nifH Gene Abundance Research Articles

Energetic supply regulates heterotrophic nitrogen fixation along a glacial chronosequence

Ice-free areas are expanding on the Tibetan Plateau and in its surroundings, and these recently exposed lands are typically deficient in nitrogen (N). Free-living N fixation (FLNF) represents a vital source of N input, especially when symbiotic N-fixing plants are absent. However, we know little about how FLNF changes with ecosystem succession after glacier retreat. In 2018, we measured the potential rates of FLNF in soil profiles at four sites (exposed since 2012, 1980, 1970 and 1930, respectively) along the Hailuogou glacier chronosequence and at a reference site with well-developed Podosols. We also tested the role of nifH gene abundance and resource availability in regulating FLNF rates. The results showed that photosynthetic cyanobacteria likely contributed the majority of FLNF in the biological soil crusts (exposed since 2012), while heterotrophic FLNF may prevail at later successional stages with closed canopies. FLNF rates were the highest in the litter layer of the soil profiles and decreased with soil depth. In the litter layer, FLNF rates were lower at the site dominated by N-fixing shrubs (exposed since 1980) than at the older sites dominated by non-N-fixing trees (exposed since 1970 and 1930, and the reference site). Carbon (C) availability was the major factor explaining variation in heterotrophic FLNF rates measured in the lab without light, while the effect of nifH gene abundance was nonsignificant. Overall, our results highlighted the energetic control on heterotrophic FLNF rates in relatively young ecosystems, which likely resulted in the poor relationship between nifH gene abundance and heterotrophic FLNF rates. The findings will help in understanding and modeling the coupled C and N cycles in glacier forefield ecosystems which are being exposed at accelerated rates.

Effects of Cellulolytic Bacteria on Nitrogen-Fixing Bacteria, 16S rRNA, nifH Gene Abundance, and Chemical Properties of Water Hyacinth Compost

This research investigated alterations to and the interdependency of nitrogen-fixing bacteria, 16S ribosomal ribonucleic acid gene (16S rRNA) and nitrogenase reductase gene (nifH) gene abundance, and chemical properties of water hyacinth compost when using cellulolytic bacteria isolated from soil and leaf litter (CSL) inoculum. The un- and inoculated treatments in the compost were designed with three replications. Microbiological analysis involved examination of the total number of bacteria and gene abundance in the compost based on quantitative real-time polymerase chain reaction (qPCR). Some chemical properties of the compost were also analyzed. The results indicated that applying cellulolytic bacteria into compost could increase the amounts of bacteria, especially nitrogen-fixing bacteria. The pH of the compost increased slightly for the first 4 weeks. The amount of nitrogen and organic matter (OM) in the compost increased continuously during the composting period. The concentration of ammonium changed markedly in the range 1.5–2 times at the 4th and 10th weeks of the composting process, which was consistent with an increase of nitrogen-fixing bacteria. The concentration of nitrate doubled at the 12th week. The abundance of 16S rRNA and nifH genes was significantly correlated with the number of bacteria, total nitrogen, ammonium, nitrate, and OM. The inoculated cellulolytic bacteria not only accelerated the nitrogen mineralization process but also promoted bacterial numbers in the compost. These bacteria also affected the transformation of nutrients and correlated positively with gene abundance.

Nitrogen transformation and microbial community structure varied in apple rhizosphere and rhizoplane soils under biochar amendment

