Abstract
BackgroundTropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology.ResultsGene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure.ConclusionsOverall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0491-8) contains supplementary material, which is available to authorized users.
Highlights
Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities
The abundance of mcrA genes involved in methane production in JFL-2 was significantly (P < 0.05) higher than in JFL-1 and JFL-3, and the abundance of pmoA genes involved in methane oxidation in JFL-2 was significantly lower (P < 0.05) compared to the other two sampling sites. These results showed that all of the metabolic processes soil bacteria mediated of related to carbon degradation, carbon fixation and methane cycle existed in these tropical rainforest soils, and some key functional gene abundances were significantly different (P < 0.05), which could lead to the differences of soil microbial metabolic potential among these sampling sites
Gene abundances related to assimilatory N reduction, denitrification, dissimilatory N reduction, nitrification, and N fixation were significantly lower in JFL-2 than these in JFL-1 and JFL-3 (P < 0.05; Fig. 3). These results showed that almost all the metabolic processes related to N cycling were present in these tropical rainforest soils, while the metabolic potential could be discrepant among three sampling sites in the tropical rainforest soils
Summary
Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. Tropical rainforests account for only 7 % of the Earth’s land surface, yet they cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, including food, drinking water, timber and medicines [1,2,3]. GeoChip 5.0, containing almost all of the key functional genes related to biogeochemical cycles, can be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential [7, 12,13,14]. Correlations between environmental microbial communities and ecosystem processes have successfully been used in different ecosystems [7, 12,13,14]
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