nifH Gene Abundance Research Articles

Moss and underlying soil bacterial community structures are linked to moss functional traits

AbstractMosses are among the first colonizing organisms after glacier retreat and can develop into thick moss mats during later successional stages. They are key players in N2 fixation through their microbiome, which is an important process for nutrient buildup during primary succession. How these moss–microbe interactions develop during succession is not well studied and is relevant in the light of climate change and increased glacier retreat. We examined how the bacterial communities associated with two moss species of the genus Racomitrium and the underlying soil, as well as moss traits and nitrogen fixation, develop along a successional gradient in the glacier forefield of Fláajökull in southeast Iceland. In addition, we tested whether moss functional traits, such as total carbon (TC) and total nitrogen (TN) contents, moss moisture content, and moss shoot length are drivers of moss and underlying soil bacterial communities. Although time since deglaciation did not affect TN and moss moisture contents, TC and shoot length increased with time since deglaciation. Moss and underlying soil bacterial communities were distinct. While the soil bacterial community structure was driven by moss C/N ratios, the moss bacterial community structure was linked to time since deglaciation, moss C/N ratio, and moss moisture content. Moss N2‐fixation rates were linked to bacterial community composition and nifH gene abundance rather than moss TN or time since deglaciation. This was accompanied by a shift from autotrophic to heterotrophic diazotrophs. Overall, our results suggest that there is little lateral transfer between moss and soil bacterial communities and that moss traits affect moss and soil bacterial community structure. Only moss bacterial community changed with time since deglaciation. In addition, moss N2‐fixation rates are determined by bacterial community structure, rather than moss traits or time since deglaciation. This study on the interplay between succession, mosses, soils, and their bacterial communities will inform future work on the fate of newly exposed areas as a result of glacier retreat.

Changes in the activities of key enzymes and the abundance of functional genes involved in nitrogen transformation in rice rhizosphere soil under different aerated conditions

Soil microorganisms play important roles in nitrogen transformation. The aim of this study was to characterize changes in the activity of nitrogen transformation enzymes and the abundance of nitrogen function genes in rhizosphere soil aerated using three different methods (continuous flooding (CF), continuous flooding and aeration (CFA), and alternate wetting and drying (AWD)). The abundances of amoA ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), nirS, nirK, and nifH genes; and the activities of urease, protease, ammonia oxidase, nitrate reductase, and nitrite reductase were measured at the tillering (S1), heading (S2), and ripening (S3) stages. We analyzed the relationships of the aforementioned microbial activity indices, in addition to soil microbial biomass carbon (MBC) and soil microbial biomass nitrogen (MBN), with the concentration of soil nitrate and ammonium nitrogen. The abundance of nitrogen function genes and the activities of nitrogen invertase in rice rhizosphere soil were higher at S2 compared with S1 and S3 in all treatments. AWD and CFA increased the abundance of amoA and nifH genes, and the activities of urease, protease, and ammonia oxidase, and decreased the abundance of nirS and nirK genes and the activities of nitrate reductase and nitrite reductase, with the effect of AWD being particularly strong. During the entire growth period, the mean abundances of the AOA amoA, AOB amoA, and nifH genes were 2.9, 5.8, and 3.0 higher in the AWD treatment than in the CF treatment, respectively, and the activities of urease, protease, and ammonia oxidase were 1.1, 0.5, and 0.7 higher in the AWD treatment than in the CF treatment, respectively. The abundances of the nirS and nirK genes, and the activities of nitrate reductase and nitrite reductase were 73.6, 84.8, 10.3 and 36.5% lower in the AWD treatment than in the CF treatment, respectively. The abundances of the AOA amoA, AOB amoA, and nifH genes were significantly and positively correlated with the activities of urease, protease, and ammonia oxidase, and the abundances of the nirS and nirK genes were significantly positively correlated with the activities of nitrate reductase. All the above indicators were positively correlated with soil MBC and MBN. In sum, microbial activity related to nitrogen transformation in rice rhizosphere soil was highest at S2. Aeration can effectively increase the activity of most nitrogen-converting microorganisms and MBN, and thus promote soil nitrogen transformation.

