Understanding the mechanisms of microbiome assembly and functionality in the different plant compartments constitutes an important step to manipulate the microbiome for the benefit of plant health and productivity. This is of special significance in the potato crop as the tuberosphere microbiome is associated with potato diseases (Van Der Wolf and De Boer 2007; Shi et al. 2019) and premature sprouting during potato storage (Buchholz et al. 2021). No research has been conducted on the concurring exploration of the bacteriome and nutrient cycling in the rhizosphere, tuberosphere and bulk soil of healthy potato plants, although these compartments are physically associated. Therefore, a complete picture of the tuberosphere bacteriome characteristics relative to the two other compartments is lacking. Here, we compared the structure, composition and abundance of the bacterial communities and their potential to perform sulfur cycling in the rhizosphere, tuberosphere and bulk soil.
Alpha diversity indexes Chao1, Shannon and Simpson were statistically similar between the three soil compartments. Hou et al. (2020), reported a decline in rhizosphere diversity as potato plants approaching the harvesting stage. In addition, İnceoğlu et al. (2011) reported that at the senescence stage the rhizosphere had similar diversity to the bulk soil. These findings are in line with the results of our study since the plant collected at the senescence stage (one week before harvest) which might have weakened the differences in alpha diversity indexes between the rhizosphere and bulk soil. The analysed tuberosphere had a diversity similar to the other two compartments, showing that by the time of full development of potato tubers differences in alpha diversity between the tuberosphere, bulk soil and rhizosphere are minimal.
Despite the similarities in alpha diversity between the compartments, we observed differences in the structure of bacterial communities between the three soil compartments, and in the bacteriome assembly in tuberospheres of two varieties. Analysis of beta diversity showed that in both varieties rhizosphere and bulk soil had distinct bacterial communities. This is a well-studied phenomenon known as the rhizosphere effect that has been already confirmed in potato (İnceoğlu et al. 2013b). Interestingly, the potato varieties presented different patterns of bacterial assembly in their tuberospheres showing that both soil type and potato genotype may determine the bacteriome dynamics in this compartment. The structure of tuberosphere communities of the variety Kerr’s Pink resemble the bulk soil communities and they were differentiated from those in the rhizosphere, indicating that tuberosphere in this variety acquires its microbiome directly from the bulk soil. The tuberosphere of Rooster on the other hand, selects a bacteriome which is different from that in the bulk soil and partially resembles that of the rhizosphere bacteriome, suggesting that it is influenced by the rhizosphere and to a lesser extent by the bulk soil.
Although we cannot determine whether the differences in tuberosphere bacteriome assembly between the varieties is due to plant genotypic differences, soil effect or the synergy between them, previous studies on the potato rhizosphere microbiome indicate that soil and to a lesser extent the genotype are the main drivers of microbiome assembly in the roots (Van Overbeek and Van Elsas 2008; İnceoğlu et al. 2011). Interaction between the two factors has also been reported and influences the amount and composition of exudates released by the plant roots. Potato tubers are growing in close proximity to the root system, hence in the variety Rooster, this interaction may lead to greater production of exudates which influence the bacterial structure of the tuberosphere. Contrary to that, in Kerr’s Pink the rhizosphere effect on the tuberosphere seemed to be weaker. A previous study also reported an effect of the genotype on the tuberosphere microbial communities which was attributed to the influence of root exudates on the soil attached to the potato tubers (Buchholz et al. 2019).
Although the structure of tuberosphere bacterial communities in the variety Kerr’s pink were similar to that of the bulk soil, an effect of the tuberosphere microenvironment on the regulation of the top 10 most abundant families was observed. In Kerr’s Pink the families Hyphomicrobiaceae, Gemmatinomonadaceae, Xanthobacteraceae and Nocordiaceae as well as the families Xanthobacteraceae and Acidothermaceae in Rooster were reduced in abundance, whereas the families Sphingomodaceae in both varieties and Shpingobacteraceae in Rooster were increased from the bulk soil to tuberosphere and rhizosphere These results indicate that regardless of the potential root exudates influence on tuberosphere, this compartment is able to affect the abundance of particular families. Consequently, the tuberosphere can be considered as an environment with transitional physicochemical characteristics between the rhizosphere and bulk soil, resulting in intermediate bacterial abundances for some bacterial families.
Nutrient cycling is an important microbial process that has been studied mainly in the rhizosphere. In the tuberosphere, there are only indirect evidences for active microbial regulation of nutrient cycling under common scab infection (Kopecky et al. 2019; Marketa et al. 2021). Here, we used the predominantly bacterial sulfur cycling activity as a representative measurement of microbial activity or potential, in disease free potato plants to investigate this further. Apart from the significant role of sulfur in suppressing fungal and bacterial potato diseases, it is also particularly important for improved potato tuber yield and quality (Klikocka et al. 2005).
Our results showed that arylsulfatase activity and the number of bacterial cells participating in arylsulfonate cycling as well as the asfA copy number were higher in the rhizosphere of both varieties compared to the bulk soil and tuberosphere. The present study also observed a tendency for higher sulfonate sulfur cycling capacity in the tuberosphere compared to the bulk soil although this trend did only reach statistical significance for asfA copy numbers in Kerr’s Pink. Our results are in accordance with previous studies which have shown that the plant capacity to control organic sulfur transformations in the soil is primarily associated with the higher microbial biomass that is present in the rhizosphere compared to the bulk soil (Castellano and Dick 1991). In addition, Diallo et al. (2011) reported similar levels of bacterial densities between the tuberosphere and rhizosphere, which might partly explain the higher sulfonate utilization potential observed in the tuberosphere relative to the bulk soil.
