iron minerals. Credit: Eye of Science, Reutlingen

Scanning electron microscope image of iron oxidizing bacteraia Acidovorax sp. BoFeN1, encrusted in iron minerals. Credit: Eye of Science, Reutlingen

Many questions remain to be answered regarding the relationship between microorganisms and weathering. What sorts of organisms can withstand being coated in minerals? What are the physiological adaptations that allow them to do so, how and when did these adaptations evolve? Traditionally, geologists have considered the lithosphere- the rocky part of the earth- to be a cold, dead place. Clearly we need to start rethinking that assumption, and considering what it may mean for our geologic understanding of the planet, if organisms can find an evolutionary space buried amidst the very rocks our biosphere sits on.

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