Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

Abstract

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.

The Nexus between Fire and Soil Bacterial Diversity in the African Miombo Woodlands of Niassa Special Reserve, Mozambique

“…Altogether, these results have shown that the bacterial diversity in the Miombo rhizosphere is highly diverse, and apparently more conserved within oxi-soils (O). These contrast with a similar study performed in another important savanna ecosystem, the Mopane woodlands [ 9 ], where the rhizobacteria were found to be less abundant (700–800 OTUs vs ca. 1000–1200) and less diverse (Shannon H index ca.…”

“…4 vs ca. 7–8) than the results found here [ 9 ]. The results also contrasted with those observed in the subtropical Laurisilva forest, where fire drastically reduced bacterial abundance (from ca.…”

“…The promiscuous tropical legume plant, Vigna unguiculata (cowpea), obtained from a local landrace from Manica, Mozambique (GUR; see [ 53 , 54 ]), was used as a trap host for rhizobia bacteria, following the protocol described by [ 9 ]. Briefly, seeds were surface-sterilized, soaked in sterilized water, and germinated in an agar and water solution of 0.8% (weight/volume).…”

“…All rhizosphere samples (SH, SL, OH, OL, RH, and RL) were used for the isolation of soil bacteria according to [ 9 ]. Briefly, 2 g aliquots of the soil samples were suspended in 18 mL of 0.85% NaCl, serially diluted (ten-fold), and plated on Tryptone-Yeast Agar (TYA) [ 58 ] and Burk’s agar [ 59 ].…”

“…Tropical soil ecosystems are particularly diverse and complex, having a unique set of microbial functions with recognized potential for developing bio-based solutions, and yet remain largely understudied [ 9 , 10 ]. The most relevant tropical ecosystems (i.e., Amazonia, Congo, New Guinea forests, and Miombo-Mopane woodlands) are ranked among the top High Biodiversity Wilderness Areas (HBWA) [ 11 , 12 ].…”