nifH Gene Copy Research Articles

Carbon type and quantity regulate soil free-living nitrogen fixation through restructuring diazotrophic community

Free-living nitrogen fixation (FLNF) is a ubiquitous and significant source of new nitrogen in ecosystems. This process requires a substantial amount of energy, and as a result, the input of labile carbon to soils may enhance FLNF. Here, we aim to explore the precise influence of different types and quantities of carbon on FLNF. We conducted experiments where sugars, carboxylic acids, and amino acids (common labile carbon inputs via root exudates) were added to cropland and forest soils. We monitored the changes in FLNF rate and diazotrophic community in response to these additions. Our findings revealed that sugars and carboxylic acids significantly stimulated FLNF rate, with an increase of up to three orders of magnitude, while amino acids either restricted FLNF or had no effect. When a mixture of sugars and carboxylic acids was added, the stimulation of FLNF was not observed until a threshold quantity of carbon was reached, indicating competition between diazotrophs and other microbes. Furthermore, the enhanced FLNF rate following carbon addition was attributable to shifts in diazotrophic community composition (e.g., increased abundance of Paenibacillus, a genus frequently used as biofertilizers), rather than to changes in the overall abundance of diazotrophs (reflected by nifH gene copy number). Our findings highlight the significant role of carbon type and quantity in regulating soil FLNF, partly through restructuring the diazotrophic community. The results have implications for predicting the response of rhizosphere FLNF to shifts in root exudation under environmental changes and can contribute to the application of diazotrophic biofertilizers in sustainable agriculture.

Short-term nitrogen addition reduces soil microbial nitrogen fixation rate in subtropical Pinus taiwanensis and Castanopsis faberi forests

Biological nitrogen (N) fixation is an important source of N in terrestrial ecosystems, but the response of soil microbial N fixation rate to N deposition in different forest ecosystems still remains uncertain. We conducted a field N addition experiment to simulate atmosphere N deposition in subtropical Pinus taiwanensis and Castanopsis faberi forests. We set up three levels of nitrogen addition using urea as the N source: 0 (control), 40 (low N), and 80 g N·hm-2·a-1(high N) to examine the chemical properties, microbial biomass C, enzyme activities, and nifH gene copies of top soils (0-10 cm). We also measured the microbial N fixation rate using the 15N labeling method. Results showed that N addition significantly reduced the soil microbial N fixation rate in the P. taiwanensis and C. faberi forests by 29%-33% and 10%-18%, respectively. Nitrogen addition significantly reduced N-acquiring enzyme (i.e., β-1, 4-N-acetylglucosaminidase) activity and nifH gene copies in both forest soils. There was a significant positive correlation between the microbial N fixation rate and soil dissolved organic C content in the P. taiwanensis forest, but a significant negative relationship between the rate of soil microbial nitrogen fixation and NH4+-N content in the C. faberi forest. Overall, soil microbial N fixation function in the P. taiwanensis forest was more sensitive to N addition than that in the C. faberi forest, and the factors affecting microbial N fixation varied between the two forest soils. The study could provide insights into the effects of N addition on biological N fixation in forest ecosystems, and a theoretical basis for forest management.

Regulation of nitrogen transformation and microbial community by inoculation during livestock manure composting.

This study examined the effects of three Bacillus strains and one Saccharomyces cerevisiae strain on nitrogen transformation and microbial communities in pig and chicken manure compost. The findings revealed that the use of compound microbial inoculants increased the compost temperature, accelerated moisture reduction, enhanced cellulase activity, and stimulated the accumulation of NH4 +-N, NO3 --N, and total nitrogen (TN), resulting in a 9% increase in TN content. The abundance of Firmicutes decreased by 3.95% at the maturation phase, while Actinobacteria and Bacteroidetes increased by 1.64% and 1.85%, respectively. Inoculation led to an increase in amoA, nxrA and nifH gene copy numbers, while simultaneously reducing the abundance of nirK, nosZ and nirS genes. It also resulted in an increase in functional enzyme levels, specifically nif and amo, with a corresponding decrease in nor. Clostridium, Phascolarctobacterium, Eubacterium and Faecalibacterium from the class Clostridium, which have a significant correlation with nifH and nxrA genes, suggest their likely crucial role in nitrogen retention and fixation. Inoculation aided in the removal of pathogenic bacteria and antibiotic resistance genes (ARGs) like fluoroquinolones, nucleosides and nitroimidazole. This study provides effective theoretical support for the mechanism of nitrogen retention and fixation, and for improving the quality of compost.

