Community assembly mechanisms and co-occurrence patterns of nitrite-oxidizing bacteria communities in saline soils

Runoff variation alters estuarine sediment microbiome and nitrogen removal processes by affecting salinity

Runoff variations shape the dynamics of the estuarine environmental factors, profoundly influencing the nitrogen cycle in estuarine sediments. However, our understanding of how these changes regulate microbially-mediated nitrogen removal processes remains limited. In this study, the impacts of changes in environmental factors caused by normal and low runoffs on denitrification and anammox in sediments of the Liao River Estuary in China, were investigated, using continuous-flow experiments combined with 15N tracing techniques and molecular methods. Results indicated that denitrification was the main nitrogen removal process in estuarine sediments under both runoff conditions. Elevated salinity under low runoff condition increased the abundance of nitrifying bacteria (Nitrospina, Nitrosomonas and Nitrosomonadaceae), thereby promoting the coupled nitrification-denitrification nitrogen removal process. Furthermore, seawater intrusion under low runoff contributed to dilute nitrite concentrations, resulting in decreased denitrification rates in sediments. Overall, this study highlighted the impacts of runoff variations on biological nitrogen removal process through affecting environmental factors, gene abundance and microbial community in the estuary.

Salinity affects microbial function genes related to nutrient cycling in arid regions

Introduction

Salinization damages soil system health and influences microbial communities structure and function. The response of microbial functions involved in the nutrient cycle to soil salinization is a valuable scientific question. However, our knowledge of the microbial metabolism functions in salinized soil and their response to salinity in arid desert environments is inadequate.

Methods

Here, we applied metagenomics technology to investigate the response of microbial carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling and the key genes to salinity, and discuss the effects of edaphic variables on microbial functions.

Results

We found that carbon fixation dominated the carbon cycle. Nitrogen fixation, denitrification, assimilatory nitrate reduction (ANRA), and nitrogen degradation were commonly identified as the most abundant processes in the nitrogen cycle. Organic phosphorus dissolution and phosphorus absorption/transport were the most enriched P metabolic functions, while sulfur metabolism was dominated by assimilatory sulfate reduction (ASR), organic sulfur transformation, and linkages between inorganic and organic sulfur transformation. Increasing salinity inhibited carbon degradation, nitrogen fixation, nitrogen degradation, anammox, ANRA, phosphorus absorption and transport, and the majority of processes in sulfur metabolism. However, some of the metabolic pathway and key genes showed a positive response to salinization, such as carbon fixation (facA, pccA, korAB), denitrification (narG, nirK, norBC, nosZ), ANRA (nasA, nirA), and organic phosphorus dissolution processes (pstABCS, phnCD, ugpAB). High salinity reduced the network complexity in the soil communities. Even so, the saline microbial community presented highly cooperative interactions. The soil water content had significantly correlations with C metabolic genes. The SOC, N, and P contents were significantly correlated with C, N, P, and S network complexity and functional genes. AP, NH4+, and NO3- directly promote carbon fixation, denitrification, nitrogen degradation, organic P solubilization and mineralization, P uptake and transport, ASR, and organic sulfur transformation processes.

Conclusion

Soil salinity in arid region inhibited multiple metabolic functions, but prompted the function of carbon fixation, denitrification, ANRA, and organic phosphorus dissolution. Soil salinity was the most important factor driving microbial functions, and nutrient availability also played important roles in regulating nutrient cycling.

Mapping multi-omics characteristics related to short-term PM2.5 trajectory and their impact on type 2 diabetes in middle-aged and elderly adults in Southern China

