Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique

Tom-Petersen, Andreas; Leser, Thomas D.; Marsh, Terence L.; Nybroe, Ole

doi:10.1016/s0168-6496(03)00192-2

Cited by 74 publications

(76 citation statements)

References 37 publications

(58 reference statements)

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“…Most of the phylotypes belonged to two phyla, the Firmicutes and the Bacteroidetes, irrespective of the anatomical site from where they were isolated. This is consistent with the situation in humans, pigs and mice, where members of the phyla Firmicutes and the Bacteroidetes are also the two largest populations found in the distal gut (Tom-Petersen et al, 2003;Xu et al, 2007). In the tammar wallaby, the two classes of Firmicutes, the Clostridia and the Lactobacillales, represented the largest bacterial populations within the openings of the urogenital and anal tracts, from the point of view of both diversity of phylotypes and the number of clones isolated, a finding that might explain the observations of Ouwerkerk et al (2005), who cultured only Firmicutes from the forestomach of an eastern grey kangaroo.…”

Section: Discussionsupporting

confidence: 90%

The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii

et al. 2008

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The bacterial diversity of the openings of the urogenital and anal tracts of the adult female tammar wallaby, Macropus eugenii, was determined in order to ascertain whether the physical proximity of the openings of these tracts within the cloaca affected the two populations of bacteria. Terminal restriction fragment length polymorphism (T-RFLP) analyses of 42 wallabies identified 81 different terminal fragments, indicative of diverse and complex microbiomes at these anatomical locations. Subsequent amplified rDNA restriction analysis (ARDRA) identified 72 phylotypes from the urogenital tract and 50 from the anal tract. Twenty-two of these phylotypes were common to both tracts. Phylogenetic analysis of sequenced 16S rDNA showed that 83 % of the phylotypes were unidentified species based on the premise that any sequence possessing ,97 % homology to a known bacterial species or phylotype was novel. Thus, despite the close proximity of the openings of the urogenital and anal tracts within the cloaca, the two sites retained a diverse range of distinct bacteria, with only a small percentage of overlapping species. INTRODUCTIONMetatherian (marsupial) mammals offer a unique biological opportunity to investigate the relationship between the microflora of the urogenital and anal tracts. In contrast to eutherian (placental) mammals, which possess separate openings of the digestive and urogenital systems, most marsupials possess a common posterior chamber for these systems -the cloaca (Tyndale-Briscoe, 2005; Fig. 1). This structural feature might imply that bacteria from one tract have easy access to the other. To date, the bacteria associated with these two sites have not been studied in marsupials, although in humans it has been noted that the bacteria of the urogenital tract may vary and can be influenced by bacteria growing in the anal tract and thus occasionally can cause urogenital disease (Reid et al., 2001;Tannock, 1999).The tammar wallaby, Macropus eugenii, is regarded as a model marsupial (Tyndale-Briscoe, 2005) with more than 30 years of fundamental research into its basic biology. Despite this, little is known about the bacterial populations of this animal, all published studies having used culture-based methods that are known to be biased in favour of a small percentage of the total microbiome (Hume, 1999; Lentle et al., 2006;Old & Deane, 1998;Yadav et al., 1972).In this study we used molecular-based methods targeting the 16S rDNA gene to document the bacteria at the openings of the urogenital and anal tracts of 42 female tammar wallabies and undertook a comprehensive comparison of the major phylotypes and their diversity. This is believed to be the first extensive report of the bacterial species within the openings of these two tracts in any marsupial. The results showed that despite the close anatomical proximity of the openings of these tracts, each opening possessed a diverse and complex bacterial population comprising mainly unidentified species.Abbreviations: ARDRA, amplified rDNA restriction analysis; T-...