Biochar amendments to tropical paddy soil increase rice yields and decrease N2O emissions by modifying the genes involved in nitrogen cycling

Water management strategies are critical in regulating nitrous oxide (N2O) emissions from paddy soils under rice cultivation. Biochar is widely used as an amendment to decrease soil N2O emissions. However, the impacts of biochar amendment on N2O emissions under different water management strategies in paddy soils have not been investigated thoroughly, and the underlying mechanisms remain poorly understood. In particular, the effects of mid-season water drainage, a strategy used for water conservation, need to be better understood. In this study, a pot experiment was conducted including six treatments: alternating dry-wet conditions during the mid-season period without and with 2% (w/w) biochar (AWD1 and AWD2, respectively), continuous flooding during the mid-season period without (CF1) and with 2% (CF2) biochar, and regular mid-season drainage during the mid-season period without (CON1) and with 2% (CON2) biochar. All treatments received inorganic nitrogen, phosphorus and potassium fertilizers (NPK) administered in a split application. We found that fluxes of N2O emission peaked after the two fertilizers’ additions. No significant difference in the first N2O flux peak was found among different treatments. There also was no difference in the second N2O flux peak in both CF treatments, whereas biochar addition significantly decreased the second N2O flux peak in AWD2 and CON2 treatments. This was mainly due to increased nosZ gene copies and decreased ratios of denitrification and amoA genes to nosZ gene copies. Biochar amendments resulted in significant stimulation of nifH gene copies in the AWD2 treatment. Lastly, biochar increased rice yields in all treatments. Our study suggested that AWD2 was the optimal management strategy for mitigating N2O emissions and improving rice production in this tropical paddy soil.

Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N2 fixation

Abstract. Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687; Shao et al., 2022).

Changes in Soil Rhizobia Diversity and Their Effects on the Symbiotic Efficiency of Soybean Intercropped with Maize

It has been established that maize/soybean intercropping can improve nitrogen use efficiency. However, few studies have addressed how maize/soybean intercropping affects nitrogen-fixing bacterial diversity and N fixation efficiency of intercropped soybean. In this study, nitrogen-fixing bacterial communities, N fixation efficiency, and their relationships with soil properties under three nitrogen fertilization application rates (N0 0 kg/ha, N1 40 kg/ha, N2 80 kg/ha) were explored through field experiments. Nitrogen fixation and nitrogen-fixing bacteria diversity were assessed using 15N natural abundance, Illumina high-throughput sequencing, and nifH (nitrogen fixation) gene copies quantification in the rhizosphere soil of intercropped soybean. The results showed that nitrogen application rates significantly decreased the nitrogen-fixing bacteria diversity, nitrogen fixation efficiency, and nifH gene copies in the rhizosphere soil. Nitrogen fixation efficiency, nodule number, and dry weight of intercropped soybean were highest in the N0 treatment, and nitrogen fixation was the highest in the N1 treatment. The nitrogen-fixing efficiency in N0, N1, and N2 treatments increased by 69%, 59%, and 42% and the nodule number of soybean was 10%, 22%, and 21%, respectively, compared with monocultures. The soybean nitrogen-fixing bacteria diversity in intercropping under N0 and N1 treatments significantly increased compared with monocultures. There was a significant positive correlation between soil nifH gene copies and N fixation efficiency and a negative correlation with soil available nitrogen. Bradyrhizobium abundance in soybean rhizosphere soil decreased significantly with the increase in nitrogen application rates and was significantly correlated with soil AN (available nitrogen) and pH content in the soybean rhizosphere. These results help us to understand the mechanisms by which nitrogen use efficiency was improved, and nitrogen fertilizer could be reduced in legume/Gramineae intercropping, which is important to improve the sustainability of agricultural production.

