Effect of Parthenium hysterophorus L. Invasion on Soil Microbial Communities in the Yellow River Delta, China

Abstract

Parthenium hysterophorus L., as an invasive plant, has negatively impacted the ecosystem functioning and stability of the terrestrial ecosystem in China. However, little information was available for its effects on microorganisms in the Yellow River Delta (YRD), the biggest newly-formed wetland in China. In the present study, high-throughput sequencing technology was used to obtain the bacterial community in soils and roots of different plant species, including P. hysterophorus and some native ones in the YRD. Our results showed that the Proteobacteria, Acidobacteriota, Gemmatimonadota, and Actinobacteriota were dominant in the rhizosphere soils of P. hysterophorus (84.2%) and Setaria viridis (86.47%), and the bulk soils (80.7%). The Proteobacteria and Actinobacteriota were dominant within the root of P. hysterophorus. A total of 2468 bacterial OTUs were obtained from different groups among which 140 were observed in all the groups; 1019 OTUs were shared by P. hysterophorus non-rhizosphere soil bacteria (YNR) P. hysterophorus rhizosphere soil bacteria (YRR) groups. The indexes of the ACE (823.1), Chao1 (823.19), Simpson (0.9971), and Shannon (9.068) were the highest in the YRR groups, showing the greatest bacterial community diversity. Random forest analysis showed that the Methylomirabilota and Dadabacteria (at the phylum level) and the Sphingomonas, and Woeseia (at the genus level) were identified as the main predictors among different groups. The LEfSe results also showed the essential role of the Acidobacteriota in the YRR group. The SourceTracker analysis of the bacterial community of the YRR group was mainly from GBS groups (average 53.14%) and a small part was from YNR groups (average 6.56%), indicating that the P. hysterophorus invasion had a more significant effect on native plants' rhizosphere microorganisms than soil microorganisms. Our observations could provide valuable information for understanding the bacterial diversity and structure of the soil to the invasion of P. hysterophorus.

Keywords: Alpha diversity; LEfSe analysis; high-throughput sequencing; rhizosphere soil.

Figure 1

Alpha diversity indices of bacteria among different species. (a) Chao1; (b) ACE; (c) Shannon; (d) Simpson. Root: root endophytes bacteria samples of P. hysterophorus; YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soils bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group.

Figure 2

Venn diagram showing the number of shared and unique OTUs among different groups. Each circle represents sampled compartments. Values within intersections represent shared OTUs, and values outside intersections represent unique OTUs. Root: root endophytes bacteria samples of P. hysterophorus; YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soils bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group.

Figure 3

The relative abundance of the top 10 bacterial communities. (a) at the phylum levels; (b) at the genus levels. Root: root endophytes bacteria samples of P. hysterophorus; YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soils bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group.

Figure 4

The PCoA based on the Bray–Curtis distance shows the variation in bacterial community structure. Different colors represent the samples from other groups. Root: root endophytes bacteria samples of P. hysterophorus; YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soils bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group.

Figure 5

The relationship between the soil physicochemical properties and bacterial community. YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soil bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group. * means significant at 0.05 level.

Figure 6

PERMANOVA analysis among different species. Root: root endophytes bacteria samples of P. hysterophorus; YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soils bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group.

Figure 7

LEfSe analysis at different bacterial taxonomic levels among different groups. Different colored dots represent the taxa with significant differences among different samples. The inner to outer circles represent taxa from phylum to species. Root: root endophytes bacteria samples of P. hysterophorus; YRR: the rhizosphere soil bacteria samples of P. hysterophorus; YNR: the bulk soils bacteria samples of P. hysterophorus; GBS: the soil bacteria samples of native plants were numbered GBS group.

Figure 8

Random forest analyses among different species. Random forest is a subclass of ensemble learning, which depends on the voting choices of decision trees to determine the final classification results. Different colors mean different bacterial species. (a) at the phylum levels; (b) at the genus levels.

Figure 9

SourceTracker analysis among different species. (a) graph represents a predicted sample, with different colored columns representing the proportions of each source in that sample. Unknow represents the unknown source classification; (b) proportional area map of predicted sample sources. One graph represents a prediction sample; different colors represent the proportion of different sources.