Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology

CJ Smith, AM Osborn - FEMS microbiology ecology, 2009 - academic.oup.com
Abstract Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in
microbial ecology to quantify the abundance and expression of taxonomic and functional …

Bias and artifacts in multitemplate polymerase chain reactions (PCR)

T Kanagawa - Journal of bioscience and bioengineering, 2003 - Elsevier
Polymerase chain reaction (PCR) is often used for the amplification of a mixture of
homologous genes. PCR bias and artifact formation can occur in multitemplate PCR, and …

QMEC: a tool for high-throughput quantitative assessment of microbial functional potential in C, N, P, and S biogeochemical cycling

B Zheng, Y Zhu, J Sardans, J Peñuelas, J Su - Science China Life …, 2018 - Springer
Microorganisms are major drivers of elemental cycling in the biosphere. Determining the
abundance of microbial functional traits involved in the transformation of nutrients, including …

The diversity and biogeography of soil bacterial communities

N Fierer, RB Jackson - Proceedings of the National Academy of Sciences, 2006 - pnas.org
For centuries, biologists have studied patterns of plant and animal diversity at continental
scales. Until recently, similar studies were impossible for microorganisms, arguably the most …

Relative roles of niche and neutral processes in structuring a soil microbial community

AJ Dumbrell, M Nelson, T Helgason, C Dytham… - The ISME …, 2010 - academic.oup.com
Most attempts to identify the processes that structure natural communities have focused on
conspicuous macroorganisms whereas the processes responsible for structuring microbial …

Evidence for Negative Effects of TiO2 and ZnO Nanoparticles on Soil Bacterial Communities

Y Ge, JP Schimel, PA Holden - Environmental science & …, 2011 - ACS Publications
Increased use of engineered nanoparticles (ENPs) raises concerns about their
environmental impacts, but the effects of metal oxide ENPs on environmental processes and …

Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis

S Kille, CG Acevedo-Rocha, LP Parra… - ACS synthetic …, 2013 - ACS Publications
Saturation mutagenesis probes define sections of the vast protein sequence space.
However, even if randomization is limited this way, the combinatorial numbers problem is …

PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample

SG Acinas, R Sarma-Rupavtarm… - Applied and …, 2005 - journals.asm.org
The contribution of PCR artifacts to 16S rRNA gene sequence diversity from a complex
bacterioplankton sample was estimated. Taq DNA polymerase errors were found to be the …

Urban aerosols harbor diverse and dynamic bacterial populations

EL Brodie, TZ DeSantis, JPM Parker, IX Zubietta… - Proceedings of the …, 2007 - pnas.org
Considering the importance of its potential implications for human health, agricultural
productivity, and ecosystem stability, surprisingly little is known regarding the composition or …

Enhanced sensitivity of DNA‐and rRNA‐based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients

T Lueders, M Manefield… - Environmental …, 2004 - Wiley Online Library
Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active
members of natural microbial populations that are involved in the assimilation of an …