Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Nitrogen fertilization and soil nitrogen cycling: Unraveling the links among multiple environmental factors, functional genes, and transformation rates

Anthropogenic nitrogen (N) inputs substantially influence the N cycle in agricultural ecosystems. However, the potential links among various environmental factors, nitrogen functional genes, and transformation rates under N fertilization remain poorly understood. Here, we conducted a five-year field experiment and collected 54 soil samples from three 0-4 m boreholes across different treatments: control, N-addition (nitrogen fertilizer) and NPK-addition (combined application of nitrogen, phosphorus and potassium fertilizers) treatments. Our results revealed pronounced variations in soil physiochemical parameters, metal concentrations and antibiotic levels under both N and NPK treatments. These alternations induced significant shifts in bacterial and fungal communities, altered NFG abundance and composition, and greatly enhanced rates of nitrate reduction processes. Notably, nutrients, antibiotics and bacteria exerted a more pronounced influence on NFGs and nitrate reduction under N treatment, whereas nutrients, metals, bacteria and fungi had a significant impact under NPK treatment. Furthermore, we established multidimensional correlations between nitrate reduction gene profiles and the activity rates under N and NPK treatments, contrasting with the absence of significant relationships in the control treatment. These findings shed light on the intricate relationships between microbial genetics and ecosystem functions in agricultural ecosystem, which is of significance for predicting and managing metabolic processes effectively.

Groundwater flow regime shapes nitrogen functional traits by affecting microbial community assembly processes in the subsurface

The complex nitrogen (N) cycle in groundwater systems is affected by both biological and environmental factors. The interactions between hydrogeological conditions and the microbial community assembly processes that impact N-cycling processes remain poorly understood. We explored the assembly patterns of N-cycling microbial communities along the groundwater flow path. The environmental heterogeneity in different hydrological phases increased along the flow path (mean Ed: 0.16-0.49), accompanied by different microbial community assembly patterns. The assembly patterns that engaged in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification changed across the water-sediment phases. Nitrifying microorganisms in the discharge area were mainly influenced by heterogeneous selection (41-69 %), and were closely correlated with dissolved oxygen (DO) concentrations. Homogeneity along flow-through increased stochastic assemblies, such as downstream drift of anammox bacterial (AnAOB) communities. Thus, the N removal pathway changed from "nitrification-denitrification" in the recharge area to "partial nitrification-anammox" in the discharge area. The increasing environmental heterogeneity brought more deterministic assembly patterns of N-cycling communities, linked to higher community turnover along the groundwater flow path. This study indicated that groundwater flow regime determined microbial community assembly patterns, providing valuable insight into the response of N transitions to environmental variations in groundwater systems.

Application of machine learning approaches to predict ammonium nitrogen transport in different soil types and evaluate the contribution of control factors

The loss of nitrogen in soil damages the environment. Clarifying the mechanism of ammonium nitrogen (NH4+-N) transport in soil and increasing the fixation of NH4+-N after N application are effective methods for improving N use efficiency. However, the main factors are not easily identified because of the complicated transport and retardation factors in different soils. This study employed machine learning (ML) to identify the main influencing factors that contribute to the retardation factor (Rf) of NH4+-N in soil. First, NH4+-N transport in the soil was investigated using column experiments and a transport model. The Rf (1.29 - 17.42) was calculated and used as a proxy for the efficacy of NH4+-N transport. Second, the physicochemical parameters of the soil were determined and screened using lasso and ridge regressions as inputs for the ML model. Third, six machine learning models were evaluated: Adaptive Boosting, Extreme Gradient Boosting (XGB), Random Forest, Gradient Boosting Regression, Multilayer Perceptron, and Support Vector Regression. The optimal ML model of the XGB model with a low mean absolute error (0.81), mean squared error (0.50), and high test r2 (0.97) was obtained by random sampling and five-fold cross-validation. Finally, SHapely Additive exPlanations, entropy-based feature importance, and permutation characteristic importance were used for global interpretation. The cation exchange capacity (CEC), total organic carbon (TOC), and Kaolin had the greatest effects on NH4+-N transport in the soil. The accumulated local effect offered a fundamental insight: When CEC > 6 cmol+ kg-1, and TOC > 40 g kg-1, the maximum resistance to NH4+-N transport within the soil was observed. This study provides a novel approach for predicting the impact of the soil environment on NH4+-N transport and guiding the establishment of an early-warning system of nutrient loss.

Methane-dependent denitrification by Methylomirabilis: an indirect nitrous oxide sink?

Methane-dependent complete denitrification primarily involves nitrate reduction to nitrite by ANME-2d archaea and nitrite reduction to dinitrogen by Methylomirabilis bacteria. 'Candidatus Methylomirabilis sinica' integrates the divisional labor. Physiological traits of this bacterium potentially enable the simultaneous reduction of N2O and CH4 emissions. This forum article explores these traits and possible microbial mechanisms for co-reduction, providing guidance for greenhouse gas management strategies.

