The bacterial community structure and N-cycling gene abundance in response to dam construction in a riparian zone

Exploring the distribution and co-occurrence of rpf-like genes and nitrogen-cycling genes in water reservoir sediments

Water reservoir sediments represent a distinct habitat that harbors diverse microbial resources crucial for nitrogen cycling processes. The discovery of resuscitation promoting factor (Rpf) has been recognized as a crucial development in understanding the potential of microbial populations. However, our understanding of the relationship between microorganisms containing rpf-like genes and nitrogen-cycling functional populations remains limited. The present study explored the distribution patterns of rpf-like genes and nitrogen-cycling genes in various water reservoir sediments, along with their correlation with environmental factors. Additionally, the co-occurrence of rpf-like genes with genes associated with the nitrogen cycle and viable but non-culturable (VBNC) formation was investigated. The findings indicated the ubiquitous occurrence of Rpf-like domains and their related genes in the examined reservoir sediments. Notably, rpf-like genes were predominantly associated with Bradyrhizobium, Nitrospira, and Anaeromyxobacter, with pH emerging as the primary influencing factor for their distribution. Genera such as Nitrospira, Bradyrhizobium, Anaeromyxobacter, and Dechloromonas harbor the majority of nitrogen-cycling functional genes, particularly denitrification genes. The distribution of nitrogen-cycling microbial communities in the reservoir sediments was mainly influenced by pH and NH4 +. Notably, correlation network analysis revealed close connections between microorganisms containing rpf-like genes and nitrogen-cycling functional populations, as well as VBNC bacteria. These findings offer new insights into the prevalence of rpf-like genes in the water reservoir sediments and their correlation with nitrogen-cycling microbial communities, enhancing our understanding of the significant potential of microbial nitrogen cycling.

Elucidation of the dominant factors influencing N2O emission in water-level fluctuation zones in a karst canyon reservoir, southwest China

The water-level fluctuations zones (WLFZs) are crucial transitional interfaces within river-reservoir systems, serving as hotspots for N2O emission. However, the comprehension of response patterns and mechanisms governing N2O emission under hydrological fluctuation remains limited, especially in karstic canyon reservoirs, which introduces significant uncertainty to N2O flux assessments. Soil samples were collected from the WLFZs of the Hongjiadu (HJD) Reservoir along the water flow direction from transition zone (T1 and T2) to lacustrine zone (T3, T4 and T5) at three elevations for each site. These soil columns were used to conduct simulation experiments under various water-filled pore space gradients (WFPSs) to investigate the potential N2O flux pattern and elucidate the underlying mechanism. Our results showed that nutrient distribution and N2O flux pattern differed significantly between two zones, with the highest N2O fluxes in the transition zone sites and lacustrine zone sites were found at 75 % and 95 % WFPS, respectively. Soil nutrient loss in lower elevation areas is influenced by prolonged impoundment durations. The higher N2O fluxes in the lacustrine zone can be attributed to increased nutrient levels resulting from anthropogenic activities. Furthermore, correlation analysis revealed that soil bulk density significantly impacted N2O fluxes across all sites, while NO3-and SOC facilitated N2O emissions in T1-T2 and T4-T5, respectively. It was evident that N2O production primarily contributed to nitrification in the transition zone and was constrained by the mineralization process, whereas denitrification dominated in the lacustrine zone. Notably, the annual N2O efflux from WLFZs accounted for 27 % of that from the water-air interface in HJD Reservoir, indicating a considerably lower contribution than anticipated. Nevertheless, this study highlights the significance of WLFZs as a vital potential source of N2O emission, particularly under the influence of anthropogenic activities and high WFPS gradient.

Response of the nitrogen processing bacterial community to water level fluctuation and nitrate availability in an intact marsh soil column

Wetlands are known to experience fluctuations in water levels and receive exogenous nitrogen inputs that affect various organisms, including soil microorganisms. To study the impact of these factors on microbial diversity, we collected intact soil columns from a Phragmites australis-dominated site in the Qixing River National Nature Reserve in Northeast China. In a laboratory experiment, we simulated water level fluctuations and exogenous nitrogen inputs to the soil columns and examined the associated changes in the relative abundance of 51 bacterial genera involved in nitrogen cycling processes. Our findings revealed that different bacterial genera exhibited varying relative abundances across treatments. Specifically, Massilia showed the highest total relative abundance at the genus level, while Planctomyces had the second highest, and Campylobacter had the lowest abundance. The DESeq2 model, based on negative binomial distribution, revealed that the tags of bacterial genera were significantly correlated with soil depth, but not with water levels or nitrogen concentrations. However, the addition of a 30 mg/L nitrate solution caused a decrease in the relative abundances of bacterial genera with decreasing water levels, while a 60 mg/L concentration of nitrogen resulted in a decrease and then an increase in the relative abundances of bacterial genera with decreasing water levels. Our study provides valuable insights into the response of nitrogen-cycling bacteria to changes in different environmental conditions.

Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China

The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.

Responses of bacterial community and N-cycling functions stability to different wetting-drying alternation frequencies in a riparian zone

Wetting-drying alternation (WD) of the soil is one of the key characteristics of riparian zones shaped by dam construction, profoundly impacting the soil microenvironment that determines the bacterial community. Knowledge concerning the stability of bacterial community and N-cycling functions in response to different frequencies of WD remains unclear. In this study, samples were taken from a riparian zone in the Three Gorges Reservoir (TGR) and an incubation experiment was conducted including four treatments: constant flooding (W), varied wetting-drying alternation frequencies (WD1 and WD2), and constant drying (D) (simulating water level of 145 m, 155 m, 165 m, and 175 m in the riparian zone respectively). The results revealed that there was no significant difference in the diversity among the four treatments. Following the WD1 and WD2 treatments, the relative abundances of Proteobacteria increased, while those of Chloroflexi and Acidobacteriota decreased compared to the W treatment. However, the stability of bacterial community was not affected by WD. Relative to the W treatment, the stability of N-cycling functions estimated by resistance, which refers to the ability of functional genes to adapt to changes in the environment, decreased following the WD1 treatment, but showed no significant change following the WD2 treatment. Random forest analysis showed that the resistances of the nirS and hzo genes were core contributors to the stability of N-cycling functions. This study provides a new perspective for investigating the impacts of wetting-drying alternation on soil microbes.

Mill dams impact microbiome structure and depth distribution in riparian sediments

Introduction

Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function.

Methods

Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States.

Results

We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification.

Discussion

Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.

Insight into the microbial nitrogen cycle in riparian soils in an agricultural region

Riparian zones are considered as an effective measure on preventing agricultural non-point source nitrogen (N) pollution. However, the mechanism underlying microbial N removal and the characteristics of N-cycle in riparian soils remain elusive. In this study, we systematically monitored the soil potential nitrification rate (PNR), denitrification potential (DP), as well as net N₂O production rate, and further used metagenomic sequencing to elucidate the mechanism underlying microbial N removal. As a whole, the riparian soil had a very strong denitrification, with the DP 3.17 times higher than the PNR and 13.82 times higher than the net N₂O production rate. This was closely related to the high soil NO₃^--N content. In different profiles, due to the influence of extensive agricultural activities, the soil DP, PNR, and net N₂O production rate near the farmland edge were relatively low. In terms of N-cycling microbial community composition, the taxa of denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction accounted for a large proportion, all related to NO₃^--N reduction. The N-cycling microbial community in waterside zone showed obvious differences to the landside zone. The abundances of N-fixation and anammox genes were significantly higher in the waterside zone, while the abundances of nitrification (amoA&B&C) and urease genes were significantly higher in the landside zone. Furthermore, the groundwater table was an important biogeochemical hotspot in the waterside zone, the abundance of N-cycle genes near the groundwater table was at a relative higher level. In addition, compared to different soil depths, greater variation in N-cycling microbial community composition was observed between different profiles. These results reveal some characteristics of the soil microbial N-cycle in the riparian zone in an agricultural region and are helpful for restoration and management of the riparian zone.

Land-Water Transport and Sources of Nitrogen Pollution Affecting the Structure and Function of Riverine Microbial Communities

The characterization of variations in riverine microbiota that stem from contaminant sources and transport modes is important for understanding biogeochemical processes. However, the association between complex anthropogenic nitrogen pollution and bacteria has not been extensively investigated owing to the difficulties faced while determining the distribution of nitrogen contaminants in watersheds. Here, we employed the Soil and Water Assessment Tool alongside microbiological analysis to explore microbial characteristics and their responses to complex nitrogen pollution patterns. Significant variations in microbial communities were observed in sub-basins with distinct land-water pollution transport modes. Point source-dominated areas (PSDAs) exhibited reduced microbial diversity, high number of denitrification groups, and increased nitrogen cycling compared with others. The negative relative deviations (-3.38) between the measured and simulated nitrate concentrations in PSDAs indicated that nitrate removal was more effective in PSDAs. Pollution sources were also closely associated with microbiota. Effluents from concentrated animal feeding operations were the primary factors relating to the microbiota compositions in PSDAs and balanced areas. In nonpoint source-dominated areas, contaminants from septic tanks become the most relevant sources to microbial community structures. Overall, this study expands our knowledge regarding microbial biogeochemistry in catchments and beyond by linking specific nitrogen pollution scenarios to microorganisms.

Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland

The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.

