Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

Acosta-Martínez, Verónica; Dowd, Scot E.; Sun, Yan-Yan; Allen, V. G.

doi:10.1016/j.soilbio.2008.07.022

Cited by 437 publications

(306 citation statements)

References 31 publications

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“…The bacterial and fungal community composition at the phylum (Table 6) and genus levels (Tables S1 & S2) in rhizosphere soils of P. notoginseng generally corresponded with previous studies carried out in agricultural or other soil types for bacteria by deep 16S rRNA pyrosequencing (Acosta-Martinez et al 2008;Roesch et al 2007), and for fungi by ITS sequencing (Buee et al 2009). Furthermore, the main bacterial and fungal phyla found in roots were in general accordance with those in rhizosphere soils.…”

Section: Discussionsupporting

confidence: 85%

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

Hao

Zeng

et al. 2015

Antonie van Leeuwenhoek

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Rhizosphere and root-associated microbial communities are known to be related to soil-borne disease and plant health. In the present study, the microbial communities in rhizosphere soils and roots of both healthy and diseased Panax notoginseng were analyzed by high-throughput sequencing of 16S rRNA for bacteria and 18S rRNA internal transcribed spacer for fungi, to reveal the relationship of microbial community structure with plant health status. In total, 5593 bacterial operational taxonomic units (OTUs) and 963 fungal OTUs were identified in rhizosphere soils, while 1794 bacterial and 314 fungal OTUs were identified from root samples respectively. Principal coordinate analysis separated the microbial communities both in the rhizosphere soils and roots of diseased P. notoginseng from healthy plants. Compared to those of healthy P. notoginseng, microbial communities in rhizosphere soils and roots of diseased plants showed a decrease in alpha diversity. By contrast, bacterial community dissimilarity increased and fungal community dissimilarity decreased in rhizosphere soils of diseased plants, while both bacterial and fungal community dissimilarity in roots showed no significant difference between healthy and diseased plants. Redundancy analysis at the phylum level showed that mycorrhizal colonization and soil texture significantly affected microbial community composition in rhizosphere soils, whereas shoot nutrition status had a significant effect on microbial community composition in root samples. Our study provided strong evidence for the hypothesis that microbial diversity could potentially serve as an indicator for disease outbreak of medicinal plants, and supported the ecological significance of microbial communities in maintaining plant healthy and soil fertility.

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Section: Discussionsupporting

confidence: 85%

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

Hao

Zeng

et al. 2015

Antonie van Leeuwenhoek

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“…The significant decrease in the relative abundance of Burkholderiales (belonging to Betaproteobacteria) at days 80 and 200 compared to day 20 of the incubation period, and the consistent decrease in the relative abundance of Sphingobacteriales (belonging to Bacteroidetes) with increasing amendment time further confirms the copiotrophic/oligotrophic model. The depletion of maize cellulose partly accounts for the decrease of actinobacterial abundance at the later stage of incubation, because Actinobacteria are an important participant in the decomposition of plant cellulose (Acosta-Martinez et al, 2008). Our result that the relative abundance of Firmicutes Statistical R and significance (P) of difference between different groups (organic manure-fertilized and unfertilized soils, stubble-amended and non-amended treatments, low and high moisture levels, and different sampling time) were calculated by analysis of similarities (ANOSIM).…”

