Showing papers on "Nitrogen fixation published in 2016"
[...]
TL;DR: Although the Haber-Bosch process more than quadrupled the productivity of agricultural crops, chemical fertilizers and other anthropogenic sources of fixed nitrogen now far exceed natural contributions, leading to unprecedented environmental degradation.
453 citations
TL;DR: In this article, a minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
Abstract: Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
394 citations
TL;DR: The results reveal a mechanism for how intercropped maize promotes nitrogen fixation of faba bean, where maize root exudates promote flavonoid synthesis in faba beans, increase nodulation, and stimulate nitrogen fixation after enhanced gene expression.
Abstract: Plant diversity in experimental systems often enhances ecosystem productivity, but the mechanisms causing this overyielding are only partly understood. Intercropping faba beans (Vicia faba L.) and maize (Zea mays L.) result in overyielding and also, enhanced nodulation by faba beans. By using permeable and impermeable root barriers in a 2-y field experiment, we show that root–root interactions between faba bean and maize significantly increase both nodulation and symbiotic N2 fixation in intercropped faba bean. Furthermore, root exudates from maize promote faba bean nodulation, whereas root exudates from wheat and barley do not. Thus, a decline of soil nitrate concentrations caused by intercropped cereals is not the sole mechanism for maize promoting faba bean nodulation. Intercropped maize also caused a twofold increase in exudation of flavonoids (signaling compounds for rhizobia) in the systems. Roots of faba bean treated with maize root exudates exhibited an immediate 11-fold increase in the expression of chalcone–flavanone isomerase (involved in flavonoid synthesis) gene together with a significantly increased expression of genes mediating nodulation and auxin response. After 35 d, faba beans treated with maize root exudate continued to show up-regulation of key nodulation genes, such as early nodulin 93 (ENOD93), and promoted nitrogen fixation. Our results reveal a mechanism for how intercropped maize promotes nitrogen fixation of faba bean, where maize root exudates promote flavonoid synthesis in faba bean, increase nodulation, and stimulate nitrogen fixation after enhanced gene expression. These results indicate facilitative root–root interactions and provide a mechanism for a positive relationship between species diversity and ecosystem productivity.
238 citations
TL;DR: It is found that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments, implying a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.
Abstract: Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.
227 citations
TL;DR: It is shown that an iron-dinitrogen complex bearing an anionic PNP-pincer ligand works as an effective catalyst towards the catalytic nitrogen fixation, where a mixture of ammonia and hydrazine is produced.
Abstract: Synthesis and reactivity of iron-dinitrogen complexes have been extensively studied, because the iron atom plays an important role in the industrial and biological nitrogen fixation. As a result, iron-catalyzed reduction of molecular dinitrogen into ammonia has recently been achieved. Here we show that an iron-dinitrogen complex bearing an anionic PNP-pincer ligand works as an effective catalyst towards the catalytic nitrogen fixation, where a mixture of ammonia and hydrazine is produced. In the present reaction system, molecular dinitrogen is catalytically and directly converted into hydrazine by using transition metal-dinitrogen complexes as catalysts. Because hydrazine is considered as a key intermediate in the nitrogen fixation in nitrogenase, the findings described in this paper provide an opportunity to elucidate the reaction mechanism in nitrogenase.
224 citations
TL;DR: It is highlighted that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use.
Abstract: Diazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high nitrogen fertilizer application. Here, we explored the impact of high nitrogen fertilizer rates on the presence of diazotrophs in field-grown sugarcane with industry-standard or reduced nitrogen fertilizer application. Despite large differences in soil microbial communities between test sites, a core sugarcane root microbiome was identified. The sugarcane root-enriched core taxa overlap with those of Arabidopsis thaliana raising the possibility that certain bacterial families have had long association with plants. Reduced nitrogen fertilizer application had remarkably little effect on the core root microbiome and did not increase the relative abundance of root-associated diazotrophs or nif gene counts. Correspondingly, low nitrogen fertilizer crops had lower biomass and nitrogen content, reflecting a lack of major input of biologically fixed nitrogen, indicating that manipulating nitrogen fertilizer rates does not improve sugarcane yields by enriching diazotrophic populations under the test conditions. Standard nitrogen fertilizer crops had improved biomass and nitrogen content, and corresponding soils had higher abundances of nitrification and denitrification genes. These findings highlight that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use.
