Diversity of nitrogenase (nifH) genes pool in soybean field soil after continuous and rotational cropping

Abstract

Diazotrophs diversity in soybean is a topic requiring thorough investigation since the previous researches have focused on only rice, forest, grass, water, etc. In this research, iron-only nitrogenase nifH gene was as genetic marker. PCR-RFLP was used to investigate the difference of diazotrophs community diversity in the soil from the continuous cropping (CC) (the 5-yr tilling of soybean) and the rotational cropping (RC) (soybean-corn) soils in the northeast of China. A total of 36 isolates were genetically characterized. Most of the isolates closely related to Azospirillum and Azotobacter. Eighty-six unique nifH gene sequences were obtained by cloning of the respective PCR products in two soil samples. It was found that the diversity of nifH genes in CC changed obviously compared with RC. Phylogenetic analysis indicated that most of the clones clustered together in a high homogeneity with some sequence retrieved from environmental representatives. The sequence diversity of nifH genes was high and the members of the Alphaproteobacteria were predominant in both samples. The experimental study also revealed the two non-proteobacterial diazotrophs, firmicutes and euryarchaeota. Through this study, it can be assumed that different tillage perhaps affected the nifH gene-containing population diversity.

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach

“…Here, we envisaged the differential distribution of diazotrophs across these habitats by targeting the nifH gene. Although nifH gene-based diazotrophy is considered to be widespread and has been recently addressed in many habitats, such as mangrove sediments (Cavalcante et al, 2012), rhizosphere soil (Chowdhury et al, 2009), soybean field soil (Xiao et al, 2010) and soil microenvironments (Izquierdo & N€ usslein, 2006), knowledge about the nitrogen cycling remains scarce in coastal barren-saline soil environments.…”

“…A few culture‐independent studies have been performed on the functional diversity of nitrogen‐fixing microbial communities in moderate, extreme, terrestrial, bulk and rhizosphere soil environments, such as rice, forest, grasses, soybean and sediments (Hirano et al ., ; Chowdhury et al ., ; Xiao et al ., ; Orr et al ., , ; Cavalcante et al ., ), but has not been equally addressed from saline soil ecosystems (Keshri et al ., ). Keshri et al .…”

“…Changes in different environmental factors, such as soil moisture, oxygen, pH, electrolytic conductivity, and carbon, nitrogen and sulphur contents have been reported to influence nitrogen fixation in soils (Hsu & Buckley, 2009). A few culture-independent studies have been performed on the functional diversity of nitrogen-fixing microbial communities in moderate, extreme, terrestrial, bulk and rhizosphere soil environments, such as rice, forest, grasses, soybean and sediments (Hirano et al, 2001;Chowdhury et al, 2009;Xiao et al, 2010;Orr et al, 2011Orr et al, , 2012Cavalcante et al, 2012), but has not been equally addressed from saline soil ecosystems (Keshri et al, 2013). Keshri et al (2013) focused on only one saline soil and also reported fewer clones (51) and operational taxonomic units (OTUs;20).…”

Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing

“…The fragments of 16S rRNA and nif H genes were amplified using the metagenomic DNA and Super-Therm Taq DNA polymerase (JMR, UK). Primer pair fM1/rC5 was used for amplification of the 16S rRNA gene [ 18 ], and PolF/PolR and PolF/ZehrR pairs were used for amplification of the nif H gene [ 19 , 20 ]. The 5’-fused primer includes an inserted 7 nucleotide ‘barcode’; the barcode is permuted for each sample and allows the identification of individual samples in a mixture in a single pyrosequencing run [ 21 ].…”

The diazotrophic community in oat rhizosphere: effects of legume intercropping and crop growth stage

“…Intercropping increased the population and diversity of the soil bacterial community in the rhizosphere soil more than sole cropping [15,16] . Xiao et al [17] reported that the abundance and diversity of nifH genes showed variations in soil with continuous and rotational soybean cropping. Sampling time also affected the diazotrophic structure in agricultural soil [18] .…”