scholarly journals Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 431 ◽  
Author(s):  
Laura M. Boggs ◽  
Melissa K. R. Scheible ◽  
Gustavo Machado ◽  
Kelly A. Meiklejohn

In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina® MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.

2007 ◽  
Vol 73 (17) ◽  
pp. 5683-5686 ◽  
Author(s):  
Dana M. Cook ◽  
Emily DeCrescenzo Henriksen ◽  
Rima Upchurch ◽  
Joy B. Doran Peterson

ABSTRACT The Tipula abdominalis larval hindgut microbial community presumably facilitates digestion of the lignocellulosic diet. The microbial community was investigated through characterization of bacterial isolates and analysis of 16S rRNA gene clone libraries. This initial study revealed novel bacteria and provides a framework for future studies of this symbiosis.


2014 ◽  
Vol 11 (4) ◽  
pp. 301-306 ◽  
Author(s):  
Jason P. Folster ◽  
Beth Tolar ◽  
Gary Pecic ◽  
Deborah Sheehan ◽  
Regan Rickert ◽  
...  

2010 ◽  
Vol 76 (12) ◽  
pp. 3863-3868 ◽  
Author(s):  
J. Kirk Harris ◽  
Jason W. Sahl ◽  
Todd A. Castoe ◽  
Brandie D. Wagner ◽  
David D. Pollock ◽  
...  

ABSTRACT Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where ≤1,000 sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel.


1998 ◽  
Vol 273 (41) ◽  
pp. 26571-26579 ◽  
Author(s):  
Elena M. Klenova ◽  
Sara Fagerlie ◽  
Galina N. Filippova ◽  
Leo Kretzner ◽  
Graham H. Goodwin ◽  
...  
Keyword(s):  

2009 ◽  
Vol 96 (4) ◽  
pp. 653-657 ◽  
Author(s):  
Maria Teresa Ceccherini ◽  
Judith Ascher ◽  
Alberto Agnelli ◽  
Federica Borgogni ◽  
Ottorino Luca Pantani ◽  
...  

2010 ◽  
Author(s):  
Michael F. Berger ◽  
Michael S. Lawrence ◽  
Kristian Cibulskis ◽  
Dorothee Pflueger ◽  
Francesca Demichelis ◽  
...  

2015 ◽  
Vol 61 (3) ◽  
pp. 171-181 ◽  
Author(s):  
Haiyan Cui ◽  
Xiaoyan Yang ◽  
Dengxue Lu ◽  
Hui Jin ◽  
Zhiqiang Yan ◽  
...  

This study is the first to describe the composition and characteristics of culturable bacterial isolates from the rhizosphere and bulk soil of the medicinal plant Stellera chamaejasme L. at different growth stages. Using a cultivation-dependent approach, a total of 148 isolates showing different phenotypic properties were obtained from the rhizosphere and bulk soil. Firmicutes and Actinobacteria were the major bacterial groups in both the rhizosphere and bulk soil at all 4 growth stages of S. chamaejasme. The diversity of the bacterial community in the rhizosphere was higher than that in bulk soil in flowering and fruiting stages. The abundance of bacterial communities in the rhizosphere changed with the growth stages and had a major shift at the fruiting stage. Dynamic changes of bacterial abundance and many bacterial groups in the rhizosphere were similar to those in bulk soil. Furthermore, most bacterial isolates exhibited single or multiple biochemical activities associated with S. chamaejasme growth, which revealed that bacteria with multiple physiological functions were abundant and widespread in the rhizosphere and bulk soil. These results are essential (i) for understanding the ecological roles of bacteria in the rhizosphere and bulk soil and (ii) as a foundation for further evaluating their efficacy as effective S. chamaejasme growth-promoting rhizobacteria.


Chemosphere ◽  
2011 ◽  
Vol 83 (6) ◽  
pp. 783-791 ◽  
Author(s):  
Muhammad Ilyas ◽  
Agus Sudaryanto ◽  
Iwan Eka Setiawan ◽  
Adi Slamet Riyadi ◽  
Tomohiko Isobe ◽  
...  

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e93374 ◽  
Author(s):  
Rodrigo Pessôa ◽  
Jaqueline Tomoko Watanabe ◽  
Youko Nukui ◽  
Juliana Pereira ◽  
Jorge Kasseb ◽  
...  

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