141 citations
TL;DR: It is concluded that the direct screening of root and nodule traits in the field as well as identification of genes, proteins and also metabolites involved in such traits will be essential in order to gain a better understanding of the regulation of root architecture, bacteroid development and lifespan in relation to drought tolerance in soybean.
Abstract: Drought is considered to be a major threat to soybean production worldwide and yet our current understanding of the effects of drought on soybean productively is largely based on studies on above-ground traits. Although the roots and root nodules are important sensors of drought, the responses of these crucial organs and their drought tolerance features remain poorly characterized. The symbiotic interaction between soybean and rhizobia facilitates atmospheric nitrogen fixation, a process that provides essential nitrogen to support plant growth and development. Symbiotic nitrogen fixation is important for sustainable agriculture, as it sustains plant growth on nitrogen-poor soils and limits fertilizer use for crop nitrogen nutrition. Recent developments have been made in our understanding of the drought impact on soybean root architecture and nodule traits, as well as underpinning transcriptome, proteome and also emerging metabolome information, with a view to improve the selection of more drought-tolerant soybean cultivars and rhizobia in the future. We conclude that the direct screening of root and nodule traits in the field as well as identification of genes, proteins and also metabolites involved in such traits will be essential in order to gain a better understanding of the regulation of root architecture, bacteroid development and lifespan in relation to drought tolerance in soybean.
132 citations
TL;DR: The need for combining rate measurements and molecular analyses of field samples with cultivation studies in order to clarify the ecology of non-cyanobacteria and their contribution to marine N2 fixation on local and global scales is highlighted.
120 citations
TL;DR: An overview of metal transport mechanisms in the plant–microbe system is proposed, emphasizing the role of arbuscular mycorrhizal fungi and endosymbiotic rhizobia in legume nodules.
Abstract: Transition metals such as iron, copper, zinc, or molybdenum, are essential nutrients for plants. These elements are involved in almost every biological process, including photosynthesis, tolerance to biotic and abiotic stress, or symbiotic nitrogen fixation. However, plants often grow in soils with limiting metallic oligonutrient bioavailability. Consequently, to ensure the proper metal levels, plants have developed a complex metal uptake and distribution system, that not only involves the plant itself, but also its associated microorganisms. These microorganisms can simply increase metal solubility in soils and making them more accessible to the host plant, as well as induce the plant metal deficiency response, or deliver directly transition elements to cortical cells. Other, instead of providing metals can act as metal sinks, such as endosymbiotic rhizobia in legume nodules that requires relatively large amounts to carry out nitrogen fixation. In this review, we propose to do an overview of metal transport mechanisms in the plant-microbe system, emphasizing the role of arbuscular mycorrhizal fungi and endosymbiotic rhizobia.
119 citations
TL;DR: Of the five test strains, Azospirillum sp.
Abstract: Rhizosphere engineering with beneficial plant growth promoting bacteria offers great promise for sustainable crop yield. Potato is an important food commodity that needs large inputs of nitrogen and phosphorus fertilizers. To overcome high fertilizer demand (especially nitrogen), five bacteria, i.e. Azospirillum sp.TN10, Agrobacterium sp.TN14, Pseudomonas sp.TN36, Enterobactersp. TN38 and Rhizobium sp. TN42 were isolated from the potato rhizosphere on nitrogen-free malate medium and identified based on their 16S rRNA gene sequences. Three strains, i.e. TN10, TN38 and TN42, showed nitrogen fixation (92.67-134.54 nmol h-1mg-1protein), while all showed the production of indole acetic acid in the presence and/or absence of L-tryptophan. Azospirillum sp. TN10 produced the highest amount of IAA, as measured by spectrophotometry (312.14 µg mL-1) and HPLC (18.3 µg mL-1). Inoculation with these bacteria under axenic conditions resulted in differential growth responses of potato. Azospirillum sp. TN10 incited the highest increase in potato fresh and dry weight over control plants, along with increased N contents of shoot and roots. All strains were able to colonize and maintain their population densities in the potato rhizosphere for upto 60 days, with Azospirillum sp. and Rhizobium sp. showing the highest survival. Plant root colonization potential was analyzed by transmission electron microscopy of root sections inoculated with Azospirillum sp. TN10. Of the five test strains, Azospirillum sp. TN10 has the greatest potential to increase the growth and nitrogen uptake of potato. Hence, it is suggested as a good candidate for the production of potato biofertilizer for integrated nutrient management with potato.
