Denitrification-related microbial functional groups in river water are shaped by anthropogenic land uses
As decomposers, microbiota play vital roles in N and P cycles in ecosystems (Dijkstra et al., 2012). Soil erosion can increase N and P in water (Ma et al., 2016). When N concentrations increase in the water environment, nitrifying and denitrifying bacteria could colonize in large numbers (Geets et al., 2007). Here, we observed that the N concentrations in river water increased with increases in proportions of agricultural and urbanized land area (Fig. 4). We speculate that anthropogenic land uses may stimulate nitrification and denitrification-related microbial functional groups. The results of functional gene prediction showed that the microbial functional groups were associated with denitrification, N cycle, and Fe and Mn respiration in the river areas under mainly agricultural and urbanized land uses, with their relative abundances positively correlated with TN, NH4+-N, NO3--N, and NO2--N concentrations in river water (Fig. 5).
Through metagenomic analysis, Wang et al. (2022) found that denitrifying bacterial community abundance was markedly improved near a sewage plant. In the present study, the impacts of anthropogenic disturbance on denitrifying bacteria in the freshwater river ecosystems were variable. The processes of N respiration, nitrate respiration, and nitrite respiration constitute denitrification, which is accompanied by the production of gaseous N such as nitric oxide (NO), N2O, and N2 (Torralbo et al., 2017). Potential strategies of reducing the emission of N2O, a GHG, have attracted considerable attention (López et al., 2013, Rafique et al., 2014). Considering N pollution and GHG emissions, it is essential to reduce TN, NH4+-N, NO3--N, and NO2--N concentrations in river areas disturbed by agricultural and urbanized land use activities.
Microbial responses to environmental change are complex (Scheuerl et al., 2020). Recently, Xun et al. (2021) found that bacterial communities with higher phylogenetic diversity tend to be more stable, implying that microbiota with higher biodiversity are more resistant to disturbance. In the present study, we predicted the microbial functions involved in the synthesis of major and trace elements required for bacterial growth. In the river area mainly under forest land, the major functional groups were related to methylotrophy (Tami et al., 2015), methanol oxidation (Pastawan et al., 2020), anoxygenic photoautotrophy S oxidation, anoxygenic photoautotrophy H2 oxidation, aerobic anoxygenic phototrophy (Sasikala et al., 1995), oxidation, nitrite ammonification (Howie-Esquivel et al., 2010), nitrate ammonification, nitrification, aerobic nitrite oxidation, anoxygenic photoautotrophy, aerobic NH3 oxidation, and microelement (Mn and Fe) oxidation. Most of the functions are involved in the synthesis of organic compounds with complex structures to support bacterial growth. The relative abundances of carbon metabolism-related functions were also higher in the river area under mainly forest land use, compared with that under mainly agriculture and urbanization (Fig. 5b). Therefore, microbial community structures under agricultural sites were simpler than those under forest sites in the river ecosystems.
In the present study, microbial community composition and functional groups were influenced not only by land-use types but also by elevation in the river areas of the Qinling tributaries. The alpha diversity of microbiota in river water was the lowest and the microbial functional groups were the fewest in the Qinling tributaries. Due to the associated low temperature and nutrient concentrations (Fig. S3), high elevations are not conducive for the normal growth of microbiota (Zhang et al., 2013). Consequently, severe natural disturbance can also reduce microbial stability in freshwater river waters.
Land-use disturbance by agriculture and urbanization has long-term impacts on microbial functional groups in river sediment
It is generally considered that microbial community functions in sediment are more diverse than those in the water column. Sediment microbiota mainly participate in organic decomposition, N and P cycling, and water pollution remediation in rivers (Kallmeyer et al., 2012, Meng et al., 2019 and Wu et al., 2021). Long-term natural evolution and human activities shape microbial community composition in sediment (Huang et al., 2021, Hung et al., 2021 and Marshall et al., 2019). In the present study, we observed that the functional composition of sediment microbiota was altered by different land-use types in the freshwater rivers. There were numerous functional groups associated with denitrification and human (e.g., multiple denitrifications, human pathogens, human gut metabolism, mammal gut metabolism, and organic synthesis) in the river ecosystems, mainly under agricultural and urbanized land use (Fig. S6). However, only organic synthesis and nitrification-related functional groups were observed in the river ecosystems under mainly forest land use, with few functional groups associated with human and denitrification.
Considering the environmental factors and microbial community composition, land-use type shapes microbial functional groups in rivers. Furthermore, the human-related microbial functional groups detected in the sediment provide strong evidence of the impact of anthropogenic land use on microbial functional groups in river sediment (Fig. 6c-d). Similarly, microbial functional groups have been applied in the measurement of microbial water quality responses to land-use type using fecal indicator bacteria and molecular source tracking in rivers and near-shore surface waters (Verhougstraete et al., 2012).
In the present study, the major functional groups of sediment microbiota were similar to those predicted in river water; the relative abundances of functional groups associated with C metabolism and metal metabolism were lower in sediment in river ecosystems under mainly agricultural and urbanized land uses than under forest land use, with opposite trends observed for functional groups associated with N metabolism and human or mammal gut metabolism. Through LEfSe analysis, we identified the microbial functional groups that were characteristic of river sediment (Fig. 6a-b). Denitrification and human-related microbial functional groups were relatively abundant in the sediment of rivers mainly under agricultural and urbanized land uses, whereas few human-related microbial functional groups were observed in the sediment of rivers mainly under forest land use. Overall, the results indicate that the microbial functional groups in freshwater river sediment were influenced by land-use type.