Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

Abstract

Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our results suggest a strong effect of the savanna soils' nutrient scarcity on all microbial communities, resulting in a distinct community structure that differs markedly from nutrient-rich, temperate grasslands, along with a high relevance of archaeal ammonia oxidation in savanna soils.

Sorgoleone release from sorghum roots shapes the composition of nitrifying populations, total bacteria, and archaea and determines the level of nitrification

“…6) showed that some bacterial phyla increased with increasing soil nutrient content, while others decreased. It is consistent with Rughöft et al (2016) who reported that nutrient availability also drives the bacterial community composition. Moreover, these results agree well with the copiotrophic hypothesis (Fierer et al 2007), which predicts that fast-growing copiotrophic soil bacteria such as Proteobacteria, Actinobacteria, and Bacteroidetes prefer nutrient-rich environments, while slowgrowing oligotrophs (e.g., Acidobacteria, Nitrospirae) would thrive in oligotrophic soils.…”

“…In contrast, differences in sorgoleone levels between sorghum lines did not influence the abundance of AOB, although plant treatments contained less AOB than controls. It has been recognized that AOA outnumber AOB in many habitats (Rughöft et al 2016;Herrmann et al 2012) and can play a Fig. 6 Relative abundance of 16S rRNAV4 bacteria based on OTU reads at 1 and 2.3 months.…”

Prokaryotic community shifts during soil formation on sands in the tundra zone

“…This family is mostly represented by uncultivable genera; its cultivable representatives are filamentous, aerobic and mesophilic [51]. Ktedonobacteraceae was previously found in young soils [20,52,53]; thus, we suggest that representatives of this family are important at initial successional stages.…”

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil specific in Texas Prairie grassland

“…Particularly, the relative abundance of the members of Planctomycetes, Chloroflexi, and Actinobacteria phyla significantly differed in sandy loam soil compared to silty clay and clay soils. These results could be linked to large variation in soil nutrient, moisture, and texture properties across soil types (Hermans et al, ; Kuramae et al, ; Rughöft et al, ).…”