92 citations
TL;DR: Results clearly indicate that P. polymyxa P2b-2R, a lodgepole pine endophyte, is capable of fixing nitrogen and promoting growth of an important oilseed crop canola, which is an indication of its broad range host capability.
Abstract: An endophytic diazotroph, Paenibacillus polymyxa P2b-2R, previously isolated from internal tissues of lodgepole pine tree was tested for its ability to colonize, fix nitrogen, and promote growth of an important oilseed crop, canola. For this, we inoculated canola seeds with P. polymyxa P2b-2R and grew them for up to 60 days. Canola seedlings were harvested thrice, 20, 40, and 60 days after inoculation, to determine the rhizospheric and endophytic P2b-2R population (colony-forming units (cfu)) and quantify the biological nitrogen fixation (15N dilution assay) and growth promotion (height and biomass). The entire experiment was repeated to confirm the treatment effects. P2b-2R colonized canola rhizosphere with a population abundance of 1.41 × 108 cfu/g dry root in the first growth trial and 7.49 × 107 cfu/g dry root in the second growth trial. P2b-2R developed a persistent endophytic population in canola root, comprising 3.48 × 105 cfu/g fresh weight in the first growth trial and 2.36 × 103 cfu/g fresh weight in the second growth trial. In the first growth trial, P2b-2R inoculation enhanced seedling height by 25 % and biomass by 30 % after 60 days of inoculation. Similarly, in the second growth trial, P2b-2R inoculation promoted seedling height by 21 % and biomass by 24 %. P2b-2R inoculated seedlings fixed 22 and 19 % of nitrogen from the atmosphere in the first and second growth trials, respectively. These results clearly indicate that P. polymyxa P2b-2R, a lodgepole pine endophyte, is capable of fixing nitrogen and promoting growth of an important oilseed crop canola, which is an indication of its broad range host capability.
TL;DR: Direct, field-based measurements of low nitrogen fixation rates in the eastern tropical South Pacific (ETSP) Ocean demonstrate that N2 fixation plays a minor role supporting export production regionally, and indicates that the ETSP hosts a minor fraction of global N2-fixation fluxes.
Abstract: An extensive region of the Eastern Tropical South Pacific (ETSP) Ocean has surface waters that are nitrate-poor yet phosphate-rich. It has been proposed that this distribution of surface nutrients provides a geochemical niche favorable for N2 fixation, the primary source of nitrogen to the ocean. Here, we present results from two cruises to the ETSP where rates of N2 fixation and its contribution to export production were determined with a suite of geochemical and biological measurements. N2 fixation was only detectable using nitrogen isotopic mass balances at two of six stations, and rates ranged from 0 to 23 µmol N m−2 d−1 based on sediment trap fluxes. Whereas the fractional importance of N2 fixation did not change, the N2-fixation rates at these two stations were several-fold higher when scaled to other productivity metrics. Regardless of the choice of productivity metric these N2-fixation rates are low compared with other oligotrophic locations, and the nitrogen isotope budgets indicate that N2 fixation supports no more than 20% of export production regionally. Although euphotic zone-integrated short-term N2-fixation rates were higher, up to 100 µmol N m−2 d−1, and detected N2 fixation at all six stations, studies of nitrogenase gene abundance and expression from the same cruises align with the geochemical data and together indicate that N2 fixation is a minor source of new nitrogen to surface waters of the ETSP. This finding is consistent with the hypothesis that, despite a relative abundance of phosphate, iron may limit N2 fixation in the ETSP.
