Molecular evidence for sediment nitrogen fixation in a temperate New England estuary

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.

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

A diazotrophy-ammoniotrophy dual growth model for the sulfate reducing bacterium Desulfovibrio vulgaris var. Hildenborough

Sulfate reducing bacteria (SRB) comprise one of the few prokaryotic groups in which biological nitrogen fixation (BNF) is common. Recent studies have highlighted SRB roles in N cycling, particularly in oligotrophic coastal and benthic environments where they could contribute significantly to N input. Most studies of SRB have focused on sulfur cycling and SRB growth models have primarily aimed at understanding the effects of electron sources, with N usually provided as fixed-N (nitrate, ammonium). Mechanistic links between SRB nitrogen-fixing metabolism and growth are not well understood, particularly in environments where fixed-N fluctuates. Here, we investigate diazotrophic growth of the model sulfate reducer Desulfovibrio vulgaris var. Hildenborough under anaerobic heterotrophic conditions and contrasting N availabilities using a simple cellular model with dual ammoniotrophic and diazotrophic modes. The model was calibrated using batch culture experiments with varying initial ammonium concentrations (0-3000 µM) and acetylene reduction assays of BNF activity. The model confirmed the preferential usage of ammonium over BNF for growth and successfully reproduces experimental data, with notably clear bi-phasic growth curves showing an initial ammoniotrophic phase followed by onset of BNF. Our model enables quantification of the energetic cost of each N acquisition strategy and indicates the existence of a BNF-specific limiting phenomenon, not directly linked to micronutrient (Mo, Fe, Ni) concentration, by-products (hydrogen, hydrogen sulfide), or fundamental model metabolic parameters (death rate, electron acceptor stoichiometry). By providing quantitative predictions of environment and metabolism, this study contributes to a better understanding of anaerobic heterotrophic diazotrophs in environments with fluctuating N conditions.

Seasonal Hypoxia Enhances Benthic Nitrogen Fixation and Shapes Specific Diazotrophic Community in the Eutrophic Marine Ranch

Recently, a growing number of studies have confirmed that biological nitrogen fixation is also an important reactive nitrogen source in coastal regions. However, how benthic nitrogen fixation and diazotrophic community in coastal regions respond to seasonal hypoxia remains largely unknown. In this study, we investigated the spatiotemporal pattern of potential nitrogen fixation rate and diazotrophic abundance and community in sediments of a eutrophic marine ranch experiencing summer hypoxia using 15N tracing and high throughput sequencing techniques. The results showed that potential nitrogen fixation rates ranged from 0.013 to 10.199 μmol kg−1 h−1, and were significantly enhanced by summer hypoxia (ANOVA, p < 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (>60%), followed by Desulfobulbaceae (13.61%). Bottom water oxygen, pH, Chl-a concentration, and sediment NH4+ significantly regulated benthic nitrogen fixation, while the variation of diazotrophic community was explained by sediment TOC, TN, and Fe content (p < 0.05). This study highlighted that hypoxia stimulated benthic nitrogen fixation, which counteracted the nitrogen removal by denitrification and anammox, and could further aggregate eutrophication of the coastal marine ranch. Moreover, the result emphasized the importance of nitrogen fixation in coastal regions for the global N budget.

Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season

Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake's water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH4 +, and NO3 -. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.

Nitrogen fixation: a poorly understood process along the freshwater-marine continuum

Although N₂ fixation is a major component of the global N cycle and has been extensively studied in open-ocean and terrestrial ecosystems, rates and ecological dynamics remain virtually unknown for the inland and coastal aquatic ecosystems (lakes, wetlands, rivers, streams, estuaries) that connect terrestrial and marine biomes. This is due to the diversity of these habitats, as well as the traditional paradigm that N₂ fixation rates were low to nonexistent, and therefore not important, in these ecosystems. We identify three major research themes to advance understanding of aquatic N₂ fixation: 1) the biological diversity of diazotrophs and variability of N₂ fixation rates, 2) the ecological stoichiometry of N₂ fixation, and 3) the upscaling of N₂ fixation rates from genes to ecosystems. Coordinating research across these areas will advance limnology and oceanography by fully integrating N₂ fixation into ecological dynamics of aquatic ecosystems from local to global scales.

