Emerging microbiome technologies for sustainable increase in farm productivity and environmental security
Brajesh K Singh A B E , Pankaj Trivedi C , Saurabh Singh D , Catriona A Macdonald A and Jay Prakash Verma A D
+ Author Affiliations
- Author Affiliations
A Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
B Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
C Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
D Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi-221005, U.P. India
E Tel: +61 2 4570 1329, Email: b.singh@westernsydney.edu.au
Microbiology Australia 39(1) 17-23 https://doi.org/10.1071/MA18006
Published: 21 February 2018
Abstract
Farming systems are under pressure to sustainably increase productivity to meet demand for food and fibre for a growing global population under shrinking arable lands and changing climatic conditions. Furthermore, conventional farming has led to declines in soil fertility and, in some cases, inappropriate and excessive use of chemical fertilisers and pesticides has caused soil degradation, negatively impacting human and environmental health. The soil and plant microbiomes are significant determinants of plant fitness and productivity. Microbes are also the main drivers of global biogeochemical cycles and thus key to sustainable agriculture. There is increasing evidence that with development of appropriate technologies, the plant microbiome can be harnessed to potentially decrease the frequency of plant diseases, increase resource use efficiencies and ultimately enhance agricultural productivity, while simultaneously decreasing the input of chemical fertilisers and pesticides, resulting in reduced greenhouse gas emissions and promoting environmental sustainability. However, to successfully translate potential to practical outcomes, both fundamental and applied research are needed to overcome current constraints. Research efforts need to be embedded in industrial requirements and policy and social frameworks to expedite the process of innovation, commercialisation and adoption. We propose that learning from the advancement in the human microbiome can significantly expedite the discovery and innovation of effective microbial products for sustainable and productive farming. This article summarises the emergence of microbiome technologies for the agriculture industry and how to facilitate the development and adoption of environmentally friendly microbiome technologies for sustainable increase in farm productivity.
References
[1] Singh, B.K. and Trivedi, P. (2017) Microbiome and the future for food and nutrient security. Microb. Biotechnol. 10, 50–53.| Microbiome and the future for food and nutrient security.Crossref | GoogleScholarGoogle Scholar |
[2] Trivedi, P. et al. (2017) Tiny microbes, big yields: enhancing food crop production with biological solutions. Microb. Biotechnol. 10, 999–1003.
| Tiny microbes, big yields: enhancing food crop production with biological solutions.Crossref | GoogleScholarGoogle Scholar |
[3] Mendes, R. et al. (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663.
| The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhsVSqtLrP&md5=6526bb0d00524382d13846cc526cbab2CAS |
[4] Leach, J.E. et al. (2017) Communication in the phytobiome. Cell 169, 587–596.
| Communication in the phytobiome.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2sXnt1Cmsb8%3D&md5=e1afc132f5dfe69ee7c9fcffbcfd71aaCAS |
[5] Berg, G. et al. (2016) The plant microbiome explored: implications for experimental botany. J. Exp. Bot. 67, 995–1002.
| The plant microbiome explored: implications for experimental botany.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28Xhs1Oqtb3I&md5=aed1a25870693cdcfe93a29abf954aeeCAS |
[6] Lemanceau, P. et al. (2017) Let the core microbiota be functional. Trends Plant Sci. 22, 583–595.
| Let the core microbiota be functional.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2sXnsl2gu7k%3D&md5=01deb7553fdd1e80a859776784348407CAS |
[7] Hamonts, K. et al. (2018) Field study reveals core plant microbiota and relative importance of their drivers. Environ. Microbiol. , .
| Field study reveals core plant microbiota and relative importance of their drivers.Crossref | GoogleScholarGoogle Scholar |
[8] Peiffer, J.A. et al. (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl. Acad. Sci. USA 110, 6548–6553.
| Diversity and heritability of the maize rhizosphere microbiome under field conditions.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXnvVOlu7o%3D&md5=41704d798641490428fbfbcd21f09cb9CAS |
[9] Edwards, J. et al. (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. USA 112, E911–E920.
| Structure, variation, and assembly of the root-associated microbiomes of rice.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXhtFKhsbw%3D&md5=2a397048da354667302daeabde30c240CAS |
[10] Vandenkoornhuyse, P. et al. (2015) The importance of the microbiome of the plant holobiont. New Phytol. 206, 1196–1206.
| The importance of the microbiome of the plant holobiont.Crossref | GoogleScholarGoogle Scholar |
[11] Agler, M.T. et al. (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 14, e1002352.
| Microbial hub taxa link host and abiotic factors to plant microbiome variation.Crossref | GoogleScholarGoogle Scholar |
[12] Trivedi, P. et al. (2017) Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Soil Biol. Biochem. 111, 10–14.
| Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2sXlsVCitbY%3D&md5=4a87a80e0e3c3aea273cdc1d8c3a46ecCAS |
[13] Singh, B.K. and Macdonald, C.A. (2010) Drug discovery from uncultivable microbes. Drug Discov. Today 15, 792–799.
| Drug discovery from uncultivable microbes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhtFCrurfN&md5=49709402aecb99e4708a58b2cac3463dCAS |
[14] Zmora, N. et al. (2016) Taking it personally: personalised utilization of the human microbiome in health and disease. Cell Host Microbe 19, 12–20.