TL;DR: Genetic analysis using biofilm formation-related Pseudomonas mutants confirmed the relevance of bacterial root adhesion in the increase in nitrogen content, biomass accumulation and nitrogen fixation rates in wheat roots, the first report of robust BNF in major cereal crops.
Abstract: A main goal of biological nitrogen fixation research has been to expand the nitrogen-fixing ability to major cereal crops. In this work, we demonstrate the use of the efficient nitrogen-fixing rhizobacterium Pseudomonas protegens Pf-5 X940 as a chassis to engineer the transfer of nitrogen fixed by BNF to maize and wheat under non-gnotobiotic conditions. Inoculation of maize and wheat with Pf-5 X940 largely improved nitrogen content and biomass accumulation in both vegetative and reproductive tissues, and this beneficial effect was positively associated with high nitrogen fixation rates in roots. 15 N isotope dilution analysis showed that maize and wheat plants obtained substantial amounts of fixed nitrogen from the atmosphere. Pf-5 X940-GFP-tagged cells were always reisolated from the maize and wheat root surface but never from the inner root tissues. Confocal laser scanning microscopy confirmed root surface colonization of Pf-5 X940-GFP in wheat plants, and microcolonies were mostly visualized at the junctions between epidermal root cells. Genetic analysis using biofilm formation-related Pseudomonas mutants confirmed the relevance of bacterial root adhesion in the increase in nitrogen content, biomass accumulation and nitrogen fixation rates in wheat roots. To our knowledge, this is the first report of robust BNF in major cereal crops.
TL;DR: A quantitative proteomic atlas of the model legume Medicago truncatula and its rhizobial symbiont Sinorhizobium meliloti is described, which includes more than 23,000 proteins, 20,000 phosphorylation sites, and 700 lysine acetylation sites, which provides insight into mechanisms regulating symbiosis.
Abstract: Legumes are essential components of agricultural systems because they enrich the soil in nitrogen and require little environmentally deleterious fertilizers. A complex symbiotic association between legumes and nitrogen-fixing soil bacteria called rhizobia culminates in the development of root nodules, where rhizobia fix atmospheric nitrogen and transfer it to their plant host. Here we describe a quantitative proteomic atlas of the model legume Medicago truncatula and its rhizobial symbiont Sinorhizobium meliloti, which includes more than 23,000 proteins, 20,000 phosphorylation sites, and 700 lysine acetylation sites. Our analysis provides insight into mechanisms regulating symbiosis. We identify a calmodulin-binding protein as a key regulator in the host and assign putative roles and targets to host factors (bioactive peptides) that control gene expression in the symbiont. Further mining of this proteomic resource may enable engineering of crops and their microbial partners to increase agricultural productivity and sustainability.
TL;DR: Reductive soil disinfestation could induced more antagonists belonging to Firmicutes under anaerobic condition, whereas Al-RSD could continuously stimulate some functional microorganisms and further improve nitrogen transformation activities in the soil at the coming cropping season.
