Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR–denaturing gradient gel electrophoresis

Abstract

Culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) was employed to assess the composition of diazotroph species from the sediments of three mangrove ecosystem sites in Sanya, Hainan Island, China. A strategy of removing humic acids prior to DNA extraction was conducted, then total community DNA was extracted using the soil DNA kit successfully for nifH PCR amplification, which simplified the current procedure and resulted in good DGGE profiles. The results revealed a novel nitrogen-fixing bacterial profile and fundamental diazotrophic biodiversity in mangrove sediments, as reflected by the numerous bands present DGGE patterns. Canonical correspondence analysis (CCA) revealed that the sediments organic carbon concentration and available soil potassium accounted for a significant amount of the variability in the nitrogen-fixing bacterial community composition. The predominant DGGE bands were sequenced, yielding 31 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were from Proteobacteria, e.g. alpha, gamma, beta, delta-subdivisions, and characterized by sequences of members of genera Azotobacter, Desulfuromonas, Sphingomonas, Geobacter, Pseudomonas, Bradyrhizobium and Derxia. These results significantly expand our knowledge of the nitrogen-fixing bacterial diversity of the mangrove environment.

Spatial variability of cyanobacterial community composition in Sanya Bay as determined by DGGE fingerprinting and multivariate analysis

“…The DGGE fingerprint results for the surface waters and bottom waters communities were analyzed according to the method prescribed by Zhang et al [26]. The band positions and intensities were both considered.…”

Microbial community shift with decabromodiphenyl ether (BDE 209) in sediments of the Pearl River estuary, China

“…That may cause the detection of low microbial diversity in our DGGE profile (Amann et al 1995). Bacterial community structure can significantly be influenced by the environmental variables, and environmental heterogeneity can drive a taxa-area relationship of bacteria (HornerDevine et al 2004;Zhang et al 2008;Hong et al 2011;Cao et al 2012). CCA has been proven to be sensitive in detecting the relationships between microbial community composition and environmental variables (Iwamoto et al 2000;Zhang et al 2008).…”

“…Bacterial community structure can significantly be influenced by the environmental variables, and environmental heterogeneity can drive a taxa-area relationship of bacteria (HornerDevine et al 2004;Zhang et al 2008;Hong et al 2011;Cao et al 2012). CCA has been proven to be sensitive in detecting the relationships between microbial community composition and environmental variables (Iwamoto et al 2000;Zhang et al 2008). Using the method of CCA, Cao et al (2012) reported that water depth and temperature were major factors shaping the community structure of ammonia-oxidizing β-Proteobacteria from the PRD to the South China Sea.…”

“…The analysis of Shannon index was according to Zhang et al (2008). Briefly, the peak areas of the fingerprint patterns in the DGGE profile were used to indicate the intensities.…”

Bacterial community structure of mangrove sediments in relation to environmental variables accessed by 16S rRNA gene-denaturing gradient gel electrophoresis fingerprinting

“…although a considerable amount is known about how culturable bacteria respond to environmental variables in mangrove ecosystems (Takizaqa et al, 1993;Wu 1993;Wang and hong 2005), little is known about how environmental variables influence the structure of mangrove sediment bacterial communities in situ. in this study, CCa was employed to explore how the changes in microbial community composition varied with environmental conditions, which has been proven to be sensitive in detecting the relationship between bacterial community composition and environmental parameters (iwamoto et al, 2000;Mouser et al, 2005;Jiang et al, 2007;Zhang et al, 2008). The previous studies reported that the cultivable bacteria composition has high similarity between mangrove soils collected from different mangrove areas (shome et al, 1995).…”