Recovery and Phylogenetic Analysis of
            <i>nifH</i>
            Sequences from Diazotrophic Bacteria Associated with Dead Aboveground Biomass of
            <i>Spartina alterniflora</i>

Lovell, Charles R.; Friez, Michael J.; Longshore, John; Bagwell, Christopher E.

doi:10.1128/aem.67.11.5308-5314.2001

Cited by 65 publications

(67 citation statements)

References 46 publications

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“…It appears that the sequence diversity in the system was relatively low compared to most estuarine and benthic systems, but the community included components that reflected open ocean, benthic and estuarine origins. Open ocean photic layer microbial communities appear to have lower nifH diversity and different community composition (Zehr et al, 1998) from coastal and estuarine (Jenkins et al, 2004), and benthic communities, including microbial mats (Omoregie et al, 2005), coral reefs (Hewson et al, 2007b) and salt marshes (Lovell et al, 2001;Moisander et al, 2005). However, in the high-diversity coastal and benthic systems, a large proportion of the community nifH genes is not expressed, at least not at detectable levels (Moisander et al, 2006;Man-Aharonovich et al, 2007;Short and Zehr, 2007).…”

Section: Discussionmentioning

confidence: 99%

Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon

et al. 2008

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The spatial heterogeneity of diversity and abundance of diazotrophs were investigated off the Vietnamese coast in the South China Sea (SCS). The study area extended from the Mekong River plume to the shelf region and beyond to stations extending to 1700 m depth. The SCS diazotroph community, based on nifH gene diversity, had components closely related to sequences from open ocean, estuarine, saltmarsh and microbial mat communities. Rarefaction analysis suggested that by using a 97% similarity operational taxonomic unit definition, the majority of nifH sequence diversity in the samples was covered by the 384 nifH clones obtained. The majority of the nifH sequences recovered fell into two clusters: one comprised of Trichodesmium sequences and the other an a-proteobacterial group. Unicellular cyanobacterial groups A and B, and symbiotic filamentous cyanobacterial diazotrophs were detected sporadically. Trichodesmium was by far the most abundant diazotroph, with up to 6 Â 10 5 nifH gene copies per liter. Quantitative PCR probe-primer sets were designed and used to quantify two proteobacterial groups, revealing abundances up to 10 3 -10 4 nifH gene copies per liter, with the highest abundances in the photic zone. Major components of the clone library were also revealed by a nifH microarray and multidimensional scaling (MDS) analysis. MDS showed that samples from the 410 lm size fraction from 0-to 5-m depths clustered separately from the rest of the samples, primarily due to the abundance of Trichodesmium sequences. The SCS diazotroph community has a relatively low diversity and is a mixture of both estuarine and oceanic fingerprints.

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Section: Discussionmentioning

confidence: 99%

Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon

et al. 2008

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“…Hsu and Buckley (2009) found that the nitrogen-fixing bacterial community structure differed across treatments as a function of vegetation biomass. Lovell et al (2001) also demonstrated that differences in the nitrogen-fixing bacterial community are closely associated with vegetation biomass. In the meadow soil beneath Carex, the nifH gene diversity was primarily affected by altitude, while abundance was primarily affected by soil-available K. Zhang et al (2006) found that altitude was one of the key factors influencing the nitrogen-fixing bacterial community in alpine prairie soil.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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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

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“…CV4 was amplified from offshore and oligotrophic stations A, D, E and F and has 99.7% nucleotide sequence similarity to sequences reported in the North Pacific (e.g., EU159536; Fong et al, 2008) and Gulf of Aqaba (DQ825729; Foster et al, 2009a). CV5 (5.1%) is most closely related (90% nucleotide similarity) to a nifH sequence from an uncultivated a-proteobacteria (AF389713) associated with a marsh cordgrass, Spartina alterniflora (Lovell et al, 2001). This phylotype is closely related (88% nucleotide similarity) to a-24809A06, which Moisander et al (2008) used in the design of a qPCR assay, but has too many mismatches in the primer/ probe region to be amplified.…”

Section: Resultsmentioning

confidence: 99%

Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic

et al. 2011

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Expression of nifH in 28 surface water samples collected during fall 2007 from six stations in the vicinity of the Cape Verde Islands (north-east Atlantic) was examined using reverse transcriptionpolymerase chain reaction (RT-PCR)-based clone libraries and quantitative RT-PCR (RT-qPCR) analysis of seven diazotrophic phylotypes. Biological nitrogen fixation (BNF) rates and nutrient concentrations were determined for these stations, which were selected based on a range in surface chlorophyll concentrations to target a gradient of primary productivity. BNF rates greater than 6 nmolN l À1 h À1 were measured at two of the near-shore stations where high concentrations of Fe and PO 4 3À were also measured. Six hundred and five nifH transcripts were amplified by RT-PCR, of which 76% are described by six operational taxonomic units, including Trichodesmium and the uncultivated UCYN-A, and four non-cyanobacterial diazotrophs that clustered with uncultivated Proteobacteria. Although all five cyanobacterial phylotypes quantified in RT-qPCR assays were detected at different stations in this study, UCYN-A contributed most significantly to the pool of nifH transcripts in both coastal and oligotrophic waters. A comparison of results from RT-PCR clone libraries and RT-qPCR indicated that a c-proteobacterial phylotype was preferentially amplified in clone libraries, which underscores the need to use caution interpreting clone-library-based nifH studies, especially when considering the importance of uncultivated proteobacterial diazotrophs.

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Recovery and Phylogenetic Analysis of nifH Sequences from Diazotrophic Bacteria Associated with Dead Aboveground Biomass of Spartina alterniflora

Cited by 65 publications

References 46 publications

Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon

Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon

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

Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic

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