| Taking it personally: personalised utilization of the human microbiome in health and disease.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhvFCltA%3D%3D&md5=a5603261adb6141f7bd6b5c28d2f5fd5CAS |
[15] Lagier, J.-C. et al. (2015) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin. Microbiol. Rev. 28, 237–264.
| The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.Crossref | GoogleScholarGoogle Scholar |
[16] Dong, B. et al. (2016) Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast. Proc. Natl. Acad. Sci. USA 113, 9716–9721.
| Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhtlGmtrfF&md5=44a0c0a4407d8c9e3e59711c2eec0e8eCAS |
[17] Nichols, D. et al. (2008) Short peptide induces an ‘uncultivable’ microorganism to grow in vitro. Appl. Environ. Microbiol. 74, 4889–4897.
| Short peptide induces an ‘uncultivable’ microorganism to grow in vitro.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXpslKktLc%3D&md5=b33b4d18e04c9eefd9462cfb47ca0145CAS |
[18] Garza, D.R. and Dutilh, B.E. (2015) From cultured to uncultured genome sequences: metagenomics and modelling microbial ecosystems. Cell. Mol. Life Sci. 72, 4287–4308.
| From cultured to uncultured genome sequences: metagenomics and modelling microbial ecosystems.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXhtlSntbzN&md5=556e9f308d1b1fdade401795b03478e1CAS |
[19] Bai, Y. et al. (2015) Functional overlap of the arabidopsis leaf and root microbiota. Nature 528, 364–369.
| Functional overlap of the arabidopsis leaf and root microbiota.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXhvFemsbjL&md5=004aa48fa95e00231358a2b44f3cdc37CAS |
[20] Mitter, B. et al. (2017) A new approach to modify plant microbiomes and traits by introducing beneficial bacteria at flowering into progeny seeds. Front. Microbiol. 8, 11.
| A new approach to modify plant microbiomes and traits by introducing beneficial bacteria at flowering into progeny seeds.Crossref | GoogleScholarGoogle Scholar |
[21] Wallenstein, M.D. (2017) Managing and manipulating the rhizosphere microbiome for plant health. A systems approach. Rhizosphere 3, 230–232.
| Managing and manipulating the rhizosphere microbiome for plant health. A systems approach.Crossref | GoogleScholarGoogle Scholar |
[22] Macdonald, C. and Singh, B. (2014) Harnessing plant-microbe interactions for enhancing farm productivity. Bioengineered 5, 5–9.
| Harnessing plant-microbe interactions for enhancing farm productivity.Crossref | GoogleScholarGoogle Scholar |
[23] Zysko, A. et al. (2012) Transcriptional response of Pseudomonas aeruginosa to a phosphate-deficient Lolium perenne rhizosphere. Plant Soil 359, 25–44.
| Transcriptional response of Pseudomonas aeruginosa to a phosphate-deficient Lolium perenne rhizosphere.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhtlGnu7fL&md5=6cc46ecb75b2af5c40f328ab68442408CAS |
[24] Sweeney, C. et al. (2017) Interplant aboveground signalling prompts upregulation of auxin promoter and malate transporter as part of defensive response in the neighbouring plants. Front. Plant Sci. 8, 595.
| Interplant aboveground signalling prompts upregulation of auxin promoter and malate transporter as part of defensive response in the neighbouring plants.Crossref | GoogleScholarGoogle Scholar |
[25] Sheth, R.U. et al. (2016) Manipulating bacterial communities by in situ microbiome engineering. Trends Genet. 32, 189–200.
| Manipulating bacterial communities by in situ microbiome engineering.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XitlSgtbw%3D&md5=5c627b40e940984b0ae0fd748c736b4dCAS |
[26] Liu, S. et al. (2016) The host shapes the gut microbiota via fecal microRNA. Cell Host Microbe 19, 32–43.
| The host shapes the gut microbiota via fecal microRNA.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XhvFClug%3D%3D&md5=89e910a45f9742ca108b029fba1abd0fCAS |
[27] Massalha, H. et al. (2017) Live imaging of root-bacteria interactions in microfluidics setup. Proc. Natl. Acad. Sci. USA 114, 4549–4554.
| Live imaging of root-bacteria interactions in microfluidics setup.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2sXkvF2itbg%3D&md5=51f92bda5b068957d1ee7453b7efc562CAS |
[28] Jobin, C. (2018) Precision medicine using microbiota Science 359, 32–34.
| Precision medicine using microbiotaCrossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC1cXhtFCntL0%3D&md5=af2d34d655b4026b6ecbc78bdbba1209CAS |
[29] Routy, B. et al. (2018) Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science 359, 91–97.
| Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC1cXjslOrsw%3D%3D&md5=50306a80435249932a286040fe3bf0cbCAS |
[30] Harris, V.C. et al. (2017) The intestinal microbiome in infectious diseases: the clinical relevance of a rapidly emerging field. Open Forum Infect. Dis. 4, ofx144.
| The intestinal microbiome in infectious diseases: the clinical relevance of a rapidly emerging field.Crossref | GoogleScholarGoogle Scholar |