Associative nitrogen fixation could be common in South African mesic grassland

Non-symbiotic nitrogen-fixing bacterial diazotrophs closely associated with the roots of grasses probably contribute most of the new nitrogen acquired to sustain productive natural grasslands, yet their ecology is poorly understood, especially in southern Africa. We looked for genetic evidence, using qPCR and gel electrophoresis, for the presence of the bacterial nifH gene associated with the roots of four grass species (20 plants each) in a mesic grassland in South Arica, which would indicate the potential for N fixation by diazotrophs. Grasses most tolerant of low N (Aristida junciformis) were predicted to harbour the most diazotrophs, especially compared to those most responsive to fertiliser N (Eragrostis curvula). However, the nifH gene was found in all 80 root samples and did not differ in copy number between species. Sequencing of a representative sample confirmed the identity of the nifH gene. The recently burned half of the grassland had 60% more relative nifH gene copy numbers than the area burned 15 months previously, suggesting that grass growth stimulated by fire could recruit diazotrophs. Given their ubiquity and importance in the N economy of grasslands, research is required to characterise root-associated diazotroph communities, quantify their N fixation rates, and understand their environmental controls.

Effects of soil treated fungicide fluopimomide on tomato (Solanum lycopersicum L.) disease control and plant growth.

Fluopimomide is a novel acid amide fungicide registered for the control of many plant pathogens. In the present study, the effects of soil-treated fluopimomide on soil micro biomass, disease incidence, plant growth, soil enzyme activity, and marketable yield of tomato (Solanum lycopersicum L.) were investigated via field trial. In addition, the application prospect in China was also evaluated. In the experiment, five treatments with three replications and a randomized complete block design were followed. The treatments were: furrow application of fluopimomide (25% suspension concentrate, SC) at the dosage of 375, 750, and 1,500 g ha−1, which was recommended, double recommended, and quadruple recommended dosages, respectively. Besides, common control fungicide fluopicolide (5% SC) furrow was applied at recommended application dosages of 750 mL ha−1, and a non-treated control was also undertaken. Results indicated that fluopimomide exhibited no effects on the amount of soil bacteria and actinomycetes, and its inhibition effect on fungi amount could be recovered at 60 days after treatment (DAT). With the recommended application dosage, fluopimomide could efficiently reduce the number of plant pathogens in soil by 79.56–85.80%, significantly reduce the disease incidences in tomato plants by 80.00–88.24%, and improve plant height by 13.25–24.05% and marketable yield by 16.88%. Furthermore, soil enzymes exhibited a complex response to fluopimomide, and AOB and nifH gene copy numbers were increased by the double and quadruple recommended dosage of fluopimomide. Based on the above results, fluopimomide could be recommended as an efficient fungicide for the tomato field.

Responses of functional genes involved in nitrogen cycling to green manuring in different paddy soils in south China

AimsWe studied the effects of green manuring on the gene level of microorganisms associated with nitrogen (N) fixation, nitrification, and denitrification in different paddy soils.MethodsField experiments were conducted in Hunan, Jiangxi, Henan, and Fujian experimental sites in south China to investigate the responses of rice yield, soil properties, and functional genes to green manuring. The four treatments were no fertilizer application (NF), using milk vetch as green manure without chemical fertilizer (GM), winter fallow with chemical fertilizer (CF), and a combination of green manure and chemical fertilizer (GMCF).ResultsThe rice yield and N uptake significantly increased in GMCF. The nifH gene copies significantly increased in GMCF in the Jiangxi and Henan sites. Soil SOM, TN, NH4+-N, NO3−-N, AP, and AK were higher in GMCF than in the other treatments. For the nitrification process, the gene copies of ammonia-oxidizing archaea were higher than those of ammonia-oxidizing bacteria in all sites. The nirK and nosZ genes involved in denitrification were negatively correlated with soil properties. With the improvement of soil properties and rice N uptake, the denitrification process was inhibited in the GMCF treatment. The nirK gene was the most critical functional gene influencing rice yield among the tested genes. SOM was the most important factor among soil properties.ConclusionsThe application of green manure improved soil properties and changed the abundance of the functional genes involved in N cycling. Green manure combined with chemical fertilizer increased rice yields and N uptake and inhibited the denitrification process.