Biochar amendment is commonly applied to ameliorate soil environment and alleviate nitrous oxide (N2O) emissions, while our understanding of biochar effects on microbial community and nitrogen transformation traits of orchard root region soil is limited. We observed the composition and diversity of bacterial, fungal, and archaeal communities in apple root region (non-rhizosphere, rhizosphere, and rhizoplane) soils amended with apple wood biochar using the Illumina sequencing methods. We used quantitative PCR to quantify the abundance of nitrogen-transforming functional marker genes involved in microbial nitrogen fixation (nifH), nitrification (archaeal amoA and bacterial amoA), and denitrification (nirK, nirS, and nosZ). Biochar amendment altered bacterial, fungal, and archaeal community compositions in apple root region soil. When compared to control, biochar additions dramatically increased the α-diversity of bacteria in the rhizoplane soil, whereas amendment significantly decreased the α-diversity of fungi and archaea in the rhizosphere soil. Moreover, the driving factors varied in non-rhizosphere, rhizosphere, and rhizoplane soils. The abundance of nitrogen-fixing microorganisms and microbial N2O reduction were enhanced by biochar amendment in rhizosphere and rhizoplane soils, which was associated with an observed reduction in N2O concentrations by 13.7 and 35.1% in the 15- and 20-cm soil layer. However, wood biochar amendment had insignificant effect on nifH and amoA gene abundances in non-rhizosphere soil. Network analysis revealed that nitrogen-transforming functional genes had an intensive potential link to multiple microbial phyla. The soil microbial community was altered in biochar-amended soil by changing soil properties, thereby regulating nitrogen transformation processes and N2O concentrations in apple root region soil.

Effect of different short-term tillage management on nitrogen-fixing bacteria community in a double-cropping paddy field of southern China.

Soil nitrogen (N)-fixing bacteria community plays an important role in the N cycling process in soil, but there is still limited information about how the soil microbes that drive this process to respond to combined application of tillage and crop residue management under the double-cropping rice (Oryza sativa L.) paddy field in southern of China. Therefore, the effects of 6-years short-term tillage treatment on soil N-fixing bacteria community under the double-cropping rice paddy field in southern China were studied by using the polymerase chain reaction-denaturing gradient gel electrophoresis method. The field experimentincluded four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), rotary tillage with crop residue removed as control (RTO). The results showed that the diversity index and richness index of cbbLR and nifH genes with CT, RT, and NT treatments were increased, compared with RTO treatment. Compared with RTO treatment, the abundance of cbbLR gene with CT, RT, and NT treatments were increased by 6.54, 4.73, and 2.78 times, respectively. Meanwhile, the abundance of nifH gene with CT, RT, and NT treatments were 5.32, 3.71, and 2.45 times higher than that of RTO treatment. The results also indicated that soil autotrophic Azotobacter and nitrogenase activity with CT and RT treatments were significantly higher (p < .05) than that of RTO treatment. There was an obvious difference in characteristic of soil N-fixing bacteria community between the application of crop residue and without crop residue input treatments. In summary, the results indicated that the abundance of N-fixing bacteria community in the double-cropping rice paddy field increased with conventional tillage and rotary tillage practice.

Projected expansion of Trichodesmium's geographical distribution and increase in growth potential in response to climate change.

Estimates of marine N2 fixation range from 52 to 73TgN/year, of which we calculate up to 84% is from Trichodesmium based on previous measurements of nifH gene abundance and our new model of Trichodesmium growth. Here, we assess the likely effects of four major climate change-related abiotic factors on the spatiotemporal distribution and growth potential of Trichodesmium for the last glacial maximum (LGM), the present (2006-2015) and the end of this century (2100) by mapping our model of Trichodesmium growth onto inferred global surface ocean fields of pCO2 , temperature, light and Fe. We conclude that growth rate was severely limited by low pCO2 at the LGM, that current pCO2 levels do not significantly limit Trichodesmium growth and thus, the potential for enhanced growth from future increases in CO2 is small. We also found that the area of the ocean where sea surface temperatures (SST) are within Trichodesmium's thermal niche increased by 32% from the LGM to present, but further increases in SST due to continued global warming will reduce this area by 9%. However, the range reduction at the equator is likely to be offset by enhanced growth associated with expansion of regions with optimal or near optimal Fe and light availability. Between now and 2100, the ocean area of optimal SST and irradiance is projected to increase by 7%, and the ocean area of optimal SST, irradiance and iron is projected to increase by 173%. Given the major contribution of this keystone species to annual N2 fixation and thus pelagic ecology, biogeochemistry and CO2 sequestration, the projected increase in the geographical range for optimal growth could provide a negative feedback to increasing atmospheric CO2 concentrations.

Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China.

Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.

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.

Abundance and community succession of nitrogen-fixing bacteria in ferrihydrite enriched cultures of paddy soils is closely related to Fe(III)-reduction

In flooded paddy soils, some metal reducers are also capable of nitrogen (N) fixation, which is essential in ensuring a reliable N-supply for rice growth. Microbial iron [Fe(III)] reduction is an important biogeochemical process that can be stimulated by ferrihydrite amendment to paddy soil. Therefore, this study aimed to investigate the abundance and succession of the N2-fixing bacterial community in ferrihydrite enriched paddy soils collected from Hunan (HN) and Sichuan (SC) provinces, China. The relationship between the N2-fixing bacterial community and Fe(III) reduction was also assessed. When compared with the control treatment, ferrihydrite enrichment significantly enhanced nitrogenase (nifH) gene abundance by 8.05 × 105 to 4.45 × 106 copies g−1 soil during the 40-day flooding of HN soil, while nifH gene abundance in SC soil was remarkably increased by 5.90 × 107 to 9.56 × 107 copies g−1 soil during day 1 to 5 in response to ferrihydrite amendment. The relative abundance of N2-fixing bacteria peaked on day 5 (21.5% in HN soil and 5.4% in SC soil) and gradually decreased to a stable abundance after day 20. Remarkable increases in relative abundance of N2-fixing bacteria during the first 10 days of flooding were detected in both soils with ferrihydrite enrichment, whereas little difference was found after day 10 of flooding. During the early stage of flooding, the Shannon and Simpson indexes of N2-fixing bacteria with ferrihydrite enrichment were significantly decreased, and the community structure changed greatly. Most N2-fixing bacteria in ferrihydrite enriched paddy soils were phylogenetically related to the order Clostridiales, with some of those potentially capable of Fe(III) reduction. The community succession of N2-fixing bacteria closely correlated with Fe(III) reduction. Thus, improving N2-fixation via stimulation of Fe(III) reduction might aid in the reduction of N-fertilizer application to paddy field.

Understanding the reestablishment of micro-ecosystem on the soil microbial community after Merapi Volcano eruption through 16S metagenomic analysis

An eruption of Merapi Volcano affected the established soil ecosystem. Succession process will recover the disrupted soil ecosystem. Soil microbial community is known as the first agent for the succession. They play essential roles to construct the micro-habitat by contributing the ecosystem recovery in nutrient cycling and subsequently initiating the plants-microbes interaction. Since the soil microbial community and its functional profiles become a response to the reestablishment process, their structure community is essential to be understood. This study was addressed to describe the soil microbial community in particular of the presence of plant communities after the eruption and to find out the functional profiles through its community. Using the 16S metagenomic culture-independent analysis, we examined the soil samples of Merapi Volcano after an eruption in three types of soil samples including soil without plants (SC), soil covered with shrubs (LP), and soil covered with high plants (HP). As a result, we obtained that the establishment following the presence of plant community type delineating the pattern diversity value increasingly from SC to LP then HC with Proteobacteria as a prominent Phylum. The presence of the plant community suggested that plants-microbes interaction constructed the establishment of microbial community structure where the microbial community in SC led the nitrogen metabolism than other soil samples due to the annotated nifH gene abundance. Therefore, we assumed that the microbial community in soil without plants is the early recovery stage and the plant community for establishing the micro-habitat after the volcano eruption.

