scholarly journals Nitrogen Fixing and Phosphate Mineralizing Bacterial Communities in Sweet Potato Rhizosphere Show a Genotype-Dependent Distribution

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 231 ◽  
Author(s):  
Joana Montezano Marques ◽  
Jackeline Rossetti Mateus ◽  
Thais Freitas da Silva ◽  
Camila Rattes de Almeida Couto ◽  
Arie Fitzgerald Blank ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Permutation Test ◽  
Nifh Gene ◽  
Gene Copy ◽  
Nitrogen Fixing ◽  
Phosphate Mineralization

We hypothesize that sweet potato genotypes can influence the bacterial communities related to phosphate mineralization and nitrogen fixation in the rhizosphere. Tuberous roots of field-grown sweet potato from genotypes IPB-149, IPB-052, and IPB-137 were sampled three and six months after planting. The total community DNA was extracted from the rhizosphere and analyzed by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR), based on the alkaline phosphatase coding gene (alp gene) and on the nitrogenase coding gene (nifH gene). The cluster analysis based on DGGE showed that plant age slightly influenced the bacterial community related to phosphate mineralization in the rhizosphere of IPB-137, although it did not affect the bacterial community related to nitrogen fixation. The statistical analysis of DGGE fingerprints (Permutation test, p ≤ 0.05) showed that nitrogen-fixing bacterial community of IPB-052 statistically differed from genotypes IPB-149 and IPB-137 after six months of planting. The bacterial community of IPB-137 rhizosphere analyzed by alp gene also showed significant differences when compared to IPB-149 in both sampling times (p ≤ 0.05). In addition, alp gene copy numbers significantly increased in abundance in the rhizosphere of IPB-137 after six months of planting. Therefore, plant genotype should be considered in the biofertilization of sweet potato.

scholarly journals Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra

2019 ◽  
Author(s):  
Ingeborg J. Klarenberg ◽  
Christoph Keuschnig ◽  
Ana J. Russi Colmenares ◽  
Denis Warshan ◽  
Anne D. Jungblut ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
The Arctic ◽  
Gene Copy ◽  
Nitrogen Fixing ◽  
Moss Species

AbstractBacterial communities form the basis of biogeochemical processes and determine plant growth and health. Mosses, an abundant plant group in Arctic ecosystems, harbour diverse bacterial communities that are involved in nitrogen fixation and carbon cycling. Global climate change is causing changes in aboveground plant biomass and shifting species composition in the Arctic, but little is known about the response of the moss microbiome. Here, we studied the total and potentially active bacterial community associated with Racomitrium lanuginosum, a common moss species in the Arctic, in response to 20-year in situ warming in an Icelandic heathland. We evaluated changes in moss bacterial community composition and diversity. Further, we assessed the consequences of warming for nifH gene copy numbers and nitrogen-fixation rates. Long-term warming significantly changed both the total and the potentially active bacterial community structure. The relative abundance of Proteobacteria increased, while the relative abundance of Cyanobacteria and Acidobacteria decreased. While warming did not affect nitrogen-fixation rates and nifH gene abundance, we did find shifts in the potentially nitrogen-fixing community, with Nostoc decreasing and non-cyanobacterial diazotrophs increasing in relative abundance. Our data suggests that the moss microbial community and the potentially nitrogen-fixing taxa are sensitive to future warming.

scholarly journals High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

2013 ◽  
Vol 10 (8) ◽  
pp. 5589-5600 ◽  
Author(s):  
X. S. Tai ◽  
W. L. Mao ◽  
G. X. Liu ◽  
T. Chen ◽  
W. Zhang ◽  
...  
Keyword(s):  
Water Conservation ◽  
Bacterial Communities ◽  
Nifh Gene ◽  
Qilian Mountains ◽  
Northwestern China ◽  
Heihe River ◽  
Meadow Soil ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Gene Copies

Abstract. Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China), located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon–Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs) of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Redundancy analysis (RDA) revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial communities beneath Potentilla were different from those beneath Carex.

Endophytic nitrogen fixation – a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites

2019 ◽  
Vol 95 (11) ◽  
Author(s):  
Kiran Preet Padda ◽  
Akshit Puri ◽  
Chris Chanway
Keyword(s):  
Nitrogen Fixation ◽  
Lodgepole Pine ◽  
Nifh Gene ◽  
Control Treatment ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Mining Sites ◽  
Greenhouse Study ◽  
Gravel Mining ◽  
Pine Trees