Metabolic adaptations underpin high productivity rates in relict subsurface water

Groundwater aquifers are ecological hotspots with diverse microbes essential for biogeochemical cycles. Their ecophysiology has seldom been studied on a basin scale. In particular, our knowledge of chemosynthesis in the deep aquifers where temperatures reach 60 °C, is limited. Here, we investigated the diversity, activity, and metabolic potential of microbial communities from nine wells reaching ancient groundwater beneath Israel's Negev Desert, spanning two significant, deep (up to 1.5 km) aquifers, the Judea Group carbonate and Kurnub Group Nubian sandstone that contain fresh to brackish, hypoxic to anoxic water. We estimated chemosynthetic productivity rates ranging from 0.55 ± 0.06 to 0.82 ± 0.07 µg C L-1 d-1 (mean ± SD), suggesting that aquifer productivity may be underestimated. We showed that 60% of MAGs harbored genes for autotrophic pathways, mainly the Calvin-Benson-Bassham cycle and the Wood-Ljungdahl pathway, indicating a substantial chemosynthetic capacity within these microbial communities. We emphasize the potential metabolic versatility in the deep subsurface, enabling efficient carbon and energy use. This study set a precedent for global aquifer exploration, like the Nubian Sandstone Aquifer System in the Arabian and Western Deserts, and reconsiders their role as carbon sinks.

Impact of copper sulphate treatment on cyanobacterial blooms and subsequent water quality risks

Control of algal blooms and associated biologically-induced water quality risks in drinking reservoirs is problematic. Copper sulphate (CuSO4) treatment is one intervention that has been utilised for >100 years. Evidence indicates a favourable short-term reduction in Cyanobacterial biomass (e.g. bloom termination), but here we indicate that it may also increase longer-term water quality risk. In 2022, we investigated the impacts of CuSO4 spraying on Cyanobacterial communities and nutrient levels within a drinking water supply reservoir using environmental DNA (eDNA) to assess community shifts, alongside monitoring nutrient fractions, orthophosphate (OP) and total phosphate (TP), post-treatment. CuSO4 application successfully reduced Cyanobacterial abundance, however elimination of Cyanobacteria resulted in a shift in bacterial dominance favouring Planctomycetota throughout the summer and a combination of Actinobacteriota and Verrucomicrobiota, throughout autumn. As Cyanobacterial abundance recovered post-treatment, Cyanobacterial genera demonstrated greater diversity compared to only three Cyanobacterial genera present across samples pre-treatment, and included taxa associated with water quality risk (e.g. taste and odour (T&O) metabolite and toxin producers). The increase in Cyanobacteria post-treatment was attributed to an increase in biologically available nutrients, primarily a significant increase in OP. Overall, findings suggest that the significant shift in biodiversity likely induces a less stable ecosystem with greater plasticity of response to changing environmental and biogeochemical variables. Legacy implications of CuSO4 spraying, in terms of shifts in ecosystem and nutrient balance over time, may have implications for drinking water quality, but importantly also for reservoir management options. As such, the effects of CuSO4 spraying should be considered carefully before consideration as a contender for in-reservoir biological control.

Evidence of Potential Anammox Activities from Rice Paddy Soils in Microaerobic and Anaerobic Conditions

Anammox, a reaction in which microorganisms oxidize ammonia under anaerobic conditions, is used in the industry to remove ammonium from wastewater in an environmentally friendly manner. This process does not produce intermediate products such as nitrite or nitrate, which can act as secondary pollutants in soil and water environments. For industrial applications, anammox bacteria should be obtained from the environment and cultivated. Anammox bacteria generally exhibit a slow growth rate and may not produce a large number of cells due to their anaerobic metabolism. Additionally, their habitats appear to be limited to specific environments, such as oxidation-reduction transition zones. Consequently, most of the anammox bacteria that are used or studied originate from marine environments. In this study, anammox bacterial evidence was found in rice paddy soil and cultured under various conditions of aerobic, microaerobic, and anaerobic batch incubations to determine whether enrichment was possible. The anammox-specific gene (hzsA) and microbial community analyses were performed on the incubated soils. Although it was not easy to enrich anammox bacteria due to co-occurrence of denitrification and nitrification based on the chemistry data, potential existence of anammox bacteria was assumed in the terrestrial paddy soil environment. For potential industrial uses, anammox bacteria could be searched for in rice paddy soils by applying optimal enrichment conditions.

The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau

The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.

Tracing the impacts of ecological water replenishment on the sources and transformation of groundwater nitrate through isotope and microbial analysis

Ecological water replenishment (EWR) changes the recharge conditions, flow fields, and physicochemical properties of regional groundwater. However, the resulting impacts on mechanisms regulating the sources and transformation of groundwater nitrate remain unclear. This study investigated how EWR influences the sources and transformation processes of groundwater nitrate using an integrated approach of Water chemistry analysis and stable isotopes (δ15N-NO3- and δ18O-NO3-) along with microbial techniques. The results showed that groundwater NO3-N decreased from 12.98 ± 7.39 mg/L to 7.04 ± 8.52 mg/L after EWR. Water chemistry and isotopic characterization suggested that groundwater nitrate mainly originated from sewage and manure. The Bayesian isotope mixing model (MixSIAR) indicated that EWR increased the average contribution of sewage and manure sources to groundwater nitrate from 46 % to 61 %, whereas that of sources of chemical fertilizer decreased from 43 % to 21 %. Microbial community analysis revealed that EWR resulted in a substantial decrease in the relative abundance of Pseudomonas spp denitrificans, from 13.7 % to 0.6 %. Both water chemistry and microbial analysis indicated that EWR weakened denitrification and enhanced nitrification in groundwater. EWR increases the contribution of nitrate to groundwater by promoting the release of sewage and feces in the unsaturated zone. However, the dilution effect caused by EWR was stronger than the contribution of sewage and fecal sources to groundwater nitrate. As a result, EWR helped to reduce groundwater nitrate concentrations. This study showed the effectiveness of integrated isotope and microbial techniques for delineating the sources and transformations of groundwater nitrate influenced by EWR.

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides

Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from Mesorhizobium sp. A09 (MeAmi_SBP) and show that MeAmi_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of MeAmi_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+ binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that MeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.

Influences of shallow groundwater depth on N2O diffusion along the soil profile of summer maize fields in North China Plain

The emissions of nitrous oxide (N2O) from agricultural fields are a significant contribution to global warming. Understanding the mechanisms of N2O emissions from agricultural fields is essential for the development of N2O emission mitigation strategies. Currently, there are extensive studies on N2O emissions on the surface of agricultural soils, while studies on N2O fluxes at the interface between the saturated and unsaturated zones (ISU) are limited. Uncertainties exist regarding N2O emissions from the soil-shallow groundwater systems in agricultural fields. In this study, a three-year lysimeter experiment (2019-2020, 2022) was conducted to simulate the soil-shallow groundwater systems under four controlled shallow groundwater depth (SGD) (i.e., SGD = 40, 70, 110, and 150 cm) conditions in North China Plain (NCP). Weekly continuous monitoring of N2O emissions from soil surface, N2O concentration in the shallow groundwater and the upper 10 cm of pores at the ISU, and nitrogen cycling-related parameters in the soil and groundwater was conducted. The results showed that soil surface N2O emissions increased with decreased shallow groundwater depth, and the highest emissions of 96.44 kg ha-1 and 104.32 kg ha-1 were observed at G2 (SGD = 40 cm) in 2020 and 2022. During the observation period of one maize growing season, shallow groundwater acted as a sink for the unsaturated zone when the groundwater depth was 40 cm, 70 cm, and 110 cm. However, when SGD was 150 cm, shallow groundwater became a source for the unsaturated zone. After fertilization, the groundwater in all treatment plots behaved as a sink for the unsaturated zone, and the diffusion intensity decreased with increasing SGD. The results would provide a theoretical basis for cropland water management to reduce N2O emissions.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions

Hadal trenches are extreme environments situated over 6000 m below sea surface, where enormous hydrostatic pressure affects the biochemical cycling of elements. Recent studies have indicated that hadal trenches may represent a previously overlooked source of fixed nitrogen loss; however, the mechanisms and role of hydrostatic pressure in this process are still being debated. To this end, we investigate the effects of hydrostatic pressure (0.1 to 115 MPa) on the chemical profile, microbial community structure and functions of surface sediments from the Mariana Trench using a Deep Ocean Experimental Simulator supplied with nitrate and oxygen. We observe enhanced denitrification activity at high hydrostatic pressure under oxic conditions, while the anaerobic ammonium oxidation - a previously recognized dominant nitrogen loss pathway - is not detected. Additionally, we further confirm the simultaneous occurrence of nitrate reduction and aerobic respiration using a metatranscriptomic dataset from in situ RNA-fixed sediments in the Mariana Trench. Taken together, our findings demonstrate that hydrostatic pressure can influence microbial contributions to nitrogen cycling and that the hadal trenches are a potential nitrogen loss hotspot. Knowledge of the influence of hydrostatic pressure on anaerobic processes in oxygenated surface sediments can greatly broaden our understanding of element cycling in hadal trenches.

How redox gradient potentially influences nitrate reduction coupled with sulfur cycling: A new insight into nitrogen cycling in the hyporheic zone of effluent-dominated rivers

The coupled N and S cycling in variable redox gradients in the hyporheic zone (HZ) of the rivers receiving effluents from wastewater treatment plants is unclear. Using two representative effluent-dominated rivers as model systems, a metagenome approach was employed to explore the spatiotemporal redox zonation of the HZ and the N/S cycling processes within the system. The results manifested that nitrate reduction represented the fundamental nitrogen pathway in the HZ. Interestingly, DNRA coupled with sulfur reduction, and denitrification coupled with sulfur oxidation were respectively abundant in the oxic and anoxic zone. Lower nitrate concentration (0-2.72 mg-N/L) and more abundant genes involved in denitrification (napB, NarGHI) and sulfur oxidation (sseA, glpE) were detected in the anoxic zone. Contrarily, the nitrate concentration (0.07-4.87 mg-N/L) and the abundance of genes involved in sulfur reduction (ttrB, sudA) and DNRA (nirBD) were observed more abundant in the oxic zone. Therefore, the results verified the oxygen-limited condition did not suppress but rather facilitated the denitrification process in the presence of active S cycling. The high relative abundances of nosZ gene encoding sequence (3-5 % relative to all nitrogen-cycling processes) in both the effluent-discharging area and downstream area highly confirmed that HZ was capable of alleviating the N2O emission in the region. The functional keystone taxa were revealed through co-occurrence network analysis. The structural equation model shows that the genes of N/S cycling were positively impacted by functional keystone taxa, especially the N cycling genes. Functional keystone taxa were proven driven by the redox gradient, demonstrating their positive roles in mediating N/S cycling processes. The promoting effect on nitrate reduction coupled with sulfur cycling was clarified when redox conditions oscillated, providing a new perspective on mitigating nitrogen pollution and greenhouse gas emissions in effluent-receiving rivers.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands

Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.

Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands

Drylands refer to water scarcity and low nutrient levels, and their plant and biocrust distribution is highly diverse, making the microbial processes that shape dryland functionality particularly unique compared to other ecosystems. Drylands are constraint for sustainable agriculture and risk for food security, and expected to increase over time. Nitrous oxide (N2O), a potent greenhouse gas with ozone reduction potential, is significantly influenced by microbial communities in drylands. However, our understanding of the biological mechanisms and processes behind N2O emissions in these areas is limited, despite the fact that they highly account for total gaseous nitrogen (N) emissions on Earth. This review aims to illustrate the important biological pathways and microbial players that regulate N2O emissions in drylands, and explores how these pathways might be influenced by global changes for example N deposition, extreme weather events, and climate warming. Additionally, we propose a theoretical framework for manipulating the dryland microbial community to effectively reduce N2O emissions using evolving techniques that offer inordinate specificity and efficacy. By combining expertise from different disciplines, these exertions will facilitate the advancement of innovative and environmentally friendly microbiome-based solutions for future climate change vindication approaches.

Arsenic biogeochemical cycling association with basin-scale dynamics of microbial functionality and organic matter molecular composition

Geogenic arsenic (As)-contaminated groundwater is a sustaining global health concern that is tightly constrained by multiple interrelated biogeochemical processes. However, a complete spectrum of the biogeochemical network of high-As groundwater remains to be established, concurrently neglecting systematic zonation of groundwater biogeochemistry on the regional scale. We uncovered the geomicrobial interaction network governing As biogeochemical pathways by merging in-field hydrogeochemical monitoring, metagenomic analyses, and ultrahigh resolution mass spectrometry (FT-ICR MS) characterization of dissolved organic matter. In oxidizing to weakly reducing environments, the nitrate-reduction and sulfate-reduction encoding genes (narGHI, sat) inhibited the dissolution of As-bearing iron minerals, leading to lower As levels in groundwater. In settings from weakly to moderately reducing, high abundances of sulfate-reduction and iron-transport encoding genes boosted iron mineral dissolution and consequent As release. As it evolved to strongly reducing stage, elevated abundance of methane cycle-related genes (fae, fwd, fmd) further enhanced As mobilization in part by triggering the formation of gaseous methylarsenic. During redox cycling of N, S, Fe, C and As in groundwater, As migration to groundwater and immobilization in mineral particles are geochemically constrained by basin-scale dynamics of microbial functionality and DOM molecular composition. The study constructs a theoretical model to summarize new perspectives on the biogeochemical network of As cycling.

Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions

The acceleration of the nitrogen cycle and the nitrogen excess observed in some coastal waters has increased interest into understanding the biochemical and molecular basis of nitrogen metabolism in various microorganisms. To investigate nitrogen metabolism of a novel heterotrophic nitrification and aerobic denitrification bacterium Klebsiella aerogenes strain (B23) under nitrogen-rich conditions, we conducted physiological and transcriptomic high-throughput sequencing analyses on strain B23 cultured on potassium nitrate-free or potassium nitrate-rich media. Overall, K. aerogenes B23 assimilated 82.47% of the nitrate present into cellular nitrogen. Further, 1,195 differentially expressed genes were observed between K. aerogenes B23 cultured on potassium nitrate-free media and those cultured on potassium nitrate-rich media. Gene annotation and metabolic pathway analysis of the transcriptome were performed using a series of bioinformatics tools, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Non-Redundant Protein Database annotation. Accordingly, the nitrogen metabolism pathway of K. aerogenes B23 was analyzed; overall, 39 genes were determined to be involved in this pathway. Differential expression analysis of the genes involved in the nitrogen metabolism pathway demonstrated that, compared to the control, FNR, NarK/14945, fdx, gshA, proB, proA, gapA, argH, artQ, artJ, artM, ArgR, GAT1, prmB, pyrG, glnS, and Ca1 were significantly upregulated in the nitrogen-treated K. aerogenes B23; these genes have been established to be involved in the regulation of nitrate, arginine, glutamate, and ammonia assimilation. Further, norV, norR, and narI were also upregulated in nitrogen-treated K. aerogenes B23; these genes are involved in the regulation of NO metabolism. These differential expression results are important for understanding the regulation process of key nitrogen metabolism enzyme genes in K. aerogenes B23. Therefore, this study establishes a solid foundation for further research into the expression regulation patterns of nitrogen metabolism-associated genes in K. aerogenes B23 under nitrogen-rich conditions; moreover, this research provides essential insight into how K. aerogenes B23 utilizes nutritional elements.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Study of bacterial population dynamics in seed culture developed for ammonia reduction from synthetic wastewater

The waterbodies have been polluted by various natural and anthropogenic activities. The aquatic waste includes ammonia as one of the most toxic pollutants. Several biological treatment systems involving anoxic and semi anoxic bacteria have been proposed for reducing nitrogen loads from wastewater and increasing the efficiency and cost effectiveness. These bacteria play a vital role in the processes involved in the nitrogen cycle in nature. However, the enrichment, sustainability and identification of bacterial communities for wastewater treatment is an important aspect. Most of the chemolithotrophs are unculturable hence their identification and measurement of abundance remains a challenging task. In this study the different bacteria involved in total nitrogen removal from the wastewater are enriched for 700 days under anoxic condition. The synthetic wastewater containing 0.382 g/L of ammonium chloride was used. Molecular identification of the bacteria involved in various steps of the nitrogen cycle was carried out based on amplification of functional genes and 16S rRNA gene Polymerase chain reaction followed by DNA sequencing. Change in the abundance of chemolithotrophs was studied using qPCR. The mutual growth of various nitrifiers along with anaerobic bacteria were identified by molecular characterisation of DNA at various time intervals with the different genes involved in the nitrogen cycle. Nitrosomonas species like Nitrosomonas europaea were identified throughout the batch scale studies possessing the genes associated with ammonia oxidizing bacteria and nitrite oxidizing bacteria which act as a complete ammonia oxidizer. The uncultured species of Nitrospira and anammox bacteria were also observed which predicts the coexistence of the anammox and comammox bacteria in a batch scale study. The coexistence of the semi anoxic and anoxic bacteria helped in the growth of these bacteria for a longer duration of time. The nitrite produced by the comammox during nitrification can be utilized by anammox as an electron carrier. The other species of denitrifiers like Pseudomonas denitrificans and Aminobacter aminovorans were also observed. It is concluded that the enrichment of semi anoxic and anoxic bacteria was faster with the increase in growth of the bacteria involved in nitrification, comammox, anammox and partial denitrification process. The bacterial growth is enhanced and the efficiency is increased which can be further used in the development of small pilot scale bioreactor for total nitrogen removal.

Microbially driven Fe-N cycle: Intrinsic mechanisms, enhancement, and perspectives

The iron‑nitrogen (FeN) cycle driven by microbes has great potential for treating wastewater. Fe is a metal that is frequently present in the environment and one of the crucial trace elements needed by microbes. Due to its synergistic role in the microbial N removal process, Fe goes much beyond the essential nutritional needs of microorganisms. Investigating the mechanisms behind the linked Fe-N cycle driven by microbes is crucial. The Fe-N cycle is frequently connected with anaerobic ammonia oxidation (anammox), nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), Feammox, and simultaneous nitrification denitrification (SND), etc. Although the main mechanisms of Fe-mediated biological N removal may vary depending on the valence state of the Fe, their similar transformation pathways may provide information on the study of certain element-microbial interactions. This review offers a thorough analysis of the facilitation effect and influence of Fe on the removal of nitrogenous pollutants in various biological N removal processes and summarizes the ideal Fe dosing. Additionally, the synergistic mechanisms of Fe and microbial synergistic N removal process are elaborated, covering four aspects: enzyme activity, electron transfer, microbial extracellular polymeric substances (EPS) secretion, and microbial community interactions. The methods to improve biological N removal based on the intrinsic mechanism were also discussed, with the aim of thoroughly understanding the biological mechanisms of Fe in the microbial N removal process and providing a reference and thinking for employing Fe to promote microbial N removal in practical applications.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12

Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests that corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids showed distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community- and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.

Denitrification genotypes of endospore-forming Bacillota

Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR, and sNOR) that may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.

Redox gradients drive microbial community assembly patterns and molecular ecological networks in the hyporheic zone of effluent-dominated rivers

The impacts of effluent discharge on receiving waterbodies have been a research hotspot. Nonetheless, limited information is available on the microbial community assembly patterns in the hyporheic zones (HZ) responding to the changes in the microenvironments, e.g., solute transport and redox gradient variations. Using two representative effluent-dominated rivers as model systems, the spatio-temporal bacterial community dynamics and assembly patterns in oxic and suboxic zones in the shallow riverbed sediments were disentangled via null model- and neutral model-based approaches. Bacterial dynamics in community composition were observed driven by environmental filtering, i.e., impacts of environmental variables, more than geographic distances, i.e., the depths of sediments. The communities in samples collected in summer were largely shaped by stochasticity, in which homogeneous selection occupied a higher proportion in oxic (∼39%) than in suboxic zone (∼23%). Deterministic processes contributed to a more complex community structure for samples from oxic zones, whereas weakened the interspecies interactions in suboxic zones. The richness and abundances of non-neutral community were confirmed governing the deterministic assembly in oxic zones. Key species ascribed to 'connectors' and 'network hubs' dominated the community assembly variations in samples collected in winter, and in oxic zones, respectively. Significant positive relationships between β-nearest taxon index and dissolved organic nitrogen (DON) and nitrate highlighted their vital roles in community assembly via deterministic selective pressures in oxic zones. The significance thresholds of nitrogen species for community transition in winter (ΔDON: 2.81 mg-N/L, ΔNO3-: 1.09 mg-N/L) were lower than in summer, probably implying that stricter effluent quality standards should be established in colder seasons. Combined, our work poses first insights on the roles of redox zonation in driving microbial community assembly in HZ, which is of significance in guiding ecological remediation processes in effluent-dominated rivers.

Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers

Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.

The influence of wet-to-dry season shifts on the microbial community stability and nitrogen cycle in the Poyang Lake sediment

In lake environments, seasonal changes can cause exposure of the lake sediment, leading to soil formation. Although previous studies have explored how environmental changes influence microbial functioning in the water-level-fluctuating zone, few studies have investigated how wholescale habitat changes affect microbial composition, community stability and ecological functions in lake environments. To address this issue, our study investigated the effects of sediment-to-soil conversion on microbial composition, community stability and subsequent ecological functioning in Poyang Lake, China. Our results revealed that, during sediment-to-soil conversion, the number of total and unique operational taxonomic units (OTUs) decreased by 40 % and 55 %, respectively. Moreover, sediment-to-soil conversion decreased the microbial community connectivity and complexity while significantly increasing its stability, as evidenced by increased absolute values of negative/positive cohesion. In sediment and soil, the abundance of dominant bacteria, and bacterial diversity strongly affected microbial community stability, although this phenomenon was not true in water. Furthermore, the specific microbial phyla and genes involved in the nitrogen cycle changed significantly following sediment-to-soil conversion, with the major nitrogen cycling processes altering from denitrification and dissimilatory nitrate reduction to ammonium to nitrification and assimilatory nitrate reduction to ammonia. Moreover, a compensation mechanism was observed in the functional genes related to the nitrogen cycle, such that all the processes in the nitrogen cycle were maintained following sediment-to-soil conversion. The oxidation-reduction potential strongly affected network complexity, microbial stability, and nitrogen cycling in the sediment and soil. These results aid in the understanding of responses of microorganisms to climate change and extreme drought. Our findings have considerable implications for predicting the ecological consequences of habitat conversion and for ecosystem management.

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.

Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms

A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.

Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities

Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.

Plant development alters the nitrogen cycle in subsurface flow constructed wetlands: Implications to the strategies for intensified treatment performance

Plant development greatly influences the composition structure and functions of microbial community in constructed wetlands (CWs) via plant root activities. However, our knowledge of the effect of plant development on microbial nitrogen (N) cycle is poorly understood. Here, we investigated the N removal performance and microbial structure in subsurface flow CWs at three time points corresponding to distinct stages of plant development: seedling, mature and wilting. Overall, the water parameters were profoundly affected by plant development with the increased root activities including radial oxygen loss (ROL) and root exudates (REs). The removal efficiency of NH4+-N was significantly highest at the mature stage (p < 0.01), while the removal performance of NO3--N at the seedling stage. The highest relative abundances of nitrification- and anammox-related microbes (Nitrospira, Nitrosomonas, and Candidatus Brocadia, etc.) and functional genes (Amo, Hdh, and Hzs) were observed in CWs at the mature stage, which can be attributed to the enhanced intensity of ROL, creating micro-habitat with high DO concentration. On the other hand, the highest relative abundances of denitrification- and DNRA-related microbes (Petrimonas, Geobacter, and Pseudomonas, etc.) and functional genes (Nxr, Nir, and Nar, etc.) were observed in CWs at the seedling and wilting stages, which can be explained by the absence of ROL and biological denitrification inhibitor derived from REs. Results give insights into microbial N cycle in CWs with different stages of plant development. More importantly, a potential solution for intensified N removal via the combination of practical operation and natural regulation is proposed.

Nitrogen fixation and diazotroph diversity in groundwater systems

Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using 15N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. 15N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L-1 h-1) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g-1 h-1, as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 103 to 1.2 × 106 copies L-1 and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4+. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.

Differential contribution of nitrifying prokaryotes to groundwater nitrification

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater

High rates of CO2 fixation and the genetic potential of various groundwater microbes for autotrophic activity have shown that primary production is an important source of organic C in groundwater ecosystems. However, the contribution of specific chemolithoautotrophic groups such as S-oxidizing bacteria (SOB) to groundwater primary production and their adaptation strategies remain largely unknown. Here, we stimulated anoxic groundwater microcosms with reduced S and sampled the microbial community after 1, 3 and 6 weeks. Genome-resolved metaproteomics was combined with 50at-% 13CO2 stable isotope probing to follow the C flux through the microbial food web and infer traits expressed by active SOB in the groundwater microcosms. Already after 7 days, 90% of the total microbial biomass C in the microcosms was replaced by CO2-derived C, increasing to 97% at the end of incubation. Stable Isotope Cluster Analysis revealed active autotrophs, characterized by a uniform 13C-incorporation of 45% in their peptides, to dominate the microbial community throughout incubation. Mixo- and heterotrophs, characterized by 10 to 40% 13C-incorporation, utilized the primarily produced organic C. Interestingly, obligate autotrophs affiliated with Sulfuricella and Sulfuritalea contained traits enabling the storage of elemental S in globules to maintain primary production under energy limitation. Others related to Sulfurimonas seemed to rapidly utilize substrates for fast proliferation, and most autotrophs further maximized their energy yield via efficient denitrification and the potential for H2 oxidation. Mixotrophic SOB, belonging to Curvibacter or Polaromonas, enhanced metabolic flexibility by using organic compounds to satisfy their C requirements. Time series data spanning eight years further revealed that key taxa of our microcosms composed up to 15% of the microbial groundwater community, demonstrating their in-situ importance. This showed that SOB, by using different metabolic strategies, are able to account for high rates of primary production in groundwater, especially at sites limited to geogenic nutrient sources. The widespread presence of SOB with traits such as S storage, H2 oxidation, and organic C utilization in many aquatic habitats further suggested that metabolic versatility governs S-fueled primary production in the environment.

Nitrogen species and microbial community coevolution along groundwater flowpath in the southwest of Poyang Lake area, China

Nitrate and ammonia overload in groundwater can lead to eutrophication of surface water in areas where surface water is recharged by groundwater. However, this process remained elusive due to the complicated groundwater N cycling, which is governed by the co-evolution of hydrogeochemical conditions and N-cycling microbial communities. Herein, this process was studied along a generalized groundwater flowpath in Ganjing Delta, Poyang Lake area, China. From groundwater recharge to the discharge area near the lake, oxidation-reduction potential (ORP), NO₃-N, and NO₂-N decreased progressively, while NH₃-N, total organic carbon (TOC), Fe²⁺, sulfide, and TOC/NO₃^- ratio accumulated in the lakeside samples. The anthropogenic influences such as sewage and agricultural activities drove the nitrate distribution, as observed by Cl^- vs. NO₃^-/Cl^- ratio and isotopic composition of nitrate. The hydrogeochemical evolution was intimately coupled with the changes in microbial communities. Variations in microbial community structures was significantly explained by Fe²⁺, NH₃-N, and sulfide, while TOC/NO₃^- controlled the distribution of predicted N cycling gene. The absence of NH₃-N in groundwater upstream was accompanied by the enrichment in Acinetobacter capable of nitrification and aerobic denitrification. These two processes were also supported by Ca²⁺ + Mg²⁺ vs. HCO₃^- ratio and isotopic composition of NO₃^-. The DNRA process downstream was revealed by both the presence of DNRA-capable microbes such as Arthrobacter and the isotopic composition of NH₄⁺ in environments with high concentrations of NH₃-N, TOC/NO₃^-, Fe²⁺, and sulfide. This coupled evolution of N cycling and microbial community sheds new light on the N biogeochemical cycle in areas where surface water is recharged by groundwater.

N/S element transformation modulating lithospheric microbial communities by single-species manipulation

BACKGROUND

The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS

Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS

The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.

Competition and interaction between DNRA and denitrification in composting ecosystems: insights from metagenomic analysis

This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO₂^--N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.

Nitrate with enriched heavy oxygen isotope linked to changes in nitrogen source and transformation as groundwater table rises

