Seasonal variation in nifH abundance and expression of cyanobacterial communities associated with boreal feather mosses

Stenotrophomonas sp. SI-NJAU-1 and Its Mutant Strain with Excretion-Ammonium Capability Promote Plant Growth through Biological Nitrogen Fixation

Legumes are well-known for symbiotic nitrogen fixation, whereas associative nitrogen fixation for nonlegume plants needs more attention. Most associative nitrogen-fixing bacteria are applied in their original plant species and need further study for broad adaptation. Additionally, if isolated nitrogen-fixing bacteria could function under fertilizer conditions, it is often ignored. Here, among 21 nitrogen-fixing bacteria isolated from barrenness-tolerance Jerusalem artichoke (JA), Stenotrophomonas sp. SI-NJAU-1 excelled in nitrogen fixation and boosted the growth of JA, wheat, barley, and rice. Additionally, SI-NJAU-1 was proven to decrease the application of compound fertilizers by 30%. To further promote plant growth, Gln K and gln B of SI-NJAU-1, which are crucial for bacterial ammonium assimilation, were mutated. Deletion of gln K but not gln B in SI-NJAU-1 reduced the activity of glutamine synthetase (GS) and the unadenylylated GS and the content of glutamine, which led to ammonium secretion outside and significantly increased the biomass of barley. This work expands the scope of associative nitrogen-fixing endophytes, affirming their potential for plant growth promotion.

Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment

Introduction

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions.

Methods

In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica).

Results

The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants.

Discussion

This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

The dominant genera of nitrogenase (nifH) affects soil biological nitrogen fixation along an elevational gradient in the Hengduan mountains

Biological nitrogen (N) fixation by diazotrophic microbes is an essential process for the N input. However, the patterns of biological N fixation and its biological or environmental mechanism along an elevational gradient in mountain ecosystems are not fully understood. In this study, a field experiment was conducted in the Hengduan Mountains to investigate the biological N fixation associated with the diversity and abundance of the nifH gene. Our results showed that both the abundance of the nifH gene and the biological N fixation displayed hump-shaped trends along an elevation gradient in the wet and dry seasons. However, the diversity of the nifH gene showed an inverse unimodal trend along an elevation gradient. We observed that biological N fixation was jointly associated with the abundance of the nifH gene, especially dominant genera, as well as soil chartacteristics. Among them, clay content played a preeminent role in the regulation of N fixation potentially through the formation of microaggregates and microenvironments. In general, our results revealed that biological N fixation was correlated with the abundance of microorganisms, especially dominant genera, and soil texture. These results highlighted the importance of dominant genera, which should be considered in the modeling and forecasting of N cycling under future environmental change.

Biological nitrogen fixation, diversity and community structure of diazotrophs in two mosses in 25 temperate forests

Many moss species are associated with nitrogen (N)-fixing bacteria (diazotrophs) that support the N supply of mosses. Our knowledge relates primarily to pristine ecosystems with low atmospheric N input, but knowledge of biological N fixation (BNF) and diazotrophic communities in mosses in temperate forests with high N deposition is limited. We measured BNF rates using the direct stable isotope method and studied the total and potentially active diazotrophic communities in two abundant mosses, Brachythecium rutabulum and Hypnum cupressiforme, both growing on lying deadwood trunks in 25 temperate forest sites. BNF rates in both mosses were similar to those observed in moss species of pristine ecosystems. H. cupressiforme fixed three times more N2 and exhibited lower diazotrophic richness than B. rutabulum. Frankia was the most prominent diazotroph followed by cyanobacteria Nostoc. Manganese, iron, and molybdenum contents in mosses were positively correlated with BNF and diazotrophic communities. Frankia maintained high BNF rates in H. cupressiforme and B. rutabulum even under high chronic N deposition in Central European forests. Moss N concentration and 15 N abundance indicate a rather minor contribution of BNF to the N nutrition of these mosses.

Comparison of the seasonal and successional variation of asymbiotic and symbiotic nitrogen fixation along a glacial retreat chronosequence

Climate change is resulting in accelerated retreat of glaciers worldwide and much nitrogen-poor debris is left after glacier retreats. Asymbiotic dinitrogen (N2) fixation (ANF) can be considered a 'hidden' source of nitrogen (N) for non-nodulating plants in N limited environments; however, seasonal variation and its relative importance in ecosystem N budgets, especially when compared with nodulating symbiotic N2-fixation (SNF), is not well-understood. In this study, seasonal and successional variations in nodulating SNF and non-nodulating ANF rates (nitrogenase activity) were compared along a glacial retreat chronosequence on the eastern edge of the Tibetan Plateau. Key factors regulating the N2-fixation rates as well as the contribution of ANF and SNF to ecosystem N budget were also examined. Significantly greater nitrogenase activity was observed in nodulating species (0.4-17,820.8 nmol C2H4 g-1 d-1) compared to non-nodulating species (0.0-9.9 nmol C2H4 g-1 d-1) and both peaked in June or July. Seasonal variation in acetylene reduction activity (ARA) rate in plant nodules (nodulating species) and roots (non-nodulating species) was correlated with soil temperature and moisture while ARA in non-nodulating leaves and twigs was correlated with air temperature and humidity. Stand age was not found to be a significant determinant of ARA rates in nodulating or non-nodulating plants. ANF and SNF contributed 0.3-51.5 % and 10.1-77.8 %, respectively, of total ecosystem N input in the successional chronosequence. In this instance, ANF exhibited an increasing trend with successional age while SNF increased only at stages younger than 29 yr and then decreased as succession proceeded. These findings help improve our understanding of ANF activity in non-nodulating plants and N budgets in post glacial primary succession.

