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

Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem

Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.

Nitrogen fate in riparian zones: Insights from experiments and analysis of sediment porosity and surface water-groundwater exchange

Riparian zones play a vital role in the river ecosystem. Solutes in vertical riparian zones are transported being by alternating hydraulic gradients between river water and groundwater, due to natural or human activities. This study investigates the impacts of porous sediments and alternating rate of surface water-groundwater on nitrogen removal in the riparian zone through experiments based on the field sampled. The experimental results, combined with dimensionless numbers (Péclet and Damköhler) and Partial Least Squares-Path Modeling, analyze the nitrogen fate responding to hydrodynamics changes. The results show that increased sediment porosity contributes to the ammonium removal, particularly when the oxygen content of river water is low, with the removal rate up to 72.57%. High ammonium content and dissolved organic carbon (DOC) in rural rivers lead to a constant low-oxygen condition (4 mg/L) during surface water-groundwater alternation, and promote denitrification. This threatens groundwater with ammonium pollution and causes accumulation at the top of vertical riparian zones during upwelling, potentially causing secondary river pollution. However, increasing the alternating rate hinders the nitrate denitrification and drastically changes in the redox environment of the riparian zone, despite contributing to ammonium removal. Rapid oxygen consumption during aerobic metabolism and nitrification in groundwater-surface water exchange created favorable conditions for denitrification. Floodplains sediment porosity is unfavorable for nitrification. This study improves understanding of coupled hydrologic and solute processes in vertical riparian zones, informing strategies for optimizing nitrogen attenuation and riparian zone construction.

Combining effects of submerged macrophytes and lanthanum-modified bentonite on sediment enzyme activity: Evidence from mesocosm study

Lanthanum-modified bentonite (LMB) combined with submerged macrophytes (SM) has been a conventional means of eutrophication management in lakes in recent years, and is one of the most important methods for P removal. However, trends in nutrients and sediment enzymes at the water-sediment interface during this process have not been systematically assessed, and there are still some gaps in how abiotic properties drive changes in enzyme activity. Here, we show changes in aquatic environmental conditions under the action of different ratios of modified bentonite (0, 10%, 20%, and 30%) in combination with SM (Vallisneria natans, Potamogeton lucens, and Hydrilla verticillate) and quantify their effects on sediment enzyme activities. The results showed that the nutrient cycling at the water-sediment interface was facilitated by the combined effect of SM and LMB, which effectively reduced the overlying water nutrient concentration, increased the sediment enzyme activity and enhanced the N cycling process. Partial least squares structural equation model (PLS-SEM) showed that sediment parameters strongly influenced changes in enzyme activity, with NO3-N as the main controlling factors. Our study fills in the process of changing environmental conditions in lake water under geoengineered materials combined with macrophyte measures, especially the changes in biological properties enzyme activities, which contributes to a clearer understanding of nutrient fluxes during the management of eutrophication in lakes.

Elucidating biogeochemical characterization of nitrogen in the vadose zone integrating geochemistry, microorganism, and numerical simulation

A thorough comprehension of nitrogen biogeochemical processes in the vadose zone is crucial for the effective prevention and remediation of soil-groundwater system contamination. Despite the growing research on this subject, the full scope of nitrogen biogeochemical characterization in different geological environments remains poorly understood. This study addresses this knowledge gap by integrating geochemical, microbiological and numerical simulation approaches to gain a deeper insight into nitrogen biogeochemistry in agriculture. Our findings indicate the biogeochemical behavior of nitrogen in the vadose zone is mediated by microorganisms, driven by hydraulics, influenced by geological conditions and environmental factors. Along the groundwater flow, NH4+-N was found to be heavily accumulated in the topsoil of 0-40 cm, while NO3--N was transported and driven by hydrodynamics from both vertical and horizontal directions. Microbial diversity, species composition and functional microorganisms were significantly influenced by soil depth, rather than geomorphological types. Oxidation-reduction potential (ORP), total organic carbon (TOC), soil moisture (MOI), bicarbonate (HCO3-), and ferrous (Fe2+) were identified as the principal environmental factors that regulate nitrogen metabolism and the dominant biochemical processes, encompassing nitrogen fixation, nitrification, and denitrification. Driven by hydrodynamics, NH4+-N, NO2--N and NO3--N tend to form distinct biochemical reaction zones in the vertical vadose zone. These areas are dynamic and subject to geomorphologies. It should be noted that NO3--N can migrate towards groundwater from the clayey sand in the Alluvial Plain, which presents a potential risk of groundwater contamination. The fissure structure of loess may serve as the major transport pathway for groundwater nitrogen contamination in the Loess Tableland. This finding highlights the importance of integrating microbiology, geochemistry and hydraulics to elucidate the biogeochemical processes of nitrogen in the vadose zone with a dynamic mindset.

The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters

Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.

Unveiling the biogeochemical mechanism of nitrate in the vadose zone-groundwater system: Insights from integrated microbiology, isotope techniques, and hydrogeochemistry

Clarifying the biogeochemical mechanism of nitrate (NO3-) in the vadose zone-groundwater system, particularly in agricultural contexts, is crucial for mitigating groundwater NO3- pollution. However, comprehensive studies on the impacts of changes in chemical indicators and microbial communities on NO3- are still lacking. This paper aims to address this gap by employing hydrogeochemistry, stable isotopes, and microbial techniques to assess the NO3- biogeochemical processes in the vadose zone-groundwater system. The findings suggested that NO3- in upper soil layers was primarily influenced by plant root absorption, assimilation, and nitrification processes. The oxygen contents gradually decreased with the nitrification process, resulting in the occurrence of the denitrification. However, denitrification predominantly occurred in the 60-80 cm soil layer in the study area. The limited thickness of the denitrification layer results in less NO3- consumption, leading to increased NO3- leaching into groundwater. Hydrochemical and isotopic characteristics further indicated that groundwater NO3- concentrations were mainly controlled by nitrification, followed by denitrification and mixing processes. The 16S rRNA sequencing analysis revealed great influences of soil sampling depths and groundwater NO3- concentrations on the microbial community structure. Additionally, the PICRUSt2-based prediction results demonstrated a stronger potential for dissimilatory reduction of NO3- to ammonium (DNRA) in both soil and groundwater compared to the other processes, potentially due to the widespread presence of the nrfH functional genes. However, the chemical indicators and isotopes used in this study did not support the occurrence of DNRA process in the vadose zone-groundwater system. This finding highlights the importance of an integrated approach combining microbiological, isotopic, and hydrogeochemical data to comprehensive understanding biogeochemical processes. The study developed a conceptual model elucidating the NO3- biogeochemical processes in the vadose zone-groundwater system within an agricultural area, contributing to enhanced comprehension and advancement of sustainable management practices for groundwater nitrogen.