Effects of tillage practices on the soil bacterial and fungal communities
We observed that tillage practices significantly impacted the bacterial community composition in 2018, which was supported by previously published research [17,37,38]. Several mechanisms could be responsible for the phenomenon. First, the vertical distribution of bacteria could be a factor. Bacteria s are generally small and easily influenced by the soil microenvironment [9], and therefore, they are distributed heterogeneously along the soil depth [9]. Both the RT and DT treatments would change the vertical distribution of soil bacteria by mixing topsoil and subsoil layers [9], thus influencing bacterial communities as compared with no-tilled soils. Second, change in the soil physiochemical variables is another factor. Soil pH has long been recognized as the main driver of the soil bacterial community [39]. Previous research confirmed that no tillage generally decreased the soil pH, owing to the accumulation of organic matter in the top soil [40,41]. Notably, the soil pH decreased in NT treatment (Supplementary Table S8) in this study. Therefore, the tillage practices may influence the bacterial community through soil pH, which was confirmed by the SEM analysis. In addition to pH, the soil oxygen level is another important factor that shapes soil bacterial community [9,24]. It has been revealed that NT systems generally reduce soil aeration porosity and oxygen content [42] by compacting the soil, while RT and DT systems alleviate soil compaction and increase the oxygen level (Supplementary Table S8). Consequently, tillage practices could possibly influence the distribution of aerobic, anaerobic and facultative anaerobic bacteria, leading to different degrees of soil C sequestration among the tillage systems [43]. Therefore, we hypothesized that the “carbon metabolism”-related bacteria would be more sensitive to tillage practices. Interestingly, our NMDS ordination revealed that bacterial functional community upon “carbon metabolism” in the NT treatment was clearly separated with DT treatment by conducting “PICRUSt” function predicting.
The shift of bacterial community was also reflected at the phylum level. Tillage practice was reported to favor fast-growing copiotrophs, while depressing oligotrophs [44]. Bacteroidetes, which typically have copiotrophic attributes and thrive in environments with high C availability, was favored by the RT and DT treatments in this study. At the OTU level, OTUs belonging to Bradyrhizobium and Candidatus Solibacter were observed to be enriched in the DT treatment in 2018, and they have been reported to be able to fix atmospheric nitrogen or reduce nitrite [45]. The genus Anoxybacillus, usually found in anaerobic or facultative anaerobic conditions [46,47], was observed to be enriched in the NT treatment, indicating that there were anaerobic or facultative anaerobic conditions in no-tilled soils.
This data showed that the effect of tillage practice on fungal communities was more evident than on bacterial communities. Not surprisingly, fungal OTU richness and community composition were unaffected by tillage practice in 2017. In 2018, we observed significantly lower fungal OTU richness in no-tillage than in deep-tillage systems. Although Degrune et al. [48] observed the same results, other studies have shown that tillage practices generally decrease fungal richness [41,49,50], primarily due to the disruption of fungal mycelia. However, fungi also produce asexual or sexual spores in addition to hyphae, conferring greater resistance to tillage disturbance than hyphae. Alternatively, since most soil-dwelling fungi are aerobic [51], the improved soil aeration in deep-tilled soils would be beneficial for fungal growth. It was noted that both the RT and DT treatments altered composition of soil fungal community compared with that of the NT. Degrune et al. [48] and Hartman et al. [3] have likewise found tillage practice is important in shaping soil fungal community composition. As revealed by SEM, the effect of tillage practice on soil fungal community was mediated through soil nutrient status. Soil nutrient factors, such as soil AP and AK, which are recognized as the important drivers for fungal communities [33], were observed to be significantly impacted by tillage practices (Supplementary Table S8). In addition, the homogenization of soil layers and improved soil aeration would be other reasons for the fungal community shift [38].
One concern for some farmers in adopting no tillage practice is a potential increase in plant diseases. In a study conducted in a black soil region, Wang et al. [22] reported that long-term NT practices increased the abundances of two pathogenic fungi (Fusarium graminearum and F. moniliforme). In the same manner, Govaerts et al. [51] conducted a 5-year field study in Mexico and concluded that the incidence of root rot under NT was higher than that under conventional tillage practice. Our results indicate that the NT treatment harbored many more pathotrophs than other treatments, which is consistent with the results of previous studies. Taken as a whole, these examples combined in our results suggest that a no-till system may favor potentially pathogenic fungi, which may threaten plant growth and crop yields. The higher abundance of pathotrophs in a no-till system might be explained, in part, by protecting them from high temperature, limited water availability and the repeated disruption of mycelia [52,53].