Nitrate is a significant constituent of the total nitrogen pool in shallow aquifers and poses an escalating threat to groundwater resources, making it crucial to comprehend the source, conversion, and elimination of nitrogen using appropriate techniques. Although dual-isotope dynamics in nitrate have been widely used, uncertainties remain regarding the asynchronously temporal changes in δ¹⁸O-NO₃^- and δ¹⁵N-NO₃^- observed in hypoxic aquifers. This study aimed to investigate changes in nitrogen sources and transformations using temporal changes in field-based NO₃^- isotopic composition, hydro-chemical variables, and environmental DNA profiling, as the groundwater table varied. The results showed that the larger enrichment in δ¹⁸O-NO₃^- (+13‰) compared with δ¹⁵N-NO₃^- (-2‰) on average during groundwater table rise was due to a combination of factors, including high ¹⁸O-based atmospheric N deposition, canopies nitrification, and soil nitrification transported vertically by rainfalls, and ¹⁸O-enriched O₂ produced through microbial and root respiration within denitrification. The strong association between functional gene abundance and nitrogen-related indicators suggests that anammox was actively processed with nitrification but in small bacterial population during groundwater table rise. Furthermore, bacterial species associated with nitrogen-associated gradients provided insight into subsurface nitrogen transformation, with Burkholderiaceae species and Pseudorhodobacter potentially serving as bioindicators of denitrification, while Candidatus Nitrotogn represents soil nitrification. Fluctuating groundwater tables can cause shifts in hydro-chemical and isotopic composition, which in turn can indicate changes in nitrogen sources and transformations. These changes can be used to improve input sources for mixture models and aid in microbial remediation of nitrate.

Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.

Removal performance, biotransformation pathways and products of sulfamethoxazole in vertical subsurface flow constructed wetlands with different substrates

For decades, sulfamethoxazole (SMX) has been frequently detected in the aquatic environments due to its high usage and refractory to degradation. Constructed wetland (CW) is regarded as an efficient advanced wastewater technology to eliminate organic pollutants including SMX. In CW system, substrate adsorption and further biodegradation are extremely important in SMX removal; however, the removal performance of SMX by CWs with different substrates varies greatly, and the biotransformation pathways, products, and mechanisms of SMX remain unclear. To address this, we constructed a CW with conventional substrate (CS, gravel) as control (C-CW) and three CWs with emerging substrates (ES, biochar, zeolite and pyrite for B-CW, Z-CW and P-CW, respectively), and explored the performance and mechanisms of SMX removal in CWs. Results illustrated that the removal performance of SMX in CWs with ES reached 94.89-99.35%, and significantly higher than that with CS of 89.50% (p < 0.05). Biodegradation contributed >90% SMX removal in all CWs. The microbial compositions and functions differed among CWs at the middle layer (mixed layer), which shaped diverse resistance pattern and metabolism pathways of microbiomes under SMX stress: P-CW and B-CW cope with SMX stress by enhancing material and energy metabolism, whereas Z-CW does that by enhancing metabolism and exocytosis of xenobiotics. Additionally, nine transformation pathways with 15 transformation products were detected in this study. A reversible process of desamino-SMX being reconverted to SMX might exist in P-CW, which caused a lower SMX removal efficiency in P-CW. This study provided a comprehensive insight into the processes and mechanisms of SMX removal in CWs with different substrates, which would be a useful guidance for substrate selection in CWs in terms of enhanced micropollutants removal.

Characterization of Enrichment Cultures of Anammox, Nitrifying and Denitrifying Bacteria Obtained from a Cold, Heavily Nitrogen-Polluted Aquifer

Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 g/L, respectively) and a very low content of organic carbon (2.5 mg/L). To assess the potential for bioremediation of polluted groundwater in situ, enrichment cultures of anammox, nitrifying, and denitrifying bacteria were obtained and analyzed. Fed-batch enrichment of anammox bacteria was not successful. Stable removal of ammonium and nitrite (up to 100%) was achieved in a continuous-flow reactor packed with a nonwoven fabric at 15 °C, and enrichment in anammox bacteria was confirmed by FISH and qPCR assays. The relatively low total N removal efficiency (up to 55%) was due to nonstoichiometric nitrate buildup. This phenomenon can be explained by a shift in the metabolism of anammox bacteria towards the production of more nitrates and less N₂ at low temperatures compared to the canonical stoichiometry. In addition, the too high an estimate of specific anammox activity suggests that N cycle microbial groups other than anammox bacteria may have contributed significantly to N removal. Stable nitrite production was observed in the denitrifying enrichment culture, while no "conventional" nitrifiers were found in the corresponding enrichment cultures. Xanthomonadaceae was a common taxon for all microbial communities, indicating its exclusive role in this ecosystem. This study opens up new knowledge about the metabolic capabilities of N cycle bacteria and potential approaches for sustainable bioremediation of heavily N-polluted cold ecosystems.

Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman

Nitrogen (N) is an essential element for life. N compounds such as ammonium ( NH 4 + ) may act as electron donors, while nitrate ( NO 3 - ) and nitrite ( NO 2 - ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H₂) generated through water-rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg²⁺- HCO 3 - type fluids comprised mostly of NO 3 - , and Ca²⁺-OH^- fluids comprised primarily of ammonia (NH₃). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - (>100 μM) with a relict meteoric oxygen isotopic composition (δ¹⁸O ~ 22‰, Δ¹⁷O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ¹⁸O of 53.7‰, Δ¹⁷O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ¹⁸O and Δ¹⁷O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH₃ (>100 μM) with little NO 3 - detectable. We interpret that NH₃ in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation (¹⁸ε / ¹⁵ε) measured in Samail Ophiolite NO 3 - was close to unity (¹⁸ε / ¹⁵ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.