The unsung hero in our living environment is the soil. It nourishes crops, provides food for humans, discharges rainwater into aquifers and serves as a habitat for various organisms. At the micro level, the soil is full of microorganisms such as fungi and bacteria, which cooperate with plants. Although it is an important element of our survival, people know little about what is under the earth's surface.
In the new study, scientists from the Pacific Northwest National Laboratory (PNNL) used bioinformatics and deep sequencing to detect soil viruses and better understand their role on earth. These viruses are believed to play a key role in the maintenance of microbial populations.
"Viruses are very abundant in nature," said Janet Jansson, chief scientist in charge of biology and researcher at PNNL laboratory. "Because there are so many viruses in each soil sample, identifying different viruses has become a challenge."
Jansson worked with Ruonan Wu, a computational scientist at PNNL's Department of Biosciences, and Kirsten hofmackel, head of the geoscientist and microbiome science team, to address this challenge.
Together with collaborators from Washington State University, Oregon University of health and science, Iowa State University and the Environmental Molecular Science Laboratory (PNNL's Department of energy science office user facility), PNNL scientists collected soil samples from grasslands in Washington, Iowa and Kansas and began in-depth research on soil composition. They found previously unknown soil viruses by using the large-scale DNA sequencing capability of the Joint Genome Institute, the computing capability of the national energy research scientific computing center and the multi omics expertise of EMSL. Their results were published in mbio and communication biology.
Janet Jansson Ruonan Wu and Kirsten hofmackel
Different viruses in different climates
Because the rainfall varies from place to place, the scientists chose Washington, Iowa and Kansas as as their soil samples. Eastern Washington is much drier than Iowa, while Kansas is somewhere in between in terms of soil moisture.
"We chose to take samples from places with different soil moisture to see if it would affect the type and number of viruses there. Wetter soil contains more bacteria, and many soil viruses infect bacteria," Wu said
Scientists have noticed that some viruses are much more abundant in dry soil than in wet soil. In dry climates, there are often fewer but more diverse microorganisms in the soil. The relative scarcity of bacterial hosts means that it is in the best interests of the virus to maintain the vitality of the host.
The researchers also found that in dry soil, viruses are more likely to contain special genes, which may be transferred to their bacterial hosts.
"These genes have the potential to confer 'super powers' on their bacterial hosts," Jansson said These viral genes can be passed on to their bacterial hosts to help them survive in dry soil.
Although more research is needed to better understand the role of these specific viral genes, the possibility of their usefulness to bacteria living in soil is exciting. These genes may be useful to bacteria, increasing their ability to recover carbon, thereby improving soil health.
This work is supported by the biological and environmental research project of the office of science of the United States Department of energy. This is the contribution of "phenotypic response of soil microbiome to environmental disturbance". Part of the study was completed by EMSL, the Joint Genome Institute and the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory.