Microbial soil live

A new study sheds 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. Little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. 

The new research is part of a project called Sustainable Systems Scientific Focus Area 2.0 (did I mention that I hate these 2.0 references?) , which is developing a predictive understanding of terrestrial environments from the genome to the watershed scale. The project's field research takes place at a research site near the town of 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. Researchers reconstructed the genomes of more than 2,500 microbes from sediment and groundwater samples collected at an aquifer in Colorado.These represent about 80 % of all known bacterial phyla, a remarkable degree of biodiversity 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.

Soil and water samples were subjected to so-called terabase metagenomic sequencing. This high-throughput method isolates and purifies DNA from environmental samples, and then sequences at least one trillion base pairs of DNA at a time. Warning - don't try this at home as the bioinformatics for this amount of data is - to say the least - challenging.

Their approach has redrawn the bacterial 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), the colleagues have doubled the number of known bacterial groups.

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.

The scientists also conducted metabolic analyses of 36% 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. 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 species 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.