Spatial and temporal variation of ARG abundance
Our results of ARG abundance emphasized that different gene elements responded differently to the same environmental variations. For example, the normalized abundance of efflux pump gene tetA showed a decreasing trend from winter to the contiguous summer. This gene was found flanked by MGEs (mobile genetic elements, MGEs); therefore, its transmission was associated with the HGT of the MGEs that carried them . The normalized abundance of floR significantly decreased, while that of mefA/E and cfr significantly increased in summer (p < 0.05). The floR and mefA/E genes encode efflux pumps, while cfr catalyzes ribosomal methylation [16, 17]. In previous studies, these three genes were also frequently found associated with MGEs, such as plasmids and transposons, suggesting MGEs were most likely involved in their variation [16, 18, 19]. In addition, intI2 showed an increasing trend from winter to the contiguous summer, this could facilitate the transmission of the linked ARGs, for integrons permit tandem integration and expression of mobile cassettes coding for ARGs .
In addition, three RPP genes—tetM, tetO and tetW were found significantly increased in soil adjacent to swine feedlots in Beijing, compared with the nearby CK soil. Previously, these three tet genes were found to be prevalent in swine intestinal microbiota and swine manure, indicating their close linkage with animal manure [21,22,23]. It was found that the distributing patterns of the three tet genes were independent of seasons, and there were also consistent distributing patterns of these genes between the adjacent soil and wastewater, implicating wastewater as the primary polluting source. These genes are commonly carried on MGEs that facilitate transfers between different bacterial taxa in an ecosystem . For example, tetM, tetO and tetW are present in numerous genera due to HGT . Especially, tetM is commonly carried on Tn916-like transposons which makes it possess the broadest host range among all tetracycline resistance genes [18, 25]. Moreover, RPP tet genes have a wider spectrum of resistance to tetracyclines than most of tet efflux pump genes . These facts highlighted the environmental risks of ARG pollution induced by swine manure into soil, since RPP tet genes are prevalent in swine manure [21, 27].
Overall, there were no significant differences in the ARG composition between topsoil and subsoil (Fig. 1 and Additional file 1: Table S3). Samples taken at greater depths might be needed to distinguish ARG composition in soils subjected to long term ARG pollution by swine wastewaters. Moreover, abandonment for 1.5 years did not alleviate ARG transfer risk compared with being abandoned for 1 year, and to the contrary, total ARG normalized abundance increased from winter to summer in this present study. These data indicated that a time span of 1.5 years was far from enough to recover a background ARG abundance. Therefore, a long-term survey is essential to study the recovery situation in soil near these abandoned feedlots.
The positive correlations between ARGs (e.g., mefA/E, cfr, sul1) and environmental factors (e.g., NH4+–N, TP, TN, NH4+–N, Cu and Zn) in Fig. 2 indicated that these factors should be concerned, especially since swine manure usually contained these components in abundance.