Influence of environmental factors on benthic nitrogen fixation and role of sulfur reducing diazotrophs in a eutrophic tropical estuary

Benthic nitrogen fixation in the tropical estuaries plays a major role in marine nitrogen cycle, its contribution to nitrogen budget and players behind process is not well understood. The present study was estimated the benthic nitrogen fixation rate in a tropical estuary (Cochin) and also evaluated the contribution of various diazotrophic bacterial communities. Nitrogen fixation was detected throughout year (0.1-1.11 nmol N g^-1 h^-1); higher activity was observed in post-monsoon. The nifH gene abundance was varied from 0.8 × 10⁴ to 0.6 × 10⁸ copies g^-1dry sediment; highest was detected in post-monsoon. The Cluster I and Cluster III were the dominant diazotrophs. Sulfur reducing bacterial phylotypes (Deltaproteobacteria) contributed up to 2-72% of total nitrogen fixation. These bacteria may provide new nitrogen to these systems, counteracting nitrogen loss via denitrification and anammox. Overall, the study explained the importance of benthic nitrogen fixation and role of diazotrophs in a monsoon influenced tropical estuarine environments.

Effects of Polyester Microfibers on Microphytobenthos and Sediment-Dwelling Infauna

Microfibers often dominate sediment microplastic samples, but little is known about their ecological effects on benthic organisms and functions. Polyethylene terephthalate) (PET) microfibers were added to 36 sediment chambers at six concentrations (0-0.5 g kg^-1 sediment) to assess the effects on microphytobenthos (MPB), a key deposit-feeding bivalve, Macomona liliana, and sediment nutrient pools. MPB photosynthesis was promoted in 18 chambers through a 12 h light/dark cycle. Another 18 chambers were maintained under dark conditions to inhibit photosynthesis. After 35 days of MPB growth and stabilization, four M. liliana were added to each chamber for a further 40 days. MPB biomass and composition were examined alongside M. liliana biochemical and behavioral properties and porewater dissolved inorganic nutrient concentrations. Increasing microfibers resulted in lower MPB biomass, fewer diatom-associated fatty acids (FAs), and an increase in cyanobacteria. The changes in MPB coincided with up to 75% lower energy reserves and reduced burrowing activity in M. liliana. In the light, nitrate + nitrate (NO_x) was significantly elevated and related to M. liliana and MPB biochemical properties. Ammoniu (NH₄⁺) concentrations increased but were variable in both the light and the dark. Our results suggest that increasing microfiber concentrations influence the interactions between M. liliana and MPB and affect biogeochemical processing in coastal marine sediments.

Nutrient stoichiometry (N:P) controls nitrogen fixation and distribution of diazotrophs in a tropical eutrophic estuary

Nitrogen fixation and its ecological regulation are poorly understood in the tropical estuaries, which are highly influenced by anthropogenic disturbances. In this study, we investigated the role of nutrient stoichiometry in the diversity, abundance and activity of N₂-fixing bacterial community and their seasonal variations in the water column of a tropical eutrophic estuary (Cochin estuary). The N₂ fixation rates in the estuary ranged from 0.1 to 2.0 nmol N₂ l^-1 h^-1, with higher activity during post-monsoon and lower during monsoon. The rates are appeared to be primarily controlled by dissolved inorganic nitrogen and phosphorous (N:P) ratio. Clone library analysis of nitrogenase (nifH) gene revealed that the major N₂ fixing phylotypes belong to Cluster I and Cluster III diazotrophs. The overall findings of this study suggest that monsoon induced seasonal changes in nutrient stoichiometry control the distribution and activity of diazotrophs in a tropical estuary.

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using ¹⁵N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.

Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China

In river-lake systems, sediment and water column are two distinct habitats harboring different bacterial communities which play a crucial role in biogeochemical processes. In this study, we employed Phylogenetic Investigation of Communities by Reconstruction of Unobserved States to assess the potential functions and functional redundancy of the bacterial communities in sediment and water in a eutrophic river-lake ecosystem, Poyang Lake in China. Bacterial communities in sediment and water had distinct potential functions of carbon, nitrogen, and sulfur metabolisms as well as phosphorus cycle, while the differences between rivers and the lake were inconspicuous. Bacterial communities in sediment had a higher relative abundance of genes associated with carbohydrate metabolism, carbon fixation pathways in prokaryotes, methane metabolism, anammox, nitrogen fixation, and dissimilatory sulfate reduction than that of water column. Bacterial communities in water column were higher in lipid metabolism, assimilatory nitrate reduction, dissimilatory nitrate reduction, phosphonate degradation, and assimilatory sulfate reduction than that of sediment bacterial communities. Furthermore, the variations in functional composition were closely associated to the variations in taxonomic composition in both habitats. In general, the bacterial communities in water column had a lower functional redundancy than in sediment. Moreover, comparing to the overall functions, bacterial communities had a lower functional redundancy of nitrogen metabolism and phosphorus cycle in water column and lower functional redundancy of nitrogen metabolism in sediment. Distance-based redundancy analysis and mantel test revealed close correlations between nutrient factors and functional compositions. The results suggested that bacterial communities in this eutrophic river-lake system of Poyang Lake were vulnerable to nutrient perturbations, especially the bacterial communities in water column. The results enriched our understanding of the bacterial communities and major biogeochemical processes in the eutrophic river-lake ecosystems.

