Diversity Of Nitrogen-fixing Bacteria Research Articles

Diversity of nitrogen-fixing bacteria in Suaeda salsa rhizosphere during reproduction in the Yellow River delta

Diversity of nitrogen-fixing bacteria in Suaeda salsa rhizosphere during reproduction in the Yellow River delta

Expanding agricultural potential through biological nitrogen fixation: Recent advances and diversity of diazotrophic bacteria

Biological nitrogen fixation (BNF) by diazotrophic bacteria is one of the oldest and most crucial processes in nature. In this process, bacteria form symbiotic associations with plants, capturing atmospheric nitrogen and making it readily available to them. The diversity of nitrogen-fixing bacteria is vast. Recent advancements in molecular biology techniques have enabled the identification of new genera and species capable of fixing nitrogen and providing other types of nutrients for plants. From an agronomic perspective, this process is fundamental in increasing crop productivity sustainably and -cost-effectively. This review aims to categorize the most recent updates on the diversity of nitrogen-fixing bacteria and showcase the main advances in the genetic improvement of legumes for this characteristic. Recent research has revealed a wide diversity of species applicable to various crops of agronomic interest, and many of these bacteria have been used either alone or in consortium with other microorganisms. This study demonstrates the agricultural potential of these new discoveries and the vast possibilities for expanding research into the diversity of microorganisms responsible for BNF in agriculture.

Characteristics of soil nitrogen and nitrogen cycling microbial communities in different alfalfa planting years

ABSTRACT Nitrogen cycling in soil and its microbial community characteristics are closely related. Characteristics of soil nitrogen, community diversity of nitrogen-fixing bacteria (NFB) and ammonia oxidizers were study with a traditional farmland as control and five treatment alfalfa fields of 1-, 2-, 3-, 4- and 5-year (a) cultivation. The results showed that total nitrogen (TN) significantly increased in 3, 4 and 5 a, alkali-hydrolysable nitrogen (AHN), NH4 +-N (AN), NO3 −-N (NN) and SOC was the highest in 3, 5, 3, 4 a, respectively. The dominant phylum of NFB and ammonia-oxidizing bacteria (AOB) belonged to Proteobacteria with a higher diversity and abundance in 3 and 4 a. Crenarchaeota was found the dominant phylum of ammonia-oxidizing archaea (AOA) with the highest abundance in the alfalfa field planted for 2 a. The dominant genus of NFB and AOB were Azohydromonas and Nitrosospira, respectively, which showed the highest abundance in the alfalfa fields planted for 2 and 3 a, respectively. The diversity of NFB and AOB showed a significantly positive correlation with TN and AHN (p < 0.05). AOA showed a significantly negative correlation with AN (p < 0.05). Many microbial species cannot be annotated in this study, which deserves future investigation.

Responses of Nitrogen-Fixing Bacteria Communities to Elevation, Season, and Slope Aspect Variations in Subtropical Forests of Yunnan, China

Nitrogen-fixing bacteria play a significant role in tropical forest ecosystems. However, little is known about the comprehensive effects of altitude gradient (1000–2600 m), seasons (October, January, April, and July), and slope aspects (east and west) on the abundance and diversity of nitrogen-fixing bacteria in subtropical forest. Q-PCR and PCR-DGGE methods were performed to explore the abundance and diversity of nitrogen-fixing bacteria, respectively, in the Ailao Mountain subtropical forest. Our results showed that the abundance of nitrogen-fixing bacteria was highest in October and December, whereas it was lowest in April and July. Moreover, there was no difference in the total number of soil nitrogen-fixing bacteria on the eastern and western slopes. The diversity of soil nitrogen-fixing bacteria is higher at low and medium altitudes, but lower at high and medium altitudes with increasing altitude, and similar variation in the eastern and western slopes as well. Moreover, the most influential factors affecting the abundance of nitrogen-fixing bacteria was NH4+-N and herbal coverage, while those most affecting the diversity of nitrogen-fixing bacteria were NH4+-N and NO3−-N. In addition, permutational multivariate analysis demonstrated that the season had the greatest effects on the abundance of nitrogen-fixing, whereas altitude had the greatest effects on the diversity of nitrogen-fixing bacteria. These findings provide evidence that the variation in nitrogen-fixing bacteria is affected by multiple factors (altitudes, seasons and slope aspects) in the subtropical forests of Yunnan, China.

