<i>nifH</i> gene diversity in the bacterial community associated with the rhizosphere of <i>Molinia coerulea</i>, an oligonitrophilic perennial grass

Hamelin, Jérôme; Fromin, Nathalie; Tarnawski, Sonia Estelle; Teyssier-Cuvelle, S.; Aragno, Michel

doi:10.1046/j.1462-2920.2002.00319.x

Cited by 74 publications

(64 citation statements)

References 31 publications

(49 reference statements)

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“…Moreover, growth of perennial grasses at the same location for several years may lead to the enrichment of the most adapted bacterial populations in both fractions. This was previously observed for dinitrogen-fixing bacteria using a molecular inventory of nifH sequences in a natural meadow [25].…”

Section: Nitrate-dissimilating Pseudomonas Frequency Under Elevated Psupporting

confidence: 74%

“…Lower frequencies of NR Pseudomonas were generally detected in the root fraction (RE) compared to soil (NRS) fraction, for both plants (Fig. 1), with statistically significant differences for some sampling dates ( In the plant-soil systems studied, being for L. perenne cultivated with low N supply [14], or for M. coerulea growing on its native oligotrophic soil [25], the nitrogen availability is clearly limiting. The availability of N is dependant on the N supply (fertilization), N uptake by the plants, and the N transformations, which can imply N losses from the system (i.e., denitrification, leaching).…”

Section: Resultsmentioning

confidence: 95%

“…M. coerulea plants (noted M) originated from a littoral meadow located at the southern shore of Lake Neuchâtel (Cudrefin, Switzerland). The local soil is a gleysol, typic haplaquoll, contained 4.7% clay, 9.5% silt, 85.8% sand, and had a pH [H2O] value of 8.4 [25]. Plants with undisturbed root systems were taken with their surrounding and underlying soil and transferred to the FACE facility in September 1999.…”

Section: Study Site and Plant Materialmentioning

confidence: 99%

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Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

et al. 2005

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A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO 2 content (pCO 2 ) at the Swiss FACE (Free Air CO 2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO 2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO 2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO 2 . Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO 2 treatment.

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Section: Nitrate-dissimilating Pseudomonas Frequency Under Elevated Psupporting

confidence: 74%

Section: Resultsmentioning

confidence: 95%

Section: Study Site and Plant Materialmentioning

confidence: 99%

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Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

et al. 2005

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“…Hamelin et al (2002) indicated that certain plants mediate favourable niches for nitrogen-fixing bacteria. Plant-specific differences in the nitrogen-fixing bacterial community may be related to plant species, biomass, the chemical composition of litter and root exudates (Shaffer et al, 2000;Bürgmann et al, 2005;Hsu and Buckley, 2009;Knelman et al, 2012).…”

Section: S Tai Et Al: High Diversity Of Nitrogen-fixing Bacteriamentioning

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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“…Surveys of nifH diversity in soil commonly reveal sequence types that correspond to the diverse unidentified diazotrophs (Ueda et al, 1995;Widmer et al, 1999;Piceno and Lovell, 2000;Shaffer et al, 2000;Poly et al, 2001). Evidence indicates that these noncultivated diazotrophs, rather than their cultivated cousins, are the dominant N-fixing organisms in many soil systems (Poly et al, 2001;Hamelin et al, 2002;Tan et al, 2003;Buckley et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Evidence for the functional significance of diazotroph community structure in soil

2008

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Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

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nifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass

Cited by 74 publications

References 31 publications

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

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

Evidence for the functional significance of diazotroph community structure in soil

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