Negative responses of terrestrial nitrogen fixation to nitrogen addition weaken across increased soil organic carbon levels

The traditional view holds that biological nitrogen (N) fixation is energetically expensive and thus, facultative N fixers reduce N fixation rates while obligate N fixers are excluded by non-N fixers as soil N becomes rich. This view, however, contradicts the phenomenon that N fixation does not decline in many terrestrial ecosystems under N enrichment. To address this paradoxical phenomenon, we conducted a meta-analysis of N fixation and diazotroph (N-fixing microorganism) community structure in response to N addition across terrestrial ecosystems. N addition inhibited N fixation, but the inhibitory effect weakened across increased soil organic carbon (SOC) concentrations. The response ratios of N fixation (including free-living, plant-associated, and symbiotic types) to N addition were lower in the ecosystems with low SOC concentrations (<10 mg/g) than in those with medium or high SOC concentrations (10-20 and > 20 mg/g, respectively). The negative N-addition effects on diazotroph abundance and diversity also weakened across increased SOC levels. Among the climatic and soil factors, SOC was the most important predictor regarding the responses of N fixation and diazotroph community structure to N addition. Overall, our study reveals the role of SOC in affecting the responses of N fixation to N addition, which helps understand the relationships of biological N fixation and N enrichment as well as the mechanisms of terrestrial C and N coupling.

Nitrogen fixation and nifH gene diversity in cyanobacteria living on feather mosses in a subalpine forest of Mt. Fuji

In the boreal forests, feather mosses such as Hylocomium splendens and Pleurozium schreberi are colonized by cyanobacteria, which provide large amounts of nitrogen to forest ecosystems through nitrogen fixation. Although these feather mosses are also ubiquitous in subalpine forests of East Asia, little is known regarding their associated cyanobacteria and their ability to fix nitrogen. In this study, we investigated (1) whether cyanobacteria co-exist and fix nitrogen in the two species of feather mosses that cover the ground surface in a subalpine forest of Mt. Fuji, (2) whether cyanobacteria belonging to a common cluster with boreal forests are found in feather mosses in Mt. Fuji, and (3) whether moss-associated nitrogen fixation rates differed among moss growing substrates, canopy openness, and moss nitrogen concentrations in the same forest area. Our results showed that cyanobacteria colonized feather mosses in the subalpine forests of Mt. Fuji and acetylene reduction rates as an index of nitrogen fixation tended to be higher in H. splendens than in P. schreberi. Based on analysis of the nifH gene, 43 bacterial operational taxonomic units (OTUs) were identified, 28 of which represented cyanobacteria. Among the five clusters of cyanobacteria classified based on their nifH gene and identified in northern Europe, four (Nostoc cluster I, Nostoc cluster II, Stigonema cluster, and nifH2 cluster) were also found at Mt. Fuji. The acetylene reduction rate differed depending on the moss growing substrate and the total nitrogen concentration of moss shoots, and a strong negative correlation was observed with the total nitrogen concentration.

Revealing the transfer pathways of cyanobacterial-fixed N into the boreal forest through the feather-moss microbiome

INTRODUCTION

Biological N₂ fixation in feather-mosses is one of the largest inputs of new nitrogen (N) to boreal forest ecosystems; however, revealing the fate of newly fixed N within the bryosphere (i.e. bryophytes and their associated organisms) remains uncertain.

METHODS

Herein, we combined ¹⁵N tracers, high resolution secondary ion mass-spectrometry (NanoSIMS) and a molecular survey of bacterial, fungal and diazotrophic communities, to determine the origin and transfer pathways of newly fixed N₂ within feather-moss (Pleurozium schreberi) and its associated microbiome.

RESULTS

NanoSIMS images reveal that newly fixed N₂, derived from cyanobacteria, is incorporated into moss tissues and associated bacteria, fungi and micro-algae.

DISCUSSION

These images demonstrate that previous assumptions that newly fixed N₂ is sequestered into moss tissue and only released by decomposition are not correct. We provide the first empirical evidence of new pathways for N₂ fixed in feather-mosses to enter the boreal forest ecosystem (i.e. through its microbiome) and discuss the implications for wider ecosystem function.