The relationship between PM2.5 and metabolic diseases, including type 2 diabetes (T2D), has become increasingly prominent, but the molecular mechanism needs to be further clarified. To help understand the mechanistic association between PM2.5 exposure and human health, we investigated short-term PM2.5 exposure trajectory-related multi-omics characteristics from stool metagenome and metabolome and serum proteome and metabolome in a cohort of 3267 participants (age: 64.4 ± 5.8 years) living in Southern China. And then integrate these features to examine their relationship with T2D. We observed significant differences in overall structure in each omics and 193 individual biomarkers between the high- and low-PM2.5 groups. PM2.5-related features included the disturbance of microbes (carbohydrate metabolism-associated Bacteroides thetaiotaomicron), gut metabolites of amino acids and carbohydrates, serum biomarkers related to lipid metabolism and reducing n-3 fatty acids. The patterns of overall network relationships among the biomarkers differed between T2D and normal participants. The subnetwork membership centered on the hub nodes (fecal rhamnose and glycylproline, serum hippuric acid, and protein TB182) related to high-PM2.5, which well predicted higher T2D prevalence and incidence and a higher level of fasting blood glucose, HbA1C, insulin, and HOMA-IR. Our findings underline crucial PM2.5-related multi-omics biomarkers linking PM2.5 exposure and T2D in humans.

Urea Fertilization Significantly Promotes Nitrous Oxide Emissions from Agricultural Soils and Is Attributed to the Short-Term Suppression of Nitrite-Oxidizing Bacteria during Urea Hydrolysis

The application of urea in agricultural soil significantly boosts nitrous oxide (N2O) emissions. However, the reason for nitrite accumulation, the period of nitrite-oxidizing bacteria (NOB) suppression, and the main NOB species for nitrite removal behind urea fertilization have not been thoroughly investigated. In this study, four laboratory microcosm experiments were conducted to simulate urea fertilization in agricultural soils. We found that within 36 h of urea application, nitrite oxidation lagged behind ammonia oxidation, leading to nitrite accumulation and increased N2O emissions. However, after 36 h, NOB activity recovered and then removed nitrite, leading to reduced N2O emissions. Urea use resulted in an N2O emission rate tenfold higher than ammonium. During incubation, Nitrobacter-affiliated NOB growth decreased initially but increased later with urea use, while Nitrospira-affiliated NOB appeared unaffected. Chlorate suppression of NOB lasted longer, increasing N2O emissions. Urease inhibitors effectively reduced N2O emissions by slowing urea hydrolysis and limiting free ammonia production, preventing short-term NOB suppression. In summary, short-term NOB suppression during urea hydrolysis played a crucial role in increasing N2O emissions from agricultural soils. These findings revealed the reasons behind the surge in N2O emissions caused by extensive urea application and provided guidance for reducing N2O emissions in agricultural production processes.

Insight into bacterial and archaeal community structure of Suaeda altissima and Suaeda dendroides rhizosphere in response to different salinity level

IMPORTANCE

Suaeda play an important ecological role in reclamation and improvement of agricultural saline soil due to strong salt tolerance. At present, research on Suaeda salt tolerance mainly focuses on the physiological and molecular regulation. However, the important role played by microbial communities in the high-salinity tolerance of Suaeda is poorly studied. Our findings have important implications for understanding the distribution patterns and the driving mechanisms of different Suaeda species and soil salinity levels. In addition, we explored the key microorganisms that played an important ecological role in Suaeda rhizosphere. We provide a basis for biological improvement and ecological restoration of salinity-affected areas.

A comprehensive insight into the abundance and community of anammox bacteria in sediments of Hangzhou Bay, China

A total of 13 surface sediments were collected from Hangzhou Bay (HZB) for an investigation into the distribution and influencing factors of anammox bacterial community. The anammox bacterial 16S rRNA and hzo genes ranged between 2.34 × 105 to 9.22 × 105 copies/g and 3.68 × 105 to 1.70 × 106 copies/g, respectively. The results of high throughput sequencing (HTS) revealed that the obtained OTUs were affiliated with five known genera, named Ca. Scalindua, Ca. Jettenia, Ca. Brocadia, Ca. Kuenenia and Ca. Anammoxoglobus. RDA analysis indicated that salinity, pH, and water depth influenced the anammox bacterial community. Furthermore, network analysis identified Ca. Scalindua as a key genus. Neutral community model (NCM) and modified stochasticity ratio (MST) indicated that the deterministic process dominated the anammox bacterial community assembly. Overall, this study offers a more comprehensive understanding of the abundance and community of anammox bacteria in the sediments of HZB.