Changes in clover rhizosphere microbial community and diazotrophs in mercury-contaminated soils

Little is known about the response of the soil microbiome (including bacteria in the rhizosphere of legumes such as clover) to mercury (Hg) despite the toxicity of Hg to soil microorganisms. Here, Hg-contaminated soils collected from Guizhou province, southwest China, were divided into three groups according to their Hg contents and were planted with clover. High-throughput sequencing of bacterial 16S rRNA and nitrogenase (nifH) genes and quantitative polymerase chain reaction (qPCR) were used to study the response of bacteria and diazotrophs to soil Hg stress and the effects of Hg on the abundance of functional genes in rhizosphere soils. High concentrations of soil Hg decreased bacterial community abundance and diversity and increased the abundance and diversity of nitrogen-fixing bacteria. LEfSe analysis indicates that Rhizobium was a biomarker at sites with high soil Hg contents and the co-occurrence network results indicate a positive relationship between the abundance of the dominant module (from the co-occurrence network analysis) of Rhizobiaceae and soil Hg concentration. Structural equation modeling (SEM) indicates that the Hg content in the clover shoots (ShootHg) was negatively correlated with the abundance of the mercury reductase (merA) gene (r = −0.26, P < 0.05) and the organomercury lyase (merB) gene (r = −0.23, P < 0.05) in rhizosphere soils. Moreover, correlation analysis and SEM indicate that soil total nitrogen (TN), nitrate‑nitrogen (NO3−N), soil organic matter (SOM), and available molybdenum (Mo) contents were also important factors affecting the structure of the microbial community and the abundance of functional genes. The results provide a basis for further study of the mechanism(s) by which microorganisms may impart tolerance of clover to Hg in contaminated soils.

¿La incorporación de residuos de diferentes especies de Lupinus, como abono verde, afecta la actividad microbiana del suelo?

In the state of Jalisco, corn and tequila agave are the most important agricultural crops. The soils to cultivate these species are characterized by low content of organic matter and nitrogen. The amendments applied to the soil provide an important source of energy and nutrients for microorganisms; promotes the diversity of nitrogen-f ixing bacteria and nitrifying bacteria, which increases nitrogen availability in the soil. The aim of this study was to evaluate the use of two species of wild legumes: Lupinus exaltatus and Lupinus rotundiflorus as green manure (AV), and its effect on soil microbial biomass. An aerobic incubation experiment (14 days) was carried out on soil samples with green manure and without green manure (control). Under laboratory conditions, the microbial activity of soil was monitored through the response in basal respiration and the concentration of C and N in the microbial biomass. The CO2 production and C and N content in the microbial biomass showed significant differences (P &lt; 0.05) due to the effect of green manure. The residues of Lupinus are considered better quality than the residues of Zea mays due to its nitrogen content and low C: N ratio. The response of microorganisms presented a positive primer effect with the input of AV. Therefore, we conclude that the input of L. exaltatus and L. rotundiflorus as a green manure to the soil increases the biological activity of the soil and promotes the enrichment of C and N of the microbial biomass.

Diversity of nitrogen-fixing bacteria in agricultural field soil along the Yamuna River, Delhi, India

Nitrogen-fixing bacteria play an important role in sustaining soil health. The diversity was studied in nitrogen-fixing bacteria using the nifH gene along the Yamuna River in Delhi-National Capital Region. The nifH gene is a part of the nif regulon, which codes for an Fe-protein of the nitrogenase enzyme complex, responsible for the reduction of dinitrogen (N2) to ammonia (NH3) during biological nitrogen fixation. Soil samples were collected from agricultural fields near the Yamuna River. Terminal restriction fragment length polymorphism analysis of soil DNA using the TReFID software package showed community comprising different nitrogen-fixing bacterial phyla, dominated by the Proteobacteria (26.87%) and Actinobacteria (2.9%). The relative abundance of these two phyla increased downstream along the river while the relative abundance of the Cyanobacteria decreased. The maximum overall microbial diversity index was lower downstream and during the summer season. It was concluded that the seasonal variation in temperature and moisture and the increases in the pollution of the water directly affected the microbial diversity as well as the relative abundance of the nitrogen-fixing bacterial population in agricultural fields along the Yamuna River.