The positive association between asfA copies and the number of arylsulfonate utilizers (MPN) suggests that these two bacterial organic sulfur cycling activities are indeed largely the same function that is quantified cultivation independently and dependently. In addition, these bacterial sulfur cycling indicators were positively correlated with the family Sphingomonadaceae in both varieties as well as with Rhizobiaceae in Kerr’s Pink and Shpinogobactereaceae in Rooster, suggesting a potential role of these families in bacterial sulfur cycling. Indeed, ssuD has been identified in members of the family Sphingomonadaceae (Aylward et al. 2013) while members of the families Rhizobiaceae (Gopalakrishnan et al. 2015) and Sphingobacteraceae (Mehnaz et al. 2007; Marques et al. 2010; Ahmed et al. 2014) are also associated with general plant growth promotion properties. However, the three families in question haven’t been associated with known sequences of asfA to date (Gahan et al. 2022). It is also evident that these families are specifically selected by the roots given that they presented the highest relative abundance in the rhizosphere and they were negatively associated with the families which had the highest relative abundance in the bulk soil and negative association with the sulfur cycling indicators. The gradual reduction in abundance of the families Rhizobiaceae Shpingomonadaceae and Sphingobacteraceae from the rhizosphere to tuberosphere and bulk soil might also partially explain the same pattern of reduction that was observed with the absolute quantities of arylsulfonate utilizers (MPN and asfA copies) in the three soil compartments.
Contrary to microbial sulfonate cycling, the tuberosphere microbial communities had almost identical or lower arylsulfatase activity compared to the bulk soil. It seems that sulphate ester utilization although positively associated with MPN and asfA played a less important role in the enrichment of the tuberosphere with sulfur. Previous studies have indicated that sulfonates are oftentimes more important for plant growth (Kertesz and Mirleau 2004; Kertesz et al. 2007) and hence this might explain the differences observed in the present study among the two microbial processes in the tuberosphere.
The mechanism that promotes microbial nutrient cycling in the tuberosphere is largely unknown to date. Lenticels on the tuber surface may not only participate in gas exchange but may also take in sulfur from the soil solution and reduce its levels in the surrounding soil. Consequently, even a modest increase in microbial sulfur mobilization in the tuberosphere may be beneficial to the plant, while at the same time depletion of nutrients in the tuber vicinity would be likely. This phenomenon is well described in rhizospheres where nutrient uptake by the roots results in a depletion zone (Wang et al. 2007) while at the same time the rhizosphere effect results in enhanced microbial nutrient cycling/mobilization (Kuzyakov and Razavi 2019).
Furthermore, the role and functional importance of sulfur cycling on the surface of the potato tubers is not clearly determined. It has been reported though that sulfur participates in metabolic pathways involved in plant resistance to pathogens (Sagova-Mareckova et al. 2017; Kopecky et al. 2019; Marketa et al. 2021). In addition, higher levels of sulfur were reported in the tuberosphere of potato cultivars resistant to common scab (Kopecky et al. 2019; Marketa et al. 2021). Consequently, enhanced microbial sulfur mobilization in the tuberosphere may take place as a plant defence mechanism. This could also explain why in the present study, where no disease incidence occurred, only a modest increase of sulfur cycling potential was observed in the tuberosphere compared to the bulk soil. Furthermore, in our study we detected up to 6x106asfA copies g− 1 soil in the organic sulfur utilizing bacterial communities while in a previous study the asfA copies of Variovorax alone reached this number in soils from the Netherlands (İnceoğlu et al. 2013a). Given that in our study Variovorax wasn’t detected in the 16S rRNA gene dataset (data not shown) we speculate that Variovorax is not a crucial contributor in sulfur cycling in the different soil compartments of the present study and that other bacteria, not yet identified, have taken over this role.
In conclusion, our results show that the tuberosphere is not just an extended environment of the bulk soil but has distinct microbial properties. Indeed, the tuberosphere putatively regulates specific characteristics of the structure and composition of the bacteriome as well as nutrient cycling, dependent on the soil characteristics and plant variety. This observation raises new questions regarding the bacteriomes of the seed tubers and of the newly emerging potato roots. Potatoes are planted as tubers (seed tubers) and following the findings from the present study, their microbiome could also influence the establishment of the plant microbiome during the stage of potato development. In addition, the root system of potato is emerging from the tuber surface and consequently the newly developed roots may acquire the microbiome from the tuber surface and the endosphere. If that is the case, the soil may be less important as a microbial reservoir at the early stages of root development in potatoes. These two hypotheses need further examination as the first stages of plant development and their interaction with soil microbes are critical for the plant vigour.
Finally, it seems that potato genotypes affect sulfur cycling in the tuberosphere to potentially increase potato resistance to common scab. Consequently, the evaluation of microbial sulfur cycling in this compartment could be incorporated in plant breeding programmes as a trait of selection, for picking genotypes with resistance to common scab and other soil pathogens.