It is still a topic of debate whether or not domestication of crops ed from wild ancestor species to cultivated species will have a specific impact on the microbial communities in the rhizosphere. Although the information revealed by different studies provides a variable picture, most studies do show that crop domestication will lead to directed selection of the rhizosphere microbiome, but such selection will vary depending on the environment [27–29]. One of the most interesting observations is that crop domestication seems to have less selective effect on bacteria than on fungi [30, 31] which is consistent with the results of our previous study on the comparison of the structure of the rhizomicrobiomes of wild and cultivated rice in natural environments .
Most comparable studies used next generation sequencing of amplicons of taxonomic phylogenetic markers of microbial diversity in order to assess the impact of crop domestication on the structure of the microbial communities in the rhizosphere. However, it is highly interesting and relevant for the future development of better crop varieties using the intrinsic characteristics of wild relatives to know how the functioning of the rhizomicrobomes has been affected by domestication. Therefore, we applied DNA shotgun metagenome sequencing to assess the most pronounced potential rhizomicrobial functions affected by crop domestication. And, indeed, we showed that domestication of rice from different origins, Asia and Africa, has clearly impacted the potential functioning of the rhizmicrobiome. Although the evolution of the rice species inform different regions in Asia and Africa has led to clearly different rice plant species, we observed a number of specific changes in the microbial functions in the rhizosphere independent of the type of rice species. Certain genes such as those related to carbon metabolism, and amino acid metabolism were mainly enriched in wild rice, while others such as those related to nitrogen metabolism, amino acid metabolism, lipid metabolism, metabolism of cofactors and vitamins, xenobiotics biodegradation and metabolism and biosynthesis of other secondary metabolites were enriched in cultivated rice as compared to wild rice. With respect to the latter we can only speculate that this is a reflection of the specific conditions in which cultivated crops are growing including increased nutrient contents in soil as a result of fertilization and the presence of xenobiotics in the form of pesticides.
It was remarkable that the pathway of methane metabolism was significantly and consistently enriched in the rhizomicrobiomes of all wild species as compared to those of cultivated rice.. This held for both genes involved in methane production and genes related to methane oxidation. Microbial methanogenesis accounts for approximately 74% of natural methane emission. The process plays a major role in global warming. It has been shown that rice paddies constitute a major source of anthropogenic CH4 emissions [33, 34]. Methane released during rice growth accounts for approximately 20% of global methane emissions which is mostly synthesized by rhizosphere methanogenic archaea [35, 36].
There were 81 KOs involved in methane metabolism (include methane synthesis and methane oxidation) and 16 KOs showed significant differences among African wild rice, African cultivated rice, Asian wild rice and Asian cultivated rice. Three types of methanogenic pathways are known: methanol to methane, CO2 to methane, and acetate to methane . We found that there were 9 significant differences KOs among African wild rice, African cultivated rice, Asian wild rice and Asian cultivated rice in the three types of methanogenic pathways. K00201, K00443 and K00399 of the CO2 to methane pathway in wild rice were more enriched in the rhizomicrobiomes of wild rice than in those of in cultivated rice. Thus, to some extent, the ability of the rhizosphere communities of wild rice to transform carbon dioxide into methane is stronger than those of cultivated rice. The genes coded K00170, K00172, K01007, K01595 and K00024 belong to the acetate to methane pathway and were also more enriched in the rhizomicrobiomes of wild rice as compare to those of cultivated rice (Fig. 6).
Three types of methanotrophic pathways are known: the serine pathway, the ribulose-P pathway and the xylulose-P pathway . We found that the genes coded K01834 and K00058 which belong to the serine pathway were significantly more enriched in the rhizosphere communities of wild riceas compare to those of cultivated rice (Figure. 7). Also K13831 and K16370, which belong to the ribulose-P pathway and K01622, which belongs to the xylulose-P pathway were significantly more enriched in the rhizomicrobiomes of wild versus those of cultivated rice (P < 0.05). We also explored the interactions of methane metabolism related functional KOs of wild rice versus cultivated rice with different functional KOs belonging to other pathways. Both in African and Asian wild rice the interactive networks were more complex than in the related cultivated rice. The methane metabolism related KOs of wild rice were mainly affected by functional KOs belonging to carbon fixation pathway, pyruvate metabolism, glycolysis/gluconeogenesis and pyrimidine metabolism which can provide energy sources and intermediates for methane metabolism [39–41]. The methane metabolisms related KO of cultivated rice were mainly affected by functional KOs belonging to phentlalanine, tyrosine and tryptophan biosynthesis as well as retinol metabolism. The aromatic amino acid phentlalanine, as well as tyrosine and tryptophan are vital constituent of proteins in all living organisms and serve as precursor for thousands of indispensable metabolites  and retinoids play an important role in controlling such vital processes as morphogenesis, development, reproduction or apoptosis . Thus, their interaction with methane oxidation pathways might be indirect.
The enriched abundance of genes involved in methane metabolism of the rhizomicrobiomes of wild rice species as compared to the abundances of these genes in the rhizomicrobiomes of cultivated relatives suggests that both methane synthesis and oxidation were more pronounced in the rhizomicrobiome of wild rice than that of cultivated rice. In wild rice, archaea utilize CO2, acetate, and formate for methane synthesis, which can help wild rice to decrease the damage of acidification caused by anaerobic condition in rhizosphere. And the produced methane can be utilized by methane oxidizer bacteria, which can help to reduce methane emission to the atmosphere. Thus, the strengthening of the ecological balance of methane production and oxidation in wild rice not only helped plant growth, but also may have also promoted the growth of methane oxidizing bacteria. Most of our data supported this hypothesis, but there were contradictory data as well. In the first place the data on the relative abundance of methanobacteria and methane consuming methanotrophs were not unambiguously. By analyzing the archaeal and bacterial community compositions of the rice rhizosphere, the relative abundance of Methanomicrobia was significantly higher in the microbial communities of the rhizospheres of both the African and Asian wild rice than in that of their related cultivated rice species. Also, the relative abundance of Methylocystaceae, which are the major methanotrophic bacteria, in the rhizomicrobiome of African wild rice was significantly higher in the that of the related cultivated rice speciess. However, the relative abundance of Methylocystaceae was lower in the rhizosphere communities of Asian wild rice than in that of the Asian cultivated rice. Moreover, the differences in the abundances KO’s in the rhizomicrobiomes of wild versus cultivated rice were, generally speaking, more pronounced for the African species than for the Asian ones. This could be due to the larger sample size in case of the Asian rice species and associated larger variability in the data on the abundances, although that was not consistent as seen in Figs. 6 and 7, but it is more likely that that is a reflection of differences in the genetic make-up of the rice species and thus, their association with the rhizosphere microbial communities. It is therefore, recommended that in future studies these aspects are dealt with in details. It may also suggest that the functional matching between plant and rhizomicrobiomes may be greater than the taxonomic selection effect [44, 45].