ABSTRACT Lodgepole pine (Pinus contorta var. latifolia) trees have been thriving on unreclaimed gravel mining sites in British Columbia, Canada, with tissue nitrogen-content and growth-rate unaffected by extremely low soil nitrogen-levels. This indicates that pine trees could be accessing a hidden nitrogen source to fulfill their nitrogen requirements – possibly via endophytic nitrogen-fixation. Endophytic bacteria originally isolated from native pine trees growing at gravel sites were selected (n = 14) for in vitro nitrogen-fixation assays and a year long greenhouse study to test the overall hypothesis that naturally occurring endophytic nitrogen-fixing bacteria sustain pine tree growth under nitrogen-limited conditions. Each of the 14 bacteria colonized the internal tissues of pine trees in the greenhouse study and fixed significant amounts of nitrogen from atmosphere (23%–53%) after one year as estimated through 15N isotope dilution assay. Bacterial inoculation also significantly enhanced the length (31%–64%) and biomass (100%–311%) of pine seedlings as compared to the non-inoculated control treatment. In addition, presence of the nifH gene was confirmed in all 14 bacteria. Our results support the possibility that pine trees associate with nitrogen-fixing bacteria, capable of endophytic colonization, to survive at unreclaimed gravel mining pits and this association could potentially be utilized for effective reclamation of highly disturbed sites in a sustainable manner.

scholarly journals Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3077 ◽  
Author(s):  
Katerin Almendras ◽  
Jaime García ◽  
Margarita Carú ◽  
Julieta Orlando
Keyword(s):  
Bacterial Communities ◽  
Fragment Length Polymorphism ◽  
Multivariate Analyses ◽  
Nifh Gene ◽  
Shannon Index ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Symbiotic Interaction ◽  
Different Types ◽  
Terricolous Lichens

Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.

Effects of Long-Term Elevated CO2 on Rhizosphere and Bulk Soil Bacterial Community Structure in Pinus sylvestriformis Seedlings Fields

2011 ◽  
Vol 343-344 ◽  
pp. 351-356
Author(s):  
Xia Jia ◽  
Chun Juan Zhou
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pinus Sylvestriformis ◽  
Soil Bacterial Community Structure ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain

The effect of long-term elevated CO2(as open top chambers) on rhizosphere and bulk bacterial community structure in Pinus sylvestriformis seedlings field was investigated in July, August, and September. The bacterial communities were processed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA fragments amplified by PCR (Polymerase Chain Reaction) from DNA extracted directly from soil. DGGE profiles from rhizosphere samples showed large changes in rhizosphere bacterial community under elevated CO2compared to ambient except for that in September. For bulk samples, bacterial community structure changed when exposed to elevated CO2in three months. With the exception of bulk samples in August, a similitude of bacterial communities structures existed between different elevated CO2concentrations by analyzing UPGMA dendrogram based on Jaccard’s coefficient.

scholarly journals mRNA Extraction and Reverse Transcription-PCR Protocol for Detection of nifH Gene Expression by Azotobacter vinelandii in Soil

2003 ◽  
Vol 69 (4) ◽  
pp. 1928-1935 ◽  
Author(s):  
Helmut Bürgmann ◽  
Franco Widmer ◽  
William V. Sigler ◽  
Josef Zeyer
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Reverse Transcription ◽  
Liquid Culture ◽  
Azotobacter Vinelandii ◽  
Nifh Gene ◽  
Rna Extraction ◽  
Soil Microbial Communities ◽  
Nitrogen Fixing ◽  
Reverse Transcription Pcr

ABSTRACT The study of free-living nitrogen-fixing organisms in bulk soil is hampered by the great diversity of soil microbial communities and the difficulty of relating nitrogen fixation activities to individual members of the diazotroph populations. We developed a molecular method that allows analysis of nifH mRNA expression in soil in parallel with determinations of nitrogen-fixing activity and bacterial growth. In this study, Azotobacter vinelandii growing in sterile soil and liquid culture served as a model system for nifH expression, in which sucrose served as the carbon source and provided nitrogen-limited conditions, while amendments of NH4NO3 were used to suppress nitrogen fixation. Soil RNA extraction was performed with a new optimized direct extraction protocol that yielded nondegraded total RNA. The RNA extracts were of high purity, free of DNA contamination, and allowed highly sensitive and specific detection of nifH mRNA by a reverse transcription-PCR. The level of nifH gene expression was estimated by PCR amplification of reverse-transcribed nifH mRNA fragments with A. vinelandii-specific nifH primers. This new approach revealed that nifH gene expression was positively correlated with bulk nitrogen fixation activity in soil (r 2 = 0.72) and in liquid culture (r 2 = 0.84) and therefore is a powerful tool for studying specific regulation of gene expression directly in the soil environment.

scholarly journals Seasonal changes in bacterial communities associated with healthy and diseasedPoritescoral in southern Taiwan

2016 ◽  
Vol 62 (12) ◽  
pp. 1021-1033 ◽  
Author(s):  
Chorng-Horng Lin ◽  
Chih-Hsiang Chuang ◽  
Wen-Hung Twan ◽  
Shu-Fen Chiou ◽  
Tit-Yee Wong ◽  
...  
Keyword(s):  
Health Status ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Southern Taiwan ◽  
The 16S Rrna Gene

