Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.)

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.

Diazotrophs for Lowering Nitrogen Pollution Crises: Looking Deep Into the Roots

During and after the green revolution in the last century, agrochemicals especially nitrogen (N) were extensively used. However, it resulted in a remarkable increase in crop yield but drastically reduced soil fertility; increased the production cost, food prices, and carbon footprints; and depleted the fossil reserves with huge penalties to the environment and ecological sustainability. The groundwater, rivers, and oceans are loaded with N excess which is an environmental catastrophe. Nitrogen emissions (e.g., ammonia, nitrogen oxide, nitrous oxide) play an important role in global climate change and contribute to particulate matter and acid rain causing respiratory problems, cancers, and damage to forests and buildings. Therefore, the nitrogen-polluted planet Earth needs concerted global efforts to avoid the disaster. Improved agricultural N management focuses on the synchronization of crop N demand and N supply along with improving the N-use efficiency of the crops. However, there is very little focus on the natural sources of N available for plants in the form of diazotrophic bacteria present inside or on the root surface and the rhizosphere. These diazotrophs are the mini-nitrogen factories that convert available (78%) atmospheric N2 to ammonia through a process known as "biological nitrogen fixation" which is then taken up by the plants for its metabolic functioning. Diazotrophs also stimulate root architecture by producing plant hormones and hence improve the plant's overall ability to uptake nutrients and water. In recent years, nanotechnology has revolutionized the whole agri-industry by introducing nano-fertilizers and coated/slow-releasing fertilizers. With this in mind, we tried to explore the following questions: To what extent can the crop N requirements be met by diazotroph inoculation? Can N input to agriculture be managed in a way leading to environmental benefits and farmers saving money? Can nanotechnology help in technological advancement of diazotroph application? The review suggests that an integrated technology based on slow-releasing nano-fertilizer combined with diazotrophs should be adopted to decrease nitrogen inputs to the agricultural system. This integrated technology would minimize N pollution and N losses to much extent.

Straw Mulching and Nitrogen Fertilization Affect Diazotroph Communities in Wheat Rhizosphere

Diazotrophs that carry out the biological fixation of atmospheric dinitrogen (N₂) replenish biologically available nitrogen (N) in soil and are influenced by the input of inorganic and organic substrates. To date, little is known about the effects of combined organic substrate addition and N fertilization on the diazotroph community composition and structure in purple soils. We investigated the effects of N fertilization and straw mulching on diazotroph communities by quantifying and sequencing the nifH gene in wheat rhizosphere. The abundance and richness of diazotrophs were greater the higher the fertilization level in the mulched treatments, whereas in the nonmulched treatments (NSMs), richness was lowest with the highest N fertilization level. The abundance and α-diversity of diazotrophs correlated with most of the soil properties but not with pH. At the genus level, the relative abundances of Azospirillum, Bacillus, and Geobacter were higher in the NSMs and those of Pseudacidovorax, Skermanella, Azospira, Paraburkholderia, Azotobacter, Desulfovibrio, Klebsiella, and Pelomonas in the mulched treatments. The differences in community composition between the mulched and the NSMs were associated with differences in soil temperature and soil organic carbon and available potassium contents and C:N ratio. Overall, straw mulching and N fertilization were associated with changes in diazotroph community composition and higher abundance of nifH gene in alkaline purple soils.

Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol

Diazotrophs play a critical role in converting air-inactive nitrogen to bio-available nitrogen. Assessing the influences of different fertilization regimes on diazotrophs is essential for a better understanding of their maintenance of soil fertility and agricultural sustainability. In this study, we targeted the nifH gene to investigate the effects of different long-term fertilization on the diazotrophic community in a vertisol, using real-time quantitative polymerase chain reaction (PCR) and MiSeq sequencing. Five fertilization regimes were tested: no fertilizer (CK), chemical nitrogen, phosphorus, and potassium fertilizer (NPK), organic fertilizer (O), chemical NPK plus organic fertilizer with an equivalent application rate of nitrogen (NPKO), and chemical NPK plus organic fertilizer with a high application rate of nitrogen (HNPKO). Our results showed that fertilization significantly affected the diazotrophic activity, abundance and composition. NPK tended to reduce the activity, abundance, operational taxonomic units (OTU)-richness and alpha-diversity of the diazotrophs, while O had the opposite effect. The effects of inorganic and organic fertilization on the diazotrophs depended on the N application rate, showing that the diazotrophic activity, abundance, and alpha-diversity in NPKO were higher than that of HNPKO. For the diazotrophic community structure, CK, O, and NPKO were grouped and separated from NPK and HNPKO. The diazotrophic community structure strongly correlated with the soil pH, electrical conductivity (EC), total carbon content (TC), and total nitrogen content (TN), among which pH was the major factor shaping the diazotrophic community structure. Different network patterns were observed between the long-term organic and non-organic fertilizers, suggesting that the organic amendment resulted in a more complicated diazotrophic community than the non-organic amendments. Rhizobium was the most important hub connecting members in the community. These results indicated that organic amendments are beneficial to diazotrophic activity, abundance, OTU richness, alpha-diversity, and the diazotrophic communities' potential interactions, which may enhance biological nitrogen fixation in vertisols.

