Beneath the Surface

Abstract by Andy Maguire (2016) CC By 2.0, on Flickr]
Abstract by Andy Maguire (2016) CC By 2.0, on Flickr

While I was watching the surface-bound shenanigans of other humans via Facebook, soil microbes have been steadily plugging away,  keeping the bio-geochemical cycles of the planet going.   A team led by scientists at the Lawrence Berkeley National Labs & UC Berkeley has reconstructed the genomes of 2500+ microbes that live in soil and groundwater of a Colorado aquifer. In addition to identifying (and naming) new phyla of bacteria, the researchers found new insights into how bacteria work together to power the carbon, nitrogen and other chemical cycles of the entire planet!

The paper appears online in Nature Communications. The soil microbiome census, using genomic techniques (“terabase-scale shotgun DNA sequencing”) to identify new taxa of bacteria in the samples, is especially important because while 1/5th of the Earth’s biomass exists underground, we still don’t know very much about about these organisms.

Once the genomes of the different bacteria were sequenced, scientists combed the data looking for genes related to microbial energy metabolism (gaining/losing electrons, carbon and nitrogen fixation, etc). By looking at which microbes with specific abilities were present in the samples, the researchers could infer what reactions (and combination of reactions) are taking place community-wide.

These combination of reactions are called “the metabolic handoffs.” Organisms may only have one or two metabolic tricks up their own sleeves (okay, I know microbes have neither hands nor sleeves, but bear with me here.) However, in the community of subterranean microbes, there are *a lot* of metabolic abilities across the different species. The waste products of one organism are food for another one that has the ability to extract energy from it. Or, as we liked to say as Teva Educators, “Waste equals food! Waste equals food! Waste equals food!”

TL;DR From the Press Release:

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.

Previously unnoticed by humans, soil microbes are hard at work shuffling electrons as a team to keep the carbon, nitrogen, sulfur and hydrogen cycling around our biosphere. They deserve a shoutout from this grateful macro-organism.

Tangents for this Post:
Okay, I wasn’t just watching humans on FB. Other organisms include:
Glockenspiel-playing chickens
Rescued Cows
Pigeons (here and here)
Left-handed snail romance
Ticklish Rats


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