Effect of mesoscale eddies on diazotroph community structure and nitrogen fixation rates in the South China Sea

Mesoscale eddies play a key role in ocean biogeochemistry, yet their effects on dinitrogen (N2) fixation are not well understood. Using quantitative polymerase chain reaction (qPCR) and dinitrogen-15 (15N2) tracer methods, we examined the abundance of nifH genes in N2-fixing microorganisms and N2 fixation rates in the upper water column (0–100 m) of mesoscale eddies in the northeastern South China Sea (SCS). High N2 fixation rates affected by an anticyclonic eddy were associated with high abundances of unicellular nitrogen-fixing cyanobacteria in groups A and B (UCYN-A, UCYN-B), while low nitrogen fixation was found in both cyclonic eddy and reference stations. The estimated N2 fixation rates met 9% ± 5% of the nitrogen demand for primary production affected by the anticyclonic eddy. Our results indicate that mesoscale eddies can affect nitrogen fixation through affecting nutrient availability and eddy transport, and play a crucial role in regulating N2 fixation in the oligotrophic SCS.

Soil microbial abundance and activity across forefield glacier chronosequence in the Northern Patagonian Ice Field, Chile

ABSTRACT In recently deglaciated soils, microbial organisms drive soil transformations by increasing carbon (C) and nitrogen (N) pools while depleting available phosphorous (P), thus improving plant colonization and soil development. However, the rate of soil development can vary in response to local environmental conditions that affect microbial abundance and activity. In this contribution we use observational and experimental approaches to evaluate the interplay between soil biogeochemical features and microbial abundance and function after approximately seventy years of soil development in the forefield of the Exploradores Glacier that is located at the northernmost end of the Northern Patagonian Ice Field. Our findings suggest that after approximately seventy years of soil development, microbial abundance and soil C and N accumulation increase with soil age, soil bulk density and pH decreased, and microbial activity measured as soil chlorophyll a and nifH gene abundance increased. In turn, decomposition increased with fungal abundance, showing higher values in the late stages of soil development where the soil C:N ratio was higher and soil pH was lower. Overall, biogeochemical changes along this chronosequence followed the predicted pattern, with gradual increases in soil nutrients and microbial abundance, in addition to decomposition processes.

Distinct Intra-lake Heterogeneity of Diazotrophs in a Deep Oligotrophic Mountain Lake.

To date, little is known about the diazotrophs in freshwater ecosystems. In this study, we examined the diversity, abundance, and distribution of the diazotrophic community in the deep oligotrophic Lake Fuxian using high-throughput sequencing and quantitative polymerase chain reaction of nifH genes. Our results showed that the diazotrophs in Lake Fuxian were diverse and were distributed among Proteobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, and other unclassified environmental sequences. For the first time, it is found that Bacteroidetes and Planctomycetes harbor diazotrophs in freshwater ecosystems. The diazotrophic community compositions were significantly different between the littoral and pelagic zones in the surface layer, and they also changed dramatically along the vertical profile. High diazotrophic abundance and diversity were mostly observed in the surface littoral zone, and overall, a significant relationship between nifH gene richness and abundance was observed. The water turbidity, nitrite, and phosphorus were the most important factors explaining the spatial changes in diversity and abundances of this important functional group. The two most dominant operational taxonomic units belonging to Betaroproteobacteria and Planctomycetes demonstrated opposite distribution patterns in abundance that were driven by non-overlapping environmental factors. This study is by far the first to uncover the high diversity and intra-lake heterogeneity of diazotrophs in a freshwater lake and illuminate the controlling factors. It provides the probability of the co-occurrence of N2 fixation and N-loss in particles.

