Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil

Poly, Franck; Monrozier, L. Jocteur; Bally, René

doi:10.1016/s0923-2508(00)01172-4

Cited by 713 publications

(555 citation statements)

References 25 publications

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“…20 ng). For the nifH gene, Power SYBR green master mix was used (12.5 ml) (Applied Biosystems), and 0.25 mM each of primer FGPH19 (Simonet et al, 1991) and primer PolR (Poly et al, 2001). The amplification reactions were performed with an initial denaturation step at 95 1C for 15 min, followed by 30 cycles of 94 1C (1 min), 55 1C (27 s) and 72 1C (1 min).…”

Section: Community Dna Extractionmentioning

confidence: 99%

“…Analysis of the structure of diazotrophic communities by PCR-DGGE The total DNA extracted from all coral samples was subjected to amplification using nifH-specific primers, as described in the literature (Simonet et al, 1991;Poly et al, 2001) for DGGE analysis of nifH genes (Pereira e Silva et al, 2011). The amplicons obtained were checked on agarose gels before DGGE analysis.…”

Section: Community Dna Extractionmentioning

confidence: 99%

“…One clone library was constructed for each subregion of sampling points, given the high similarity of replicates in DGGE analysis. The template DNA was subjected to amplification with the nifH gene primers FGPH19 (Simonet et al, 1991) and PolR (Poly et al, 2001), according to previously described methodology (Taketani et al, 2009). The amplicons were purified using the Wizard SV gel and PCR clean-up system (Promega, Madison, WI, USA) and cloned in plasmid pGEM-T using the pGEM-T Easy Vector system kit (Promega) according to the manufacturer's instructions.…”

Section: Construction and Analysis Of Nifh Gene Clone Librariesmentioning

confidence: 99%

See 2 more Smart Citations

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

Santos

Carmo

Duarte³

et al. 2014

The ISME Journal

124

111

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Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study investigated the effects of increased seawater temperature on bacteria able to fix nitrogen (diazotrophs) that live in association with the mussid coral Mussismilia harttii. Consistent increases in diazotroph abundances and diversities were found at increased temperatures. Moreover, gradual shifts in the dominance of particular diazotroph populations occurred as temperature increased, indicating a potential future scenario of climate change. The temperature-sensitive diazotrophs may provide useful bioindicators of the effects of thermal stress on coral reef health, allowing the impact of thermal anomalies to be monitored. In addition, our findings support the development of research on different strategies to improve the fitness of corals during events of thermal stress, such as augmentation with specific diazotrophs.

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Section: Community Dna Extractionmentioning

confidence: 99%

Section: Community Dna Extractionmentioning

confidence: 99%

Section: Construction and Analysis Of Nifh Gene Clone Librariesmentioning

confidence: 99%

See 1 more Smart Citation

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

Santos

Carmo

Duarte³

et al. 2014

The ISME Journal

124

111

View full text Add to dashboard Cite

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“…Reaction mixtures were heated to 95°C for 15 min before completing 40 cycles of denaturation (95°C, 15 s), annealing (60°C, 30 s) and extension (72°C, 15 s) with the Applied biosystems Viia7 (USA). PolF and PolR primers were used for nifH qPCR [16]. For normalization, 16S rRNA gene was chosen and 357F/518R primers were consumed.…”

Section: Rna Extraction and Real Time Pcrmentioning

confidence: 99%

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

Sharma

Singh

2016

Indian J Microbiol

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

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“…The 16S rRNA gene sequence was amplified using PCR with two sets of universal bacterial primers, 27F (5¢-AGAGTTTGATCMTGGCTCAG-3¢) and 1492R (5¢-TACGYTACCTTGTTACGACTT-3¢), as well as 518F (5¢-CCAGCAGCCGCGGTAATACG-3¢) and 800R (5¢-TACCAGGGTATCTAATCC-3¢) [12]. The PolF (5¢-TGCGAYCCSAARGCBGACTC-3¢) and PolR (5¢-ATSGC-CATCATYTCRCCGGA-3¢) primer set was used for the PCR of the nifH gene as described by Poly et al [13]. Sequencing of the 16S rRNA gene was conducted as described previously [14].…”

mentioning

confidence: 99%

Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil

Kim

Kang

Ahn

2017

International Journal of Systematic and Evolutionary Microbiology

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A novel aerobic, Gram-stain-negative and non-motile bacterial strain, designated ED7 T , was isolated from grass-field soil in Cheonan, Korea. Strain ED7 T utilized methanol and methylamine, but not formate, as carbon and energy sources. The strain was able to grow at 20-42 C (optimum 30-35 C), at pH 7.0-8.5 (optimum pH 7.5-8.0), and in the absence of NaCl. According to the similarities of the 16S rRNA gene sequences, strain ED7 T was most closely related to the genera Labrenzia ( 93.3 % 16S rRNA gene sequence similarity), Pleomorphomonas ( 93.1 %) and Prosthecomicrobium ( 93.1 %). A phylogenetic analysis based on the 16S rRNA gene sequence of strain ED7 T revealed that it was affiliated with the family Methylocystaceae, being most closely related to the genus Pleomorphomonas. In contrast to Pleomorphomonas koreensis and Pleomorphomonas oryzae, strain ED7 T did not contain the nifH gene. The DNA G+C content of the genomic DNA of strain ED7 T was 71.8 mol%.The predominant fatty acids of strain ED7 T were summed feature 8 (C 18 : 1 !7c and/or C 18 : 1 !6c), summed feature 2 (C 14 : 0 3-OH, and/or C 16 : 1 iso I), 11-methyl C 18 : 1 !7c and C 16 : 0 3-OH. The major isoprenoid quinone was ubiquinone 10 (Q-10). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. Based on phenotypic, chemotaxonomic and genotypic characteristic data, strain ED7 T could be differentiated from other genera, suggesting that strain ED7 T represents a novel species of a new genus in the family Methylocystaceae, for which the name Chthonobacter albigriseus gen. nov., sp. nov. is proposed. The type strain of the type species is ED7 T (=JCM 30603 T =KCTC 42450 T ).

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Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil

Cited by 713 publications

References 25 publications

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

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

Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil

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