Dam construction alters planktonic microbial predator‒prey communities in the urban reaches of the Yangtze River

While dam construction supports social and economic development, changes in hydraulic conditions can also affect natural aquatic ecosystems, especially microbial ecosystems. The compositional and functional traits of multi-trophic microbiota can be altered by dam construction, which may result in changes in aquatic predator-prey interactions. To understand this process, we performed a large-scale sampling campaign in the urban reaches of the dam-impacted Yangtze River (1 995 km) and obtained 211 metagenomic datasets and water quality data. We first compared the compositional traits of planktonic microbial communities upstream, downstream, and in a dam reservoir. Results showed that Bacteroidetes (R-strategy) bacteria were more likely to survive upstream, whilst the reservoir and downstream regions were more conducive to the survival of K-strategy bacteria such as Actinobacteria. Eukaryotic predators tended to be enriched upstream, whilst phototrophs tended to be enriched in the reservoir and downstream regions. Based on bipartite networks, we inferred that the potential microbial predator-prey interactions gradually and significantly decreased from upstream to the downstream and dam regions, affecting 56% of keystone microbial species. Remarkably, functional analysis showed that the abundance of the photosynthetic gene psbO was higher in the reservoir and downstream regions, whilst the abundance of the KEGG carbohydrate metabolic pathway was higher upstream. These results indicate that dam construction in the Yangtze River induced planktonic microbial ecosystem transformation from detritus-based food webs to autotroph-based food webs.

Submergence in the Dry Season Alters Microbial Nitrogen Transformations in the Root Zone of Carex cinerascens: A Mesocosm Study in One Floodplain Lake

The increasing demand for water resources has triggered a series of water level regulation (WLR) projects, which exerts considerable effects on local hydrologic conditions. In particular, artificial impoundments, which may occur during the dry season in wetlands, increase the periods of waterlogging. However, little is known about their potential effects on biogeochemical cycling. To evaluate how impoundments affect nitrogen (N) cycling in the floodplain ecosystem, we conducted a mesocosm experiment to investigate N dynamics and the potential N-gene changes in the root-zone soil of the dominant plant in one large floodplain lake (Poyang Lake, China). The results indicated that, compared with the control, the 12 cm submergence treatment (SP₁₂) caused NH₄ ⁺-N accumulation in the root-zone soil on day 14 and day 41. On the contrary, NO₃ ^--N levels in SP₁₂ were statistically lower than those in the control from day 7 to day 28. The curve of organic N had a tendency of declining as a whole. Changes in N-gene abundances revealed that SP₁₂ significantly inhibited nitrification and enhanced denitrification in root-zone soil. Moreover, SP₁₂ enhanced the links and complexity of the N-gene network, reflecting the increased correlations among the N transformations under flooding stress. Considering the increasing demand for WLR worldwide, the study about the effects of anti-seasonal submergence on biogeochemical cycling in floodplains provides insight into the ecological impacts of anthropogenic activities.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13157-022-01656-1.

The mechanism of C-N-S interconnection degradation in organic-rich sediments by Ca(NO3)2 - CaO2 synergistic remediation

The rebound of black-odorous occurred in organic-rich sediments has become a critical issue due to its great harm to the ecological environment. Elements such as S, C, and N play a crucial role in the biogeochemical cycle of black-odorous rivers. As electronic acceptors, Ca(NO₃)₂ and CaO₂ can effectively remove acidified volatile sulfide (AVS) and organic matter to control the black-odorous rebound. However, the remediation mechanisms in organic-rich sediments by Ca(NO₃)₂ and CaO₂ are unclear. The present study explored the mechanism of C-N-S interconnection degradation in organic-rich urban river sediments by adding different ratios and sequences of Ca(NO₃)₂ and CaO₂. The results showed that Ca(NO₃)₂ remediation followed by CaO₂ and the accepted electron ratio 1:1 of Ca(NO₃)₂ to CaO₂ is an effective method for controlling the rebound of black-odorous and reducing the accumulation NO₂^--N. Mainly attributed to that, CaO₂ enhanced the degradation of organic matter by stimulating enzymatic activities in the sediments, which is also the main reason for controlling the rebound of black-odorous. Since CaO₂ releases O₂ and •OH, which inhibit nosZgenes, NO₂^--N accumulates when remedied simultaneously with Ca(NO₃)₂ and CaO₂. Co-occurrence network analysis illustrated that sulfur-driven autotrophic denitrification bacteria, heterotrophic denitrifying bacteria, and sulfate-reducing bacteria interact strongly inside one module, clarifying a solid interaction of C-N-S substances among these bacteria. Our results reveal the C-N-S interconnection degradation mechanism and provide a new perspective on applying biochemical remediation in organic-rich urban river sediments.