Periphytic biofilms function as a double-edged sword influencing nitrogen cycling in paddy fields

It remains unclear whether periphytic biofilms are beneficial to N cycling in paddy fields. Here, based on a national-scale field investigation covering 220 rice fields in China, the N accumulation potential of periphytic biofilms was found to decrease from 8.8 ± 2.4 to 4.5 ± 0.7 g/kg and 3.1 ± 0.6 g/kg with increasing habitat latitude and longitude, respectively. The difference in abundant and rare subcommunities likely accounts for their geo-difference in N accumulation potential. The N cycling pathways involved in periphytic biofilms inferred that soil N and N₂ were two potential sources for N accumulation in periphytic biofilms. Meanwhile, some of the accumulated N may be lost via N₂ , N₂ O, NO, or NH₃ outputs. Superficially, periphytic biofilms are double-edged swords to N cycling by increasing soil N through biological N fixation but accelerating greenhouse gas emissions. Essentially, augmented periphytic biofilms increased change of TN (ΔTN) content in paddy soil from -231.9 to 31.9 mg/kg, indicating that periphytic biofilms overall benefit N content enhancement in paddy fields. This study highlights the contribution of periphytic biofilms to N cycling in rice fields, thus, drawing attention to their effect on rice production and environmental security.

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America

Feather mosses are abundant cryptogams of the boreal forest floor and shelter a broad diversity of bacteria who have important ecological functions (e.g., decomposition, nutrient cycling). In particular, nitrogen (N₂-) fixation performed by feather moss-associated diazotrophs constitutes an important entry of nitrogen in the boreal forest ecosystem. However, the composition of the feather moss bacteriome and its environmental drivers are still unclear. Using cDNA amplicon sequencing of the 16S rRNA and nifH genes and cyanobacterial biomass quantification, we explored the active global and diazotrophic bacterial communities of two dominant feather moss species (i) at the ecosystem scale, along a 500-km climatic and nutrient deposition gradient in the North American boreal forest, and (ii) at the plant scale, along the moss shoot senescence gradient. We found that cyanobacteria were major actors of the feather moss bacteriome, accounting for 33% of global bacterial communities and 65% of diazotrophic communities, and that several cyanobacterial and methanotrophic genera were contributing to N₂-fixation. Moreover, we showed that bacteria were occupying ecological niches along the moss shoot, with phototrophs being dominant in the apical part and methanotrophs being dominant in the basal part. Finally, climate (temperature, precipitation), environmental variables (moss species, month, tree density) and nutrients (nitrogen, phosphorus, molybdenum, vanadium, iron) strongly shaped global and diazotrophic bacteriomes. In summary, this work presents evidence that the feather moss bacteriome plays crucial roles in supporting moss growth, health, and decomposition, as well as in the boreal forest carbon and nitrogen cycles. This study also highlights the substantial effects of climate and nutrients on the feather moss bacteriome, suggesting the importance of understanding the impacts of global change on moss-associated bacterial growth and activity.

Biotic and abiotic controls of nitrogen fixation in cyanobacteria-moss associations

Most mosses are colonized by nitrogen (N)-fixing cyanobacteria. This discovery is relatively recent, which can explain the large knowledge gaps the field is now tackling. For instance, while we have a good understanding of the abiotic controls (e.g. nutrient availability, increased temperature), we still do not know much about the biotic controls of N₂ fixation in mosses. I propose here that we should endeavour to position moss-cyanobacteria associations along the mutualism-parasitism continuum under varying abiotic conditions (e.g. nutrient availability). This would finally unravel the nature of the relationship between the partners and will be a big leap in our understanding of the evolution of plant-bacteria interactions using moss-cyanobacteria associations as a model system.

Chemical Stimulation of Heterocyte Differentiation by the Feather Moss Hylocomium splendens: a Potential New Step in Plant-Cyanobacteria Symbioses

Cyanobacteria associated with mosses play a key role in the nitrogen (N) cycle in unpolluted ecosystems. Mosses have been found to release molecules that induce morphophysiological changes in epiphytic cyanobionts. Nevertheless, the extent of moss influence on these microorganisms remains unknown. To evaluate how mosses or their metabolites influence N₂ fixation rates by cyanobacteria, we assessed the nitrogenase activity, heterocyte frequency and biomass of a cyanobacterial strain isolated from the feather moss Hylocomium splendens and a non-symbiotic strain when they were either growing by themselves, together with H. splendens or exposed to H. splendens water, acetone, ethanol, or isopropanol extracts. The same cyanobacterial strains were added to another moss (Taxiphyllum barbieri) and a liverwort (Monosolenium tenerum) to assess if these bryophytes affect N₂ fixation differently. Although no significant increases in nitrogenase activity by the cyanobacteria were observed when in contact with H. splendens shoots, both the symbiotic and non-symbiotic cyanobacteria increased nitrogenase activity as well as heterocyte frequency significantly upon exposure to H. splendens ethanol extracts. Contact with T. barbieri shoots, on the other hand, did lead to increases in nitrogenase activity, indicating low host-specificity to cyanobacterial activity. These findings suggest that H. splendens produces heterocyte-differentiating factors (HDFs) that are capable of stimulating cyanobacterial N₂ fixation regardless of symbiotic competency. Based on previous knowledge about the chemical ecology and dynamics of moss-cyanobacteria interactions, we speculate that HDF expression by the host takes place in a hypothetical new step occurring after plant colonization and the repression of hormogonia.

