Dataset Information

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.

SUBMITTER: Rughoft S

PROVIDER: S-EPMC5069293 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

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

Rughöft Saskia S Herrmann Martina M Lazar Cassandre S CS Cesarz Simone S Levick Shaun R SR Trumbore Susan E SE Küsel Kirsten K

Frontiers in microbiology 20161019

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 nutr ...[more]

PMID: 27807431

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Project description:Application of nitrogen (N) fertilizers, predominantly as urea, is a major source of reactive N in the environment, with wide ranging effects including increased greenhouse gas accumulation in the atmosphere and aquatic eutrophication. The soil microbial community is the principal driver of soil N cycling; thus, improved understanding of microbial community responses to urea addition has widespread implications. We used next-generation amplicon sequencing of the 16S rRNA gene to characterize bacterial and archaeal communities in eight contrasting agricultural soil types amended with 0, 100, or 500 μg N g-1 of urea and incubated for 21 days. We hypothesized that urea amendment would have common, direct effects on the abundance and diversity of members of the microbial community associated with nitrification, across all soils, and would further affect the broader heterotrophic community resulting in decreased diversity and variation in abundances of specific taxa. Significant (P < 0.001) differences in bacterial community diversity and composition were observed by site, but amendment with only the greatest urea concentration significantly decreased Shannon indices. Expansion in the abundances of members of the families Microbacteriaceae, Chitinophagaceae, Comamonadaceae, Xanthomonadaceae, and Nitrosomonadaceae were also consistently observed among all soils (linear discriminant analysis score ≥ 3.0). Analysis of nitrifier genera revealed diverse, soil-specific distributions of oligotypes (strains), but few were correlated with nitrification gene abundances that were reported in a previous study. Our results suggest that the majority of the bacterial and archaeal community are likely unassociated with N cycling, but are significantly negatively impacted by urea application. Furthermore, these results reveal that amendment with high concentrations of urea may reduce nitrifier diversity, favoring specific strains, specifically those within the nitrifying genera Nitrobacter, Nitrospira, and Nitrosospira, that may play significant roles related to N cycling in soils receiving intensive urea inputs.

Project description:To identify factors that drive plant species richness in South-African savanna and explore their relative importance, we sampled plant communities across habitats differing in water availability, disturbance, and bedrock, using the Kruger National Park as a model system. We made plant inventories in 60 plots of 50 × 50 m, located in three distinct habitats: (i) at perennial rivers, (ii) at seasonal rivers with water available only during the rainy season, and (iii) on crests, at least ~ 5 km away from any water source. We predicted that large herbivores would utilise seasonal rivers' habitats less intensely than those along perennial rivers where water is available throughout the year, including dry periods. Plots on granite harboured more herbaceous and shrub species than plots on basalt. The dry crests were poorer in herb species than both seasonal and perennial rivers. Seasonal rivers harboured the highest numbers of shrub species, in accordance with the prediction of the highest species richness at relatively low levels of disturbance and low stress from the lack of water. The crests, exposed to relatively low pressure from grazing but stressed by the lack of water, are important from the conservation perspective because they harbour typical, sometimes rare savanna species, and so are seasonal rivers whose shrub richness is stimulated and maintained by the combination of moderate disturbance imposed by herbivores and position in the middle of the water availability gradient. To capture the complexity of determinants of species richness in KNP, we complemented the analysis of the above local factors by exploring large-scale factors related to climate, vegetation productivity, the character of dominant vegetation, and landscape features. The strongest factor was temperature; areas with the highest temperatures reveal lower species richness. Our results also suggest that Colophospermum mopane, a dominant woody species in the north of KNP is not the ultimate cause of the lower plant diversity in this part of the park.

Dataset Information

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

Publications

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

Similar Datasets

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