Abstract: Reductive soil disinfestation (RSD) has been proven to be an effective and environmentally friendly way to control many soilborne pathogens and diseases. In this study, the RSDs using ethanol (Et-RSD) and alfalfa (Al-RSD) as organic carbons were performed in a Rhizoctonia solani-infected soil, and the dissimilarities of microbial communities during the RSDs and after planting two seasons of cucumber seedlings in the RSDs-treated soil were respectively investigated by MiSeq pyrosequencing. The results showed that, as for bacteria, Coprococcus, Flavisolibacter, Rhodanobacter, Symbiobacterium, and UC-Ruminococcaceae became the dominant bacterial genera at the end of Al-RSD. In contrast, Et-RSD soil involved more bacteria belonging to Firmicutes, such as Sedimentibacter, UC-Gracilibacteraceae, and Desulfosporosinus. For fungi, Chaetomium significantly increased at the end of RSDs, while Rhizoctonia and Aspergillus significantly decreased. After planting two seasons of cucumber seedlings, those bacteria belonging to Firmicutes significantly decreased, but Lysobacter and Rhodanobacter belonging to the phylum Proteobacteria as well as UC-Sordariales and Humicola belonging to Ascomycota alternatively increased in Al- and Et-RSD-treated soils. Besides, some nitrification, denitrification, and nitrogen fixation genes were apparently increased in the RSD-treated soils, but the effect was more profound in Al-RSD than Et-RSD. Overall, Et-RSD could induced more antagonists belonging to Firmicutes under anaerobic condition, whereas Al-RSD could continuously stimulate some functional microorganisms (Lysobacter and Rhodanobacter) and further improve nitrogen transformation activities in the soil at the coming cropping season.
TL;DR: The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions.
Abstract: N2 fixation should be a critical process in the nitrogen-poor surface water of the eastern Mediterranean Sea. Despite favorable conditions, diazotroph abundance and N2 fixation rates remains low for reasons yet explained. The main goal of this study was to investigate the limiting nutrients for diazotrophy in this oligotrophic environment. Hence, we conducted dedicated bottle-microcosms with eastern Mediterranean Sea water that were supplemented with mono and polysaccharides as well as inorganic nitrogen and phosphorous. Our results indicate that the diazotrophic community expressing nifH was primarily represented by heterotrophic Proteobacteria. N2 fixation and heterotrophic bacterial activity increased up-to tenfold following two days of dark incubations, once seawater was supplemented with organic carbon substrate in the form of glucose (monosaccharides) or gum-xanthan (polysaccharide surrogate). Furthermore, our results point that carbon-rich polysaccharides, such as transparent exopolymer particles, enhance heterotrophic N2 fixation, by forming microenvironments of intense metabolic activity, high carbon: nitrogen ratio, and possibly low O2 levels. The conclusions of this study indicate that diazotrophs in the eastern Mediterranean coast are primarily limited by organic carbon substrates, as possibly in many other marine regions.
TL;DR: It is demonstrated that transporter function in N export from nodules is a key step for enhancing atmospheric N2 fixation and nodule function and for improving shoot N nutrition and seed development in legumes.
TL;DR: DNA stable isotope probing with15N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate 15N2 in early successional crusts and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development.
Abstract: Biological soil crusts (BSCs) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface In particular, BSC N2-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems In mature crusts, N2-fixation is largely attributed to heterocystous cyanobacteria; however, early successional crusts possess few N2-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development DNA stable isotope probing with (15)N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate (15)N2 in early successional crusts The Clostridiaceae identified are divergent from previously characterized isolates, though N2-fixation has previously been observed in this family The Proteobacteria identified share >985% small subunit rRNA gene sequence identity with isolates from genera known to possess diazotrophs (for example, Pseudomonas, Klebsiella, Shigella and Ideonella) The low abundance of these heterotrophic diazotrophs in BSCs may explain why they have not been characterized previously Diazotrophs have a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSCs in arid ecosystems
TL;DR: A high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO2T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management.
TL;DR: This work reports the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat, and indicates that associative N2-fixation occurred within wild poplar.
Abstract: The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms However, a variety of non-nodulating plant species can also thrive in natural, low-N settings Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation Similarly, acetylene was reduced to ethylene in some samples The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees
TL;DR: The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice.
Abstract: The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi-controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field-grown plants under a conventional flooded system of rice intensification (SRI) and in dry-seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α-proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2 μg·ml(-1) ) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non-heterocystous filaments under aerobic as well as anaerobic conditions. PCR-DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice.
TL;DR: The reconstructed network substantially expands the existing knowledge of transcriptional regulation in nitrogen-fixing microorganisms and can be used for genetic experiments, metabolic reconstruction, and evolutionary analysis.