Unraveling host-microbe interactions and ecosystem functions in moss-bacteria symbioses

Mosses are non-vascular plants usually found in moist and shaded areas, with great ecological importance in several ecosystems. This is especially true in northern latitudes, where mosses are responsible for up to 100% of primary production in some ecosystems. Mosses establish symbiotic associations with unique bacteria that play key roles in the carbon and nitrogen cycles. For instance, in boreal environments, more than 35% of the nitrogen fixed by diazotrophic symbionts in peatlands is transferred to mosses, directly affecting carbon fixation by the hosts, while moss-associated methanotrophic bacteria contribute 10-30% of moss carbon. Further, half of ecosystem N input may derive from moss-cyanobacteria associations in pristine ecosystems. Moss-bacteria interactions have consequences on a global scale since northern environments sequester 20% of all the carbon generated by forests in the world and stock at least 32% of global terrestrial carbon. Different moss hosts influence bacteria in distinct ways, which suggests that threats to mosses also threaten unique microbial communities with important ecological and biogeochemical consequences. Since their origin ~500 Ma, mosses have interacted with bacteria, making these associations ideal models for understanding the evolution of plant-microbe associations and their contribution to biogeochemical cycles.

Long-term warming effects on the microbiome and nifH gene abundance of a common moss species in sub-Arctic tundra

Bacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of moss microbiomes in these environments. Here, we studied the total and potentially active bacterial communities associated with Racomitrium lanuginosum in response to a 20-yr in situ warming in an Icelandic heathland. We evaluated the effect of warming and warming-induced shrub expansion on the moss bacterial community composition and diversity, and nifH gene abundance. Warming changed both the total and the potentially active bacterial community structure, while litter abundance only affected the total bacterial community structure. The abundance of nifH genes was negatively affected by litter abundance. We also found shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and noncyanobacterial diazotrophs increasing in relative abundance. Our data suggest that the moss microbial community and potentially nitrogen fixing taxa will be sensitive to future warming, partly via changes in litter and shrub abundance.

Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species but may also be shaped by environmental conditions related with tree dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. The overall composition of moss phyllosphere was defined by the interaction of both factors, though most of bacterial phyla were determined by a strong effect of forest type. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the cyanobacteria family Nostocaceae differing the most between forest types. Our results advance the understanding of moss-associated microbial communities among coniferous and broadleaf deciduous forests, which are important with the increasing changes in tree dominance in the boreal system. This article is protected by copyright. All rights reserved.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems

Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of ¹³CH₄ and ¹⁵N₂ isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.

In Vivo Temperature Dependency of Molybdenum and Vanadium Nitrogenase Activity in the Heterocystous Cyanobacteria Anabaena variabilis

The reduction of atmospheric dinitrogen by nitrogenase is a key component of terrestrial nitrogen cycling. Nitrogenases exist in several isoforms named after the metal present within their active center: the molybdenum (Mo), the vanadium (V), and the iron (Fe)-only nitrogenase. While earlier in vitro studies hint that the relative contribution of V nitrogenase to total BNF could be temperature-dependent, the effect of temperature on in vivo activity remains to be investigated. In this study, we characterize the in vivo effect of temperature (3-42 °C) on the activities of Mo nitrogenase and V nitrogenase in the heterocystous cyanobacteria Anabaena variabilis ATTC 29413 using the acetylene reduction assay by cavity ring-down absorption spectroscopy. We demonstrate that V nitrogenase becomes as efficient as Mo nitrogenase at temperatures below 10-15 °C. At temperatures above 22 °C, BNF seems to be limited by O₂ availability to respiration in both enzymes. Furthermore, Anabaena variabilis cultures grown in Mo or V media achieved similar growth rates at temperatures below 20 °C. Considering the average temperature on earth is 15 °C, our findings further support the role of V nitrogenase as a viable backup enzymatic system for BNF in natural ecosystems.