Fertilization regimes affect crop yields through changes of diazotrophic community and gene abundance in soil aggregation

Soil aggregates are extremely vulnerable to agricultural intensification and are important drivers of soil health, microbial diversity, and biogeochemical cycling. Despite its importance, there is a dearth of studies revealing how fertilization regimes influence diazotrophic community behind soil aggregates, as well as the potential consequences for crop yields. To do this, a two-decade fertilization of wheat-maize intercropping field experiment was conducted in Loess Plateau of China semiarid area under three treatments: no fertilizer, chemical and organic fertilizer. Moreover, we categorized soil aggregates as large macroaggregates (>2 mm), medium macroaggregates (1–2 mm), small macroaggregates (0.25–1 mm), microaggregates (< 0.25 mm) and rhizosphere soils aggregates. We found that soil aggregates exerted a much more influence on the nifH gene abundance than fertilization practices. Particularly, nifH gene abundance has been promoted with increasing the size of soil aggregates fraction without blank soil in the organic fertilization while its abundance presented contrast patterns in the chemical fertilization. Bipartite association networks indicated that different soil aggregates shaped niche differentiation of diazotrophic community behind fertilization regimes. Additionally, we found that organic fertilization strengthens the robustness of diazotrophic communities as well as increases the complexity of microbial networks by harboring keystone taxa. Mantel test results suggested that specific soil factors exerted more selective power on diazotrophic community and nifH gene abundance in the chemical fertilization. Furthermore, β-diversity and nifH gene abundance of diazotrophic communities in the soil microaggregates jointly determine the crop yields. Collectively, our findings emphasize the key role of functional community diversity in sustaining soil cycling process and crop yields under long-term fertilization, and facilitate our understanding of the mechanisms underlying diazotrophic community in response to agricultural intensification, which could pave the way to sustainable agriculture through manipulating the functional taxa.

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 &lt; 0.05). However, nifH gene abundance peaked in June. The diazotrophic community was dominated by Geobacteraceae (&gt;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 &lt; 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.

Empirical relationship between nifH gene abundance and diazotroph cell concentration in the North Pacific Subtropical Gyre.

Cyanobacterial N2 -fixing microorganisms (diazotrophs) play a critical role in nitrogen and carbon cycling in the oceans; hence, accurate measurements of diazotroph abundance are imperative for understanding ocean biogeochemistry. Marine diazotroph abundances are often assessed using qPCR of the nifH gene, a sensitive, taxa-specific, and time/cost-efficient method. However, the validity of nifH abundance as a proxy for cell concentration has recently been questioned. Here, we compare nifH gene abundances to cell counts for four diazotroph taxa (Trichodesmium, Crocosphaera, Richelia, and Calothrix) on two cruises to the North Pacific Subtropical Gyre, one of the largest habitats for marine diazotrophs. nifH:cell relationships were strong and significant for Crocosphaera, Richelia, and Calothrix (nifH:cell 1.51-2.58; R2 = 0.89-0.96) but were not significant for Trichodesmium, despite previous studies reporting significant nifH:cell relationships for this organism. Limited available data suggest that empirical nifH:cell can vary among studies but that relationships are usually significantly linear and >1:1. Our study indicates that nifH geneabundance, while not a direct measure of cells, is a useful quantitative proxy for diazotroph abundance.

The response of diazotrophs to nutrient amendment in the South China Sea and western North Pacific

