Nutrient analysis of sediments in Bahe River Basin
The TN contents in the sediments of Bahe River ranged from 24 to 1,812 mg/kg, with an average of 524 mg/kg (Table 1). The TN contents at B2, B5, B8, B16 and B18 ranged from 1000 to 2000 mg/kg (Additional file 1: Fig. S1), indicating moderate pollution according to the Environmental Protection Agency (EPA) classification and grading standard for the sediments, while those at the remaining points were lower than 1000 mg/kg, indicating mild pollution (Additional file 1: Fig. S1; Table 1). The TP contents in the sediments ranged from 216 to 1177 mg/kg, with an average of 734 mg/kg (Table 1). The TP contents at B1 and B3 were less than 420 mg/kg, indicating mild pollution according to the EPA classification and grading standard for sediments; while that at points B6 and B14 were 420–650 mg/kg, indicating moderate pollution; and at the remaining points were greater than 650 mg/kg, indicating severe pollution (Additional file 1: Fig. S1). Compared with the TN and TP contents in the sediments of rural rivers, the nutrients were higher, while the pollution level was lower compared to other urban rivers [21].
The water quality at points B1–B4 belongs to that of a Class IV water body and at points B5–B18 to that of a Class III water body according to the Environmental Quality Standards for Surface Water (GB 3838-2002). The primary reason for this result is that a rubber dam downstream has slowed the water flow and decreased the DO concentration. The OM content in the sediments in the lower reaches of the river ranged from 2.37 to 50.58 g·kg−1, with an average of 9.85 g·kg−1(Additional file 1: Fig. S1; Table 1). This result is primarily due to the anthropogenic interferences in the lower reaches of the river, which has affected the soil mass in the long term and frequently disturbed the sediments. The TN contents in the lower reaches of the river ranged from 0.05 to 2.78 g·kg−1, with an average of 0.64 g·kg−1 (Additional file 1: Fig. S1). The TP contents in the lower reaches of the river ranged from 0.40 to 3.06 g·kg−1, with an average of 2.10 g·kg−1 (Additional file 1: Fig. S1). The TP contents are at a moderate-to-high level due to phosphorus enrichment from urban construction, domestic waste discharge and irrigation using sewage [54]. Since microbial community is significantly influenced by environmental factors, especially nutrient content, these physiochemical properties could be more meaningful in the following RDA analysis.
Analysis of species diversity of sediment microbial communities in Bahe River Basin
Pan/core species analyses
According to the high-throughput sequencing technique, there are 63 phyla, 201 classes, 464 orders, 770 families, 1590 genera, 3477 species, and 10,127 OTUs in the sediments of the Bahe River Basin. Using pan-OTU, we observed an increase in the total OTU number as the number of samples increased. It was used to observe the decrease in the number of common OTUs as the number of samples increased. As illustrated in Additional file 1: Fig. S2, for the 18 sequenced samples obtained from the pan/core species analyses, the curves gradually flatten out, indicating that the sample size is sufficient and can be used to determine the abundance of the sediment microbial communities of the Bahe River Basin and for the subsequent evaluation and analysis of the number of core species.
Alpha diversity analysis
The species richness in the sediment microbial communities of the Bahe River Basin was obtained using diversity index analysis and was expressed using statistical analysis indices (Sobs, Chao, and Ace), which can also reflect the biotic and microbiological activities. The Sobs index represents the actual observed abundance, and the Chao and Ace indices represent the species richness. As displayed in Fig. 2a–c, the average values of the three indices at the OTU classification level were higher than 2000, indicating that the selected sequencing samples reflect the species richness of the sediment microbial communities of the Bahe River Basin. The Shannon index primarily reflects the diversity of microbial communities with a higher Shannon value indicating high community diversity. As illustrated in Fig. 2d, the Shannon index of the Bahe River Basin was higher than the average value of 6, indicating that the microbial community diversity in the sediments of the Bahe River Basin is high.
Microbial community composition analysis in sediments of Bahe River Basin
Venn diagram analysis of microbial species in sediments of Bahe River Basin
Ten dominant microbial populations, including Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidota, were tested for their differences. The microbial community characteristics of Bacteroidota in the upper, middle and lower reaches of the Bahe River Basin were significantly different (P < 0.05) (Fig. 3). Some literatures showed that many species of bacteroidetes live in the intestines of humans and animals and sometimes become pathogens, in feces, Bacteroides is the main microorganism in terms of the number of cells, flavobacteriaceae exist mainly in aquatic environments, which can degrade cellulose [56, 13, 41]. Bacteroidota were all detected in the upper, middle and lower reaches of the Bahe River Basin, it showed that domestic sewage or aquaculture wastewater (such as feces) was the important source in the Bahe River Basin. Venn diagram can be seen in Additional file 1: Fig. S3 that the river is divided into the upper (points B1–B6), middle (points B7–B12), and lower reaches (points B13–B18). There were 3259 common species of microorganisms in the Bahe River Basin sediments. The unique microbial sequences in the sediments of the upper, middle, and lower reaches of the Bahe River Basin included 963 species, 800 species, and 1150 species, respectively. The microbial diversity of the sediments in the Bahe River Basin was in the following order: lower reaches > middle reaches > upper reaches (Additional file 1: Fig. S3).