Domestic Wastewater for Forage Cultivation in Cerrado Soil

Fertigation of agricultural crops that are not directly used in human food, with domestic wastewater is a viable alternative for the sustainable use of water resources. The development of agricultural practices that provide high productivity with the sustainability of agroecosystems has been a great challenge. Thus, our aims were to use of domestic wastewater in the planting of Brachiaria brizantha cv Marandu, as an alternative for animal feed production in Cerrado soils, and to study the physical-chemical and microbiological impacts of the fertigation. These impacts were evaluated, respectively, by physical-chemical indicators content and diversity of nitrogen fixing bacteria (NFB) and arbuscular mycorrhizal fungi (AMF) in the DGGE profile. The NPK contents of the wastewater were used to determine the five fertigation managements (M1 to M5). M1 and M2 managements had no wastewater and M3 to M5 contained 20, 40 and 60% of NPK from the wastewater. The managements in a completely randomized design with 20 plots and 4 replicates were distributed. Soil samplings prior to fertigation and at the end of the experiment were performed. Leaf biomass productivity was determined in three different grass cuts. After fertigation, changes in physical-chemical indicators and in the viable microbial cells counts were observed. The NPK of wastewater increased the abundance of NFBs and AMFs. Leaf biomass productivity per hectare was directly proportional to NPK concentration. In addition, wastewater did not alter the nutritional composition of Marandu grass. Therefore, the fertigation with domestic wastewater showed to be a viable and promising alternative for reuse of this water in Cerrado soil for animal feed production.

&lt;b&gt;Symbiosis of rhizobia with &lt;i&gt;Gliricidia sepium &lt;/i&gt; and &lt;i&gt;Clitoria fairchildiana&lt;/i&gt; in an Oxisol in the pre-Amazon region of Maranhão State

Gliricidia ( Gliricidia sepium ) and sombreiro ( Clitoria fairchildiana ) have been recommended for agroforestry systems and reforestation of degraded areas due to their fast growth and symbiosis with rhizobia. However, little is known about native populations that nodulate these species. The objective of this study was to evaluate the phenotypic and genetic diversity of nitrogen-fixing bacteria isolated from nodules of gliricidia and sombreiro in alley cropping systems located in the pre-Amazon region of Maranhao State and to confirm their nodulation ability. Nodules were field collected from 20 plants of each species. The isolated strains were characterized morphologically, their 16S rRNA gene was partially sequenced, and their symbiotic ability was authenticated in siratro ( Macroptilium atropurpureum ). Despite being in the same climate and soil conditions, gliricidia and sombreiro are nodulated by different rhizobia genera, with Rhizobium predominant in gliricidia and Bradyrhizobium in sombreiro. Endophytic strains also colonized nodules in the field. Approximately 60% of Rhizobium strains did not nodulate siratro, whereas all Bradyrhizobium strains did. Native strains isolated from gliricidia nodules had low efficiency, and only four strains isolated from sombreiro nodules were efficient in siratro. These results highlight the importance of symbiotic relationships in the regulation of biological nitrogen fixation.

Effect of biofertilizer on the diversity of nitrogen-fixing bacteria and total bacterial community in lowland paddy fields in Sukabumi West Java, Indonesia

Effect of biofertilizer on the diversity of nitrogen-fixing bacteria and total bacterial community in lowland paddy fields in Sukabumi West Java, Indonesia

Effects of intercropping with soybean on bacterial and nitrogen-fixing bacterial diversity in the rhizosphere of sugarcane