Abstract. The availability of iron (Fe) and phosphorus (P) has been shown to be a key factor regulating rates of nitrogen fixation in the western subtropical Pacific. However, the relative importance of Fe and P at finer spatial scales between the northern South China Sea (NSCS) and the western boundary of the North Pacific is poorly constrained. Furthermore, nutrient limitation of specific diazotroph types has not yet been assessed. Here we investigated these unknowns by (i) carrying out measurements of finer-scale spatial variabilities in N2 fixation rates and diazotroph nifH gene abundances throughout these regions and (ii) conducting eight additional Fe and phosphate addition bioassay experiments where both changes in N2 fixation rates and the nifH gene abundances of specific diazotrophs were measured. Overall, nitrogen fixation rates and nifH gene abundances were lower in the NSCS than around the Luzon Strait and the western North Pacific. The nutrient addition bioassay experiments demonstrated that N2 fixation rates in the central NSCS were co-limited by Fe and P, whereas at the western boundary of the North Pacific they were P-limited. Changes in the abundances of nifH in response to nutrient addition varied in how well they correlated with changes in N2 fixation rates, and in six out of eight experiments the largest responses in nifH gene abundances were dominated by either Trichodesmium or UCYN-B (unicellular diazotrophic cyanobacteria group B). In general, nutrient addition had a relatively restricted impact on the composition of the six phylotypes that we surveyed apart from on UCYN-B. This unicellular cyanobacterium group showed increased contribution to the total nifH gene abundance following P addition at sites where N2 fixation rates were P-limited. Our study provides comprehensive evidence of nutrient controls on N2 fixation biogeography in the margin of the western North Pacific. Future research that more accurately constrains nutrient supply rates to this region would be beneficial for resolving what controls diazotroph community structure.

Biological nitrogen fixation and nifH gene abundance in deadwood of 13 different tree species

Deadwood is an extremely nitrogen (N) poor plant litter whose decomposition may rely on external N sources. Biological N2 fixation (BNF) by free-living diazotrophs, encoded with the nifH gene, is a potential pathway of N acquisition in deadwood. Still, the control of this process by tree species specific traits is hardly known. Here, we examined (1) BNF rates and nifH gene abundances in deadwood of 13 tree species after 12 years of decomposition and (2) how BNF was related to nutrient concentrations and non-structural carbohydrates (NSC). Comparing our BNF rates with the literature revealed no difference for angiosperms but gymnosperms. Large variability prevented any significant difference in BNF and nifH gene abundance between tree species identities of deadwood. Still, higher BNF and nifH gene abundances occurred in the group of diffuse-porous angiosperms compared to ring-porous angiosperms and gymnosperms. Positive relationships between BNF rates and molybdenum, phosphor, sulfur, and N suggested co-limitation of BNF by several nutrients in deadwood. Relatively high NSC concentrations indicated good carbon availability for diazotrophs. Furthermore, structural equation modeling highlighted the importance of water content for BNF and nifH gene abundance, although the overall explanatory power was low. In conclusion, BNF is a ubiquitous microbial process in deadwood of native European tree species and the comparison with other studies suggests no down-regulation of BNF by high N deposition in Central Europe.

Soil nutrient dynamics relate to Epichloë endophyte mutualism and nitrogen turnover in a low nitrogen environment

Colonization by foliar fungal endophytes can assist host plants in the acquisition of soil nutrients, however understanding of the effects of Epichloë endophytes on soil nutrient dynamics and their consequences for nitrogen cycling remains fragmentary. Here, we studied the microbial functional genes involved in the soil nitrogen cycle and soil nutrient dynamics along a nitrogen gradient in rhizosphere soil of ryegrass infected by the endophyte Epichloë festucae var. lolii. High-throughput sequencing was used to determine the community of microbial functional genes. Plant nutrients and soil N2O flux were measured. The endophyte presence reduced the plant nutrient traits (shoot organic carbon, total nitrogen and total phosphorus, and root total phosphorus) under low nitrogen, while it increased the soil nutrient accumulation and altered the microbial environment. Plants with fungal endophyte showed higher community diversity in the AOB-amoA gene (ammonia-oxidation bacteria), had lower absolute and relative abundances in the nirK gene (nitrite reduction bacteria), and improved relative abundances and community diversity of the nosZ (nitrous oxide reduction bacteria). The nifH gene (N2 fixing bacteria) showed higher absolute and relative abundances, and diversity in rhizosphere soil of endophyte-infected plants. Changes in plant and soil traits mediated by endophyte infection were closely related to N2O fluxes and nifH gene abundance. The changes in CO2 flux by changing in soil microbial biomass nitrogen mediated by shoot biomass (induced by endophyte infection), which further altered the soil pH and NO3− content and lead to an increased in NH4+ accumulation. The current study demonstrated that the possible mechanism for endophyte-mediated nutrient uptake might promote the NH4+ accumulation through nitrogen mineralization and NO3− isomerization rather than enhancing in the nitrogen fixation process and inhibiting the denitrification process in N limited samples. By underlining the importance of endophyte infection for nutrient accumulation in plant and soil and biomass, these findings suggested that nutrient availability could initiate endophyte infection effects to mitigate the damage of low N stress for the host.

