Abstract:
Increasing livestock densities and more severe drought events challenge sustainable
management in South Africa’s semi-arid savannas. Effective mitigation strategies require
accurate assessments of livestock foraging behaviour. By utilising high-throughput
sequencing technology, this study evaluated the use of a dual-locus metabarcoding
approach (trnL and rbcL) together with study-area-specific reference libraries, to analyse
cattle diets in two bioregions of the eastern semi-arid South African savanna. Both
markers demonstrated the ability to identify various plant families, but trnL exhibited a
higher diversity in terms of family and genus identification at both sampling sites. Forbs,
although comprising a diverse component of savanna plant communities, have relatively
small above-ground biomass, but can still serve as crucial forage items, especially
during dry periods. Our study underscores the significant role of forbs in cattle diets,
demonstrating a shift in cattle foraging preferences from grass-based diets to higher
inclusions of forbs and woody taxa during the drier season. Although grasses, such as
Setaria, were still prevalent, forbs, belonging to the genera Malvastrum, Asparagus, Pollichia
and Ipomoea were also important food items for cattle as well as woody taxa belonging to
Fabaceae, Combretaceae, Ebenaceae, and Malvaceae with a selection of food items from
trees and shrubs from genera Albizia, Combretum, Euclea and Vachellia. Furthermore, our
study highlights the value of a dual-locus metabarcoding approach for understanding
herbivorous diets. Using trnL and rbcL markers, with study-area-specific reference
libraries, improves taxonomic resolution for accurately reconstructing cattle diets in semiarid savannas. This study may improve biodiversity estimates and inform sustainable
rangeland management strategies in semi-arid African savanna ecosystems.
Description:
DATA AVAILABILITY STATEMENT: All of the data that support the findings of this study are available in the main text or Supplementary Information.
SUPPLEMENTARY MATERIAL 1 : The sequences of the forward and reverse primers of the barcodes with their Illumina overhang adapters amplified from herbivorous faeces in this study.
SUPPLEMENTARY MATERIAL 2 : Overview of the main steps followed in the materials and methods section for the mock community analysis conducted in Botha (2023). Explanation note: * An external quality filter was added to the VSEARCH approach since this workflow does not incorporate one in its various steps. ** “OTU” in this diagram may refer to operational taxonomic units as retrieved from the clustering of sequences based on 97% similarity in the VSEARCH approach, amplicon sequence variants retrieved by the inference of an error model in the DADA2 approach or grouping of strictly identical sequences as in the OBITOOLS approach.
SUPPLEMENTARY MATERIAL 3 : Bar plots generated from the taxonomic assignments of the Welverdiend rbcL (rbcL_WV) and trnL dataset (trnL_WV). Explanation note: Bar plots generated from the taxonomic assignments of the Welverdiend rbcL (rbcL_WV) and trnL dataset (trnL_WV) showing the absolute abundance of reads assigned to families (A and B) and genera (C and D) identified as well as the proportions of unassigned reads.
SUPPLEMENTARY MATERIAL 4 : Bar plots generated from the taxonomic assignments of the Syferkuil rbcL (rbcL_SK) and trnL dataset (trnL_SK). Explanation note: Bar plots generated from the taxonomic assignments of the Syferkuil rbcL (rbcL_SK) and trnL dataset (trnL_SK) showing the absolute abundance of reads assigned to families (A and B) and genera (C and D) identified as well as the proportions of unassigned reads.
