A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction

Liles, Mark R.; Türkmen, Özgür; Manske, Brian F.; Zhang, Mingzi M.; Rouillard, Jean Marie; George, Isabelle; Balser, Teri C.; Billor, Nedret; Goodman, Robert M.

doi:10.1016/j.soilbio.2010.01.007

Cited by 12 publications

(12 citation statements)

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“…Several findings point to the fact that not all subdivisions within the phylum Acidobacteria share the same traits. Examples of these are the occurrence of numerically dominant as well as metabolically active Acidobacteria in rhizospheric soil [45], the lineage-dependent variations in relative abundance within a clay fraction of soil versus bulk soil [48] and the differences in the pH preferences for growth [44]. Interestingly, Mummey et al found that Acidobacteria were poorly represented in the inner fraction of aggregates [49], but were more abundant in soil macroaggregates and the outer fractions of microaggregates, i.e.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production

et al. 2012

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The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP) and Poor no-till Agricultural Practices (PAP) were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable vs. non-sustainable agricultural practices in the Pampa region.

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Section: Discussionmentioning

confidence: 99%

Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production

et al. 2012

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“…A given probe was only considered to be truly hybridized when at least three of four replicate spots provided a strong positive hybridization (Sanguin et al 2006). The pixel intensity of positive hybridization was then normalized relative to a mean hybridization signal observed from the set of positive control (PC) probes to provide the best array-to-array consistency, because PC probes were universal for every hybridized PCR amplicon (Liles et al 2010). …”

Section: Scanning and Data Analysismentioning

confidence: 99%

“…2). The differences in the hybridization signals for expected-positive features between different rRNA gene sequences (e.g., clone 1 vs. clone 3) might be a consequence of different probe hybridization kinetics (Liles et al 2010). …”

Section: Validation Of Probe Set With Pure Culturesmentioning

confidence: 99%

“…It should be noted that the probe hybridization signals could not be used to characterize the quantitative abundance of any group in an environmental sample due to potential kinetic differences between individual probes (Liles et al 2010). However, if a comparison was conducted in the same set of probes with different environmental samples, a shift in probe hybridization strength from one sample to another could indicate a real shift in bacterial relative abundance (Liles et al 2010). Mycobacteriaceae includes pathogens known to cause serious diseases in mammals.…”

Section: Hybridization Of Water Samplesmentioning

confidence: 99%

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Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

et al. 2017

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Many reports have shown that the composition of the bacterioplankton community can serve as a biological indicator to evaluate the occurrence of shrimp diseases. However, the distribution, diversity, and function of planktonic actinobacteria in shrimp ponds are still poorly understood. In this study, a prototype of a 16S rRNA gene-based taxonomic microarray was developed and evaluated for monitoring of planktonic actinobacteria in shrimp ponds. The prototype microarray is composed of 30 probes that target ten dominant families of planktonic actinobacteria found in shrimp ponds. The specificity of the actinobacterial microarray was validated by a set of control hybridizations with 16S rRNA genes clones. The prototype microarray was subsequently tested with two seawater samples from ponds with diseased shrimp populations (PDS) and ponds with healthy shrimp populations (PHS). The actinobacteria hybridization profiles revealed a lower abundance of Microbacteriaceae and a higher abundance of Mycobacteriaceae in PDS than in PHS. The changes in planktonic actinobacterial communities were validated by pyrosequencing data. These results support the utility of the microarray for monitoring planktonic actinobacteria in shrimp ponds and aquaculture environments.

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“…The use of PCR has become routine for molecular phylogenetic analysis based on ribotype diversity (Woese, 1987), often used in combination with community analysis methods such as denaturing gradient gel electrophoresis (e.g., Muyzer et al, 1993), 16S rRNA gene clone libraries (e.g., Chandler, 1997), or more recently microarrays (DeSantis et al, 2007; Liles et al, 2010). Although in many cases such studies are described as “metagenomic”, since indeed the template DNA used is derived from diverse genomes, such phylogenetic surveys of a single evolutionarily conserved gene are not truly metagenomic in nature and will not be further considered in this review.…”

Section: Analyzing the Soil Metagenomementioning

confidence: 99%

Size does matter: Application-driven approaches for soil metagenomics

Kakirde

Parsley

Liles

2010

Soil Biology and Biochemistry

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106

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Metagenomic analyses can provide extensive information on the structure, composition, and predicted gene functions of diverse environmental microbial assemblages. Each environment presents its own unique challenges to metagenomic investigation and requires a specifically designed approach to accommodate physicochemical and biotic factors unique to each environment that can pose technical hurdles and/or bias the metagenomic analyses. In particular, soils harbor an exceptional diversity of prokaryotes that are largely undescribed beyond the level of ribotype and are a potentially vast resource for natural product discovery. The successful application of a soil metagenomic approach depends on selecting the appropriate DNA extraction, purification, and if necessary, cloning methods for the intended downstream analyses. The most important technical considerations in a metagenomic study include obtaining a sufficient yield of high-purity DNA representing the targeted microorganisms within an environmental sample or enrichment and (if required) constructing a metagenomic library in a suitable vector and host. Size does matter in the context of the average insert size within a clone library or the sequence read length for a highthroughput sequencing approach. It is also imperative to select the appropriate metagenomic screening strategy to address the specific question(s) of interest, which should drive the selection of methods used in the earlier stages of a metagenomic project (e.g., DNA size, to clone or not to clone). Here, we present both the promising and problematic nature of soil metagenomics and discuss the factors that should be considered when selecting soil sampling, DNA extraction, purification, and cloning methods to implement based on the ultimate study objectives.

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A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction

Cited by 12 publications

References 50 publications

Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production

Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production

Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds

Size does matter: Application-driven approaches for soil metagenomics

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