Cultivation may not dramatically alter rhizobial community diversity or structure associated with rooibos tea (Aspalathus linearis Burm.f.) in South Africa

Abstract

Rooibos tea, Aspalathus linearis (Burm.f.), represents one of South Africa's most important indigenous crops, and monotypic plantations are rapidly replacing wild populations. Dwindling wild rooibos populations may drastically reduce possible, but hitherto overlooked, natural resources to bolster commercial productivity and long-term sustainability. Here, using next generation sequencing data, we seek to determine whether cultivation impacts on the diversity and community structure of mutualistic nitrogen fixing bacteria (rhizobia) associated with rooibos plants. We do this by generating operational taxonomic units (OTUs) from nodulation (nodC) and nitrogenase (nifH) DNA sequence data from rhizobia within root nodules of rooibos plants from cultivated and wild populations. For these rhizobial communities we found significant differences for various OTU diversity metrics due to geography (site), the interaction between site and status (cultivated vs. wild), but not for status. We also sequenced nodC soil microbiomes and found evidence for compositional differences in soil rhizobial communities due to geography, status (cultivated vs. wild), and the interaction between geography and status. Our data adds to existing evidence suggesting that tea cultivation in South Africa may have limited impacts on soil microbial community diversity and structure, and that such changes are mainly driven by larger geographic processes rather than human-mediated disturbances such as cultivation.