Source: School of Life Sciences
Edited by: Tan Rongyu, Wang Dongmei

Microbes are the most abundant and diverse cellular life forms on Earth and colonize a wide range of environmental niches. However, more than 99% of bacterial and archaeal species have not been obtained in pure culture and we have only glimpsed the surface of this mysterious microbial world. This is so-called Microbial Dark Matter (MDM): the enormous diversity of yet-uncultivated microbes that microbiologists can only study by using cultivation-independent techniques. Recently, a number of international projects have dramatically increased our understanding of the extent and distribution of microbial diversity; however, the functional diversity of MDM is still mysterious.

Recently, Wen-Jun Li’s group published a perspective paper “Microbial dark matter coming to light: challenges and opportunities” in National Science Review. This perspective addresses why MDM deserves scientific effort and illustrates challenges and opportunities in the future study of these enigmas. The authors mention that single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) obtained from single-cell genomic and metagenomic approaches, respectively, have become the most effective methods that enable organism-level genomic analysis of complex microbial ecosystems without the need for cultivation, which brings light to MDM. They outline three major challenges of MDM research: The first challenge is that communication about MDM is currently difficult because the taxonomy and nomenclature are unstable. The second challenge is that it remains very difficult to extrapolate functions from genomic information. The third challenge is that cultivation of MDM remains difficult. They advocate three approaches to promote future MDM research. First, large-scale investigations of MDM integrating various omics approaches are still needed to explore a variety of natural environments, especially extreme habitats, which will stretch our imaginations with regard to the taxonomic and functional diversity of microbial life. Second, researchers need to strengthen connections between species and their functions in situ. This can now be studied by integrating omics, FISH, MAR, NanoSIMS, Raman and heterologous expression techniques, which offer insights into mechanisms of species. Third, researchers need to establish and explore the new cultivation approaches guided by multi-omics information and network approaches, in order to test hypotheses and obtain enrichments or pure cultures. Further understanding of MDM requires a combination of many disciplines and multidimensional knowledge; they also highlight the need to establish MDM research centers to tackle these challenges in different ways, from developing research facilities and providing technical assistance, to training the next generation of scientists, and providing academic communication platforms.

The exploration of MDM is likely to open a magic box, in which a bag full of surprises could be displayed. The study of MDM is still in its infancy and further exploration of MDM will continue to provide unanticipated and exciting answers about the evolution and roles of MDM in nature. However, as a scientist, the wonderful things displayed by the ‘box’ are not the final answer of MDM research but rather a starting point for further exploration of ecological and evolutionary mechanisms.

Dr. Jian-Yu Jiao from the School of Life Sciences of Sun Yat-sen University is the first author of this perspective, and Prof. Wen-Jun Li is the corresponding author. Dr. En-Min Zhou (Current position: Assistant Professor at Yunnan University), Dr. Zheng-Shuang Hua (Current position: Research Professor at the University of Science and Technology of China), Dr. Bao-Zhu Fang (Current position: Associate Research Professor at the Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences), Dr. Nimaichand Salam, Dr. Lan Liu and Prof. Brian P. Hedlund (University of Nevada, Las Vegas) are the co-authors of this article. Sun Yat-sen University is the first unit to complete this achievement. This study was supported by National Natural Science Foundation of China (nos. 91951205, 31972856, 31850410475 and 31670009), Natural Science Foundation of Guangdong Province, China (no. 2016A030312003), Guangzhou Municipal People’s Livelihood Science and Technology Plan (no. 201803030030) and the US National Science Foundation (NSF DEB 1557042 and NSF DEB 1841658).

Link to the paper: https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa280/6027462