Wen-sheng Shu

Effect of Environmental Variation on Estimating the Bacterial Species Richness

Estimating the species richness of microorganisms is of great importance in predicting, maintaining and managing microbial communities. Although the roles of environmental heterogeneity and geographical distance in structuring soil microbial communities have been studied intensively, the effects of environmental and spatial variation on the species richness estimation have not been examined. To this end, we have explored their effects on estimating the belowground soil bacterial species richness within a 50 ha forest dynamic plot (FDP) using a published massive sequencing dataset with intensive sampling scheme. Our resampling analyses showed that, for a given sequencing depth, increasing the sample size could significantly enhance the detection of rare species by capturing more of the environmental and spatial variation, thus obtaining higher observed and estimated species richness. Additionally, the estimates of bacterial species richness were significantly and positively correlated with environmental variation among samples, indicating that environmental filtering was the main mechanism driving the processes of community assembly for belowground soil bacterial communities in the plot. Moreover, this effect of environmental variation could be markedly alleviated when the sample size was higher than 450, and thus we predicted that there were at least 42,866 soil bacterial species based on 8,296,878 sequences from 550 samples in the whole 50 ha FDP. Furthermore, we built a power law environmental heterogeneity equation (EHE) as a decision-tool to determine an approximate sample size for comprehensively capturing the environmental gradient within a given habitat. Collectively, this work further links the inherent environmental and spatial variation to the estimation of soil bacterial species richness within a given region, and provides a useful tool of sampling design for a better understanding of microbial biogeographic patterns and estimation of microbial biodiversity.

Effects of a bacterial consortium from acid mine drainage on cadmium phytoextraction and indigenous soil microbial community

Background and aimsA major concern in developing microbially-assisted phytoextraction (MAP) is that the effects of introduced microbes on indigenous soil microbial community are profound and irreversible. To date, however, the microbial properties of soils subjected to MAP remain poorly understood. Therefore, we explored the effects of inoculation with a bacterial consortium enriched from acid mine drainage on not only the cadmium (Cd) phytoextraction efficiency of Averrhoa carambola but also the microbial properties of the Cd-contaminated soil.MethodsWe conducted a field experiment and characterized the microbial community in the contaminated soil using next generation sequencing technology (Illumina MiSeq).ResultsThe bacterial inoculation increased the Cd concentration in A. carambola shoot tissues by 20%–65%, leading to a relatively high Cd removal efficiency (4.63% annually). Meanwhile, there were no significant differences between the treatments in soil bacterial diversity and community composition one year after the initiation of the bacterial inoculation treatment. The most abundant genera of the introduced bacteria were found to either disappear from, or be present in similar relative abundance, in the soils of the different treatments, except Sulfobacillus.ConclusionsCollectively, our results provide evidence that MAP could be practiced with minor effects on indigenous soil microbial community.