Bacterial community variation in winter and summer
Combining the results of NMDS analysis in Fig. 3 at the genus level and comparison of relative abundance of bacterial community between two seasons at the phylum level, our present study indicated that seasonal change did not substantially alter the bacterial community structure from winter to summer, even though the weather characteristics were quite different (Table 1). The reason might be that the complex soil colloid offered a relative stable environment for bacterial community. However, further studies are needed in future to verify this speculation as previous studies seldom focus on the bacterial community alteration over season. Among the seven phyla that did show a significant alteration in relative abundance between winter and summer (Table 2), Actinobacteria decreased, while Acidobacteria increased for Beijing but not for Hefei. This discrepancy might be the result of climatic differences based on geography. Beijing has four distinct seasons with larger temperature fluctuations between winter and summer and is much drier. These factors would exert stress on the soil bacterial community resulting in a competitive advantage for Actinobacteria in winter, since they possessed high GC content and could robustly resist these stressors. However, Hefei in southern China experienced fewer temperature extremes between winter and summer and received more rainfall than Beijing. For example, the average daily temperatures in December and June in Beijing are − 6–3 and 19–30 °C, while in Hefei, they are 1–9 and 21–29 °C, respectively (Table 1). The average rainfall from December to May in Beijing was only 74.1 mm, while in Hefei, it was 362 mm. In Beijing, the relative humidity varied from 44 to 77% compared with Hefei at 73–80% (China Meteorological Bureau, available at https://www.weather-atlas.com/). The soil types also differed, and together these components were reflected in the combined Actinobacteria population trend. Moreover, unlike other bacterial phyla in soil, Actinobacteria relative abundance was negatively correlated with soil moisture. In contrast, Acidobacteria populations were positively correlated to soil moisture content . Actinobacteria were drought resistant and could proliferate in arid soil conditions . These variables were probably major contributors to the seasonal variation of Actinobacteria and Acidobacteria in Beijing, because the rainfall is extremely concentrated in summer and winter is a dry season there (China Meteorological Bureau). However, the lack of a gradient and continuous alteration of soil moisture data as a variable in the present study made it impossible to determine whether soil moisture directly altered bacterial phyla. Therefore, further experiments are needed to address this question.
Moreover, ref.  concluded that Firmicutes were the predominant phylum in swine intestinal microflora, and the long-term exposure of swine manure to soil is linked to Firmicutes abundance. In our study, the persistence of Firmicutes in soils adjacent to swine feedlots in Beijing suggested that this is a result of long-term manure pollution from the adjacent wastewater. The above characteristics of Actinobacteria and Firmicutes were also most likely to contribute to ARG profiles in the corresponding soil sites, because Actinobacteria and Firmicutes were among the major phyla that host ARGs and caused their transmission [31, 32].
Co-occurrence patterns of bacterial taxa with ARGs
In this present study, there were more potential genera hosts on the network of the working swine feedlots than those of the abandoned swine feedlots in the same season. The possible reason for this might be that the HGT level was higher in summer than in winter both in abandoned and working feedlots, as several studies have shown that HGT was highly temperature-dependent [33,34,35,36]. There were also studies showed that higher ambient temperatures favor HGT between bacterial taxa, and transfer frequencies have been linked to specific temperatures [35, 37,38,39]. For example, the transformation level of Pseudomonas stutzeri at 12 °C was 0.7% of that at 30 °C . An increase in temperature across different regions was conceived to facilitate the HGT of antibiotic resistance level for common pathogens . However, this assumption could not serve as a conclusion for sure in the current scenario, because HGT level could not be speculated merely based on co-occurrence network analysis. More studies are needed to infer the correlation between HGT level and season in soil microbiota.
Overall, the potential ARG hosts at the phylum level in the soil adjacent to swine feedlots in both seasons were quite similar (Additional file 1: Fig. S5). They were primarily composed of Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Acidobacteria, which are in accordance with previous studies [4, 32]. In addition, the frequency of phyla presented on the above networks was not proportional to their relative abundance in our soil, wastewater, or sediment showed in Additional file 1: Fig. S4. More specifically, Firmicutes possessed the most nodes in summer, underlining the significant input of antimicrobial-resistant bacterial from swine manure to the wastewater. Because Firmicutes were proved to be the most dominant phylum in the swine feces (> 90% in adult swine) . The above result was consistent with the results of wastewater and sediment samples in winter from our previous study . The above results suggested that the host taxa were constrained to a group of particular phyla that included Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria and Cloroflexi. Proteobacteria, Firmicutes and Actinobacteria had also been implicated as main ARG carriers and played important roles in disseminating ARGs in previous studies, [41,42,43]. This implied some barriers exist in horizontally transferring ARGs to other phyla within soil microbiota. The mechanisms that might act as these barriers included host restriction–modification systems, plasmid incompatibly, and the lack of integrative conjugative element target sites .