Analysis of community composition in sediments of Ba river basin
The community composition histogram visually presents two types of information: (1) the dominant species contained in each sample at a certain taxonomic level and (2) the relative abundance of each dominant species in the sample (Fig. 4). As can be seen from Fig. 4a, at the phylum level, the dominant species of the sediment microbial communities in the river basin are Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Acidobacterota, Bacteroidota and Desulfobacterota, accounting for over 90% of the total microbial community. Of these, Desulfobacterota can oxidise reduced sulphides (e.g. H2S, \({\text{S}}_{2} {\text{O}}_{3}^{2 - }\), etc.) and elemental sulphur. The existence of Desulfobacterota reduces the content of sulphides in the river water and thus reduces the risk of polluted water, which is of significance in improving the river water quality [29,30,31].
As can be seen from Fig. 4a, the microbial population in the sediments of the Bahe River Basin is primarily composed of Proteobacteria (13.86–69.14%), Firmicutes (1.45–58.33%), Chloroflexi (3.68–26.18%), Actinobacteriota (2.7–21.51%), Acidobacterota (0.73–16.36%), Bacteroidea (1.53–14.11%), and Thermodesulfobacteria (0.1–8.9%). Such community composition is consistent with other urban rivers, indicating Baha River is a typical urban river [1, 9]. Some researchers found that benthic bacterial communities were clearly more diverse and uniform than surface bacterioplankton communities [14]. The relative abundances of Acidobacteria, proteobacteria and Chloroflexi were higher in sediment than in water samples [35]. In particular, several sewer- and fecal-pollution bacterial indicators were observed in sediment samples, implying that the water bodies of Bahe river were contaminated by sewer- and fecal-pollution.
The average abundance of the Proteobacteria population in the Bahe River Basin is high, particularly at points B1, B2, and B14, accounting for over 50% of the microbial population, and it is one of the dominant species at the other points. Figure 4a, the analysis of the species distribution and proportions at the phylum level demonstrated that the phyla in the microbial community at point B1 in the Bahe River Basin from high to low are Proteobacteria (51.8%), Actinobacteriota (22.3%), Acidobacterota (7.68%), Chloroflexi (5.55%), Firmicutes (4.83%) and others. Proteobacteria was the main component of microorganisms, which was consistent with previous research results [23, 30, 34]. At point B7, the population of Firmicutes accounts for over 50% of the microbial community, indicating that more OM is decomposed at this point. Firmicutes is important biological resources for degrading carbohydrates [34]. The distribution proportions of phyla in the microbial community at point B18 in the Bahe River Basin are Proteobacteria (28.5%) > Chloroflexi (15.1%) > Acidobacteriota (13.9%) > Actinobacteriota (12.0%) > Firmicutes (7.5%) > Desulfobaacteria and others. The relative abundance of the other predominate phyla is lower than that of Proteobacteria and Firmicutes, indicating that the relative contents of organic carbon and nitrates may be lower at these points. As can be seen from Fig. 4b, the dominant species in the sediment microbial communities of the Bahe River Basin are Gammaproteobacteria, Alphaproteobacteria, Anaerolineae, Bacilli, Bacteroidota, Actinobacteriota, Clostridia, and Vicinamibacteria, accounting for over 70% of the total microbial community. Similar results were also observed by a prior field research of microbial community in sediments by 16S rRNA sequences [24, 14].
Hierarchical clustering analysis of sediments in Bahe River Basin
Figure 5 displays the hierarchical clustering analysis of the sediment microbial communities in the Bahe River Basin at the phylum, class, family, and genus classification levels. From Fig. 5, it can be seen that there are significant differences between point B7 and the microbial communities at the other sampling points at all classification levels. The population of Firmicutes accounts for over 50% of the microbial community (Fig. 5a), Some reports showed that Firmicutes and Bacteroidetes communities are important biological resources for degrading carbohydrates such as rice straw and dietary fiber [34]. Under anaerobic conditions, Firmicutes and Bacteroidetes communities can degrade simple or complex organics (such as cellulose, hemicellulose and lactic acid) into pyruvate and acetyl coenzyme A, and then produce metabolites such as ethanol and methane [3].
