Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants

Abstract

Over the past several decades, we have come to appreciate that healthy plants host, within and on the surfaces of their tissues, endophytic and epiphytic fungi and bacteria that do not cause disease. Individual species (typically endophytes) of plants have been found to fall largely into one or more of three major functional groups: 1) Microbes that alleviate abiotic stress of the host; 2) Microbes that defend hosts from biotic stress (pathogens and herbivores); and 3) Microbes that support the host nutritionally through increased nitrogen, phosphorus, iron, etc. This functional aspect of plant microbiomes raises the potential to design and construct microbiomes for crop plants in order to enhance their cultivation with reduced agrochemical inputs and at lower cost. In order to design and construct functional microbiomes, we must first develop an understanding of the mechanisms by which plant microbiomes function. Examples of hypotheses for the abiotic stress tolerance mechanism include: 1) Oxidative stress protection by increased production of antioxidants produced either by the microbes or by hosts in response to microbes; 2) Ethylene reduction by production of ACC deaminase; and 3) Ammonia or ammonium detoxification and consequent oxidative stress avoidance. Mechanisms to explain biotic stress resistance generally include production of anti-herbivore or anti-pathogen defensive compounds by the microbe or by the host in response to the microbe (i.e., induced systemic resistance). Examples of hypothesized mechanisms to explain microbe-mediated enhanced plant growth include: 1) Stimulation of plant growth due to growth regulator production by microbes; 2) Increased absorption of nutrients by plants from the rhizosphere due to activities of microbes on roots; and 3) Increased supply of nitrogen obtained directly from diazotrophic microbes in plants. Factors by which plant endophyte communities are regulated are hypothesized to involve host-produced compounds that modify behavior of endophytic microbes, often reducing growth rates and suppressing pathogenic behaviors. These behavior-modifying compounds are proposed to include phenolic acids, quorum quenching compounds, and perhaps other secondary metabolites.