Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

Staley et al. Microbiome (2017) 5:65 DOI 10.1186/s40168-017-0287-1 RESEARCH Open Access Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism Christopher Staley1, Abigail P. Ferrieri2, Malak M. Tfaily2, Yaya Cui3, Rosalie K. Chu2, Ping Wang1, Jared B. Shaw2, Charles K. Ansong4, Heather Brewer2, Angela D. Norbeck2, Meng Markillie2, Fernanda do Amaral3, Thalita Tuleski3, Tomás Pellizzaro3, Beverly Agtuca3, Richard Ferrieri5, Susannah G. Tringe6, Ljiljana Paša-Tolić2*†, Gary Stacey3† and Michael J. Sadowsky1*† Abstract Background: The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community. Microbial communities associated with Brachypodium distachyon (BD21) were also evaluated. Results: Significantly different bacterial community structures (P = 0.031) were observed in the rhizosphere of wild-type plants between light and dark cycle samples. Furthermore, 13% of the community showed cycling, with abundances of several families, including Burkholderiaceae, Rhodospirillaceae, Planctomycetaceae, and Gaiellaceae, exhibiting fluctuation in abundances relative to the light cycle. However, limited-to-no cycling was observed in the acyclic CCAox34 line or in soil controls. Significant cycling was also observed, to a lesser extent, in Brachypodium. Functional gene inference revealed that genes involved in carbohydrate metabolism were likely more abundant in near-dawn, dark samples. Additionally, the composition of organic matter in the rhizosphere showed a significant variation between dark and light cycles. Conclusions: The results of this study suggest that the rhizosphere bacterial community is regulated, to some extent, by the circadian clock and is likely influenced by, and exerts influences, on plant metabolism and productivity. The timing of bacterial cycling in relation to that of Arabidopsis further suggests that diurnal dynamics influence plant-microbe carbon metabolism and exchange. Equally important, our results suggest that previous studies done without relevance to time of day may need to be reevaluated with regard to the impact of diurnal cycles on the rhizosphere microbial community. Keywords: Bacterial community structure, Diurnal rhythm, Rhizosphere, Arabidopsis * Correspondence: ; † Equal contributors 2 Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA 1 BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave, Saint Paul, MN 55108, USA Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Staley et al. Microbiome (2017) 5:65 Background The plant rhizosphere contains a complex microbial community that directly impacts plant growth, health, and development [1]. The rhizosphere bacterial community composition is predominantly determined by the soil community, and associated environmental factors (e.g., climate), but is also influenced to some extent by plant host genotype [2, 3]. Relative to bulk soil, a “rhizosphere effect” results in a plant-root-associated microbial community that is more numerous and shows greater metabolic activity that is shaped by exudation of carbon and other metabolites from the plant root [4]. Thus, mutations in genes related to plant nutrient metabolism may in turn influence the rhizosphere microbial community, with implications for plant growth and health [5]. Furthermore, manipulation of host-associated microbial communities is receiving increasing attention as a biological mechanism to improve plant growth and stress resistance [6]. Important to the determination of what constitutes a beneficial microbial community is the characterization of how diverse soil bacteria interact with host plant species [7]. The rhizosphere effect that exerts some control on the rhizosphere community composition is mediated by metabolic exchange between the roots and soil [4]. The partitioning of nutrients to the roots and their exchange with the soil environment is controlled by the response of plants to environmental signals, such as light and temperature [8]. These responses are modulated by a plant’s innate ability to estimate time within an approximately 24-h period and synchronize biological events via the circadian clock [8]. The importance of light in shaping the outcome of host-microbe interactions is becoming increasingly evident. Recent studies show that the intestinal microbiota of humans [9] and mice [10, 11] undergo diurnal oscillations under the control of host feeding time and diet, and silencing of a host’s molecular clock genes causes gut dysbiosis [12]. The circadian clock is an important regulator of numerous basic plant functions including central carbon metabolism [13], gene expression, stomatal function, and the timing component of photoperiodism, which regulates seasonal reproduction [14, 15]. The clock is also subject to extensive natural variation both within and between species, and this is reported to influence plant fitness and performance [16–20]. As a result, the circadian clock is considered a key regulator of plant physiology and adaptation to different geographic environments, enabling an organism to anticipate periodic environmental changes and adapt its physiological and developmental states accordingly [8, 21]. Indeed, the life cycles of pathogens are closely associated with diurnally regulated host plant metabolism, and the circadian clock has been suggested to contribute to enhanced plant Page 2 of 13 fitness by balancing innate immune responses with cellular metabolism [22, 23]. In Arabidopsis, the circadian clock consists of a series of intertwined feedback loops, regulated both transcriptionally and post-transcriptionally, through posttranslational modification and protein turnover [8]. This mechanism appears to be c (...truncated)