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

Spatial and temporal changes in the assembly mechanism and co-occurrence network of the chromophytic phytoplankton communities in coastal ecosystems under anthropogenic influences

As a typical semiclosed coastal sea area in China, the ecological environment of Bohai Bay has been significantly disturbed by human activities. As primary producers, the chromophytic phytoplankton are the basis of ecosystems, especially in coastal ecosystems, and changes in the chromophytic phytoplankton community can affect the stability of the entire ecosystem. In this study, we investigated the effects of the human activity-induced spatial and temporal environmental heterogeneity on the community composition, diversity, assembly mechanisms, and co-occurrence networks of chromophytic phytoplankton in Bohai Bay during the wet season and the dry season. The results showed that in both seasons, there was obvious environmental heterogeneity between the nearshore area and the offshore area, and the nearshore areas were more affected by human disturbance. Although higher diversity was supported by the abundance of nutrients in nearshore areas, co-occurrence network analysis revealed that the chromophytic phytoplankton were less closely connected to each other in nearshore areas than in offshore areas due to chemical oxygen demand (COD), eutrophication index (EI), and dissolved inorganic nitrogen (DIN). The nearshore network was less stable than the offshore co-occurrence network in both seasons, which was related to the concentration of dissolved oxygen and COD. Both stochastic and deterministic processes dominated the assembly of the chromophytic phytoplankton communities, with different importance rankings of stochastic and deterministic processes in the nearshore and offshore areas. Drift dominated the assembly of the communities in nearshore areas, while variable selection dominated the assembly of the communities in offshore areas. DIN, EI, and COD, rather than geographic distance, were the main environmental factors affecting the phylogenetic turnover of the chromophytic phytoplankton. Our study showed that environmental heterogeneity caused by human disturbance had a greater impact on the chromophytic phytoplankton communities in Bohai Bay than natural factors such as temperature and salinity.

Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments

Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.

Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea

The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.

Ammonia level influences the assembly of dissimilatory nitrate reduction to ammonia bacterial community in soils under different heavy metal remediation treatments

Heavy metal remediation treatments might influence functional microbial community assembly. Dissimilatory nitrate reduction to ammonia (DNRA) contributes to the nitrogen retention processes in soil ecosystems. We assumed that remediation might reduce heavy metal toxicity and increase some available nutrients for the DNRA microbes, thus balancing the deterministic and stochastic process for DNRA community assembly. Here, we investigated the process of DNRA bacterial community assembly under different heavy metal remediation treatments (including control, biochar, limestone, rice straw, rice straw + limestone, and biochar + limestone) in an Alfisol soil. The abundance of DNRA bacteria diverged across treatments. The α-diversity of the DNRA bacterial community was correlated with pH, available phosphorus (AP), ammonium (NH₄⁺), and extractable Fe (EFe). Metal Cd and Fe significantly affected the abundance of the nrfA gene. The β-diversity was associated with pH, NH₄⁺, and EFe. Deterministic processes dominantly drove the assembly processes of the DNRA bacterial community. NH₄⁺ level played an essential role in the assembly processes than the other soil physicochemical properties and metal availability. High, moderate, and low levels of NH₄⁺ could advocate stochastic process plus selection, heterogeneous selection to stochastic process, and heterogeneous selection, respectively. Network analysis highlighted a predominant role of NH₄⁺ in regulating DNRA bacterial community assembly. However, the relative abundance of modules and some keystone species also were influenced by pH and EFe, respectively. Therefore, the DNRA bacterial community assembly under different heavy metal remediation treatments in this study was dominantly driven by nitrogen availability. pH, phosphorus, and metal availability were auxiliary regulators on DNRA bacterial community.

High nitrite-nitrogen stress intensity drives nitrite anaerobic oxidation to nitrate and inhibits methanogenesis

Nitrite is an important intermediate in nitrogen metabolism. We explored the effect of nitrite-nitrogen stress intensity (NNSI) on nitrite metabolism and methanogenesis in anaerobic digestion. The results showed that the NNSI regulated microbial diversity, composition, and functions, and microbial community assembly was primarily shaped by stochastic processes. Moreover, the NNSI was negatively correlated with α-diversity and positively correlated with non-metric multi-dimensional scaling distance. Denitrification gradually increased with increasing NNSI; however, methanogenesis was gradually inhibited, which was primarily due to the inhibition of the aceticlastic methanogenesis pathway (i.e., Methanosaeta) and methylotrophic methanogenesis pathway (i.e., Candidatus_Methanofastidiosum). High NNSI (1882 ± 98.99 mg/L NO₂^--N) promoted nitrite anaerobic oxidation to nitrate and was favorable for dissimilatory nitrate reduction to ammonia (DNRA). We present evidence for the microbial transformation of nitrite under anaerobic conditions, with potential geochemical and evolutionary importance. As nitrogen oxides were already present on early Earth, our finding presents the possibility of a nitrogen cycle before the evolution of oxygenic photosynthesis.

Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China

Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.

Response of substrate kinetics and biological mechanisms to various pH constrains for cultured Nitrobacter and Nitrospira in nitrifying bioreactor

Nitrite (NO₂^-) oxidation is an essential step of biological nitrogen cycling in natural ecosystems, and is performed by chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Although Nitrobacter and Nitrospira are regarded as representative NOB in nitrification systems, little attention has focused on kinetic characterisation of the coexistence of Nitrobacter and Nitrospira at various pH values. Here, we evaluate the substrate kinetics, biological mechanism and microbial community dynamics of an enrichment culture including Nitrobacter (17.5 ± 0.9%) and Nitrospira (7.2 ± 0.6%) in response to various pH constrains. Evaluation of the Monod equation at pH 6.0, 6.5, 7.0, 7.5, 8.0 and 8.5 showed that the enrichment had maximum rate (r_max) and maximum substrate affinity (K_S) for NO₂^- oxidation at pH 7.0, which was also supported by the largest absolute abundance of Nitrobacter nxrA (5.26 × 10⁷ copies per g wet sludge) and Nitrospira nxrB (1.975 × 10⁹ copies per g wet sludge) genes. Moreover, the predominant species for the Nitrobacter-like nxrA were N. vulgaris and N. winogradskyi, while for the Nitrospira-like nxrB, the predominant species were N. japonica, N. calida and Ca. N. bockiana. Furthermore, the r_max was strongly and positively correlated with the abundance of the Nitrobacter nxrA or Nitrospira nxrB genes, or N. winogradsk, whereas K_S was positively correlated with the abundance of Nitrobacter nxrA or Nitrospira nxrB genes or Ca. N. bockiana. Overall, this study could improve basis kinetic parameters and biological mechanism of NO₂^- oxidation in WWTPs.

Antibiotic resistance genes alternation in soils modified with neutral and alkaline salts: interplay of salinity stress and response strategies of microbes

Growing evidence points to the pivotal roles of salt accumulation in mediating antibiotic resistance genes (ARGs) spread in soil, whereas how salt mediates ARGs dissemination remains unknown. Herein, the effects of neutral or alkaline (Ne/Al) salt at low, moderate and high levels (Ne/Al-L, Ne/Al-M, Ne/Al-H) on the dissemination of ten typical ARGs in soils were explored, by simultaneously considering the roles of salinity stress and response strategies of microbes. In the soils amended with Ne/Al-L and Al-M salt, the dissemination of ARGs was negligible and the relative abundances of ARGs and mobile genetic elements (MGEs) were decreased. However, Ne-M and Al-H salt contributed to the dissemination of ARGs in soils, with the significantly increased absolute and relative abundances of ARGs and MGEs. In Ne-H soil, although the absolute abundance of ARGs declined drastically due to serious oxidative damage, their relative abundances were promoted. The facilitated ARGs transfer was potentially related to the excessive generation of intracellular reactive oxygen species and increased activities of DNA repair enzymes involved in SOS system. In addition, the activated intracellular protective response including quorum sensing and energy metabolism largely provided essential factors for ARGs dissemination. The co-occurrence of ARGs and over-expressed salt-tolerant genes in specific halotolerant bacteria further suggested the selection of salt stress on ARGs. Moreover, less disturbance of alkaline salt than neutral salt on ARGs evolution was observed, due to the lower abiotic stress and selective pressure on microbes. This study highlights that soil salinity-sodicity could dose-dependently reshape the dissemination of ARGs and community structure of microbes, which may increase the ecological risks of ARGs in agricultural environment.

Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata

The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.

High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling

Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m^-1). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.