Data‐Driven Modeling of the Distribution of Diazotrophs in the Global Ocean

AbstractDiazotrophs play a critical role in the biogeochemical cycling of nitrogen, carbon, and other elements in the global ocean. Despite their well‐recognized role, the diversity, abundance, and distribution of diazotrophs in the world's ocean remain poorly characterized largely due to limited observations. Here we update the database of diazotroph nifH gene abundances and assess how environmental factors may regulate diazotrophs at the global scale. Our meta‐analysis more than doubles the number of observations in the previous database. Using linear and nonlinear regressions, we find that the abundances of Trichodesmium, UCYN‐A, UCYN‐B, and Richelia relate differently to temperature, light, and nutrients. We further apply a random forest algorithm to estimate the global distributions of these diazotrophic groups, identifying undersampled potential hot spots of diazotrophy in the South Atlantic and southern Indian Ocean, and in coastal waters. The distinct ecophysiologies of diazotrophs highlighted here argue for separate parameterizations of different diazotrophs in model simulations.

Effects of grazing exclusion on the abundance of functional genes involved in soil nitrogen cycling and nitrogen storage in semiarid grassland

We investigated the effects of grazing exclusion on the abundance of functional genes (nifH, amoA-AOA, amoA-AOB, narG, nirK, nirS, and nosZ) involved in soil nitrogen cycling in soil profiles (0-10, 10-20, 20-40 and 40-60 cm) from a chronosequence of grazing exclusion (0, 7, 18, 27 and 35 years) in the semiarid grasslands of the Loess Plateau. The relationship between abundance of functional genes and soil nitrogen storage was evaluated. The results showed that 35 years exclusion increased the abundance of nifH and amoA-AOB genes by 67.8% and 17.6% compared with the grazed grassland, respectively, and decreased that of nirK genes. The abundance of nifH, narG, and nirS genes in surface soil (0-10 cm) were significantly higher than that in deep soil (20-40 and 40-60 cm), indicating that those genes had surface accumulation effects. Grazing exclusion increased soil nitrogen storage. Soil nitrogen storage in 0-60 cm layer was the highest at 27 years (20.96 mg·hm-2), indicating that 27 years might be the optimum for grazing exclusion. The abundance of nifH, amoA-AOA and amoA-AOB had a significant linear relationship with nitrogen storage, suggesting that microbes harboring these genes played an important role in soil nitrogen accumulation. Total nitrogen, bulk density, and available phosphorus content were the dominant factors affecting the abundance of functional genes involved in soil nitrogen cycling. Our results provided a scientific reference for understanding soil nitrogen cycling and restoration of degraded grassland.

Biogeography of N2 Fixation Influenced by the Western Boundary Current Intrusion in the South China Sea

AbstractThe N2 fixation and primary production rates were measured simultaneously using 15N2 and 13C incubation assays in the northern South China Sea influenced by the Kuroshio intrusion (KI) seasonally. The degree of KI (KI index, range from 0 to 1) was assessed by applying an isopycnal mixing model. The water column integrated N2 fixation and primary production for stations with KI index larger than 0.5 were 463 ± 260 μmol N·m−2·day−1 and 62 ± 19 mmol C·m−2·day−1, respectively, significantly higher than those for stations with KI index lower than 0.5 (50 ± 10 μmol N·m−2·day−1 and 28 ± 10 mmol C·m−2·day−1, respectively). Trichodesmium was the dominant diazotroph at stations with KI index larger than 0.5, with 2 orders of magnitude higher nifH gene abundance than that at stations with KI index lower than 0.5. However, the highest N2 fixation rates were found in waters with moderate KI index around 0.6, suggesting that frontal zone mixing might stimulate N2 fixation. Our results demonstrated that diazotrophs (mainly Trichodesmium) were tightly associated with the KI, which modulated the biogeographic distribution of N2 fixers. In summary, we found the transportation of Trichodesmium by KI, then, we quantified the fraction of KI and N2 fixation rates in the northern South China Sea. The results suggested that KI generated a new biogeographic regime which could significantly influence the carbon and nitrogen cycles far away from the main stream.

Plant Diversity and Fertilizer Management Shape the Belowground Microbiome of Native Grass Bioenergy Feedstocks.