Empirical and Earth system model estimates of boreal nitrogen fixation often differ: A pathway toward reconciliation

The impacts of global environmental change on productivity in northern latitudes will be contingent on nitrogen (N) availability. In circumpolar boreal ecosystems, nonvascular plants (i.e., bryophytes) and associated N₂ -fixing diazotrophs provide one of the largest known N inputs but are rarely accounted for in Earth system models. Instead, most models link N₂ -fixation with the functioning of vascular plants. Neglecting nonvascular N₂ -fixation may be contributing toward high uncertainty that currently hinders model predictions in northern latitudes, where nonvascular N₂ -fixing plants are more common. Adequately accounting for nonvascular N₂ -fixation and its drivers could subsequently improve predictions of future N availability and ultimately, productivity, in northern latitudes. Here, we review empirical evidence of boreal nonvascular N₂ -fixation responses to global change factors (elevated CO₂ , N deposition, warming, precipitation, and shading by vascular plants), and compare empirical findings with model predictions of N₂ -fixation using nine Earth system models. The majority of empirical studies found positive effects of CO₂ , warming, precipitation, or light on nonvascular N₂ -fixation, but N deposition strongly downregulated N₂ -fixation in most empirical studies. Furthermore, we found that the responses of N₂ -fixation to elevated CO₂ were generally consistent between models and very limited empirical data. In contrast, empirical-model comparisons suggest that all models we assessed, and particularly those that scale N₂ -fixation with net primary productivity or evapotranspiration, may be overestimating N₂ -fixation under increasing N deposition. Overestimations could generate erroneous predictions of future N stocks in boreal ecosystems unless models adequately account for the drivers of nonvascular N₂ -fixation. Based on our comparisons, we recommend that models explicitly treat nonvascular N₂ -fixation and that field studies include more targeted measurements to improve model structures and parameterization.

The relationship of C and N stable isotopes to high-latitude moss-associated N2 fixation

Moss-associated N₂ fixation by epiphytic microbes is a key biogeochemical process in nutrient-limited high-latitude ecosystems. Abiotic drivers, such as temperature and moisture, and the identity of host mosses are critical sources of variation in N₂ fixation rates. An understanding of the potential interaction between these factors is essential for predicting N inputs as moss communities change with the climate. To further understand the drivers and results of N₂ fixation rate variation, we obtained natural abundance values of C and N isotopes and an associated rate of N₂ fixation with ¹⁵N₂ gas incubations in 34 moss species collected in three regions across Alaska, USA. We hypothesized that δ¹⁵N values would increase toward 0‰ with higher N₂ fixation to reflect the increasing contribution of fixed N₂ in moss biomass. Second, we hypothesized that δ¹³C and N₂ fixation would be positively related, as enriched δ¹³C signatures reflect abiotic conditions favorable to N₂ fixation. We expected that the magnitude of these relationships would vary among types of host mosses, reflecting differences in anatomy and habitat. We found little support for our first hypothesis, with only a modest positive relationship between N₂ fixation rates and δ¹⁵N in a structural equation model. We found a significant positive relationship between δ¹³C and N₂ fixation only in Hypnales, where the probability of N₂ fixation activity reached 95% when δ¹³C values exceeded - 30.4‰. We conclude that moisture and temperature interact strongly with host moss identity in determining the extent to which abiotic conditions impact associated N₂ fixation rates.

The bacterial communities of Alaskan mosses and their contributions to N2-fixation

BACKGROUND

Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information.

RESULTS

Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades.

CONCLUSIONS

The strong effect of host identity on moss-associated bacterial communities demonstrates mosses' utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems. Video Abstract.

Comparable canopy and soil free-living nitrogen fixation rates in a lowland tropical forest

Biological nitrogen fixation (BNF) is a fundamental part of nitrogen cycling in tropical forests, yet little is known about the contribution made by free-living nitrogen fixers inhabiting the often-extensive forest canopy. We used the acetylene reduction assay, calibrated with ¹⁵N₂, to measure free-living BNF on forest canopy leaves, vascular epiphytes, bryophytes and canopy soil, as well as on the forest floor in leaf litter and soil. We used a combination of calculated and published component densities to upscale free-living BNF rates to the forest level. We found that bryophytes and leaves situated in the canopy in particular displayed high mass-based rates of free-living BNF. Additionally, we calculated that nearly 2 kg of nitrogen enters the forest ecosystem through free-living BNF every year, 40% of which was fixed by the various canopy components. Our results reveal that in the studied tropical lowland forest a large part of the nitrogen input through free-living BNF stems from the canopy, but also that the total nitrogen inputs by free-living BNF are lower than previously thought and comparable to the inputs of reactive nitrogen by atmospheric deposition.