Aims In order to investigate the effects of intercropping with soybean on the diversities of bacteria and nitrogenfixing bacteria in the rhizosphere of sugarcane(Saccharum officinarum), to collect and exploit nitrogen-fixing bacterial resources, and to screen for efficient sugarcane-associative nitrogen fixation system, an experiment was conducted by cultivating three sugarcane cultivars ‘ROC22', ‘GT21', and ‘B8' with a soybean(Glycine max) cultivar ‘Guizao 2'. Methods Rhizospheric soil bacteria and nitrogen-fixing bacteria were measured in the rhizosphere of sugarcane intercropped with soybean by using a nested-PCR combined with denaturing gradient gel electrophoresis(DGGE) technique. The specific bacterial 16 S rRNA gene fragments and nitrogen-fixing bacteria nifH gene fragments were amplified for phylogenetic and diversity analyses. Important findings Cluster analysis of bacterial communities showed that the sugarcane-soybean intercropping changed the community composition of rhizospheric soil bacteria and nitrogen-fixing bacteria, with the effect being greater on nitrogen-fixing bacterial communities than on the soil bacterial communities. The intercropping system had a significant effect on the diversity of the rhizospheric bacteria and nitrogen-fixing bacteria; the impact on the diversity of nitrogen-fixing bacteria was greater than on the soil bacteria, and was only minor on the dominance of the bacterial species. Analyses of Shannon-Wiener index and Simpson index showed that thenitrogen-fixing bacteria differed in diversity among the treatments with different sugarcane varieties, and that the sugarcane cultivar ‘ROC22'-soybean intercropping had the greatest diversity. The diversity of soil bacteria in the rhizosphere of sugarcane varied greatly among different stages of crop growth; the booming stage of soybean had the greatest diversity and variations in the diversity among treatments in soil bacteria in the rhizosphere of sugarcane, and thereafter the two variables decreased. In conclusion, the sugarcane-soybean intercropping system had significant effects on the community structures and diversities of soil bacteria and nitrogen-fixing bacteria in the rhizosphere of sugarcane. This is of help for understanding the beneficial effects of sugarcane-soybean intercropping and for identifying efficient sugarcane-associative nitrogen fixation systems.

基于RFLP技术的鹿角杯形珊瑚共附生固氮菌多样性分析

基于RFLP技术的鹿角杯形珊瑚共附生固氮菌多样性分析

Isolation and characterization of nitrogen fixing heterotrophic bacteria from the rhizosphere of pioneer plants growing on mine tailings

Mine tailings are extreme environments containing high concentrations of heavy metals and deficient in nitrogen and organic matter. However, some plant species tolerant to heavy metals are capable of growing on mine tailings. In this environment, it is expected that biological nitrogen fixation is the major source of nitrogen available for plants. In this work, three different nitrogen-free culture media were used to isolate nitrogen-fixing bacteria associated with nine plant species growing on mine tailings in Zacatecas, Mexico. Acetylene reduction assays (ARA) with and without heavy metals were carried out, as were the determination of minimum inhibitory concentration (MIC) of Ni, Cu, Co, Cr and Zn, and plant growth promotion (PGP) activities of each bacterial isolate. The major nitrogen-fixing bacteria distributed among rhizospheres of Juniperus sp., Aster gymnocephalus, Gringelia sp., Lygodesmia sp., and Haplopappus sp. were members of the genus Paenibacillus. However, Azospirillum lipoferum and Bradyrhizobium japonicum were also isolated from the rhizosphere of Haplopappus sp., and Viguiera linearis. Functionally, Paenibacillus durus BR_30 had the highest ARA and PGP activities, but was highly sensitive to heavy metals. However, Paenibacillus graminis BR_35 and Paenibacillus borealis BR_32 maintained a significant ARA activity in the presence of relatively high concentrations of Ni and Zn. Also, B. japonicum KYR_C5 and A. lipoferum showed moderate ARA and PGP activities. The majority of the isolates grew in moderate concentrations of heavy metals but ARA activities were inhibited at low Co and Cr concentrations. The diversity of nitrogen-fixing bacteria in the rhizosphere of pioneer plants may contribute to their adaptation to toxic stress and nutrient-deficiency in environments such as mine tailings.