Cyanobacterial Diazotroph Distributions in the Western South Atlantic

Inputs of new nitrogen by cyanobacterial diazotrophs are critical to ocean ecosystem structure and function. Relative to other ocean regions, there is a lack of data on the distribution of these microbes in the western South Atlantic. Here, the abundance of six diazotroph phylotypes: Trichodesmium, Crocosphaera, UCYN-A, Richelia associated with Rhizosolenia (Het-1) or Hemiaulus (Het-2), and Calothrix associated with Chaetoceros (Het-3) was measured by quantitative PCR (qPCR) of the nifH gene along a transect extending from the shelf-break to the open ocean along the Vitória-Trindade seamount chain (1200 km). Using nifH gene copies as a proxy for phylotype abundance, Crocosphaera signals were the most abundant, with a broad distribution throughout the study region. Trichodesmium signals were the second most abundant, with the greatest numbers confined to the warmer waters closer to the coast, and a significant positive correlation with temperature. The average signals for the host-associated diazotrophs (UCYN-A, Het-1, and Het-2) were consistently lower than for the other phylotypes. These findings expand measurements of cyanobacterial diazotroph distribution in the western South Atlantic, and provide a new resource to enhance modeling studies focused on patterns of nitrogen fixation in the global ocean.

Biochar-induced changes in the soil diazotroph community abundance and structure in a peanut field trial

Biological nitrogen fixation (BNF) can help replenish available nitrogen (N) in cropland and reduce the use of chemical N fertilizers, with diazotrophs playing an important role. However, the response of diazotroph community and BNF activity in biochar amendment soil, especially in the deep soil horizon, are poorly understood. In this study, soil samples were collected from topsoil (0–20 cm) and subsoil (20–40 cm) in the field experiment (established in 2013) comprising treatments with no chemical fertilizer (CK), chemical fertilizer (NPK), biochar (BC), and biochar plus chemical fertilizers (BNPK). Here, we investigated the diazotroph community using real-time PCR and high-throughput sequencing of the nifH gene, and assessed the soil N2 fixation rate (RNfix) using acetylene reduction assay (ARA). Results showed that in the topsoil, the treatments with biochar significantly increased nifH gene copies and RNfix, which was consistent with the increased soil organic matter (SOM), total carbon-to-nitrogen ratio (C/N), dissolved organic carbon (DOC) and pH. In the subsoil, applying chemical fertilizers (NPK) strongly decreased RNfix, but had no effect on diazotroph abundance; in contrast, biochar application (BC) had no effect on RNfix, but suppressed the growth of bacteria and diazotrophs while increasing the abundance of Rhizobiales order. Diazotroph and bacterial gene copies were significantly and positively correlated in both top- and sub-soil, and they were mainly influenced by SOM and total nitrogen (TN). In addition, soil nitrate nitrogen (NO3−–N) was the major factor in shaping the vertical stratification of diazotroph community structure. Although nifH gene abundance was significantly correlated with RNfix in the topsoil, the structure equation modeling (SEM) showed the highest correlation between diazotroph community structure and RNfix. Hence, we suggested that soil carbon and nitrogen sources were the key factors correlated with changes in the vertical pattern of diazotroph abundance. Biochar induced the dominant diazotroph community succession and increased soil carbon content and pH, which contributed to the BNF activity. Changes in the BNF activity were driven by the variation in diazotroph community structure.

Anomalously high abundance of Crocosphaera in the South Pacific Gyre.