Quantification of Moss-Associated Cyanobacteria Using Phycocyanin Pigment Extraction

In the boreal forest, cyanobacteria can establish associations with feather moss and realize the biological nitrogen fixation (BNF) reaction, consisting in the reduction of atmospheric dinitrogen into bioavailable ammonium. In this ecosystem, moss-associated cyanobacteria are the main contributors to BNF by contributing up to 50% of new N input. Current environmental changes driven by anthropogenic activities will likely affect cyanobacteria activity (i.e., BNF) and populations inhabiting mosses, leading to potential important consequences for the boreal forest. Several methods are available to efficiently measure BNF activity, but quantifying cyanobacteria biomass associated with moss is challenging because of the difficulty to separate bacteria colonies from the host plant. Attempts to separate cyanobacteria by shaking or sonicating in water were shown to be poorly efficient and repeatable. The techniques commonly used, microscopic counting and quantitative PCR (qPCR) are laborious and time-consuming. In aquatic and marine ecosystems, phycocyanin (PC), a photosynthesis pigment produced by cyanobacteria, is commonly used to monitor cyanobacteria biomass. In this study, we tested if PC extraction and quantification can be used to estimate cyanobacteria quantity inhabiting moss. We report that phycocyanin can be easily extracted from moss by freeze/thaw disturbance of cyanobacteria cells and can be quickly and efficiently measured by spectrofluorometry. We also report that phycocyanin extraction is efficient (high recovery), repeatable (relative SD < 13%) and that no significant matrix effects were observed. As for aquatic systems, the main limitation of cyanobacteria quantification using phycocyanin is the difference of cellular phycocyanin content between cyanobacteria strains, suggesting that quantification can be impacted by cyanobacteria community composition. Nonetheless, we conclude that phycocyanin extraction and quantification is an easy, rapid, and efficient tool to estimate moss-associated cyanobacteria number.

Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism

In nitrogen-limited boreal forests, associations between feathermoss and diazotrophic cyanobacteria control nitrogen inputs and thus carbon cycling, but little is known about the molecular regulators required for initiation and maintenance of these associations. Specifically, a benefit to the cyanobacteria is not known, challenging whether the association is a nutritional mutualism. Targeted mutagenesis of the cyanobacterial alkane sulfonate monooxygenase results in an inability to colonize feathermosses by the cyanobacterium Nostoc punctiforme, suggesting a role for organic sulfur in communication or nutrition. Isotope probing paired with high-resolution imaging mass spectrometry (NanoSIMS) demonstrated bidirectional elemental transfer between partners, with carbon and sulfur both being transferred to the cyanobacteria, and nitrogen transferred to the moss. These results support the hypothesis that moss and cyanobacteria enter a mutualistic exosymbiosis with substantial bidirectional material exchange of carbon and nitrogen and potential signaling through sulfur compounds.

Seasonal variation of epiphytic bacteria in the phyllosphere of Gingko biloba, Pinus bungeana and Sabina chinensis

Phyllosphere harbors diverse microorganisms, which influence plant growth and health. In order to understand the extent to which environmental factors affect epiphytic microbial communities, we characterized microbial communities on leaves of three separate tree species present on the college campus, and also present within a forest park over two seasons. Quantitative PCR analysis showed the quantity of 16S rRNA genes was lower in May compared with October, while the abundances of functional genes (nifH and bacterial amoA genes) were extremely high in May. High-throughput sequencing revealed a large variation in the diversity and composition of bacterial and diazotrophic communities over the two seasons, and showed the abundance of functional genera, such as Nocardioides, Bacillus and Zoogloea were significantly elevated in May. In addition, xenobiotic biodegradation pathways of bacterial communities were clearly elevated in May. Network analysis showed the correlations between phyllospheric bacteria in May were more complex than that in October and showed greater negative correlations. These results were consistent in all tree species in this study. This study showed that phyllospheric bacteria varied greatly in different seasons, which implies that different growing seasons should be considered in the exploitation of the interactions between phyllospheric microorganisms and host plants.

Experimental assessment of tree canopy and leaf litter controls on the microbiome and nitrogen fixation rates of two boreal mosses

Nitrogen (N₂ )-fixing moss microbial communities play key roles in nitrogen cycling of boreal forests. Forest type and leaf litter inputs regulate moss abundance, but how they control moss microbiomes and N₂ -fixation remains understudied. We examined the impacts of forest type and broadleaf litter on microbial community composition and N₂ -fixation rates of Hylocomium splendens and Pleurozium schreberi. We conducted a moss transplant and leaf litter manipulation experiment at three sites with paired paper birch (Betula neoalaskana) and black spruce (Picea mariana) stands in Alaska. We characterized bacterial communities using marker gene sequencing, determined N₂ -fixation rates using stable isotopes (¹⁵ N₂ ) and measured environmental covariates. Mosses native to and transplanted into spruce stands supported generally higher N₂ -fixation and distinct microbial communities compared to similar treatments in birch stands. High leaf litter inputs shifted microbial community composition for both moss species and reduced N₂ -fixation rates for H. splendens, which had the highest rates. N₂ -fixation was positively associated with several bacterial taxa, including cyanobacteria. The moss microbiome and environmental conditions controlled N₂ -fixation at the stand and transplant scales. Predicted shifts from spruce- to deciduous-dominated stands will interact with the relative abundances of mosses supporting different microbiomes and N₂ -fixation rates, which could affect stand-level N inputs.