Manure applications alter the abundance, community structure and assembly process of diazotrophs in an acidic Ultisol

The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha−1) application, rather than medium-rate (18 Mg ha−1) and high-rate (27 Mg ha−1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.

Nutrient status of integrated rice-crayfish system impacts the microbial nitrogen-transformation processes in paddy fields and rice yields.

Increasing rice yield is essential for alleviating global food crisis. High soil nutrient level guarantees high rice yields in conventional rice monoculture (RM) systems, but excessive unconsumed nutrients act as pollutants and can even threaten rice growth. The integrated rice-crayfish (IRC) system aims to transfer the excess nutrients from crayfish to paddy fields to improve the comprehensive utilization rate of nutrients and create additional profits, while the responding characteristics of IRC microbial communities in paddy fields and rice yields to the nutrient status remain unclear. Considering the crucial roles of microbiomes in promoting nutrient cycling for crop absorption in rice production progresses, the composition and functional characteristics of soil microbial communities from six IRC farms with variant nutrient statuses in the Yangtze River Delta were surveyed in this study. Compared with RM systems, IRC systems with appropriately improved (p < 0.05) soil quality created favorable nutrient (FN) status accompanied by 15% rice yields increase, while IRC systems with extremely high nutrients (HN) status (p < 0.01) accompanied by 14% rice yields reduction. Soil microbial diversity and network complexity were maintained in FN-IRC systems, but declined in HN-IRC systems, with the Shannon index significantly decreased by 9.2% and network density decreased from 0.135 (in RM) to 0.062. In the FN-IRC systems, the keystone taxa identified by co-occurrence networks displayed inextricably positive correlations with soil nitrification potential (calculated by normalization of amoA gene abundance) and rice yields. While in HN-IRC systems, the large loss of keystone taxa might limit soil nitrogen fixation potential (calculated by normalization of nifH gene abundance), and further rice yields. Our study indicates that soil nutrient management in IRC systems claim attention, and the improvement of nitrogen metabolism is the key to realize agricultural cleaner production.

Contrasting Roles of DOP as a Source of Phosphorus and Energy for Marine Diazotrophs

The oceanic dissolved organic phosphorus (DOP) pool is mainly composed of P-esters and, to a lesser extent, equally abundant phosphonate and P-anhydride molecules. In phosphate-limited ocean regions, diazotrophs are thought to rely on DOP compounds as an alternative source of phosphorus (P). While both P-esters and phosphonates effectively promote dinitrogen (N2) fixation, the role of P-anhydrides for diazotrophs is unknown. Here we explore the effect of P-anhydrides on N2 fixation at two stations with contrasting biogeochemical conditions: one located in the Tonga trench volcanic arc region (“volcano,” with low phosphate and high iron concentrations), and the other in the South Pacific Gyre (“gyre,” with moderate phosphate and low iron). We incubated surface seawater with AMP (P-ester), ATP (P-ester and P-anhydride), or 3polyP (P-anhydride) and determined cell-specific N2 fixation rates, nifH gene abundance, and transcription in Crocosphaera and Trichodesmium. Trichodesmium did not respond to any DOP compounds added, suggesting that they were not P-limited at the volcano station and were outcompeted by the low iron conditions at the gyre station. Conversely, Crocosphaera were numerous at both stations and their specific N2 fixation rates were stimulated by AMP at the volcano station and slightly by 3polyP at both stations. Heterotrophic bacteria responded to ATP and 3polyP additions similarly at both stations, despite the contrasting phosphate and iron availability. The use of 3polyP by Crocosphaera and heterotrophic bacteria at both low and moderate phosphate concentrations suggests that this compound, in addition to being a source of P, can be used to acquire energy for which both groups compete. P-anhydrides may thus leverage energy restrictions to diazotrophs in the future stratified and nutrient-impoverished ocean.