The unicellular diazotrophic cyanobacterium Crocosphaera contributes significantly to fixed nitrogen inputs in the oligotrophic ocean. In the western tropical South Pacific Ocean (WTSP), these diazotrophs abound thanks to the phosphorus-rich waters provided by the South Equatorial Current, and iron provided aeolian and subsurface volcanic activity. East of the WTSP, the South Pacific Gyre (SPG) harbors the most oligotrophic and transparent waters of the world's oceans, where only heterotrophic diazotrophs have been reported before. Here, in the SPG, we detected unexpected accumulation of Crocosphaera at 50m with peak abundances of 5.26×105nifH gene copies l-1. The abundance of Crocosphaera at 50m was in the same order of magnitude as those detected westwards in the WTSP and represented 100% of volumetric N2 fixation rates. This accumulation at 50m was likely due to a deeper penetration of UV light in the clear waters of the SPG being detrimental for Crocosphaera growth and N2 fixation activity. Nutrient and trace metal addition experiments did not induce any significant changes in N2 fixation or Crocosphaera abundance, indicating that this population was not limited by the resources tested and could develop in high numbers despite the oligotrophic conditions. Our findings indicate that the distribution of Crocosphaera can extend into subtropical gyres and further understanding of their controlling factors is needed.

Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere.

Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.

Succession of diazotroph community and functional gene response to inoculating swine manure compost with a lignocellulose-degrading consortium

Diazotroph community contributes to the nitrogen mass and improves the agronomic quality of composting product, but their responses to microbial inoculation during composting are unclear. In this study, the lignocellulose-degrading consortium was inoculated at different levels (0%: CK (control) and 10%: T) to investigate their effects on the variations in the diazotroph community and functional gene during composting. In the later composting phase, the nifH gene copy number was 17.50−25.28% higher in T than CK. The nitrogenase abundance in CK and T were 0.042% and 0.046% in composting product, respectively. Network analysis indicated that inoculation affected the co-occurrence patterns of the diazotroph community and changed the keystone species composition. Partial least-squares path modeling showed that available carbon sources and the succession of the diazotroph community mainly determined the increased abundance of nifH gene. Microbial inoculation stimulated the diazotrophs activities, and was conducive to the nitrogen production in composting product.

Composition and Activity of N2-Fixing Microorganisms in Mangrove Forest Soils

Mangrove forests are considered to be a highly productive ecosystem, but they are also generally nitrogen (N)-limited. Thus, soil N2 fixation can be important for the stability of both mangrove ecosystem functions and upland N supply. This study evaluates the N2 fixation activity and composition of relevant microorganisms in two coastal mangrove forests—the Guandu mangrove in an upstream estuary and the Bali mangrove in a downstream estuary—using the acetylene reduction method, real-time polymerase chain reaction, and next-generation sequencing. The results demonstrated that ambient nitrogenase activity was higher in downstream mangrove forests (13.2–15.6 nmol h−1 g−1 soil) than in upstream mangrove forests (0.2–1.4 nmol h−1 g−1 soil). However, both the maximum potential nitrogenase activity and nitrogenase gene (nifH gene) copy number were found to be higher in the upstream than in the downstream mangrove forests, implying that the nitrogenase activity and diazotrophic abundance may not necessarily be positively correlated. In addition, amended MoO4 (which inhibits the activity of sulfate-reducing bacteria in N2-fixation) yielded low nitrogenase activity, and sulfate-reducing bacteria made up 20–50% of the relative diazotrophic abundance in the mangrove forests, indicating that these bacteria might be the major active diazotrophs in this environment.

Microbial inoculation elicited changes in phyllosphere microbial communities and host immunity suppress Magnaporthe oryzae in a susceptible rice cultivar

The hemibiotrophic fungal pathogen Magnaporthe oryzae causes serious crop losses in rice. As phyllospheric microbes share a common habitat with this foliar pathogen, they can be deployed as the change-agents for engineering desired phyllospheric microbial communities to inhibit the disease progression. Comparative evaluation of a set of native microbes, when applied as foliar spray or soil drench was undertaken, showed significant interactive effects on the concentrations of chlorophyll a and b, and carotenoids. A significant enhancement was recorded in the activities of chitosanase, β-1,3-endoglucanase and β-1,4-endoglucanase (CMCase) in the disease challenged plants, as compared to healthy plants. Among the treatments, Bacillus sp. (B1) inoculation recorded lowest values of the activities of all three hydrolytic enzymes, while Bacillus sp. (B4) and Nostoc-Anabaena consortium (C1) led to 30–60% decreases, both as foliar and soil drench modes of application. Distinct changes in the abundances of eubacterial and phylum Cyanobacterial 16S rRNA gene copies, nifH and bacterial amoA illustrated the significance of foliar over the soil drench method. The nifH gene copies were significantly higher due to the foliar method of Calothrix sp. (C2) inoculation, and values were significantly at par values with both the soil drench application of B1 (Bacillus sp.) and C1 (Nostoc-Anabaena consortium) treatments. This study illustrates the significance of the root-shoot linkages in the effective biocontrol of these promising, indigenous microbes, applied as soil drench or foliar agents, which can be useful in abating the incidence of the fungal pathogen in an environment –friendly manner.

