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1. During soil development, bacteria and fungi can be differentially affected by changes in soil biogeochemistry. Since the chemistry of parent material affects soil pH, nutrient availability, and indirectly litter quality, we hypothesize that parent material has an important influence on microbial community patterns during long-term soil development. In this paper, we tested for the effect of parent material, as well as, soil and litter properties upon microbial community patterns in three c. 20000-year-old semi-arid chronosequences developed on sedimentary and volcanic (i.e. Andesitic and Dacitic) soils in the Dry Puna of Bolivia. We evaluated microbial patterns by analysing the terminal restriction fragment length polymorphism from amplified bacterial 16S rRNA genes, and the fungal internal transcribed spacer region, and quantitative real-time polymerase chain reaction.

2. Soil and litter characteristics differed significantly between the Sedimentary and volcanic chronosequences. In particular, soil pH was alkaline in all stages of the Sedimentary chronosequence; whereas it changed from alkaline to near neutral across stages in both volcanic chronosequences. Composition of bacterial communities changed across volcanic chronosequences, and this change was associated with a reduction in soil pH and increases in litter quality, whereas no differences were found in the Sedimentary chronosequence. Fungal community composition, in contrast, did not change across any chronosequence.

4. Relative microbial abundance, expressed as the fungal:bacterial ratio, declined across stages of the Sedimentary chronosequence in association with decreases in TC and TP, whereas in the Andesitic chronosequence decreases in fungal:bacterial ratios were related with increases in litter quality and declines in soil pH.

5. Synthesis. Our results show the importance of parent material in affecting bacterial and fungal communities during soil development. Further, in semi-arid chronosequences, fungal:bacterial ratios tend to decline given that soil pH in young soils is rather alkaline. Our results also are consistent with the general framework that highlights the importance of above-ground (i.e. litter quality) and below-ground (i.e. soil properties) in affecting microbial relative abundance and community composition during soil development.