Recent progress on the community structure, assembly and functions of rhizosphere microbiome
Author:   Source: Research Institute of subtropical Forestry  Time: 2016-09-14

More than 100 years of research suggests that in natural ecosystems, most plants are symbiotic with fungal endophytes, which can in turn regulate the host phenotype (plant growth and stress). From an ecological perspective, the plant microbiome is considered a second plant genome (also called the pan-genome) with the capacity to enhance host health and stress tolerance. Mycorrhizal fungal and root nodule symbiosis have been widely recognized, however, the complexity of root-associated microbes indicates that diverse types of root-microbial symbiotic relationships may exist. As a step in this direction, Dr. Zhilin Yuan, a researcher from Chinese Academy of Forestry and his group has addressed the community structure and ecological significances of endophytes.

First at all, they found that the dark septate endophytes (DSEs) are frequently found in extreme environments and act as a new groupf of root symbioticfungi, including Harpophora oryzae, Montagnulacea sp. and Curvularia sp. Based on the colonization pattern, plant- fungal co-cultivation and inoculation under saline condition, DSEs are believed to play an important role to help plants adapt to stressful environments. Interestingly, a mechanism of nitrogen-status dependent effects on plant growth was found in the plant-DSEs symbiosis. DSEs can only significantly promote plant growth when organic nitrogen is supplied, suggesting that these fungi can readily utilize organic nitrogen and mineralize it inorganic nitrogen, which is easily accessible for plant uptake. As the excessive use of inorganic nitrogen poses a great threat to natural ecosystems and tree and crop yields, our findings underscore the enormous potentials for utilizing organic N mineralizing microbes in sustainable forestry and agriculture. Furthermore, a DSE from rhizosphere can even transfer to the above-ground parts of plant and become the dominant endophyte of seeds. Inoculation test revealed its role in improving host seed germination rate and enhancing growth of non-host trees. These insights indirectly suggest that rhizosphere microbiome has a remote control in plant growth and reproduction.

Root microbiota is a crucial determinant of plant productivity and stress tolerance. They further revealed the microbial structure, assembly and functions of a halophyte microbiota based on pyrosequencing approach. Results supported the evidence that the superior halo-tolerance of seepweed Suaeda salsa was tightly linked to a specialized below-ground microbiome. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity. Moreover, they argued that reconstruction of the synthetic microbial communities (SMCs) or pan-SMC will be an important strategy to develop novel microbial agents. In addition, they established two-step nested PCR to detect the endophytic fungal ITS sequences from plant tissues efficiently, which greatly reduced the non-specific amplification.

These results have been published in Scientific Reports (doi: 10.1038/srep32467), Biotechnology Advances (doi: 10.1016/j.biotechadv.2016.08.005), Fungal Ecology (doi: 10.1016/j.funeco.2016.08.011). Two national invention patents (ZL201410045895.0, ZL201410045774.6) and one utility model patent (ZL201520638815.2) have also been authorized. This work was financially supported by the Non-Profit Sector Special Research Fund of the Chinese Academy of Forestry (RISF2013005), the National Natural Science Foundation of China (No. 31370704) and the Programme of Introducing Talents of State Forestry Administration (20140327017).