Hierarchical clustering analysis of microbial communities in the sediments of the Bahe River Basin at the family level (Fig. 5d) revealed that Sphingomonadaceae, Xanthomonadaceae, Camobactericaeae, Rhodobacteraceae of alpha-3-Proteobacteria, Comamonadaceae, and Clostridlaceae are the dominant species in the sediment microbial communities of the Bahe River Basin at the family level, and the other microbial communities account for over 50% of the total microbial community. Of these, the sediment microbial communities at points B11 and B14 of the Bahe River Basin show similarity, and those at points B2, B4, and B6 show similarity.
Response relationship between environmental factors and microbial communities
The RDA results reflect the relationship between the sediment bacterial population and environmental factors. The principal components in Fig. 6a explained 57.1% and 18.4% of the variation in the sediment bacterial communities at the phylum level while the principal components in Fig. 6b explain 42.56% and 19.48% of the variation in the sediment bacterial communities at the class level. Of these, the environmental factors pH, EC, MC, OM, TP, DO were positively correlated each other, and these environmental factors controlled the abundance of microbial community at the phylum level at points B5, B8, B9, B10, B13, B15, B17, and B18 of sediments in the Bahe River, while these environmental factors were negatively correlated with ORP, \({\text{NH}}_{4}^{ + }\)-N, T, and they limited the abundance of microbial community at the phylum level at points B1, B2, B11, B14 of sediments in the Bahe River (Fig. 6a). Analysis based on Additional file 1: Fig. S4, the concentration of TN was significant positive correlation with part of microbial community (i.e., Dependentiae, Nitrospirota, Planctomycetota and DTN120) at the phylum level in the Bahe River Basin. The RDA indicated that population, industrial wastewater, domestic sewage, livestock production were positively correlated with nitrogen pollution of river waters [33]. It was speculated that the concentration of nitrogen maybe impact on the structure of microbial community. Some researchers found that nutrients (e.g., nitrogen and phosphorus) was influential on the bacterial community structures [35]. Meanwhile, microbial community structure was related to land type and source, namely the human influence in Bahe basin. The previous reports shown that forestlands and grasslands were negatively correlated with nitrogen pollution of river water [33]. It was reported that in Turag River, pollution from factories along the river significantly changed the environmental conditions such as DO, COD and BOD5 nearby, which could be the key factors determining the longitudinal distribution pattern of the microbial community [32]. The strength of stressor inflow, namely the volume, also had crucial influence on the distribution of nutrient and microorganisms [61]. However, that habitat probably have more influence than pollution on microorganisms [1]. It can be seen from the land type around sampling points in Fig. 1 that B17 and B18 were close to forestlands, while sampling points B3, B5, B8 and B10 were close to grasslands, which was similar to the results presented by Shi et al. [33].
The environmental factors pH, MC, OM, and TP are positively correlated with each other, and these environmental factors controlled the abundance of microbial community at the class level at points B5-6, B8-10, B12-13, B15-18 of sediments in the Bahe River, while these environmental factors were negatively correlated with COD, ORP, \({\text{NH}}_{4}^{ + }\)-N, T, and they limited the abundance of microbial community at the class level at points B1, B2, B11, B14 of sediments in the Bahe River (Fig. 6b). Microbial abundance and diversity are particularly critical to the control of the denitrification rate [59]. The bacterial communities in the sediments of the Bahe River Basin exhibit high diversity, and the seven primary bacterial families discovered in the present study are consistent with previous reports [58, 60]. Researches have proved that environmental factors could be changeable in different season, which could significantly influence the microbial community [39]. Therefore, future research about seasonal transformation of dynamics between environmental factors and microbial community is highly recommended.
Management measures for water quality improvement in the urban river
The nitrogen and phosphorus in the upper and lower reaches of the Bahe river mainly came from domestic sewage treatment plant. The nutrients pollution was considerably affected by human activities in the Bahe river. The water quality of the Bahe river at the downstream of B5 point and the upstream of B8 point were better than other sample points, and were less affected by the tail water of the sewage treatment plant. The inlet water of the sewage treatment plant should control the mixing of external water (i.e., rainwater, groundwater and river water) into the sewage pipe network. It is necessary to continue to rectify the mixing and misconnecting of the pipe network and improve the efficiency of the sewage transmission system. Meanwhile, optimizing chemical fertilizer application rates and employing deep fertilizing techniques will improve fertilizer use efficiency.