Effect of poplar ecological retreat project on soil bacterial community structure in Dongting Lake wetland

As an important environmental protection measure, the Poplar Ecological Retreat (PER) project aims to restore the ecology of the Dongting Lake (DL, China’s second largest freshwater lake) wetland. And its ecological impact is yet to be revealed. This study selected soil bacterial community structure (BCS) as an indicator of ecological restoration to explore the ecological impact of PER project on DL wetland. Soil samples were collected from reed area (RA, where poplar had never been planted, as the end point of ecological restoration for comparison in this study), poplar planting area (PA), poplar retreat for 1-year area (PR1A) and poplar retreat for 2 years area (PR2A), then their soil properties and BCS were measured. The results showed that the PER project caused significant changes in soil properties, such as the soil organic matter (SOM) and moisture, and an increase in the diversity and richness index of soil BCS. The Shannon-wiener index of RA, PA, PR1A and PR2A were 3.3, 2.63, 2.75 and 2.87, respectively. The number of operational taxonomic units (OTUs) changed similarly to the Shannon-wiener index. The Pearson correlation analysis and redundancy analysis (RDA) showed that the poplar retreat time, SOM and moisture content were the main factors leading to the increase of BCS diversity. All of these indicated that after the implementation of the PER project, the ecology of the lake area showed a trend of gradual recovery.

Response of CO2 and CH4 transport to damming: A case study of Yulin River in the Three Gorges Reservoir, China

The growing number of dams in the Three Gorges Reservoir (TGR) make tributaries of TGR into spatially complex and temporally dynamic systems. To assess the influence of damming on the carbon emission in the tributary of TGR, we investigated the spatial heterogeneity of CO₂, CH₄, organic carbon, inorganic carbon, and evaluated the transport mechanisms of CO₂ and CH₄ within water column during different TGR operation periods. We found that mean CO₂ and CH₄ concentrations in water downstream (44.04 and 0.44 μmol L^-1 for CO₂ and CH₄, respectively) were lower than upstream (48.36 and 1.63 μmol L^-1 for CO₂ and CH₄, respectively) in the impoundment period of TGR, which was consistent with the spatial variations of organic carbon. In the drainage period of TGR, the mean CO₂ concentration of upstream (58.71 μmol L^-1) was significantly lower than that of downstream (88.92 μmol L^-1). The higher CO₂ concentration downstream was attributed to terrestrial input and higher microbial diversity of the water column, while the lower CO₂ concentration upstream was due to the photosynthesis of phytoplankton. Furthermore, low CH₄ concentrations (less than 0.1 μmol L^-1) of both upstream and downstream were detected in the drainage period. Based on results of 16s rRNA sequencing, quantitative PCR, and functional prediction, it was indicated that aerobic CH₄ oxidation predominantly in the bottom water layer reduced CH₄ of the water column in drainage period. Our results expand the theory of CO₂ and CH₄ transport within the water column in complex river systems and provide theoretical references for the distribution of carbon in the dammed tributaries of TGR.

Spatial distribution of antibiotic resistance genes of the Zaohe-Weihe Rivers, China: exerting a bottleneck in the hyporheic zone

The hyporheic zone (HZ) is an active biogeochemical region where groundwater and surface water mix and a potential reservoir for antibiotic resistance genes (ARGs). In this paper, the relative abundance and spatial distribution of ARGs in the HZ media were investigated, taking into consideration both the five speciation of six metals and the local characteristics. The samples of surface water, groundwater, and sediment were collected from Zaohe-Weihe Rivers of Xi'an City, which is a representative city with characteristics of the northwest region of China. Of 271 ARGs associated with 9 antibiotics, 228 ARGs were detected, with a total detection rate of 84%. Sulfonamide and aminoglycoside ARGs were the dominant types of ARGs. The top 6 ARGs and mobile genetic elements (MGEs) in terms of abundance were tnpA-04, cepA, sul1, aadA2-03, sul2 and intI1. The results of principal component analysis (PCA) showed that the distribution characteristics of ARGs were not associated with the sampling sites but with the environmental medias. Similarity in the water phases and significant differences in the water and sediment phases were found. The redundancy analysis (RDA) identified the key factors controlling ARG pollution, including dissolved oxygen (DO) in surface water, total nitrogen (TN) in groundwater, and total organic carbon (TOC) in sediment. In terms of the speciation of heavy metals, we further revealed the promotion effect between ARGs and heavy metals, especially the residual fraction of Ni. In terms of horizontal transfer mechanism, ARGs were significantly correlated with tnpA-03 in water phase and tnpA-04 in sediment. In the three media, intI1 and ARGs all show a significant correlation. These findings showed that hyporheic zone exerted a bottleneck effect on the distribution and transfer of ARGs.