Difficult-to-culture bacteria in the rhizosphere: The underexplored signature microbial groups
Section snippets
INTRODUCTION
Microbial biodiversity in terrestrial ecosystems potentially influences important ecophysiological processes because microbes play crucial roles in driving biogeochemical cycles. Soil harbors a complex microbial consortium with an abundant bacterial population. The complex below-ground plant-bacterial interactions, especially in the rhizosphere, are major determining factors of plant health and soil fertility. Rhizosphere bacteria that benefit plants through nitrogen fixation, phosphate
RHIZOSPHERE MICROBIAL COMMUNITIES
Soil is a complex, dynamic, and diverse environment populated with a plethora of diverse microbes that keep it healthy and productive. Rhizosphere soil is under the direct influence of plant roots and differs considerably from the bulk soil in terms of its physico-biochemical properties (Hinsinger, 1998) and associated microbial communities. The rhizosphere is home to a wide range of prokaryotic and eukaryotic taxa, of which bacteria and fungi comprise the most abundant groups (Buée et al., 2009
MISSED DIVERSITY: THE RARE BIOSPHERE AND MICROBIAL DARK MATTER
Novel or unrecognized bacterial taxa are present in low abundance within a microbial community and constitute the largely unexplored rare biosphere (Sogin et al., 2006; Lynch and Neufled, 2015; Bull and Goodfellow, 2019). Unprecedented access to this rare biosphere has been accomplished with the aid of amplicon-based 16S rRNA gene biodiversity studies, including pyrosequencing (Janssen, 2006; Jones et al., 2009; Shade et al., 2012) and Illumina sequencing (Bartram et al., 2011). Despite its
OVERVIEW OF CULTURE-DEPENDENT AND INDEPENDENT APPROACHES TO STUDY DIFFICULT-TO-CULTURE BACTERIA
Overmann et al. (2017) reviewed the techniques available for culturing difficult-to-culture bacterial phyla and predicted that such underexplored phyla could represent new and innovative research opportunities. Culture-dependent studies revealed that conventional cultivation media favor the growth of fast-growing bacteria, masking the growth of slow growers, including oligotrophs (Koch, 1997; Connon and Giovannoni, 2002); however, the use of dilute nutrient media has been successful in
INSIGHTS INTO THE ECOLOGICAL ROLES OF PREDOMINANT DIFFICULT-TO-CULTURE BACTERIAL PHYLA
Physiologic, genomic, and metagenomic studies provide evidence of the crucial roles played by difficult-to-culture bacterial phyla inhabiting the soil environment. Nutrient cycling is one of the most essential ecological processes in which microorganisms play a crucial role. Determining rhizospheric difficult-to-culture bacterial interactions and their dynamics within soil ecosystems is of high priority from an ecological perspective. The predominant difficult-to-culture bacterial phyla
DIFFICULT-TO-CULTURE BACTERIA AS POTENTIAL PGPR
The difficult-to-culture bacterial taxa have been widely reported from rhizosphere soils, suggesting that they may have PGP abilities (da Rocha et al., 2010a, b). As already stated, free-living soil bacteria that inhabit the rhizosphere and improve overall plant health, leading to augmented plant growth, are referred to as PGPR (Dutta and Podile, 2010; Goswami et al., 2016). The PGPR are considered to be important plant probiotics (Flores-Félix et al., 2015) as they increase crop yields, act as
CONCLUSIONS AND FUTURE CHALLENGES
The varied metabolic and ecophysiological functions of the difficult-to-culture bacterial phyla in soil open the scope to finding the bright side of microbial dark matter. Culture-dependent and -independent approaches together provide a holistic approach to the study of the soil microbial community, especially the difficult-to-culture phyla. As rhizosphere soils are a major reservoir of microbial consortia, more attention sensu stricto should be paid to the rhizospheric difficult-to-culture
CONTRIBUTION OF AUTHORS
Sadaf KALAM and Anirban BASU contributed equally to this work and shared the first authorship.
ACKNOWLEDGEMENTS
This work was supported by the Department of Science and Technology (DST), Government of India (GoI), in the form of DST-WOS-A Women Scientist Fellowship for Sadaf KALAM (Grant no. SR/WOS-A/LS-294/2012(G)) and in the form of J. C. Bose Fellowship for Appa Rao PODILE (Grant no. JCB/2017/000053). We gratefully acknowledge the DST-FIST level II and University Grants Commission Special Assistance Programme (UGC-SAP) support for the Department of Plant Sciences, School of Life Sciences, University
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