Evaluation of the diversity of nitrogen-fixing bacteria in soybean rhizosphere by nifH gene analysis

Biological nitrogen fixation plays an important role in the nitrogen balance of agricultural ecosystems and provides an essential part of nitrogen nutrition for plants, even in conditions of intensive fertilization. The main agrobiotechnological method for soybean cultivation (Glycine max (L.) Merril) is an application of microbial preparations based on Bradyrhizobium japonicum. Successful inoculation strongly depends on the interactions between the introduced microorganism and the aboriginal rhizosphere microorganisms. To evaluate the composition of diazotrophic communities, a study of the diversity of the molecular marker for nitrogen fixation, the nifH gene, in the samples of soybean rhizosphere soil was carried out. Experiments were performed in the variants when soybean was cultivated without inoculation and after adding bacterial preparations, as well as in enrichment cultures of diazotrophs. The revealed diazotrophic microorganisms demonstrated low level of similarity to the known microorganisms (74–95% identity by nucleotides), and were identified as species of the phyla Firmicutes and Proteobacteria. In the composition of nitrogen-fixing communities in the rhizosphere soil, the microorganisms of the genera Clostridium, Paenibacillus, and Spirochaeta were shown to prevail.

Abundance and diversity of ammonia-oxidizing bacteria in rhizosphere and bulk paddy soil under different duration of organic management

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) approaches were used to assess respectively the molecular diversity and quantity of the nifH gene sequences in rhizosphere and bulk paddy soil under conventional management and different duration of organic management (2, 3, 5, 9 years). The phylogenetic distribution of clones based on nifH gene sequence showed that taxonomic groups were consisted of Alphaproteobacteria (27.6%), Betaproteobacteria (24.1%) and Gammaproteobacteria (48.3%). Members of the order Rhizobiales and Pseudomonadales were prevalent among the dominant diazotrophs. When the quantity of the nifH gene sequences was determined by qPCR, 2.27 × 105 to 1.14 × 106 copies/g of soil were detected. Except for 2 years organically managed soil, nifH gene copy numbers in organic soil, both rhizosphere and bulk, were significantly higher than in CM soil. Moreover, nifH gene copy numbers in the organic rhizosphere soil (3, 5, 9 years) were significantly higher than in bulk soil. The abundance and diversity of nitrogen-fixing bacteria tended to increase with duration of organic management but the highest number of nifH gene copies was observed in the rhizosphere and bulk soil of 5 years organic management. In addition, analysis of variance and canonical correspondence analysis (CCA) showed that C/N, C and N were important factors influencing the abundance and community structure of nitrogen-fixing bacterial.

New evidence for nitrogen fixation within the Italian white truffle Tuber magnatum

Diversity of nitrogen-fixing bacteria and the nitrogen-fixation activity was investigated in Tuber magnatum, the most well-known prized species of Italian white truffle. Degenerate PCR primers were applied to amplify the nitrogenase gene nifH from T. magnatum ascomata at different stages of maturation. Putative amino acid sequences revealed mainly the presence of Alphaproteobacteria belonging to Bradyrhizobium spp. and expression of nifH genes from Bradyrhizobia was detected. The nitrogenase activity evaluated by acetylene reduction assay was 0.5–7.5 μmol C 2H 4 h −1 g −1, comparable with early nodules of legumes associated with specific nitrogen-fixing bacteria. This is the first demonstration of nitrogenase expression gene and activity within truffle.

Diversity of nitrogen-fixing bacteria in cyanobacterial mats

The structure of the microbial community and the diversity of the functional gene for dinitrogenase reductase and its transcripts were investigated by analyzing >1400 16S rRNA gene and nifH sequences from two microbial mats situated in the intertidal zone of the Dutch barrier island Schiermonnikoog. Although both microbial mat communities were dominated by Cyanobacteria, they differed with respect to the composition of the total bacterial community. Proteobacteria-related sequences were retrieved as the second most abundant group higher up in the littoral (Station I), whereas Bacteroidetes were the second most abundant group at the low water mark (Station II). The diazotrophic (nitrogen-fixing) communities at both stations were also different, but had more operational taxonomic units in common than the total bacterial community. Denaturing gradient gel electrophoresis also revealed differences in the total bacterial and diazotrophic community in two consecutive years. Analysis of the expression of nifH at Station I showed a discrepancy between the present and the active diazotrophic community. Transcript abundances of the different diazotrophs changed over a 24-h cycle and were dominated by cyanobacterial lineages in the daytime, while Gammaproteobacteria peaked at night. These variations might be responsible for the pattern in nitrogenase activity observed in these mats.

