Influence of Different Cultivars on Populations of Ammonia-Oxidizing Bacteria in the Root Environment of Rice

Briones, Aurelio; Okabe, Satoshi; Umemiya, Yoshiaki; Ramsing, Niels B.; Reichardt, Wolfgang; Okuyama, Hidetoshi

doi:10.1128/aem.68.6.3067-3075.2002

Cited by 152 publications

(106 citation statements)

References 59 publications

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“…Studies from a variety of habitats document that AOB communities vary over space (Kowalchuk and Stephen, 2001) and that this variation is correlated with a variety of factors, including salinity (Stehr et al, 1995;Sahan and Muyzer, 2008), temperature (Avrahami and Conrad, 2005;Fierer et al, 2009), nutrients (Webster et al, 2002;Mosier and Francis, 2008), plant composition (Briones et al, 2002;Mintie et al, 2003;Dollhopf et al, 2005), soil moisture (Hastings et al, 2000) and pH (Kowalchuk et al, 2000;Nicol et al, 2008). Field experiments confirm that pH (Stephen et al, 1998;Backman et al, 2003) and nitrogen availability (Phillips et al, 2000;Webster et al, 2002) can directly influence AOB composition and/or abundance.…”

Section: Introductionmentioning

confidence: 61%

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

et al. 2010

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Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

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Section: Introductionmentioning

confidence: 61%

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

et al. 2010

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“…In other cases in which statistical significance were demonstrated, differences were approximately twofold. It is generally and reasonably believed that for changes in microorganism populations to be biologically significant, differences in numbers need to be at least by a power of 10 (Curl and Truelove 1986;Briones et al 2002). However, trends also have drawn notice (Gu and Mazzola 2003;McSpadden-Gardener 2007) and, especially in field studies, even statistical significance may have been difficult to demonstrate (Schwerinski et al 2007).…”

Section: Discussionmentioning

confidence: 99%

Effect of sorghum seedlings, and previous crop, on soil fluorescent Pseudomonas spp.

2008

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Hypotheses in which sorghum seedlings [Sorghum bicolor (L.) Moench] of different genotypes will differentially modify soil microorganisms and will affect subsequent planting of wheat (Triticum aestivum L.) seedlings, were tested. Wheat cultivar Lewjain, and sorghum genotypes Redlan and RTx433, were planted into soils previously planted with wheat or sorghum in growth chamber experiments. Total culturable fungi and oomycetes, and fluorescent Pseudomonas spp. numbers (cfu) were determined. Pseudomonads were screened for hydrogen cyanide (HCN) production, for the presence of the phlD gene for 2,4-diacetylphloroglucinol production (Phl) and for a region of the operon involved in phenazine-1-carboxylic acid (PCA) production. Pasteurized soils were inoculated with rifampicin-marked strains of Pseudomonas fluorescens then planted with Lewjain, Redlan and RTx433 to assess rhizosphere and soil colonization. Effects of plant species, sorghum genotype and previous crop on culturable fungi and oomycetes, and pseudomonad numbers (cfu g −1 soil) were statistically significant. Soils planted with RTx433 or Lewjain had greater numbers of fungal cfu than soils planted with Redlan. When Lewjain seedlings were grown in soil previously planted with RTx433, there were greater numbers of fungal cfu than when Lewjain was planted into Redlan soil. Wheat planted into wheat soil resulted in statistically significantly fewer numbers of pseudomonads than when planted into sorghum soil. Overall, percentages of HCN-producing pseudomonads increased, especially when wheat seedlings were planted in wheat soil. For most treatments, percent of isolates with Phl declined, except when Redlan was planted into Redlan soil, which resulted in increased Phl isolates. When rifampicin-marked P. fluorescens isolates were applied to pasteurized soil, sorghum seedlings sustained rhizosphere and soil populations similar to those on wheat. Sorghum genotypes may differ in associations with soil microorganisms, Plant Soil

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“…Thus in rice, water uptake is hydraulic in nature and oxygen losses are diffusive (Colmer et al 1998). Some rice cultivars were found to allow oxygen diffusion from aerenchyma to outer surface of roots in order to keep the rhizosphere aerobic during anoxia (Briones et al 2002). Lack of induction of the barrier to radial oxygen loss is also a positive response of aerenchyma formation to hypoxia and ethylene.…”

Section: Soil Waterlogging and Aerenchyma Developmentmentioning

confidence: 99%

Lysigenous aerenchyma formation involves non-apoptotic programmed cell death in rice (Oryza sativa L.) roots

Joshi

Kumar

2011

Physiol Mol Biol Plants

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In waterlogged soil, deficiency of oxygen triggers development of aerenchyma in roots which facilitates gas diffusion between roots and the aerial environment. However, in contrast to other monocots, roots of rice (Oryza sativa L.) constitutively form aerenchyma even in aerobic conditions. The formation of cortical aerenchyma in roots is thought to occur by either lysigeny or schizogeny. Schizogenous aerenchyma is developed without cortical cell death. However, lysigenous gas-spaces are formed as a consequence of senescence of specific cells in primary cortex followed by their death due to autolysis. In the last stage of aerenchyma formation, a 'spoked wheel' arrangement is observed in the cortical region of root. Ultrastructural studies show that cell death is constitutive and no characteristic cell structural differentiation takes place in the dying cells with respect to surrounding cells. Cell collapse initiation occurs in the center of the cortical tissues which are characterized by shorter with radically enlarged diameter. Then, cell death proceeds by acidification of cytoplasm followed by rupturing of plasma membrane, loss of cellular contents and cell wall degradation, while cells nuclei remain intact. Dying cells releases a signal through symplast which initiates cell death in neighboring cells. During early stages, middle lamella-degenerating enzymes are synthesized in the rough endoplasmic reticulum which are transported through dictyosome and discharged through plasmalemma beneath the cell wall. In rice several features of root aerenchyma formation are analogous to a gene regulated developmental process called programmed cell death (PCD), for instance, specific cortical cell death, obligate production of aerenchyma under environmental stresses and early changes in nuclear structure which includes clumping of chromatin, fragmentation, disruption of nuclear membrane and apparent engulfment by the vacuole. These processes are followed by crenulation of plasma membrane, formation of electron-lucent regions in the cytoplasm, tonoplast disintegration, organellar swelling and disruption, loss of cytoplasmic contents, and collapse of cell. Many processes in lysing cells are structural features of apoptosis, but certain characteristics of apoptosis i.e., pycnosis of the nucleus, plasma membrane blebbing, and apoptotic bodies formation are still lacking and thus classified as non-apoptotic PCD. This review article, describes most recent observations alike to PCD involved in aerenchyma formation and their systematic distributions in rice roots.

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Influence of Different Cultivars on Populations of Ammonia-Oxidizing Bacteria in the Root Environment of Rice

Cited by 152 publications

References 59 publications

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

Effect of sorghum seedlings, and previous crop, on soil fluorescent Pseudomonas spp.

Lysigenous aerenchyma formation involves non-apoptotic programmed cell death in rice (Oryza sativa L.) roots

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