
Changes of microbiome in response to sugars in a wilt pathogen-infested soil
Gaidi Ren, Guangfei Wang, Dejie Guo, Chao Lu, Yan Ma
Soil Ecology Letters ›› 2023, Vol. 5 ›› Issue (1) : 46-65.
Changes of microbiome in response to sugars in a wilt pathogen-infested soil
• Sugar addition caused vigorous proliferation of wilt pathogen.
• Sugar addition modified bacterial community structure and decreased the diversity.
• Sugar addition caused more complex and connected networks.
• Keystone taxa formed positive links with wilt pathogen in sugar-spiked networks.
Sugars are frequently and abundantly found in root exudates, but influence of specific sugars on the fate of soil-borne pathogens, microbiome structure, and particularly microbial interactions are not well understood. A 42-day of microcosm incubation was conducted with two soils: a natural watermelon Fusarium wilt pathogen (i.e., Fusarium oxysporum f. sp. niveum (FON))-infested soil (Low-FON soil) and the soil further receiving the wilt pathogen inocula (High-FON soil). Both soils were supplemented with four simple sugars before incubation. The results show that, in both soils, FON was enriched by all sugars although co-living with tremendously diverse microbes; and bacterial richness, evenness, and diversity were decreased and bacterial community structure was changed by all sugars. Bacterial richness and evenness were negatively correlated with FON quantity in both Low-FON and High-FON soils, indicating that FON may tend to live in soil with low alpha-diversity. In both Low-FON and High-FON soils, the sugar-spiked networks had more links, higher density, larger modules, and shorter harmonic geodesic distance, suggesting greater potentials for microbial interaction and niche-sharing. The positive links between some of the keystone taxa and FON indicates that these keystone taxa may have promoted FON. This may be one of reasons why FON could proliferate vigorously after sugar supplementation.
Root exudate / Sugar / Fusarium oxysporum f. sp. niveum / Microbial community structure / Molecular ecological network / Keystone taxa
Fig.1 Fusarium oxysporum f. sp. niveum quantity dynamics over a 42 d period in Low-FON (A) and High-FON (B) soils determined by quantifying the ITS gene of F. oxysporum f. sp. niveum with real-time PCR technique. The soil without or with F. oxysporum f. sp. niveum was referred to as Low-FON or High-FON soil, respectively. The designations CK, Gluc, Fruc, Suc, and Mal indicate that the soils were added with H2O, glucose, fructose, sucrose solutions, respectively. The designation FON denotes the soils with FON inoculation. The designations FON+Gluc, FON+Fruc, FON+Suc, FON+Mal denote that the soil was not only inoculated with FON but also supplied with glucose, fructose, sucrose, and maltose solution, repsectivley. T0 denotes zero time and 1 d, 2 d, 3 d, …42 d denote samples collected after 1 day, 2 days, 3 days, …42 days of incubation. Different letters indicate significant differences by Duncan’s multiple range test (P<0.05). |
Fig.2 Observed OTU number, Heip’s evenness index, and Shannon index in Low-FON (i.e., FON-uninoculated) and High-FON (i.e., FON-inoculated) soils. The OTUs, Heip’s evenness index, and Shannon index were obtained by using 10290 subsampled sequences from each sample. The designations Gluc, Fruc, Suc, and Mal denote the soil with the supplementation with glucose, fructose, sucrose, and maltose solutions, respectively, while CK denotes the soil with the supplementation with water. FON denotes the soil with FON inoculation. FON+Gluc, FON+Fruc, FON+Suc, and FON+Mal represent the soils that were not only inoculated with FON but also supplied with glucose, sucrose, fructose, and maltose solutions, respectively. T0 denotes zero time, and 1 d, 3 d, 5 d, 9 d, and 42 d indicate that the samples were collected after 1 day, 3 days, 5 days, 9 days, and 42 days of incubation. Different letters denote significant differences by Duncan’s multiple range test (P<0.05). The error bars represent the standard deviation of the means. |
Fig.3 Principal coordinates ananlysis (PCoA) of bacterial communities from the samples collected at zero time (A) and after 1 day (B), 3 days (C), 5 days (D), 9 days (E), and 42 days (F) of incubation. The percentages in parentheses for each axis represent the proportion of total variation explained. The PCoA plot was obtained based on the Bray-Curtis distances at a depth of 10290 subsampled sequence reads per sample. All other designations are the same as those in Fig. 2. |
Fig.4 Relative abundance of bacterial phylotypes at the phylum or class (only for Proteobacteria) level in Low-FON (A) and High-FON (B) soils. The phylotypes which had relative abundance >0.5% in at least one treatment are presented. All other designations are the same as those in Fig. 2. |
Fig.5 Abundance of the significantly enriched genera and fold changes after sugar addition. The significantly enriched genera refer to those bacterial population (shown in Fig. S6) which had a significantly (P<0.05) higher abundance in sugar-spiking treatment than in no-sugar treatment throughout 42 d of incubation. The data shown are the mean value of three replicates±the standard deviation. The abundance of the genus was calculated as the relative abundance of each genus × the total bacterial abundance determined by qPCR technique (shown in Fig. S2). The values in blue bold font indicate a higher fold increase for the genera than FON. Different letters indicate significant differences by Ducan’s multiple range test (P<0.05). All the other designations are the same as those in Fig. 2. |
Fig.6 Network interactions of microbial communities in FON-uninoculated (A–F) and FON-inoculated (H–M) soils over time, and links between keystone taxa and FON. Those keystone OTUs (i.e., connectors, module hubs, or network hubs) which were connected with FON are indicated by the black arrow in panels A–F and H–M, and the links between these keystone taxa and FON shown in panels G and N. The red line denotes a positive connection (link), and the blue line denotes a negative connection (link). The designations CK and Sugar indicate that the soil was supplied with water and sugars (i.e., glucose, fructose, sucrose, and maltose), respectively. FON indicates the soil inoculated with FON. The samples collected after 0 day (i.e., zero time), 1 day, 3 days, 5 days, 9 days, and 42 days are referred to as 0, 1d, 3d, 5d, 9d, and 42d, respectively. |
Fig.7 Classification of nodes to identify putative keystone species within the networks. Each symbol represents an OTU. Module hubs have Zi >2.5, whereas connectors have Pi >0.62. Network hubs have Zi >2.5 and Pi >0.62. The number of peripherals, connectors, module hubs, or network hubs and their proportion in the network are shown below or next to the symbols “Peripherals”, “Connectors”, “module hubs”, or “Network hubs”. The Low-FON denotes the FON-uninoculated soil and the High-FON denotes the FON-inoculated soil. OTUs from Low-FON (dots) and High-FON (squares) soils were colored by genus membership. CK and Sugar represent the soil supplied with water and sugars (i.e., glucose, fructose, sucrose, and maltose), respectively. FON denotes the soil inoculated with FON. The samples collected after 0 day (i.e., zero time), 1 day, 3 days, 5 days, 9 days, and 42 days are referred to as 0, 1 d, 3 d, 5 d, 9 d, and 42 d, respectively. |
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