Heterotrophic Nitrogen Fixation at the Hyper-Eutrophic Qishon River and Estuary System

Cold seep nitrogen fixation and its potential relationship with sulfur cycling

Dinitrogen (N2) fixation is a crucial source of bioavailable nitrogen in carbon-dominated cold seep systems. Previous studies have shown that diazotrophy is not necessarily dependent on sulfate-dependent anaerobic oxidation of methane for energy, and diverse catabolism can fuel the high-energy-demanding process in sediments. However, it remains unclear whether diazotroph can obtain energy by sulfur oxidation in sulfur-rich cold seep water column. Here, field investigations and in situ experiments were conducted in Haima cold seep to examine the effects of diverse sources of dissolved organic matter (DOM) on N2 fixation, specifically containing sulfur, carbon, nitrogen, and phosphorus. We found that active N2 fixation occurred in the water column above the Haima cold seep, with the Dechloromonas genus dominating the diazotroph community as revealed by nifH gene using high-throughput sequencing. In situ experiments showed an increased rate of N2 fixation (1.15- to 12.70-fold compared to that in control group) and a greater relative abundance of the Dechloromonas genus following enrichment with sulfur-containing organic matter. Furthermore, metagenomic assembly and binning revealed that Dechloromonas sp. carried genes related to N2 fixation (nifDHK) and sulfur compound oxidation (fccAB and soxABCXYZ), implying that the genus potentially serves as a multifunctional mediator for N2 fixation and sulfur cycling. Our results provide new insights regarding potential coupling mechanism associated with sulfur-driven N2 fixation in methane- and sulfide-rich environments.

IMPORTANCE

N2 fixation is an important source of biologically available in carbon-dominated cold seep systems as little nitrogen is released by hydrocarbon seepage, thereby promoting biological productivity and the degradation of non-nitrogenous organic matter. Cold seeps are rich in diverse sources of dissolved organic matter (DOM) derived from the sinking of photosynthetic products in euphotic layer and the release of chemosynthesis products on the seafloor. However, it remains unclear whether N2 fixation is coupled to the metabolic processes of DOM, as determined by e.g., carbon, nitrogen, phosphorus, and sulfur content, for energy acquisition in sulfur-rich cold seeps. In this study, diazotroph community structure and its response to DOM compositions were revealed. Moreover, the metagenomics analysis suggested that Dechloromonas genus plays a dominant role in potential coupling N2 fixation and sulfur oxidation. Our study highlighted that sulfur oxidation in deep-sea cold seeps may serve as an energy source to drive N2 fixation.

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.

Spatial and temporal variations of geochemical processes and toxicity of water, sediments, and suspended solids in Sibuti River Estuary, NW Borneo

A comprehensive geochemical study was conducted in the Sibuti River estuary by considering water, suspended solids (SS), and sediment samples from 36 stations during southwest monsoon (SWM) and northeast monsoon (NEM). In this study, the distribution of in situ parameters, major ions, nutrients, trace metals, and isotopes (δD, δ18O) were analyzed in water samples, whereas sediments and SS were studied for trace metals. The distribution revealed that suspended solids were the major carrier of Cd, Zn, and Mn, whereas sediments worked as a major source of Co, Cr, Ba, Se, Cu, and Pb. Na-Cl water type and ion exchange dominated the lower part of the estuary during both seasons. However, the mixed mechanism of Ca-Cl, Ca-Mg-Cl, and higher weathering indicated reverse ion exchange in the intermediate and upper parts of the estuary. Isotopic signatures of δD and δ18O in estuarine water indicate that the precipitation over the Limbang area dominates during SWM, whereas higher evaporation was confirmed during NEM. The factor analysis revealed that seawater influence in the estuary majority controlled the water chemistry irrespective of seasons. Major ions were mainly regulated by the tidal influence during the low flow time of the river (SWM), whereas the mixing mechanism of weathering and seawater controlled the concentrations during NEM. Nutrients such as NO3, SO42-, NH3, and NH4+ mainly originated from the agricultural fields and nitrification along with ammonification were responsible for the recycling of such nutrients. Trace metals except Cd were found to be geogenic in nature and originating mainly from the oxidation of pyrites present in the sandstone and mudstones of the Sibuti Formation. Redox condition was catalyzed by microorganisms near the river mouth, whereas Al-oxyhydroxides and Fe-oxyhydroxides complexes in the intermediate and upper part under oxygenated conditions controlled the absorption of metals. Overall, the estuary was found to be absorptive in nature due to ideal pH conditions and was confirmed by the saturation index (SI) of minerals.

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.

Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre

Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surface water, while hypothesized to be important, has yet to be demonstrated. In this study, we used simultaneous 15N-dinitrogen and 13C-bicarbonate incubations combined with nanoscale secondary ion mass spectrometry analysis to screen tens of thousands of mostly particle-associated, cell-like regions of interest collected from the North Pacific Subtropical Gyre. These dual isotope incubations allow us to distinguish between non-cyanobacterial and cyanobacterial nitrogen-fixing microorganisms and to measure putative cell-specific nitrogen fixation rates. With this approach, we detect nitrogen fixation by putative non-cyanobacterial diazotrophs in the oxygenated surface ocean, which are associated with organic-rich particles (<210 µm size fraction) at two out of seven locations sampled. When present, up to 4.1% of the analyzed particles contain at least one active putative non-cyanobacterial diazotroph. The putative non-cyanobacterial diazotroph nitrogen fixation rates (0.76 ± 1.60 fmol N cell-1 d-1) suggest that these organisms are capable of fixing dinitrogen in oxygenated surface water, at least when attached to particles, and may contribute to oceanic nitrogen fixation.

Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens

Biological dinitrogen (N₂) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N₂ fixation by NCDs and propose a conceptual framework for aggregate-associated N₂ fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.

Contribution of Heterotrophic Diazotrophs to N2 Fixation in a Eutrophic River: Free-Living vs. Aggregate-Associated

Recent studies have indicated that heterotrophic diazotrophs are highly diverse and fix N₂ in aquatic environments with potentially adverse conditions for diazotrophy, such as oxic and rich in total nitrogen. In this study, we compared the activity and diversity of heterotrophic diazotrophs associated with aggregates (>12 μm) to free-living cells in the eutrophic Qishon River during the winter and summer seasons. Overall, measured heterotrophic N₂ fixation rates in the Qishon River ranged between 2.6–3.5 nmol N L^–1 d^–1. Heterotrophic N₂ fixation was mainly associated with aggregates in the summer samples (74 ± 24%), whereas during the winter the bulk diazotrophic activity was mostly ascribed to the free-living fraction (90 ± 6%). In addition, immunolabeled micrographs indicated the presence of aggregate-associated heterotrophic diazotrophs in both seasons, while phototrophic diazotrophs were also captured during the winter. The richness of free-living and aggregate-associated heterotrophic diazotrophs were overall similar, yet the evenness of the later was significantly smaller, suggesting that few of the species gained advantage from particle lifestyle. The differences in the activity, micro-localization and diversity of the diazotrophic community were mostly attributed to spatiotemporal changes in the ambient C:N ratios (total organic carbon, TOC: total nitrogen) and the TOC concentrations. Taken together, our results shed new light on the contribution of heterotrophic diazotroph associated with aggregates to total heterotrophic N₂ fixation in oxic, highly eutrophic aquatic environments.

Purification effect evaluation of the designed new volcanic soil adsorption material containing bioreactor for eutrophic water treatment

The purpose of this study was to investigate the purification effect of a new adsorption material containing bioreactor and the critical role of viable but non-culturable (VBNC) bacteria in a eutrophication ecosystem. Major water quality parameters of the prepared eutrophic water were determined, and the microbial community was analyzed during 2 years. The results showed that removal rates of total phosphorus (TP), total nitrogen (TN), chlorophyll-a (Chl-a), and chemical oxygen demand (COD) were 90.7-95.9%, 84.5-92.4%, 87.9-95.8%, and 68.3-82.7%, respectively, indicating the high efficiency of the bioreactor in the eutrophic water treatment. Although the bioreactor had been operated for 2 years, water from the treatment group was much clearer and odorless than from the control group, exhibiting the long service life of the bioreactor. Stopping operation in August caused significant decrease of the removal rates of major water quality parameters (p < 0.05). This operational stop event and high temperature in summer exerted a dual effect on the bioreactor, whereas the impact could be minimized when the bioreactor was running. Moreover, the total bacteria under +Rpf (active resuscitation-promoting factor) treatment were higher than under -Rpf (inactive resuscitation-promoting factor) treatment, implying that Rpf could resuscitate VBNC bacteria in the eutrophication ecosystem. Nine strains of VBNC bacteria were isolated based on the BLAST results of the 16S rRNA gene. Also, these bacteria might contribute to the eutrophic water treatment based on their functions of phosphorus collecting and denitrification. These results provided new insights for engineering technology innovations, and consequently these findings had benefits in eutrophic water treatment.

Low diffusive nitrogen loss of urban inland waters with high nitrogen loading

Little is known about the exchange of gaseous nitrogen (N2) with the atmosphere from urban inland waters, which are characterized by low carbon-to‑nitrogen ratios and low nitrogen-to‑phosphorus ratios. Here, we studied diffusive nitrogen loss based on the measurement of dissolved N2 concentrations and related gene abundance of N2 production and fixation in rivers and lakes in the megacity of Beijing, China, between 2018 and 2020. The excess dissolved N2 (△N2) ranged from -51.2 to 56.8 μmol L-1 (average - 0.03 ± 13.8 μmol L-1), and approximately 43% of the river samples and 72% of the lake samples being undersaturated with N2, suggesting that the lakes mainly acted as a role of N2 sink. The N2 removal fraction (△N2/DIN, average 3.5 ± 4.3%) at the sites of rivers with positive △N2 was lower than that in other rivers around the world. The average N2 flux (0.8 ± 23.9 mmol m-2 d-1) in the urban rivers was also lower than that in other rivers. The low carbon-to‑nitrogen ratios in Beijing inland waters are not beneficial for N2 production during denitrification, and low nitrogen-to‑phosphorus ratios potentially favor N2 fixation with a high abundance of the nitrogenase nifH gene in the sediment, resulting in low net N2 production. The traditional paradigm is that rivers constantly lose vast N to the atmosphere via denitrification and anammox, but this study indicates that urban inland rivers emit negligible N even under high nitrogen loading.

Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles

Nitrogen ([Formula: see text]) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix [Formula: see text] under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding [Formula: see text] and [Formula: see text] concentrations determine the [Formula: see text] fixation rate inside particles. [Formula: see text] fixation inside sinking particles is mainly fueled by [Formula: see text] respiration rather than [Formula: see text] respiration. Our model suggests that anaerobic processes, including heterotrophic [Formula: see text] fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled [Formula: see text] fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic [Formula: see text] fixation contributes significantly to oceanic [Formula: see text] fixation.