Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments

www.nature.com/scientificreports OPEN Received: 15 October 2018 Accepted: 1 March 2019 Published: xx xx xxxx Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments Qian Zhang1, Jacquelinne J. Acuña2,3, Nitza G. Inostroza2,3, María Luz Mora3, Sergio Radic4, Michael J. Sadowsky 1,5 & Milko A. Jorquera 2,3 Several studies have demonstrated the relevance of endophytic bacteria on the growth and fitness of agriculturally-relevant plants. To our knowledge, however, little information is available on the composition, diversity, and interaction of endophytic bacterial communities in plants struggling for existence in the extreme environments of Chile, such as the Atacama Desert (AD) and Patagonia (PAT). The main objective of the present study was to analyze and compare the composition of endophytic bacterial communities associated with roots and leaves of representative plants growing in Chilean extreme environments. The plants sampled were: Distichlis spicate and Pluchea absinthioides from the AD, and Gaultheria mucronata and Hieracium pilosella from PAT. The abundance and composition of their endophytic bacterial communities was determined by quantitative PCR and high–throughput sequencing of 16S rRNA, respectively. Results indicated that there was a greater abundance of 16S rRNA genes in plants from PAT (1013 to 1014 copies g−1 DNA), compared with those from AD (1010 to 1012 copies g−1 DNA). In the AD, a greater bacterial diversity, as estimated by Shannon index, was found in P. absinthioides, compared with D. spicata. In both ecosystems, the greater relative abundances of endophytes were mainly attributed to members of the phyla Proteobacteria (14% to 68%), Firmicutes (26% to 41%), Actinobacteria (6 to 23%) and Bacteroidetes (1% to 21%). Our observations revealed that most of operational taxonomic units (OTUs) were not shared between tissue samples of different plant species in both locations, suggesting the effect of the plant genotype (species) on the bacterial endophyte communities in Chilean extreme environments, where Bacillaceae and Enterobacteriacea could serve as keystone taxa as revealed our linear discriminant analysis. Numerous studies have revealed that bacteria living within plant tissues, collectively called endophytic bacteria, play a crucial role in the growth and fitness of a wide variety of monocot and dicot plant species, among others1,2. Beneficial functions attributed to endophytic bacteria include plant growth promotion by supplying nutrients (e.g., nitrogen fixation), protection against biotic- (e.g., pathogens) and abiotic-stresses (e.g., salinity and drought), detoxification of harmful compounds (e.g., NH3 or CN), and the production of bioactive compounds (e.g., secondary metabolites and hormones)3,4. Various endophytic microorganisms have been categorized as plant growth–promoting bacteria (PGPB) and they are currently used in the formulation of diverse bioproducts (e.g., biofertilizers and biofungicides) or to modify and/or introduce beneficial bacteria into the plant phytomicrobiome for agricultural purposes5,6. To date, however, many microbiome studies have been done using model 1 The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 551086106, USA. 2Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. 3Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. 4Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Ave. Bulnes 01855, Punta Arenas, Chile. 5Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA. Correspondence and requests for materials should be addressed to M.A.J. (email: milko. ) Scientific Reports | (2019) 9:4950 | https://doi.org/10.1038/s41598-019-41160-x 1 www.nature.com/scientificreports www.nature.com/scientificreports/ plant (e.g., Arabidopsis thaliana), commercially relevant plants for agriculture (e.g., wheat, soybean, rice, maize, etc.) and wild plant species (e.g., weeds and trees) grown under laboratory, greenhouse and fields conditions1,2,7,8. Consequently, we only have limited knowledge on the composition and interactions of microbiota and plants, especially endophytic bacterial communities, on native plant vegetation growing in extreme environments, such as hot and/or cold deserts. Thus, our understanding on microbial interactions in plant holobiont will be key in the develop of efficient strategies for native plant conservation and/or exploit the full yield potential of crop plants under climate change scenario9. The country of Chile is long (4,270 km) and narrow (mean width 177 km) and harbors a great variety of pristine ecosystems. The Atacama Desert (AD) is located in the northern region of Chile (from 18°24′S to 29°55′S) and is considered among the driest places on earth. In contrast, the Chilean Patagonia (from 41°08S to 56°30′S) is located in the far south of the country and is a sub Antarctic region. Both regions have extreme environments and their plant-associated bacterial communities have been barely studied thus far. In this context, we have reported that members of the orders Enterobacteriales, Actinomycetales, and Rhizobiales comprise dominant groups of the bacterial communities in the rhizosphere (the soil influenced by plant roots) of shrubs grown in AD and Patagonia (PAT), namely Atriplex sp. and Chuquiraga sp., respectively10. Results of this study also suggested that some isolates, belonging to the genera Enterobacteria, Pseudomonas, and Bacillus, were putative PGPB. The ability of the native isolates from AD to act as PGPB was confirmed by formulation and inoculation of a bacterial consortium onto plants. These studies revealed that wheat plants inoculated with the consortium produced greater biomass under water shortage and field conditions, compared with uninoculated seedlings11. A recent study also showed a greater protection against salt stress in wheat plants inoculated with rhizosphere bacteria isolated from Andean Altiplano native plant (Parastrephia quadrangularis) in AD12. However, these studies did not take into account the composition and interaction of native endophytic bacteria in Chilean extreme environments, as well as their potential use as PGPB. During the last several years, advances in high–throughput DNA sequencing (HTS) technologies (e.g., Illumina , PacBio and Oxford Nanopore ) have opened new windows into the microbial ecology of a variety of environments, allowing the detailed study of complex bacterial communities in nature as never seen before. Thus, H (...truncated)