Nitrogen fertilizer and Amorpha fruticosa leguminous shrub diversely affect the diazotroph communities in an artificial forage grassland

Soil diazotrophs have been known to be essential in biological nitrogen (N) fixation, which contributes to the sustainability of agricultural ecosystems. However, there remains an inadequacy of research on the effects of different N inputs from N fertilization and from symbiotic N fixation associated with legumes on the diazotroph communities in agricultural ecosystems. Hence, we investigated the variations in diazotroph abundance and community composition as well as the soil properties with different N inputs in the Guimu-1 hybrid elephant grass cultivation on karst soils in China. We conducted six different N treatments: control, Amorpha fruticosa planting at a spacing of 1.5 × 2 m (AFD1), A. fruticosa planting at a spacing of 1 × 2 m (AFD2), N fertilization (N), A. fruticosa planting at a spacing of 1.5 × 2 m with N fertilization (AFD1N), and A. fruticosa planting at a spacing of 1 × 2 m with N fertilization (AFD2N). Our results showed that the interaction between sampling time and N fertilization significantly affected the diazotroph abundance. In July, the diazotroph abundance significantly decreased in the N fertilization treatments: N, AFD1N, and AFD2N, compared to that in the control. The richness and Chao1 estimator of diazotrophs significantly increased in AFD2N and AFD1 correspondingly in December and July, relative to those in the control. Co-occurrence networks showed species-species interactions with high negative correlations that occurred more in the control than in the N input plots. The N input from N fertilization and legume planting directly increased the ammonium N and nitrate N and consequently affected the dissolved organic N and pH of the soil, thereby altering the diazotroph abundance and richness. Our findings demonstrated that both N fertilization and legumes could reduce the interspecific competition among diazotroph species by providing greater N availability in the forage grass.

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss

The pleurocarpous feather moss Pleurozium schreberi is a ubiquitous moss species which plays a fundamental role in many terrestrial ecosystems, for instance within the boreal forest, the Earth's largest terrestrial biome, this species plays a significant role in driving ecosystem nitrogen and carbon inputs and fluxes. By hosting dinitrogen (N₂)-fixing cyanobacteria, the moss-cyanobacteria symbiosis constitutes the main nitrogen input into the ecosystem and by the high productivity and the low decomposability of the moss litter, P schreberi contributes significantly to build-up soil organic matter, and therefore long-term C sequestration. Knowledge on P. schreberi genome will facilitate the development of 'omics' and system's biology approaches to gain a more complete understanding of the physiology and ecological adaptation of the moss and the mechanisms underpinning the establishment of the symbiosis. Here we present the de novo assembly and annotation of P. schreberi genome that will help investigating these questions. The sequencing was performed using the HiSeq X platform with Illumina paired-end and mate-pair libraries prepared with CTAB extracted DNA. In total, the assembled genome was approximately 318 Mb, while repetitive elements account for 28.42% of the genome and 15,992 protein-coding genes were predicted from the genome, of which 84.23% have been functionally annotated. We anticipate that the genomic data generated will constitute a significant resource to study ecological and evolutionary genomics of P. schreberi, and will be valuable for evo-devo investigations as well as our understanding of the evolution of land plants by providing the genome of a pleurocarpous moss.

Experimental warming alters the community composition, diversity, and N2 fixation activity of peat moss (Sphagnum fallax) microbiomes

Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.

Global pattern and controls of biological nitrogen fixation under nutrient enrichment: A meta-analysis

Biological nitrogen (N) fixation (BNF), an important source of N in terrestrial ecosystems, plays a critical role in terrestrial nutrient cycling and net primary productivity. Currently, large uncertainty exists regarding how nutrient availability regulates terrestrial BNF and the drivers responsible for this process. We conducted a global meta-analysis of terrestrial BNF in response to N, phosphorus (P), and micronutrient (Micro) addition across different biomes (i.e, tropical/subtropical forest, savanna, temperate forest, grassland, boreal forest, and tundra) and explored whether the BNF responses were affected by fertilization regimes (nutrient-addition rates, duration, and total load) and environmental factors (mean annual temperature [MAT], mean annual precipitation [MAP], and N deposition). The results showed that N addition inhibited terrestrial BNF (by 19.0% (95% confidence interval [CI]: 17.7%-20.3%); hereafter), Micro addition stimulated terrestrial BNF (30.4% [25.7%-35.3%]), and P addition had an inconsistent effect on terrestrial BNF, i.e., inhibiting free-living N fixation (7.5% [4.4%-10.6%]) and stimulating symbiotic N fixation (85.5% [25.8%-158.7%]). Furthermore, the response ratios (i.e., effect sizes) of BNF to nutrient addition were smaller in low-latitude (<30°) biomes (8.5%-36.9%) than in mid-/high-latitude (≥30°) biomes (32.9%-61.3%), and the sensitivity (defined as the absolute value of response ratios) of BNF to nutrients in mid-/high-latitude biomes decreased with decreasing latitude (p ≤ 0.009; linear/logarithmic regression models). Fertilization regimes did not affect this phenomenon (p > 0.05), but environmental factors did affect it (p < 0.001) because MAT, MAP, and N deposition accounted for 5%-14%, 10%-32%, and 7%-18% of the variance in the BNF response ratios in cold (MAT < 15°C), low-rainfall (MAP < 2,500 mm), and low-N-deposition (<7 kg ha^-1  year^-1 ) biomes, respectively. Overall, our meta-analysis depicts a global pattern of nutrient impacts on terrestrial BNF and indicates that certain types of global change (i.e., warming, elevated precipitation and N deposition) may reduce the sensitivity of BNF in response to nutrient enrichment in mid-/high-latitude biomes.