Effects of residue management on soil bacterial and fungal communities
Residue retention is an effective management technique to enhance SOM content and improve soil nutrient availability [12,54,55] However, the climate in Northeast China is characterized by an extremely long and cold winter [33]. Therefore, the residue buried in soil after harvest in mid October had difficulty decomposing during the winter, owing to the deficiency of water and heat [8]. Together with the relatively short duration of the experiment, the SOM and nutrient contents (e.g., AP, AK and NH4+-N) were not obviously improved by residue management in this study (Supplementary Table S8). As reported previously, the beneficial effect of residue retention on soil variables was usually not apparent in short-term studies [56]. Therefore, the soil bacterial richness and community composition was unaffected by residue retention in both years. These results were not surprising considering the lack of change in most soil physiochemical variables (Supplementary Table S8). Alternatively, the rich SOM content in black soil [33] may explain the absence of any effect of residue management on bacterial communities; the organic carbon content in maize residues could be negligible compared to the total carbon content present in soil [48]. This confirms the findings of De la Cruz-Barrón et al. [57] and Fernandez et al. [58], who reported no effect or minor effects of residue application on the bacterial community structure. However, we observed some bacterial OTUs that were enriched or depleted by residue retention. Interestingly, we observed that OTUs belonging to multiple cellulolytic genera, including Burkholderia, Luteibacter, Sphingomonas, Bacillus, Streptomyces and Stenotrophomonas [59], were enriched in the +R treatment in 2018 (Supplementary Table S3).
Unlike the observations with bacteria, we observed a significant effect of residue management on the fungal community in 2018. Similarly, Wang et al. [22] conducted a long-term field study and concluded that no tillage with residue retention altered the soil fungal community composition, while the bacterial community was less impacted. Fungi are better able to degrade cellulose than bacteria [60]. Therefore, they would be more sensitive to residue management. As revealed by SEM, the effect of residue retention on fungal community was also mediated through nutrient availability. Although these soil nutrient variables were barely affected by residue retention, we observed that the content of soil nitrate was decreased by residue retention (Supplementary Table S6). Maize straw is notable for its high C/N ratio [13]. Therefore, soil microorganisms would absorb additional N from the soil when decomposing maize straw, resulting in a reduction of the available N in soil [13]. Additionally, we observed that some putative plant pathogens were depressed by residue retention. For instance, the populations of Gaeumannomyces radicicola and Setosphaeria pedicellata, which are recognized as maize root pathogens [61,62], were significantly lower in the +R treatment. However, Rhizophlyctis rosea and Sphaerobolus ingoldii [63,64], which are reported to have the potential to degrade cellulose, were favored by residue retention.
Bacterial and fungal co-occurrence networks
To our knowledge, this study is the first that addresses both bacterial and fungal co-occurrence network patterns in response to different tillage practices. Our findings have important implications for understanding how complex soil microbial communities respond to tillage practices. Tillage practices, particularly deep tillage, shift soil bacteria-fungi co-occurrence networks towards bacterial domination rather than fungal domination. Fungal-dominated microbial communities are common in less intensively managed land use systems [41] where the intensive land use consistently reduces the biomass of soil fungi and increases the dominance of bacteria [65]. Fungal-dominated communities would result in greater storage of carbon in no-tilled soils [65], while bacteria-dominated communities would drive decomposition and nutrient cycles in the rotary or deep tillage systems [66]. Thus, the relatively lower soil nutrient availability in DT systems could be explained by the network analysis in this study.
Our results indicated that soil bacterial and fungal network patterns respond differently to tillage practices, with rotary and deep tillage complicating the bacterial networks but simplifying fungal networks. Evidently, the amplitudes of the changes in soil bacterial networks increased, while fungal networks decreased with time after the adoption of tillage practices. Compared with the NT treatment, the bacterial interactions were strengthened in the RT and DT treatments in both years, confirmed by their higher average degree and connectedness, more negative connections and more keystone OTUs in the co-occurrence networks. The changes in the soil physical conditions can influence network tightening [67]. As indicated by stepwise regression, SC was the most important determinant for the bacterial network average degree in this study (Supplementary Table S9). The compacted soils in NT treatment would thus restrict soil aeration and bacterial interactions. Additionally, the higher network complexity of bacterial community under RT and DT practices might be explained in part by the homogenization of top and bottom soil, providing more opportunities for different species to interact with each other [68]. In addition, bacteria live in the center of aggregates and were separated by the soil pores in no-tilled soils, restricting the extensive interactions among bacteria. In contrast, tillage practices would break apart soil aggregates [69] and allow more interactions among bacteria in the tilled soils. For fungal networks, we hypothesized that the disturbance of the soil profiles would physically damage fungal mycelia [18] and reduce fungal interactions in 2017. However, this pattern was not apparent in 2018. Since we adopted the tillage practice each year, this result was not because of the recovery of fungal mycelia. Resource availabilities are important drivers of microbial network structures [70]. Soil nutrient availabilities appeared higher in 2018 than in 2017 (Supplementary Table S8). The environment that is richer in nutrients may alleviate the physical disturbance and tighten the fungal interactions. Additionally, we found that the P/N ratio gradually decreased with tillage intensity for both bacterial and fungal networks, suggesting that many bacterial and fungal species in the RT and DT soils competed for resources or spaces and repelled each other.
Since organic inputs provide a substantial supply of substrates and nutrients for soil microorganisms, previous studies indicated that organic inputs generally increased the complexity of soil microbial networks [33,35,36]. In contrast, we observed that residue retention simplified both soil bacterial and fungal co-occurrence networks in 2018. However, the studies described above used animal manure or compost as organic inputs, which were easily decomposed in soils compared with maize straw, making it difficult to compare them with this study. One likely explanation for this pattern is that the reduction of available N in residue retained soils may simplify the microbial networks [13]. Alternatively, the maize residues incorporated in soils may disrupt the microbial habitats and prevent their interaction.