Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome?

Author:

Davies Tarryn1ORCID,Cando‐Dumancela Christian1ORCID,Liddicoat Craig1ORCID,Dresken Romy2,Damen Rudolf H.13,Edwards Robert A.1ORCID,Ramesh Sunita A.1ORCID,Breed Martin F.1ORCID

Affiliation:

1. College of Science and Engineering Flinders University Bedford Park South Australia Australia

2. School of Biological Sciences and the Environment Institute University of Adelaide Adelaide South Australia Australia

3. HAN University of Applied Sciences Nijmegen Netherlands

Abstract

AbstractSoil microbiota underpin ecosystem functionality yet are rarely targeted during ecosystem restoration. Soil microbiota recovery following native plant revegetation can take years to decades, while the effectiveness of soil inoculation treatments on microbiomes remains poorly explored. Therefore, innovative restoration treatments that target soil microbiota represent an opportunity to accelerate restoration outcomes. Here, we introduce the concept of ecological phage therapy—the application of phage for the targeted reduction of the most abundant and dominant bacterial taxa present in degraded ecosystems. We propose that naturally occurring bacteriophages—viruses that infect bacteria—could help rapidly shift soil microbiota towards target communities. Bacteriophages sculpt the microbiome by lysis of specific bacteria, and if followed by the addition of reference soil microbiota, such treatments could facilitate rapid reshaping of soil microbiota. Here, we experimentally tested this concept in a pilot study. We collected five replicate pre‐treatment degraded soil samples, then three replicate soil samples 48 hours after phage, bacteria, and control treatments. Bacterial 16S rDNA sequencing showed that phage‐treated soils had reduced bacterial diversity; however, when we combined ecological phage therapy with reference soil inoculation, we did not see a shift in soil bacterial community composition from degraded soil towards a reference‐like community. Our pilot study provides early evidence that ecological phage therapy could help accelerate the reshaping of soil microbiota with the ultimate aim of reducing timeframes for ecosystem recovery. We recommend the next steps for ecological phage therapy be (a) developing appropriate risk assessment and management frameworks, and (b) focussing research effort on its practical application to maximise its accessibility to restoration practitioners.

Publisher

Wiley

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