Effects of applying maize stover on soil diazotroph community diminish with depth

Biological nitrogen fixation (BNF) is a vital approach to replenishing soil nitrogen (N) pools by converting atmospheric N2. Agronomic practice of growing legumes frequently includes stover return, which generally induces the growth of N2-fixers (i.e., diazotrophs) and stimulates BNF; however, there is uncertainty regarding the stover return effects along soil depth. Here, soil samples were collected from 0 to 10, 10–20 and 20–30 cm in the peanut (Arachis hypogaea) field experiment (established in 2013) comprising treatments with no fertilizer (CK), maize (Zea mays) stover (MS), and MS + chemical fertilizers (SNPK). The abundance of 16S rRNA and nifH genes was determined by real-time PCR, the rate of N2 fixation in soil (RNfix) was measured by acetylene reduction assay, and diazotroph community structure was explored by high-throughput sequencing. Results showed that maize stover application alone increased nifH gene abundance in the 0–10 cm layer, and combined with chemical fertilizer application increased RNfix in the 0–20 cm layers, affecting diazotroph community structure succession in the 0–20 cm layers. This is consistent with the effects of stover on soil properties such as dissolved organic carbon and nitrogen, soil organic matter (SOM) and carbon-to‑nitrogen ratio, with SOM playing a dominant role in governing the abundance, structure and activity of diazotroph communities in the soil. In addition, total nitrogen (TN) was the key factor in shaping the vertical stratification of diazotroph community structure, the abundance of diazotrophs and bacteria as well as the structure and RNfix of the diazotroph community were highly correlated. This study demonstrated that maize stover incorporation caused significant positive changes in the vertical stratification of soil diazotroph communities; although these effects decreased with soil depth and were minor when stover was combined with chemical fertilizers, they still highlighted the crucial role of stover return in enhancing BNF in soil where legumes were present.

Response of bacterial communities and nitrogen-cycling genes in newly reclaimed mudflat paddy soils to nitrogen fertilizer gradients.

Conversion of coastal mudflats into paddy soils is an effective measure to alleviate the pressures on land resources. However, few studies have evaluated the effects of nitrogen (N) fertilizers on bacterial communities in newly reclaimed mudflat paddy soils. We performed a field plot experiment with six N fertilizer rates (0, 210, 255, 300, 345, and 390kgNha-1) in a newly reclaimed mudflat paddy for 2 consecutive years and used Illumina sequencing and qPCR to investigate the effects of N fertilizers on bacterial communities and N-cycling genes. Results showed that high N fertilization (above 300kgNha-1) increased the contents of organic matter (OM), total N (TN), ammonium (NH4+), and nitrate (NO3-) and significantly decreased the diversity and richness of bacteria. Furthermore, high N fertilization had a stronger effect on bacterial communities than low N fertilization, probably due to high concentrations of NH4+, OM, and NO3-. Additionally, in paddy soils with high N fertilizer application, the relative abundances of Bacteroidetes, γ-proteobacteria, and Actinobacteria increased significantly, but the reverse was true for those of Chloroflexi, Firmicutes, δ-proteobacteria, α-proteobacteria, Acidobacteria, and β-proteobacteria. The results of qPCR indicated that high N fertilization significantly increased the relative abundance of nifH genes involved in N fixation and decreased that of amoA-archaea involved in ammonia oxidation, nirS genes involved in nitrite reduction, and nosZ genes involved in nitrous oxide reduction, which suggested that high N fertilization increased the potential of available N retention and reduced the potential of nitrous oxide emission. Overall, N fertilizers with an N fertilizer rate of above 300kgNha-1 significantly altered the bacterial communities and N-cycle of mudflat paddy soils.

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.