Abstract: Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. Being a complex and sensitive process, nitrogen fixation requires a complicated regulatory system, also, on the level of transcription. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class Alphaproteobacteria. This regulatory network includes the activator of nitrogen fixation NifA, working in tandem with the alternative sigma-factor RpoN as well as oxygen-responsive regulatory systems, one-component regulators FnrN/FixK and two-component system FixLJ. Here we used a comparative genomics analysis for in silico study of the transcriptional regulatory network in 50 genomes of Alphaproteobacteria. We extended the known regulons and proposed the scenario for the evolution of the nitrogen fixation transcriptional network. The reconstructed network substantially expands the existing knowledge of transcriptional regulation in nitrogen-fixing microorganisms and can be used for genetic experiments, metabolic reconstruction, and evolutionary analysis.
TL;DR: Five isolates promoted plant growth in greenhouse experiments, showing potential as biofertilizers and characterizing plant growth-promoting bacteria associated with sugarcane.
Abstract: Microorganisms play a vital role in maintaining soil fertility and plant health. They can act as biofertilizers and increase the resistance to biotic and abiotic stress. This study aimed at isolating and characterizing plant growth-promoting bacteria associated with sugarcane, as well as assessing their ability to promote plant growth. Endophytic bacteria from leaf, stem, root and rhizosphere were isolated from the RB 867515 commercial sugarcane variety and screened for indole acetic acid (IAA) production, ability to solubilize phosphate, fix nitrogen and produce hydrogen cyanide (HCN), ammonia and the enzymes pectinase, cellulase and chitinase. A total of 136 bacteria were isolated, with 83 of them presenting some plant growth mechanism: 47 % phosphate solubilizers, 26 % nitrogen fixers and 57 % producing IAA, 0.7 % HCN and chitinase, 45 % ammonia, 30 % cellulose and 8 % pectinase. The seven best isolates were tested for their ability to promote plant growth in maize. The isolates tested for plant growth promotion belong to the Enterobacteriaceae family and the Klebsiella, Enterobacter and Pantoea genera. Five isolates promoted plant growth in greenhouse experiments, showing potential as biofertilizers.
TL;DR: Permutational multivariate analyses demonstrated that soil depth, rather than the sampling time or fertilization regime, was the important factor that influence the diazotrophic structures.
TL;DR: ISARA analyses indicate significant contributions of alternative nitrogen fixation in boreal cyanolichens and salt marshes and suggest significant interactions between the cycles of nitrogen and trace metals, which affect the quantitative interpretation of natural abundance 15N data or traditional acetylene reduction assays.
Abstract: Biological nitrogen fixation, the main natural input of fixed nitrogen into the biosphere, is catalyzed by Mo-, V-, or Fe-only nitrogenase metalloenzymes. Although “alternative” V- and Fe-only nitrogenase genes are found in many environments, the contribution of these isoenzymes to N2 fixation is unknown. Here we present a new method (ISARA, isotopic acetylene reduction assay) that distinguishes canonical Mo and alternative nitrogenase activities based on in vivo 13C fractionation of acetylene reduction to ethylene (13eMo = 13.1–14.7 ‰, 13eV = 7.5–8.8 ‰, 13eFe = 5.8–6.5 ‰). ISARA analyses indicate significant contributions of alternative nitrogen fixation in boreal cyanolichens and salt marshes (~10–40 % acetylene reduction, ~20–55 % N2 fixed). These results affect the quantitative interpretation of natural abundance 15N data or traditional acetylene reduction assays. They also invite a reexamination of the conditions under which the different nitrogenase isozymes are active and suggest significant interactions between the cycles of nitrogen and trace metals.
TL;DR: The results suggest that S. alterniflora invasion can increase soil N fixation in the high N-loading estuarine ecosystem, and thus may further mediate soil N availability.