Microbiome structure and function in rhizosphere of Jerusalem artichoke grown in saline land

The improvement and development of saline-alkali soils is currently a hot economic and scientific issue, and exploring the correlation between rhizosphere microorganisms of plants growing on saline-alkali soils and their salt tolerance has become the key point of related research. In our study, the community structure of microorganism and various properties of saline soils were characterized in which Jerusalem artichoke grown along a soil salinity gradient. A variety of basic soil properties were measured and the amplicon was performed as well as metagenomic sequencing on coastal saline soils using various techniques (such as RDA analysis and the assembly of genomes) to evaluate microbial functions. In addition, WGCNA (Weighted gene coexpression network analysis) method was used to identify the species related to salt stress and the sequence binning to assemble two enriched putative bacterial genomes. The research showed the cultivation of Jerusalem artichoke on saline soil changed soil physico-chemical and enzymatic properties; most of the rapidly changing as well as the long-term stable properties differed significantly between the rhizosphere and bulk soils. The amplicon and metagenomic sequencing revealed the function and structure of microorganisms varied between the rhizosphere and bulk soils, with greater microbial diversity in the rhizosphere. Catalase activity and the moisture content were the factors with the greatest impact on microorganisms. The putative genomes of two species of microorganisms (belong to Nitrospira and Gemmatimonas) were assembled, identified microbial species that were highly responsive to salt stress and that may play a key role in saline soil, stressed the important role of archaea in microbial communities in response to salt stress. The study provides a comprehensive understanding of the microbial community structure in the rhizosphere of Jerusalem artichoke to enable the improvement and economic development of saline land.

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi

High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.

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.

Plant growth promotion properties of bacterial strains isolated from the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.) adapted to saline-alkaline soils and their effect on wheat growth

The Jerusalem artichoke (JA; Helianthus tuberosus), known to be tolerant to saline-alkaline soil conditions, has been cultivated for many years in the Yellow River delta, Shandong Province coastal zone, in China. The aim of our study was to isolate nitrogen-fixing bacteria colonizing the rhizosphere of JA and to characterize other plant growth promotion properties. The ultimate goal was to identify isolates that could be used as inoculants benefiting an economic crop, in particular for improving wheat growth production in the Yellow River delta. Bacterial strains were isolated from the rhizosphere soil of JA on the basis of growth on nitrogen-free Ashby medium. Identification and phylogenetic analysis was performed after nucleotide sequencing of 16S rRNA gene. Plant-growth-promoting traits, such as nitrogen fixation activity, phosphate solubilization activity, indole-3-acetic acid production, were determined using conventional methods. Eleven strains were isolated and 6 of them were further examined for their level of salt tolerance and their effect on plant growth promotion. Inoculation of Enterobacter sp. strain N10 on JA and wheat led to significant increases in both root and shoot dry mass and shoot height. Enterobacter sp. strain N10 appeared to be the best plant-growth-promoting rhizobacteria to increase wheat productivity in future field applications.

A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin?