Nitrogen cycling processes within stormwater control measures: A review and call for research

Stormwater control measures (SCMs) have the potential to mitigate negative effects of watershed development on hydrology and water quality. Stormwater regulations and scientific literature have assumed that SCMs are important sites for denitrification, the permanent removal of nitrogen, but this assumption has been informed mainly by short-term loading studies and measurements of potential rates of nitrogen cycling. Recent research concluded that SCM nitrogen removal can be dominated by plant and soil assimilation rather than by denitrification, and rates of nitrogen fixation can exceed rates of denitrification in SCM sediments, resulting in a net addition of nitrogen. Nitrogen cycling measurements from other human-impacted aquatic habitats have presented similar results, additionally suggesting that dissimilatory nitrate reduction to ammonium (DNRA) and algal uptake could be important processes for recycling nitrogen in SCMs. Future research should directly measure a suite of nitrogen cycling processes in SCMs and reveal controlling mechanisms of individual rate processes. There is ample opportunity for research on SCM nitrogen cycling, including investigations of seasonal variation, differences between climatic regions, and trade-offs between nitrogen removal and phosphorus removal. Understanding nitrogen dynamics within SCMs will inform more efficient SCM design and management that promotes denitrification to help mitigate negative effects of urban stormwater on downstream ecosystems.

Nitrogen fixation in surface sediments of the East China Sea: Occurrence and environmental implications

Sediment nitrogen fixation and associated functional gene in the East China Sea were investigated using nitrogen-isotope tracing and molecular techniques. Potential rates of nitrogen fixation were detected, with values of 0.06-5.51 nmol N g^-1 h^-1. Abundance of functional gene (nifH) ranged from 0.36 × 10⁶ to 5.39 × 10⁷ copies g^-1. Nitrogen fixation rates were not related to the abundance of nifH gene but to temperature, salinity, sulfide, iron and C/N, indicating that the sediment properties rather than microbial abundance dominated the nitrogen fixation. It is also estimated that sediment nitrogen fixation annually contributed about 3.43 × 10⁵ to 3.10 × 10⁷ tons nitrogen to the East China Sea, which accounted for 8.2-22.6% of the total inorganic nitrogen input. Overall, this study highlights the importance of benthic nitrogen fixation in controlling nitrogen budget in the East China Sea and improves our knowledge on nitrogen cycling in the coastal marine environments.

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.

Coastal stormwater wet pond sediment nitrogen dynamics

Wet ponds are a common type of stormwater control measure (SCM) in coastal areas of the southeastern US, but their internal nitrogen dynamics have not been extensively studied. Using flow-through intact sediment core incubations, net sediment N₂ fluxes before and after a nitrate addition from five wet ponds spanning a range of ages (3.25-10years old) were quantified through membrane inlet mass spectrometry during early summer. Multiple locations within a single wet pond (6.16years old) were also sampled during ambient conditions in late summer to determine the combined effects of depth, vegetation, and flow path position on net N₂ fluxes at the sediment-water interface. All pond sediments had considerable rates of net nitrogen fixation during ambient conditions, and net N₂ fluxes during nitrate-enriched conditions were significantly correlated with pond age. Following a nitrate addition to simulate storm conditions, younger pond sediments shifted towards net denitrification, but older ponds exhibited even higher rates of net nitrogen fixation. The pond forebay had significantly higher rates of net nitrogen fixation compared to the main basin, and rates throughout the pond were an order of magnitude higher than the early summer experiment. These results identify less than optimal nitrogen processing in this common SCM, however, data presented here suggest that water column mixing and pond sediment excavation could improve the capacity of wet ponds to enhance water quality by permanently removing nitrogen.

Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism

The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.