Actinobacteria from the Atacama desert for promoting tomato growth under drought

Abstract

Actinobacteria are a large group of beneficial Gram-positive bacteria play an important role for promoting plant growth for sustainable agriculture. Desert, an extreme ecosystem, is known to harbour diverse actinobacteria with biotechnological potential. The worldwide agricultural products have been sharply decreased due to waste land conditions caused by global climate change, especially crop plants. The use of plant growth promoting bacteria is one alternative for sustainable agriculture and food security through plant-microbe interactions. The arid environment of desert offers an underexplored resource for diverse actinobacteria with high level of drought tolerance and potential plant growth promoting activities. This project aims to investigate unique actinobacteria from the Atacama Desert with potential plant growth promoting properties under drought condition. Three soil samples were collected from the Atacama Desert, including Aguas Calientes (AC3), Lomas Bayas (LB3) and Yungay (Y6, CAB0). Nine isolates from AC3 were assigned to 2 multi- and 3 single-membered colour-groups. The 34 strains from LB 3 were assigned to 7 multi- and 2 single-membered colour-groups, while 240 strains from Y6 were assigned to 31 multi- and 33 single-membered colour-groups. The 53 representatives isolated from were belonging to 24 validly named species, 13 genera, including Blastococcus, Brevibacterium, Geodermatophilus, Kocuria, Lentzea, Modestobacter, Microbacterium, Micromonospora, Nocardioides, Pseudonocardia, Rhodococcus, Streptomyces and Tsukamurella. Comparative 16S rRNA sequencing studies showed 5 representatives from the Atacama Desert shared 16S similarity values below 98.7%, a threshold for establishing new species of Blastotoccus, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces. Six beneficial plant growth-promoting traits were evaluated for: indole-3-acetic acid (IAA) production, phosphate solubilization, siderophore production, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, nitrogen fixation and drought tolerant ability. Most strains displayed in vitro PGP capabilities with different proportions. All desert isolates were grown below the aw of 0.919, considered as drought-tolerant. It is surprising that Micromonospora chalcea strain 66-1 was able to survive in drought treated soil based on growth observation in soil, despite the fact that PGP traits were negatively influenced by drought stress. The adaption of actinobacteria to desert lifestyle was supported by genomic analysis, revealed that Amycolatopsis vastitatis strain H5T, Micromonospora chalcea strain 66-1, Modestobacter caceresii strain KNN 45-2bT from the Atacama Desert contains substantial genes related to plant growth promotion and stress response. Amycolatopsis vastitatis strain H5T and Modestobacter caceresii KNN 45-2bT were selected and used as bioinoculants to promote growth of tomato (Lycopersicum esculentum Mill.) under drought conditions. Both strains successfully increased tomato growth as observed from the morphological features such as root length, total fresh and dry weight, fruit weight, and biochemical characteristics such as proline accumulation and total soluble sugar content in the greenhouse trial with drought treatment. To minimize the negative effects of reactive oxygen species (ROS), the accumulation of hydrogen peroxide was reduced with the inoculation of actinobacteria under drought condition. Hence, these results provide supporting evidence that diverse actinobacteria in the Atacama Desert have plant growth promoting activities. They offer potential resources as plant growth promoter for sustainable agriculture, especially in arid land or water deficit areas which are increasingly affected by climate change.