Seasonal Shifts in Diazotrophs Players: Patterns Observed Over a Two-Year Time Series in the New Caledonian Lagoon (Western Tropical South Pacific Ocean)

Coastal and open ocean regions of the Western Tropical South Pacific ocean have been identified as a hotspot of N2 fixation. However, the environmental factors driving the temporal variability of abundance, composition, and activity of diazotrophs are still poorly understood, especially during the winter season. To address this, we quantified N2 fixation rates and the abundance of seven diazotroph phylotypes (UCYN-A1 symbiosis, UCYN-B, UCYN-C, Trichodesmium, Het-1, Het-2 and Het-3) on a monthly basis during two full years (2012 to 2014) at four stations along a coast to open ocean transect in the New Caledonian lagoon. The total nifH gene concentration (sum of all nifH gene copies) clearly decreased from the barrier reef to the shore. Apart from UCYN-B, which peaked at very high abundances (106-108nifH gene copies L-1) at two occasions at the coastal station, the UCYN-A1 symbiosis was the most abundant group at all stations, accounting for 79 % of the total nifH gene copy counts along the transect (average abundance 4.2 ± 10.3 x 104 nifH gene copies L-1). The next most abundant groups were in order Trichodesmium (accounting for 14% of the total nifH gene copies), Het-groups (6% of the total) and UCYN-C (1% of the total). Statistical analyses reveal that the UCYN-A1 symbiosis and Het groups were associated with cold ( 25°C) waters, low NOx and PO43- concentrations, strong and (mostly) easterly winds. Average N2 fixation rates over the survey were 6.5 ± 6.7 nmol N L-1 d-1 and did not differ significantly among seasons. The interannual variability was more pronounced with average integrated rates significantly higher the second year of the survey (162 ± 122 μmol N m-2 d-1) than the first year (66 ± 91 μmol N m-2 d-1), likely due to higher seawater temperature. This dataset suggests that seasonality is less pronounced than previously thought, and that relatively high N2 fixation rates are maintained in the New Caledonian lagoon all year long, despite seasonal changes in the diazotroph community composition.

Carbon substrates exert a stronger role than mineral nitrogen application in structuring soil diazotroph communities during Chinese milk vetch growth

Carbon (C) quality and quantity and nitrogen (N) availability are known to play a crucial role in influencing diazotroph community structure in soils and they are commonly affected by crop residue management and fertilizer application. However, a full understanding of how C and N interactions contribute to shaping soil diazotroph communities remains elusive. An experiment comparing two different C substrates (rice straw vs. glucose) plus low to high rates of mineral N application was conducted in two paddy soils with contrasting pH (pH = 6.05 and 7.85) with Chinese milk vetch (CMV) growth. Soils were sampled during the full blooming stage of CMV and diazotroph community structure was characterized using the nifH marker gene. The results showed that the diazotroph community responded differently to C substrates (straw and glucose) depending upon the C availability. In both soils, mineral N addition decreased nifH gene copy numbers in the straw-included treatments, but not in the glucose-included soils. Compared to the straw-included soils, glucose addition resulted in less α-diversity of diazotroph. Meanwhile, diazotroph community structure was clustered into different groups by the C sources, and marginally affected by N levels. These results suggested that the responses of the diazotroph community to N supply were regulated by C availability. Glucose addition decreased the relative abundance of Bradyrhizobium compared to straw incorporation (16.0%–25.9% vs. 19.5%–38.2%), but significantly increased the abundance of the second most dominant genus Geobacter (12.8%–23.7% vs. 4.1%–8.7%). In addition, the diazotroph diversity and community structure were less responsive to straw, glucose and mineral N addition in the lower vs. high pH soils. Overall, the results suggest that the responses of diazotrophs to N availability rely on C availability in paddy soils, and that C substrates exert a stronger influence than mineral N application in structuring diazotroph communities.