Plants may actively cultivate microorganisms in their roots and rhizosphere that enhance their nutrition. To develop cropping strategies that substitute mineral fertilizers for beneficial root symbioses, we must first understand how microbial communities associated with plant roots differ among plant taxa and how they respond to fertilization. Arbuscular mycorrhizal (AM) fungi and rhizobacteria are of particular interest because they enhance nutrient availability to plants and perform a suite of nutrient cycling functions. The purpose of this experiment is to examine the root and soil microbiome in a long-term switchgrass (Panicum virgatum) biofuel feedstock experiment and determine how AM fungi and rhizobacteria respond to plant diversity and soil fertility. We hypothesize that intra- and interspecific plant diversity, nitrogen fertilization (+N), and their interaction will influence the biomass and community composition of AM fungi and rhizobacteria. We further hypothesize that +N will reduce the abundance of nitrogenase-encoding nifH genes on the rhizoplane. Roots and soils were sampled from three switchgrass cultivars (Cave-in-Rock, Kanlow, Southlow) grown in monoculture, intraspecific mixture, and interspecific planting mixtures with either Andropogon gerardii or diverse native tallgrass prairie species. Molecular sequencing was performed on root and soil samples, fatty acid extractions were assessed to determine microbial biomass, and quantitative polymerase chain reaction (qPCR) was performed on nifH genes from the rhizoplane. Sequence data determined core AM fungal and bacterial microbiomes and indicator taxa for plant diversity and +N treatments. We found that plant diversity and +N influenced AM fungal biomass and community structure. Across all plant diversity treatments, +N reduced the biomass of AM fungi and nifH gene abundance by more than 40%. The AM fungal genus Scutellospora was an indicator for +N, with relative abundance significantly greater under +N and in monoculture treatments. Community composition of rhizobacteria was influenced by plant diversity but not by +N. Verrucomicrobia and Proteobacteria were the dominant bacterial phyla in both roots and soils. Our findings provide evidence that soil fertility and plant diversity structure the root and soil microbiome. Optimization of soil communities for switchgrass production must take into account differences among cultivars and their unique responses to shifts in soil fertility.

Non‐cyanobacterial diazotrophs dominate nitrogen‐fixing communities in permafrost thaw ponds

AbstractThere is a growing concern about the implications of accelerated thawing of permafrost for regional biogeochemical cycling of carbon and other bioreactive elements. One such element of concern is nitrogen, and in this study, we investigated the diversity and biogeography of potential diazotrophs within a series of thaw ponds representing different ontogenetic stages in pond development. Using metagenomic sequence data from subarctic thaw ponds, we identified an array of nitrogenase genes across the ponds. The iron‐only nitrogenase gene (anfH) was positively correlated with sulfate, while there was no correlation with methane despite previous findings that organisms carrying anfH can simultaneously participate in nitrogen fixation and methanogenesis. Sulfate is known to inhibit microbial uptake of molybdate, an element essential for the activity of the nifH (molybdenum‐iron) nitrogenase and this may explain the high potential for nitrogen fixation utilizing anfH in sulfate‐rich ponds. NifH was particularly abundant in the hypolimnion of the deeper and older ponds, with Deltaproteobacteria and Chlorobi as the putative dominant diazotrophs. In the epilimnetic waters, nifH composition was more variable, with various Gammaproteobacteria as abundant representatives, while cyanobacterial diazotrophs were scarce. Interestingly, nifH gene abundance was significantly positively correlated with in situ methane concentration. Based on genome‐resolved metagenomics, we hypothesize that diazotrophs and methanogens engage in syntrophic interactions in anoxic waters, possibly via propionate oxidation or (in Geobacter) by interspecies electron transfer. Our results also suggest that nitrogen fixers may supply bioreactive nitrogen compounds to the thaw pond communities, thereby enhancing growth and activity of methanogens.