Organism body size has been demonstrated to be a discriminating element in shaping the response of living beings to environmental factors, thus playing a fundamental role in community structuring. Despite the importance of studies elucidating relations among communities of different size levels in ecosystems, the attempts that have been made in this sense are still very scarce and a reliable approach for these research still has to be defined. We characterized the benthic communities of bacteria, microbial eukaryotes, meiofauna and macrofauna in a coastal environment, encompassing a 10000-fold gradient in body size, testing and discussing a mixed approach of molecular fingerprinting for microbes and morphological observations for meio- and macrofauna. We found no correlation among structures of the different size-level communities: this suggests that community composition at one size-level could have no (or very low) influence on the community composition at other size-levels. Moreover, each community responds in a different way to the environmental parameters and with a degree of sensitivity which seems to increase with organism size. Therefore, our data indicate that the characterization of all the different size levels is clearly a necessity in order to study the dynamics really acting in a system.

Colonization by endophytic Ochrobactrum anthropi Mn1 promotes growth of Jerusalem artichoke

The Ochrobactrum anthropi Mn1 strain, taxonomically identified using 16S ribosomal DNA sequence, was isolated from roots of Jerusalem artichoke. Its endophytic colonization was investigated microscopically using green fluorescent protein introduced by vector pHC60. The strain entered Jerusalem artichoke tissues through the root, and was localized in the roots and stems. The plant growth-promoting (PGP) effects of O. anthropi Mn1 were assessed in greenhouse as well as field trials with different nitrogen supplies. Only under moderate to ample nitrogen supply, could O. anthropi Mn1 promoted growth of host plant. The PGP effects of the strain were symbiotic nitrogen fixation, root morphological optimization and enhanced nutrient uptake. We hypothesize that the symbiotic interspecies interaction might be quorum sensing related.

Dynamics of soil diazotrophic community structure, diversity, and functioning during the cropping period of cotton (Gossypium hirsutum)

The soil sampled at different growth stages along the cropping period of cotton were analyzed using various molecular tools: restriction fragment length polymorphism (RFLP), terminal restriction length polymorphism (T-RFLP), and cloning-sequencing. The cluster analysis of the diazotrophic community structure of early sampled soil (0, 15, and 30 days) was found to be more closely related to each other than the later sampled one. Phylogenetic and diversity analysis of sequences obtained from the first (0 Day; C0) and last soil sample (180 day; C180) confirmed the data. The phylogenetic analysis revealed that C0 was having more unique sequences than C180 (presence of γ-Proteobacteria exclusively in C0). A relatively higher richness of diazotrophic community sequences was observed in C0 (S(ACE) : 30.76; S(Chao1) : 20.94) than C180 (S(ACE) : 18.00; S(Chao1) : 18.00) while the evenness component of Shannon diversity index increased from C0 (0.97) to C180 (1.15). The impact of routine agricultural activities was more evident based on diazotrophic activity (measured by acetylene reduction assay) than its structure and diversity. The nitrogenase activity of C0 (1264.85 ± 35.7 ηmol of ethylene production g(-1) dry soil h(-1) ) was statistically higher when compared to all other values (p < 0.05). There was no correlation found between diazotrophic community structure/diversity and N2 fixation rates. Thus, considerable functional redundancy of nifH was concluded to be existing at the experimental site.

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial signatures of the agricultural land-use. The three sites included in this study are the Broadbalk Experiment at Rothamsted Research, UK, the Everglades Agricultural Area, Florida, USA, and the Kellogg Biological Station, Michigan, USA. The effects of agricultural management on the abundance and diversity of bacteria and archaea were determined using high throughput, barcoded 16S rRNA sequencing. In addition, the relative abundance of these organisms was correlated with soil features. Two groups of microorganisms involved in nitrogen cycle were highly correlated with land use at all three sites. The ammonia oxidizing-archaea, dominated by Ca. Nitrososphaera, were positively correlated with agriculture while a ubiquitous group of soil bacteria closely related to the diazotrophic symbiont, Bradyrhizobium, was negatively correlated with agricultural management. Analysis of successional plots showed that the abundance of ammonia oxidizing-archaea declined and the abundance of bradyrhizobia increased with time away from agriculture. This observation suggests that the effect of agriculture on the relative abundance of these genera is reversible. Soil pH and NH3 concentrations were positively correlated with archaeal abundance but negatively correlated with the abundance of Bradyrhizobium. The high correlations of Ca. Nitrososphaera and Bradyrhizobium abundances with agricultural management at three long-term experiments with different edaphoclimatic conditions allowed us to suggest these two genera as signature microorganisms for agricultural land use.