The inhibitory effects of sunlight on nitrogen removal in riverine overlying water with suspended particles

Overlying water with suspended particles is a hot spot for nitrogen removal in river systems. Although light exposure affects nitrogen transformations and nitrogen removal in some environments, such effects have rarely been explored and quantified in riverine overlying water. Herein, we examined the difference between dark and light conditions in the community composition and abundance of nitrogen transformation microbes in simulated overlying water by high-throughput sequencing and qPCR. Moreover, 15N-labeling techniques were used to investigate variation in nitrogen removal rates (N2 and N2O) as well as nitrification rates between dark and light conditions. We found apparent differences in the bacterial community between light and dark microcosms. The abundance of Cyanobacteria was greatly elevated in light microcosms, with the diazotroph nifH gene abundance being 7.4-fold higher in the light microcosm (P < 0.01). However, due to the vulnerability of some specifies to UV damage, the diazotroph species richness was reduced. The abundances of ammonia-oxidizing archaeal amoA, ammonia-oxidizing bacterial amoA, and denitrifying nirS genes were 80.1%, 46.3%, and 50.7% lower in the light microcosm, respectively, owing to the differential inhibition of sunlight exposure on these microbes. Both 15N–N2 and 15N–N2O were significantly produced regardless of conditions with or without light. Due to the combined effects of reduced nitrification and denitrification, as well as potentially enhanced nitrogen fixation, the accumulated amounts of 15N–N2 and 15N–N2O were 6.2% and 44.8% lower, respectively, in the light microcosm. This study quantifies the inhibitory effect of sunlight exposure on nitrogen removal in riverine overlying water and reveals the underlying mechanisms, providing insights into our understanding of nitrogen transformations in river systems.

Nutrient regulation of biological nitrogen fixation across the tropical western North Pacific.

Nitrogen fixation is critical for the biological productivity of the ocean, but clear mechanistic controls on this process remain elusive. Here, we investigate the abundance, activity, and drivers of nitrogen-fixing diazotrophs across the tropical western North Pacific. We find a basin-scale coherence of diazotroph abundances and N2 fixation rates with the supply ratio of iron:nitrogen to the upper ocean. Across a threshold of increasing supply ratios, the abundance of nifH genes and N2 fixation rates increased, phosphate concentrations decreased, and bioassay experiments demonstrated evidence for N2 fixation switching from iron to phosphate limitation. In the northern South China Sea, supply ratios were hypothesized to fall around this critical threshold and bioassay experiments suggested colimitation by both iron and phosphate. Our results provide evidence for iron:nitrogen supply ratios being the most important factor in regulating the distribution of N2 fixation across the tropical ocean.

Constraining uncertainties of diazotroph biogeography from nifH gene abundance

AbstractMarine diazotrophs fix dinitrogen gas into bioavailable nitrogen that drives the ocean nitrogen cycle; yet, efforts to infer global diazotroph distributions have been limited by a sparsity of observations. In situ measurements of nifH gene abundance (essential for nitrogen fixation) are increasingly being used to inform the biogeography of diazotrophs. However, comparing such gene abundances spatially, temporally and between diazotroph species remains difficult. We synthesize existing data on gene‐to‐cell and cell‐to‐biomass conversions for four major diazotroph groups to convert nifH gene counts to abundance‐ and biomass‐based biogeographic “currencies.” Results suggest up to two orders of magnitude uncertainty converting from nifH gene abundance to cell abundance, and up to four orders of magnitude uncertainty from nifH gene abundance to biomass. Uncertainty arises due to large taxonomic variation in cell size and presumed polyploidy, that is, variability in the number of genomes per cell. Such uncertainties hinder comparing biogeographies of different species. Additionally, numerical models need biogeographies for validation, typically in the currency of carbon biomass. Here, we show that conversion uncertainty from nifH gene abundance to biomass overwhelms biomass variability simulated in such models. These results demonstrate a basic currency problem in converting gene abundance observations to biogeographically meaningful quantities for synthesizing studies and modeling approaches. Such issues may also have relevance to other genes and organisms beyond diazotrophs. To avoid biases in interpreting gene counts as a measure of abundance, we suggest converting gene counts to a binary presence/non‐detect metric to map broad biogeographical distributions more robustly.

Land use indirectly affects the cycling of multiple nutrients by altering the diazotrophic community in black soil.

