Contents lists available at ScienceDirect Applied Soil Ecology journal homepage: www.elsevier.com/locate/apsoil Review Plant growth promoting bacteria in agriculture: Two sides of a coin Wusirika Ramakrishna a, ⁎ , Radheshyam Yadav a , Kefeng Li b a Department of Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, India b School of Medicine, University of California, San Diego, CA 92103-8467, United States of America ARTICLE INFO Keywords: Plant growth promoting bacteria Microbial community Antibiotics resistance Omics ABSTRACT Plant growth promoting bacteria (PGPB) provide multiple benefits in agriculture by enhancing crop productivity and nutrient content and suppressing the growth of pathogens. Development of beneficial plant-microbe in- teractions based on genomics, transcriptomics, proteomics and metabolomic data of both PGPB and host will lead to optimized microbial inoculants for enhancing crop yield and nutrient content. PGPB are promoted as a green technology which will reduce the use of chemical fertilizers thereby improving soil health. Although a significant increase in the use of PGPB in agriculture was observed in the last two decades, there is a dearth of long-term studies addressing the effects of PGPB on existing microbial community structure. It is likely that most or all PGPB are resistant to common antibiotics used to treat human diseases. Antibiotic resistance of PGPB may be due to the presence of antibiotic resistance genes and intrinsic resistance due to the presence of efflux pumps. The biological significance of resistance to antibiotics and metals and their relation to plant growth promoting activity, if any, is not known. The consequences of harboring antibiotic resistance may be negative if the trait is transferred to other soil or environmental bacteria. Strategies to develop PGPB strains with useful traits of plant growth promotion but without resistance to common antibiotics used by humans, would enhance agricultural productivity without the negative effects on the environment. Alternately, harboring antibiotic resistance may be positive if it is due to intrinsic resistance involving proteins which also have other functions. Antibiotic resistance of PGPB may be an essential trait if it is related to their plant growth promoting activity. Overall, there is a need to conduct large-scale screening of PGPB for antibiotic resistance and long-term studies to see the effect of the introduction of biofertilizers on native soil microbial community. 1. Introduction Modern agriculture practices have sharply increased crop yields in the last 50 years, mainly resulting from the application of fertilizers, chemical pest control, irrigation, and development of hybrids. The in- tensive use of synthetic chemical fertilizers and pesticides in current agricultural practices created a range of environmental problems that include ground water contamination, soil quality degradation and biodiversity reduction (Tilman et al., 2001; Tilman et al., 2002; Diaz and Rosenberg, 2008). In addition, environmental factors such as drought, elevated temperature and CO 2 caused by the global climate change pose a growing threat to current agriculture (Ahuja et al., 2010). There is an increasing need for global crop production to meet the food, industrial processes and biofuel demands of our growing po- pulation, which will reach about 9 billion by 2050. Stimulated by the increasing demand, and the awareness of negative environmental and human health impact caused by current agriculture practices, world- wide agriculture is moving to a more sustainable and eco-friendly approach. Soil microorganisms as a component of soil ecosystem play an im- portant role in regulating soil fertility, nutrient cycling and maintaining plant diversity (Fitzsimons and Miller, 2010). Plant growth-promoting bacteria (PGPB) refer to free living bacteria in the soil and rhizobacteria that colonize root rhizosphere. The use of naturally occurring PGPB in sustainable agriculture has gained importance in the past decade due to their beneficial effects on soil and crop productivity. In addition to enhancing plant growth, PGPB help plants to cope with biotic and abiotic stresses. PGPB tend to harbor genes for antibiotic and metal resistance. Antibiotic resistance can be an intrinsic property or it can be acquired. Intrinsic resistance can be attributed to the presence of specific char- acteristics such as the presence of multidrug efflux pumps, which are involved in performing metabolic processes in bacteria. This is sup- ported by phylogenetic analysis of some genes involved in antibiotic resistance which suggest a long evolutionary history originating prior to the ‘antibiotic era’ (D'Costa et al., 2011; Van Goethem et al., 2018). https://doi.org/10.1016/j.apsoil.2019.02.019 Received 17 October 2018; Received in revised form 16 February 2019; Accepted 21 February 2019 ⁎ Corresponding author. E-mail addresses: rk.wusirika@cup.edu.in (W. Ramakrishna), kli@ucsd.edu (K. Li). Applied Soil Ecology xxx (xxxx) xxx–xxx 0929-1393/ © 2019 Elsevier B.V. All rights reserved. Please cite this article as: Wusirika Ramakrishna, Radheshyam Yadav and Kefeng Li, Applied Soil Ecology, https://doi.org/10.1016/j.apsoil.2019.02.019