New Tool for Tracking Bathyarchaeota in Marine Sediments

The Bathyarchaeota are a widespread and abundant group of Archaea commonly found in marine sediments. Researchers suspect that they play an important role in carbon cycling, but the details of their activities have thus far remained elusive. Scientists cannot, as yet, culture Bathyarchaeota in the lab, and their incredibly small size makes them difficult to visualize under the microscope.

In a new paper in Environmental Microbiology Reports [1] Fengping Wang (Shanghai Jiao Tong University, China) and colleagues, report an improved method for detecting and quantifying Bathyarchaeota in the environment. They demonstrated that their method detects a wider variety of Bathyarchaeota subgroups than previously possible and that it can help uncover relationships between abundance and environmental conditions. Wang is a member of the Deep Life Community and Scientific Steering Committee. This work is part of a DCO-supported pilot project to understand the Archaea playing significant roles in carbon cycling in marine sediments.

Wang first became interested in Bathyarchaeota more than 15 years ago. In the early 2000s, when researchers first began finding their DNA in marine sediments, lakes, and salt marshes, no one knew the identity or function of these organisms. By sequencing the DNA of these microbes and comparing the sequences to other Archaea, Wang’s group determined that they constitute their own novel phylum. In 2014, they named them Bathyarchaeota because “Bathy” means “deep” in Greek, and the cells live in deep marine sediments.

In the new study, Wang and colleagues tested out primers that they specially designed based on the latest Bathyarchaeota sequencing data. Primers are short segments of DNA that bind to specific sequences in the genome. Sets of primers customized to different organisms are used to copy and detect DNA in environmental samples, and are therefore one way of figuring out where microscopic organisms live. They offer a snapshot of which organisms live in an ecosystem and how numerous they are.

“We can now use this tool to quantify Bathyarchaeota,” said Wang. “Hopefully through this and together with other methods, we can know more of their ecological functions in the environment and meanwhile, bring them into lab culture to better understand them.”

The researchers used their new primers to quantify Bathyarchaeota abundance at different depths from two sediment cores from the South China Sea. The new primers successfully picked up certain subgroups that previous primer sets could not adequately detect. The authors also considered carbon content along the core samples, and for the first time, showed directly that Bathyarchaeotal abundance correlates with organic carbon levels in marine sediments.

These findings “suggest that those Bathyarchaeota in the South China Sea sediments are heterotrophic,” said Wang. “They are probably eating the organic carbon in marine sediments.”

With these accurate detection methods in place, Wang’s group aims to quantify Bathyarchaeota in different habitats and depths to better understand their metabolic roles in the environment. The new primers also will enable the researchers to pinpoint the conditions that Bathyarchaeota need to live so they can culture these supposedly “unculturable” organisms in the lab.

Ultimately, this work will uncover details of Bathyarchaeota’s physiological functions and yield greater understanding of how these abundant Archaea are involved in carbon cycling in deep marine sediments.

Reference:

1. Yu T, Liang Q, Niu M, Wang F (2017) High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers. Environmental Microbiology Reports doi: 10.1111/1758-2229.12539