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Section: Discussionsupporting

confidence: 90%

The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii

et al. 2008

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“…The T-RFLP approach has been applied in the analysis of bacterial (McMahon et al 2011;Tom-Petersen et al 2003;Blackwood and Paul 2003;Hartmann et al 2005), archaeal (Moeseneder et al 2001; Leybo et al 2006), and fungal (Bennett et al 2008;Genney et al 2006) rRNA genes, as well as functional genes such as ammoniaoxidizing (Fan et al 2011), nitrogen-denitrifying (Wolsing and Priemé 2004), and dissimilatory (bi)sulfite reductase genes (Liu et al 2009), among others. The profiles of T-FRLP were analyzed using different methods, such as principal component analysis for the interpretation of the significance of the effects of complex T-RFLP patterns (Blackwood and Paul 2003;Wang et al 2004;Park et al 2006;, redundancy analysis for the analysis of T-RFLP data exhibiting a linear response to the environmental variables (Fan et al 2011), canonical correspondence analysis (CCA) for the validation of the unimodal relationship between microbial communities and environmental factors (Chang et al 2010), and multidimensional scaling (MDS) (Wolsing and Priemé 2004) and Nonmetric MDS (Bennett et al 2008;Lee et al 2010;McMahon et al 2011) methods for estimating the similarities among samples.…”

Section: Introductionmentioning

confidence: 99%

Succession of plant and soil microbial communities with restoration of abandoned land in the Loess Plateau, China

Zheng

Yan

et al. 2013

J Soils Sediments

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Purpose There have been a number of studies on the succession of vegetation; however, the succession of soil microbes and the collaborative relationships between microbes and vegetation during land restoration remain poorly understood. The objectives of this study were to characterize soil microbial succession and to explore the collaborative mechanisms between microbes and vegetation during the restoration of abandoned land through quantitative ecology methods. Materials and methods The present research was carried out in the succession of a 5-year abandoned land and its conversion to Hippophae rhamnoides shrubs, Larix principisrupprechtii plantation, and a naturally regenerated forest (mixed forest). Soil bacterial, archaeal and fungal characteristics were tested by real-time quantitative PCR assays and terminal restriction fragment length polymorphism. The richness, diversity, and evenness indices were employed to analyze plant and microbial communities' structure. The stability of plant and microbial communities was tested using Spearman's rank correlation. The relationships between the regeneration scenarios and environmental factors were determined through canonical correspondence analysis. Results and discussion The aboveground biomass was significantly different among the sites. Soil bacterial, archaeal, and fungal rRNA gene abundances did not increase significantly with increasing soil organic carbon content. There were higher correlation coefficients between plant and total microbial communities on the richness, diversity, and evenness indices and ratios of positive to negative association compared to ones between plant and individual bacteria, archaea, and fungi. Soil bulk density, clay, pH, and litter were the primary significant environmental factors affecting the structure of plant and microbial communities. The positive relationships between plant and soil bacteria, fungi, and total microbe communities, as well as the negative relationships between plant and archaea, were demonstrated. Conclusions The results suggested that plants promote the growth of soil bacteria and fungi during the process of community succession on a small scale; however, plants inhibit the growth of soil archaea.

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“…Among the heavy metals, cadmium (Cd), mercury (Hg), and copper (Cu) are known to have deleterious effects on the density, activity, and diversity of soil microflora (8,11,16). However, most of the experiments dealing with the impact of metals on soil microorganisms have been field experiments in which there has been polymetal contamination, generally associated with inorganic nutrients and organic matter, which has made it difficult to distinguish the effect of one metal from the effect of another (3,7,14,17).…”

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Cumulative Effects of Short-Term Polymetal Contamination on Soil Bacterial Community Structure

Ranjard

Lignier

Chaussod

2006

Appl Environ Microbiol

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In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu ؉ Cd ؉ Hg) > > Hg > Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the "hump-backed" relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, and S.

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Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique

Cited by 74 publications

References 37 publications

The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii

The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii

Succession of plant and soil microbial communities with restoration of abandoned land in the Loess Plateau, China

Cumulative Effects of Short-Term Polymetal Contamination on Soil Bacterial Community Structure

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