Diazotrophic bacteria, as one of most important group of soil microorganisms, play critical roles in multiple ecosystem functions (i.e., multifunctionality). However, little information is available about the diazotrophic community in driving soil nutrient cycling and multifunctionality at different depths with distinct vegetation in the black soil region of northeastern China. To learn the interactions among land use, cycling of multiple nutrients and the diazotrophic community, we performed this study in grassland (GL), forested land and a cropland (CL) in soils at depths of 0-15 cm and 15-35 cm. The highest nifH gene abundances were found in the CL treatment, while the highest diazotrophic species richness and diversity were detected in the GL in both soil layers. The nifH gene abundance was directly/positively correlated with soil bulk density and negatively correlated with land use and soil depth. The index of multiple nutrient cycling was directly/negatively affected by soil depth and indirectly/positively affected by land use. Land use directly/negatively affected soil pH and thus indirectly affected the diazotrophic community composition and the nutrient cycling index. The diversity and community composition of the diazotrophs together accounted for 95% of the differences in the multiple nutrient cycling index. Soil diazotrophic communities undertake important roles in maintaining nutrient cycling and soil multifunctionality at depths of 0-15 cm and 15-35 cm layers with different land uses of the black soil region of China. © 2021 Society of Chemical Industry.

Alpine meadow degradation depresses soil nitrogen fixation by regulating plant functional groups and diazotrophic community composition

Biological nitrogen fixation (BNF), a function performed by diazotrophic microbes, plays an essential role in nitrogen (N) bioavailability in terrestrial ecosystems. However, little is known about the effects of meadow degradation on soil BNF and diazotrophic communities in alpine meadows. We investigated changes in soil BNF and their potential drivers in alpine meadows along a degradation gradient on the Tibetan Plateau (non-degraded, lightly degraded, moderately degraded, and severely degraded meadows) using real-time quantitative PCR and amplicon sequencing. Soil BNF rates decreased significantly along the meadow degradation gradient with a range of 17.34–79.84 nmol C2H4 g−1 dry soil d−1 across all sites. The highest BNF rate in the non-degraded meadow was 1.5–4.6-fold higher than that in the degraded meadows. The abundance and diversity of diazotrophs measured by nifH abundance and Shannon diversity was also decreased in the degraded meadows, accompanied by decreases in plant biomass, soil moisture, and nutrient content (C, N). Soil BNF rate was correlated with plant biomass, soil nutrient content, and diazotrophic abundance (including Nostoc, Scytonema, Rhodopseudomonas, and unidentified genera within the Rhizobiales and Proteobacteria). The community composition of diazotrophs differed markedly among sites with different levels of degradation, with both autotrophic (Cyanobacteria) and heterotrophic (Proteobacteria) diazotrophs contributing significantly to BNF. The plant functional groups, particularly the sedge family, were the primary drivers of soil BNF rates via mediating soil moisture, nutrient content (dissolved organic C and N), nifH gene abundance, and diazotrophic community composition. Our results reveal the main drivers of decreased BNF during alpine meadow degradation and emphasize the importance of plant functional groups in shaping the diazotrophic community and regulating the BNF rate. This information can be applied to the restoration of degraded meadow ecosystems.

Biochar Enhanced Growth and Biological Nitrogen Fixation of Wild Soybean (Glycine max subsp. soja Siebold &amp; Zucc.) in a Coastal Soil of China

The high salinity and nutrient deficiency in degraded coastal soil restricts crop growth and grain production. The development of effective and novel technology for coastal soil remediation is of great requirement. The effect of wood waste biochar (WB) on the growth and biological nitrogen fixation of wild soybean (Glycine max subsp. soja Siebold &amp; Zucc.), a legume with high economic values and salt tolerance in coastal soil, were explored using a 42-day pot experiment. With the optimal rate of WB addition (1.5%, w/w), the biomass and plant height of wild soybean increased by 55.9% and 28.3%, respectively. WB addition enhanced the photosynthesis (chlorophyll content) and biological nitrogen fixation (nodule number) of the wild soybean. These results may attribute to the improvement of the soil properties including the SOM, NO3−-N content, and WHC. In addition, the shifted bacterial community following WB addition in the coastal soil favored the nitrogen fixation of wild soybean, which was evidenced by the increased abundance of nifH gene and Pseudarthrobacter, Azospirillum, and Rhizobiales. The results of our study suggested the potential of using biochar-based technology to reclaim the coastal degraded soils and enhance the crop growth to ensure food security.