Physical Forcing Controls the Basin‐Scale Occurrence of Nitrogen‐Fixing Organisms in the North Pacific Ocean

AbstractBiological nitrogen fixation is increasingly recognized as an important source of new nitrogen in a warming ocean. However, the basin‐scale spatiotemporal distribution of nitrogen‐fixing organisms (diazotrophs) in the ocean and its controlling environmental factors remain unclear. Here we examined the basin‐scale seasonal distribution patterns of major diazotrophs (filamentous cyanobacterial Trichodesmium, unicellular cyanobacterial UCYN‐A1, and proteobacterial Gamma‐A) in surface waters of the North Pacific from 2014 to 2016 with unprecedented coverage and resolution. In general, UCYN‐A1, Trichodesmium, and Gamma‐A were abundant during spring‐autumn, summer‐autumn, and spring respectively. Regarding latitudinal patterns of abundance, UCYN‐A1 showed dome shape; Trichodesmium was gradually decreasing from low‐ to high‐latitude regions; and Gamma‐A did not show a clear pattern, which were coincident with the distinct correlations between the diazotrophs and temperature. All three diazotrophs were abundant (reached 106–107 nifH gene copy number L−1) in the North Pacific transition zone and subtropical gyre, where the cyanobacterial diazotrophs were more abundant in both the western and eastern North Pacific than in the central North Pacific. The diazotroph abundance in the western North Pacific was positively correlated with eddy kinetic energy and sea surface height anomaly, which implies an enhancement of diazotrophs in mesoscale eddies associated with the western boundary current Kuroshio and its extension. The cyanobacterial diazotrophs were positively correlated with wind stress curl, a measurable parameter of wind‐driven upwelling, in the eastern North Pacific. Our study refines the biogeography of three major diazotrophs and highlights the importance of physical forcing in mediating their dynamics.

Latitudinal constraints on the abundance and activity of the cyanobacterium UCYN‐A and other marine diazotrophs in the North Pacific

AbstractThe number of marine environments known to harbor dinitrogen (N2)‐fixing (diazotrophic) microorganisms is increasing, prompting a reassessment of the biogeography of marine diazotrophs and N2fixation rates (NFRs). Here, we investigate the diversity, abundance, and activity of diazotrophic microorganisms in the North Pacific Subtropical Gyre (NPSG), a diazotrophic habitat, and the North Pacific Transition Zone (NPTZ), a region characterized by strong physical, chemical, and biological gradients. Samples were collected on two springtime meridional cruises during 2016 and 2017, spanning from 23.5°N to 41.4°N along 158°W. We observed an abrupt decrease in diazotrophic abundances near the southern edge of the NPTZ, which coincided with a salinity front and with a ∼10‐fold increase inSynechococcusabundance, but without a concomitant change in phosphate or nitrate concentrations. In NPSG waters south of this diazotrophic boundary,nifHgenes and NFRs were consistently detected and diazotrophic communities were dominated by UCYN‐A, an uncultivated, symbiotic cyanobacterium (2.8 × 103to 1.0 × 106nifHgene copies L−1). There was a significant positive relationship between quantitative polymerase chain reaction‐derived UCYN‐AnifHgene abundances and community NFRs in the NPSG, suggesting a large contribution of UCYN‐A to community NFRs. In the NPTZ waters to the north, NFRs were low or undetected andnifHgenes were rare, with the few detected sequences represented by UCYN‐A and noncyanobacterial diazotrophs. The patterns we observed in UCYN‐A abundance in the context of local biogeochemistry suggest that the environmental controls of this organism may differ from those of cultivated marine cyanobacterial diazotrophs.