Railroad derived nitrogen and heavy metal pollution does not affect nitrogen fixation associated with mosses and lichens at a tundra site in Northern Sweden

Traffic derived nitrogen (N) and heavy metal pollution is a well-known phenomenon, but little explored in otherwise pristine ecosystems such as subarctic tundra. Here, the main source of N input to the ecosystem is via N₂ fixation by moss- and lichen-associated bacteria. While inhibitory effects of N deposition on moss-associated N₂ fixation have been reported, we still lack understanding of the effects of traffic derived N and heavy metal deposition on this ecosystem function in an otherwise pristine setting. To test this, we established a distance gradient (0-1280 m) away from a metal pollution source -a railway transporting iron ore that passes through a subarctic birch forest. We assessed the effects of railway-derived pollution on N₂ fixation associated with two moss species Pleurozium schreberi, Hylocomium splendens and with the lichen Peltigera aphthosa. Deposition and availability of N and heavy metals (Fe, Cu, Zn, Pb) as well as the respective contents in moss, lichen and soil was assessed. While we found a steep gradient in metal concentration in moss, lichen and soil with distance away from the pollution source, N deposition did not change, and with that, we could not detect a distance gradient in moss- or lichen-associated N₂ fixation. Hence, our results indicate that N₂ fixing bacteria are either not inhibited by heavy metal deposition, or that they are protected within the moss carpet and lichen tissue.

Novel bacterial lineages associated with boreal moss species

Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbour diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local site conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with seven boreal moss species collected near Fairbanks, AK, USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbour diverse lineages of potential N₂ -fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.

Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont

Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.

Molybdenum and phosphorus limitation of moss-associated nitrogen fixation in boreal ecosystems

Biological nitrogen fixation (BNF) performed by moss-associated cyanobacteria is one of the main sources of new nitrogen (N) input in pristine, high-latitude ecosystems. Yet, the nutrients that limit BNF remain elusive. Here, we tested whether this important ecosystem function is limited by the availability of molybdenum (Mo), phosphorus (P), or both. BNF in dominant mosses was measured with the acetylene reduction assay (ARA) at different time intervals following Mo and P additions, in both laboratory microcosms with mosses from a boreal spruce forest and field plots in subarctic tundra. We further used a ¹⁵ N₂ tracer technique to assess the ARA to N₂ fixation conversion ratios at our subarctic site. BNF was up to four-fold higher shortly after the addition of Mo, in both the laboratory and field experiments. A similar positive response to Mo was found in moss colonizing cyanobacterial biomass. As the growing season progressed, nitrogenase activity became progressively more P limited. The ARA : ¹⁵ N₂ ratios increased with increasing Mo additions. These findings show that N₂ fixation activity as well as cyanobacterial biomass in dominant feather mosses from boreal forests and subarctic tundra are limited by Mo availability.

Temporal Variations in Diazotrophic Communities and nifH Transcripts Level Across the Agricultural and Fallow Land at Jaipur, Rajasthan, India

Biological nitrogen fixation is one of the most important nutrient processes in the ecosystem. Many studies have estimated the variations in soil diazotrophic communities across the globe. To understand the dynamics of nitrogen fixing bacterial communities and their response to the environmental changes, it is important to study the temporal variability of these communities. Using DNA fingerprinting method, denaturing gradient gel electrophoresis and real time polymerase chain reaction of the nifH gene, we have found that the agricultural land harbored unique nitrogen fixing communities that revealed different temporal patterns and abundance. Variation in soil moisture, organic carbon content, ammonium and nitrate concentrations may be the main factors which influenced the diazotrophic community composition and nifH gene abundance. Azospirillum species were more dominant in the agricultural soil. Unique environmental factors and agricultural practices were responsible for the temporal shifts in bacterial community structures and nifH transcripts level. Our study expands understanding of the influence of environmental factors on diazotrophic population that contributes to the nitrogen pool.