Effects of clay on nitrogen cycle related functional genes abundance during chicken manure composting

The objective of this study was to identify the effect of clay additive to explore the nitrogen cycling related ammonification, denitrifying genes and their relation N2O and ammonia emission during the chicken manure (CM) composting. The consequences indicated that the additive clay could optimize the environment and improve the NH4+-N into NO3−-N transformation. Meanwhile, the results observed that 8% clay amendment was significant correlated the abundance of nifH and nosZ genes. Compared with the other treatments, the 6% and 10% clay treatments observed low abundance of nifH. The heat map indicated that clay amendment could enhance the function genes abundance. The redundancy analysis showed that N2O and ammonia emission among all physiochemical parameters had great relationship with functional genes. Therefore, the addition of 10% clay into CM composting system could efficiently enhance the abundance of nirK and narG genes, and improve the composting with its application.

Long-term N fertilization imbalances potential N acquisition and transformations by soil microbes.

Nitrogen (N) fertilization in agricultural soils has been receiving worldwide attention due to its detrimental effects on ecosystem services, particularly on microbial N transformation. However, few studies provide a complete picture of N-fertilization effects on the N transformation cycle within a single agricultural ecosystem. Here, we explored the main steps of the microbial N cycle, using targeted gene abundances as proxies, in relation to soil properties, following 35 years of N-fertilization at increasing rates (0, 202 and 269 kg N/ha) in continuous corn (Zea mays L.) and corn-soybean [Glycine max (L.) Merr.] rotations. We used real-time quantitative polymerase chain reaction (qPCR) for the quantification of phylogenetic groups and functional gene screening of the soil microbial communities, including genes encoding critical enzymes of the microbial N cycle: nifH (N2 fixation), amoA (first step of nitrification), nirK and nirS (first step of denitrification), and nosZ (last step of denitrification). Our results showed that long term N-fertilization increased the abundance of fungal communities likely related to decreases in pH, and an enrichment of Al3+ and Fe3+ in exchange sites at the expense of critical macro and micronutrients. At the same time, long term N-fertilization damaged potential biological N2 fixation by significantly reducing the abundance of nifH genes in both continuous and rotated corn systems, while accelerating potential nitrification activities under continuous corn by increasing the abundance of bacterial amoA. Fertilization did not affect the abundance of denitrifying groups. Altogether, these results suggest that N fertilization in corn crops potentially decreases N2 acquisition by free-living soil microbes and stimulates nitrification activities, thus creating a vicious loop that makes the overall agricultural system even more dependent on external N inputs.

Relative Diazotroph Abundance in Symbiotic Red Sea Corals Decreases With Water Depth

Microbial dinitrogen (N2) fixation (diazotrophy) is a trait critical for coral holobiont functioning. The contribution of N2 fixation to holobiont nitrogen (N) supply likely depends on the ecological niche of the coral holobiont. Consequently, coral-associated diazotroph communities may exhibit distinct activity patterns across a water depth gradient. We thus compared relative abundances of diazotrophs in the tissues of two common hard coral species, Podabacia sp. and Pachyseris speciosa, along their water depth distribution (10 – 30 m and 30 – 50 m, respectively) in the Central Red Sea. The relative gene copy numbers of the nifH gene (i.e. referenced against the eubacterial 16S rRNA gene), as proxy for N2 fixation potential, were assessed via quantitative PCR. We hypothesized that relative nifH gene copy numbers would decrease with water depth, assuming a related shift from autotrophy to heterotrophy. Findings confirmed this hypothesis and revealed that nifH gene abundances for both corals decreased by ~97 % and ~90 % from the shallowest to the deepest collection site. However, this result was not significant for Pachyseris speciosa due to high biological variability. The observed decrease in nifH gene abundances may be explained by the relative increase in heterotrophy of the coral animal at increasing water depths. Our results underline the importance of interpreting microbial functions and associated nutrient cycling processes within the holobiont in relation to water depth range reflecting steep environmental gradients.