We compared the bacterial communities associated with healthy scleractinian coral Porites sp. with those associated with coral infected with pink spot syndrome harvested during summer and winter from waters off the coast of southern Taiwan. Members of the bacterial community associated with the coral were characterized by means of denaturing gradient gel electrophoresis (DGGE) of a short region of the 16S rRNA gene and clone library analysis. Of 5 different areas of the 16S rRNA gene, we demonstrated that the V3 hypervariable region is most suited to represent the coral-associated bacterial community. The DNA sequences of 26 distinct bands extracted from DGGE gels and 269 sequences of the 16S rRNA gene from clone libraries were determined. We found that the communities present in diseased coral were more heterogeneous than the bacterial communities of uninfected coral. In addition, bacterial communities associated with coral harvested in the summer were more diverse than those associated with coral collected in winter, regardless of the health status of the coral. Our study suggested that the compositions of coral-associated bacteria communities are complex, and the population of bacteria varies greatly between seasons and in coral of differing health status.

scholarly journals Bacteria diversity and microbial biomass in forest, pasture and fallow soils in the southwestern Amazon basin

2009 ◽  
Vol 33 (4) ◽  
pp. 907-916 ◽  
Author(s):  
Karina Cenciani ◽  
Marcio Rodrigues Lambais ◽  
Carlos Clemente Cerri ◽  
Lucas Carvalho Basílio de Azevedo ◽  
Brigitte Josefine Feigl
Keyword(s):  
Microbial Biomass ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Amazon Basin ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Chemical Properties ◽  
Total Carbon ◽  
Wet Season ◽  
Al Content ◽  
C And N

It is well-known that Amazon tropical forest soils contain high microbial biodiversity. However, anthropogenic actions of slash and burn, mainly for pasture establishment, induce profound changes in the well-balanced biogeochemical cycles. After a few years the grass yield usually declines, the pasture is abandoned and is transformed into a secondary vegetation called "capoeira" or fallow. The aim of this study was to examine how the clearing of Amazon rainforest for pasture affects: (1) the diversity of the Bacteria domain evaluated by Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE), (2) microbial biomass and some soil chemical properties (pH, moisture, P, K, Ca, Mg, Al, H + Al, and BS), and (3) the influence of environmental variables on the genetic structure of bacterial community. In the pasture soil, total carbon (C) was between 30 to 42 % higher than in the fallow, and almost 47 % higher than in the forest soil over a year. The same pattern was observed for N. Microbial biomass in the pasture was about 38 and 26 % higher than at fallow and forest sites, respectively, in the rainy season. DGGE profiling revealed a lower number of bands per area in the dry season, but differences in the structure of bacterial communities among sites were better defined than in the wet season. The bacterial DNA fingerprints in the forest were stronger related to Al content and the Cmic:Ctot and Nmic:Ntot ratios. For pasture and fallow sites, the structure of the Bacteria domain was more associated with pH, sum of bases, moisture, total C and N and the microbial biomass. In general microbial biomass in the soils was influenced by total C and N, which were associated with the Bacteria domain, since the bacterial community is a component and active fraction of the microbial biomass. Results show that the genetic composition of bacterial communities in Amazonian soils changed along the sequence forest-pasture-fallow.

scholarly journals Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill

2009 ◽  
Vol 75 (11) ◽  
pp. 3407-3418 ◽  
Author(s):  
Jorge Alonso-Gutiérrez ◽  
Antonio Figueras ◽  
Joan Albaigés ◽  
Núria Jiménez ◽  
Marc Viñas ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Oil Spill ◽  
Bacterial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Mycolic Acids ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis ◽  
Northwestern Spain

ABSTRACT The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.

scholarly journals Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis

2002 ◽  
Vol 68 (10) ◽  
pp. 5142-5150 ◽  
Author(s):  
Hiroyuki Sekiguchi ◽  
Masataka Watanabe ◽  
Tadaatsu Nakahara ◽  
Baohua Xu ◽  
Hiroo Uchiyama
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Clone Library ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Changjiang River ◽  
The Changjiang River ◽  
Clone Library Analysis ◽  
Gradient Gel Electrophoresis

ABSTRACT Bacterial community structure along the Changjiang River (which is more than 2,500 km long) was studied by using denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal bacterial primer sets. DGGE profiles and principal-component analysis (PCA) demonstrated that the bacterial community gradually changed from upstream to downstream in both 1998 and 1999. Bacterial diversity, as determined by the Shannon index (H′), gradually decreased from upstream to downstream. The PCA plots revealed that the differences in the bacterial communities among riverine stations were not appreciable compared with the differences in two adjacent lakes, Lake Dongting and Lake Poyang. The relative stability of the bacterial communities at the riverine stations was probably due to the buffering action of the large amount of water flowing down the river. Clone library analysis of 16S rDNA revealed that the dominant bacterial groups changed from β-proteobacteria and the Cytophaga-Flexibacter-Bacteroides group upstream to high-G+C-content gram-positive bacteria downstream and also that the bacterial community structure differed among the stations in the river and the lakes. The results obtained in this study should provide a reference for future changes caused by construction of the Three Gorges Dam.

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