Effects of Waterlogging on Soybean Rhizosphere Microbial Community Profiled Using Illumina MiSeq, LoopSeq, and PacBio 16S rRNA Genes Sequences

Abstract Background: Waterlogging on the global environment has led to a significant decline in crop yields. However, the response of plant-associated microbes to waterlogging stress on different soils is not known. Moreover, there are few reports on whether this response is influenced by different sequencing methods. In this study, the effects of waterlogging on soybean rhizosphere microbial structure on two types of soil were examined, using a short reading 16S rRNA sequencing variable region V4 and two full-length 16S rRNA sequencing variable regions V1-V9.Results: The results revealed some similarities and differences in three sequencing methods for soybean rhizosphere microbial response to waterlogging stress. Based on CPCoA analysis, all the sequencing methods showed that waterlogging on both types of soil significantly affected the bacterial community structure of the soybean rhizosphere, and increased the relative abundance of Geobacter. However, the full-length sequencing methods had higher classification resolution than short-read sequencing (except phylum level of all sequencing methods and class level of LoopSeq sequencing). Further, analysis on OTU level and network showed that waterlogging increased the abundance of some microorganisms related to nitrogen cycle using V4 sequencing, and microorganisms related to phosphorus cycling when using two full-length sequencing methods. This is in line with the core microbial analysis. Environmental factors affecting the structure of microbial communities differed among sequencing methods.Conclusions: In summary, this piece of work detected the effects of waterlogging on soybean rhizosphere microbes using three sequencing methods. Some functional microbes were enriched in the rhizosphere, which may benefit soybean in resisting waterlogging stress. On the other hand, there were several differences in results among the three sequencing methods which might affect the response of rhizosphere microbial structure to stress. Our analysis of sequencing methods on various levels provides some useful information on environmental samples sequencing.