Abstract: Biological nitrogen fixation (BNF) is the major natural process of nitrogen (N) input to ecosystems. To understand how plant invasion and N enrichment affect BNF, we compared soil N-fixation rates and N-fixing microbes (NFM) of an invasive Spartina alterniflora community and a native Phragmites australis community in the Yangtze River estuary, with and without N addition. Our results indicated that plant invasion relative to N enrichment had a greater influence on BNF. At each N level, the S. alterniflora community had a higher soil N-fixation rate but a lower diversity of the nifH gene in comparison with the native community. The S. alterniflora community with N addition had the highest soil N-fixation rate and the nifH gene abundance across all treatments. Our results suggest that S. alterniflora invasion can increase soil N fixation in the high N-loading estuarine ecosystem, and thus may further mediate soil N availability.
TL;DR: Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazOTrophs, which is consistent with the physical isolation nature of symbiotic nifH genes from the environment by root nodules.
Abstract: Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems.
TL;DR: It is concluded that although N deposition negatively affects N2 fixation as also shown in previous studies, long-term effects of N deprivation on the diazotrophic activity and community are more complex.
Abstract: Background and aims
In pristine ombrotrophic Sphagnum-dominated peatland ecosystems nitrogen (N) is often a limiting nutrient, which is replenished by biological N2 fixation and atmospheric N deposition. It is, however, unclear which impact long-term N deposition has on microbial N2 fixing activity and diazotrophic diversity, and whether phosphorus (P) modulates the response. Therefore, we studied the impact of increased N deposition and N depletion on microbial N2 fixation and diazotrophic diversity associated with the peat moss Sphagnum magellanicum, and their interaction with P availability.
TL;DR: In this paper, the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot were sequenced and compared, and it was found that the Rhizobium species coexist with low genetic recombination across their core genomes.
Abstract: Cultivated common beans are the primary protein source for millions of people around the world who subsist on low-input agriculture, enabled by the symbiotic N2 -fixation these legumes perform in association with rhizobia. Within a single agricultural plot, multiple Rhizobium species can nodulate bean roots, but it is unclear how genetically isolated these species remain in sympatry. To better understand this issue, we sequenced and compared the genomes of 33 strains isolated from the rhizosphere and root nodules of a particular bean variety grown in the same agricultural plot. We found that the Rhizobium species we observed coexist with low genetic recombination across their core genomes. Accessory plasmids thought to be necessary for the saprophytic lifestyle in soil show similar levels of genetic isolation, but with higher rates of recombination than the chromosomes. However, the symbiotic plasmids are extremely similar, with high rates of recombination and do not appear to have co-evolved with the chromosome or accessory plasmids. Therefore, while Rhizobium species are genetically isolated units within the microbial community, a common symbiotic plasmid allows all Rhizobium species to engage in symbiosis with the same host in a single agricultural plot.
TL;DR: Select diazotrophic isolates may be potentially beneficial but they should be tested more in greenhouse and field conditions with maize to confirm their potential for application as biofertilizers.
Abstract: Poor soil fertility is one of the major constraints for crop production. Nitrogen is the most limiting nutrient for increasing crop productivity. Therefore, there is a need to identify diazotrophic inoculants as an alternative or supplement to N-fertilizers for sustainable agriculture. In the current study, a number of free-living diazotrophic bacteria were isolated from soils collected from maize rhizosphere and from leaves and roots of maize within the KwaZulu-Natal Province, Republic of South Africa. Ninety two isolates were selected for further screening because they were able to grow on N-free media containing different carbon sources. Isolates that were very slow to grow on N-free media were discarded. The isolates were screened in vitro for diazotrophic potential tests for ammonia production and acetylene reduction. Ethylene (C2H4) production was quantified and ranged from 4 to 73 nmoles of C2H4 h-1 culture-1. The top twenty isolates were re-screened on maize seedlings, and eight isolates significantly (P=0.001) enhanced some growth parameters of maize above the un-inoculated control. Isolates that showed significant effect on at least two growth parameters were identified at species or genera level. In conclusion, selected diazotrophic isolates may be potentially beneficial but they should be tested more in greenhouse and field conditions with maize to confirm their potential for application as biofertilizers.