Section: Discussionmentioning

confidence: 99%

Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

Lin

Zhang

Zhao

et al. 2015

Applied Soil Ecology

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It is of ecological significance to investigate microbial communities in response to straw amendment and moisture in arable soils. However, in Chinese fluvo-aquic soils, these responses are still poorly understood. We designed an incubation experiment involving two soils with and without the addition of maize stubble at two moisture levels, and bacterial community structure at days 20, 80, and 200 after the start of incubation was assessed via bar-coded pyrosequencing of the 16S rDNA amplicons. In the presence of stubble with identical moisture level, we observed higher bacterial diversity and richness in long-term organic manure-fertilized soil compared with the unfertilized soil at days 20 and 80, which we attributed to the different quality and quantity of organic matter between the two soils. However, there was no significant difference in bacterial diversity and richness between the two soils at day 200, indicating that long-term straw amendment probably lessens the difference in bacterial community structure between the two soils. In the amended soils bacterial diversity, richness, and community composition at 25% of the water-holding capacity distinctly differed from those at 55% of the waterholding capacity, indicating that moisture strongly affects bacterial distribution in the amended soils. As stubble-C availability declined over time, the dominance of copiotrophic population weakened, and oligotrophic population was moderately abundant. Finally, our study suggests that dissolved organic carbon, which drives redistribution in copiotrophic and oligotrophic categories in response to the varying water and stubble-C availability, is a determinant of bacterial community composition in the amended soils.

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“…Graphite targets were made from the DNA and were measured at the Center for AMS at Lawrence Livermore National Laboratory. Multiplex tag-encoded pyrosequencing (32,33) and 454 shotgun metagenomic sequencing were performed to examine the microbial community of the high As well (F6-25.4m). Complete methods are available and all data are described in SI Text.…”

Section: Methodsmentioning

confidence: 99%

Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater

Mailloux

Trembath‐Reichert

Cheung

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

107

103

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Chronic exposure to arsenic (As) by drinking shallow groundwater causes widespread disease in Bangladesh and neighboring countries. The release of As naturally present in sediment to groundwater has been linked to the reductive dissolution of iron oxides coupled to the microbial respiration of organic carbon (OC). The source of OC driving this microbial reduction-carbon deposited with the sediments or exogenous carbon transported by groundwater-is still debated despite its importance in regulating aquifer redox status and groundwater As levels. Here, we used the radiocarbon ( 14 C) signature of microbial DNA isolated from groundwater samples to determine the relative importance of surface and sediment-derived OC. Three DNA samples collected from the shallow, high-As aquifer and one sample from the underlying, low-As aquifer were consistently younger than the total sediment carbon, by as much as several thousand years. This difference and the dominance of heterotrophic microorganisms implies that younger, surface-derived OC is advected within the aquifer, albeit more slowly than groundwater, and represents a critical pool of OC for aquifer microbial communities. The vertical profile shows that downward transport of dissolved OC is occurring on anthropogenic timescales, but bomb 14 C-labeled dissolved OC has not yet accumulated in DNA and is not fueling reduction. These results indicate that advected OC controls aquifer redox status and confirm that As release is a natural process that predates human perturbations to groundwater flow. Anthropogenic perturbations, however, could affect groundwater redox conditions and As levels in the future.A quifer redox status is a major factor affecting groundwater composition and its suitability for human consumption. The most egregious example is the dire health impact of elevated levels of arsenic (As) in groundwater drawn with inexpensive handpumped tube wells by more than 100 million villagers across South, Southeast, and East Asia (1, 2). Aquifer redox status is largely controlled by microbial respiration of organic carbon (OC) coupled to the utilization of terminal electron acceptors. Reduction of iron (Fe) oxides containing As coupled with the oxidation of OC is the dominant process causing the accumulation of As in groundwater (1), but there is no consensus on the source of OC that fuels these transformations. Such information is critical to understanding subsurface carbon cycling, redox reactions, and the vulnerability of groundwater aquifers to perturbation.Human perturbations have long been suggested to exacerbate the problem of elevated As in groundwater in several ways. Given the connectivity between contaminated surface waters and aquifers, widespread pumping could redistribute As from the surface to depth (3, 4) or between aquifers (5). This pumping could potentially also deliver reactive OC from ponds and latrines to depth, causing microbial reduction and As release (3, 4). Fluorescent spectra of dissolved organic carbon (DOC), correlations between sedimentary ...

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Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

Cited by 437 publications

References 31 publications

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

Bacterial community structure in maize stubble-amended soils with different moisture levels estimated by bar-coded pyrosequencing

Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater

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