Seasonal analyses of arbuscular mycorrhizae, nitrogen-fixing bacteria and growth performance of the salt marsh grass Spartina patens

Seasonal variation of arbuscular mycorrhizal fungi (AMF) in roots of the high salt marsh plant Spartina patens, the diversity of nitrogen-fixing bacteria in the rhizosphere and plant growth performance was studied at key stages of the growing season coinciding with major plant phenological stages, i.e., vegetative growth, reproduction and senescence. AMF colonization was highest during vegetative growth, with values declining during the growing season to the same level seen at plant dormancy. AMF colonization was reduced at lower depths in the sediments where anoxic conditions were observed and in plants treated with the systemic fungicide Benomyl. Only small changes in diversity of nitrogen-fixing bacteria in general and more specifically of those belonging to the e-subdivision of Proteobacteria were detected during the season or between treatments by PCR-RFLP of nifH gene fragments with DNA as template for amplification; however, greater seasonal changes were displayed when cDNA was used as template for amplification as a proxy for gene expression and thus active bacteria. DGGE analyses of nifH gene fragments representing nitrogen-fixing bacteria of the e-subdivision of Proteobacteria using both using DNA and cDNA as template showed highly diverse profiles that changed during the season and in response to treatment. Seasonal changes were observed for a suite of plant growth attributes and differences were observed between treatments, with higher values generally obtained on non-treated plants compared to Benomyl-treated plants. These differences were most pronounced during vegetative growth; however, differences between non-treated and Benomyl-treated plants were reduced seasonally and disappeared by the onset of senescence. This study demonstrates seasonal changes in AMF colonization on S. patens and in the community structure of nitrogen-fixing members of the e-subdivision of Proteobacteria in the plant root zone. Plant growth performance changed seasonally with some effects of Benomyl-treatment.

Diversity ofnifHgene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). The nifH gene was amplified directly from DNA extracted from the rhizospheres, and the PCR products cloned and sequenced. Four clone libraries were generated from the nifH fragments and 245 sequences were obtained. Most of the clones (57%) were closely related to nifH genes of uncultured bacteria. NifH clones affiliated with Azohydromonas spp., Ideonella sp., Rhizobium etli and Bradyrhizobium sp. were found in all libraries. Sequences affiliated with Delftia tsuruhatensis were found in the rhizosphere of both cultivars sown with high levels of nitrogen, while clones affiliated with Methylocystis sp. were detected only in plants sown under low levels of nitrogen. Moreover, clones affiliated with Paenibacillus durus could be found in libraries from the cultivar IS 5322-C sown either in high or low amounts of fertilizer. This study showed that the amount of nitrogen used for fertilization is the overriding determinative factor that influenced the nitrogen-fixing community structures in sorghum rhizospheres cultivated in Cerrado soil.

Distribution of Extensive nifH Gene Diversity Across Physical Soil Microenvironments

The diversity of nitrogen-fixing bacteria is well described for aquatic environments; however, terrestrial analyses remain mostly biased to rhizobial plant-microbe associations. We maximized the level of resolution for this study through the use of nucleotide sequence information extracted from a series of soil microenvironments, ranging from macroaggregates at 2000 microm to the clay fraction at < 75 microm in diameter. In addition, we attempted to create an overview of the distribution of terrestrial nitrogen fixers across such microenvironments by combining culture-independent techniques with a suite of natural soil environments from uniquely different origins. Soil diazotroph diversity was analyzed phylogenetically for 600 terrestrial nifH sequences from 12 midsized clone libraries based on microenvironments of three separate soils across a global scale. Statistical analyses of nifH gene clone libraries were used to estimate coverage, establish degrees of sequence overlap, and compare cluster distributions. These analyses revealed an extensive diversity in a tropical (19 phylotypes) and an arctic soil (17 phylotypes), and moderate diversity in a temperate soil (11 phylotypes). Within each soil, comparisons across aggregate size fractions delineated nifH gene cluster shifts within populations and degrees of sequence overlap that ranged from significantly different (arctic, tropical) to significantly similar (temperate). We suggest that this is due to population separation across aggregates of different size classes, which results from differences in the temporal stability of aggregates as niches for microbial communities. This study not only provides new knowledge of the arrangement of diazotrophic communities at the soil microscale, but it also contributes to the underrepresented knowledge of soil nifH sequences in the public databases.