Microbiomes of Top and Sub-Layers of Semi-Arid Soils in North-Eastern Nigeria Are Rich in Firmicutes and Proteobacteria with Surprisingly High Diversity of Rare Species

Abstract

Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46˚C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32˚C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria; however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.