scholarly journals Development of a Common Oligonucleotide Reference Standard for Microarray Data Normalization and Comparison across Different Microbial Communities

2009 ◽  
Vol 76 (4) ◽  
pp. 1088-1094 ◽  
Author(s):  
Yuting Liang ◽  
Zhili He ◽  
Liyou Wu ◽  
Ye Deng ◽  
Guanghe Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microarray Data ◽  
Genomic Dna ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Data Normalization ◽  
Reference Standard ◽  
Complementary Sequence ◽  
Normalization Methods ◽  
Reference Target

ABSTRACT High-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. However, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic DNA) for the study of pure cultures are not applicable. In this study, we developed a common oligonucleotide reference standard (CORS) method to address this problem. A unique 50-mer reference oligonucleotide probe was selected to co-spot with gene probes for each array feature. The complementary sequence was synthesized and labeled for use as the reference target, which was then spiked and cohybridized with each sample. The signal intensity of this reference target was used for microarray data normalization and comparison. The optimal amount or concentration were determined to be ca. 0.5 to 2.5% of a gene probe for the reference probe and ca. 0.25 to 1.25 fmol/μl for the reference target based on our evaluation with a pilot array. The CORS method was then compared to dye swap and genomic DNA normalization methods using the Desulfovibrio vulgaris whole-genome microarray, and significant linear correlations were observed. This method was then applied to a functional gene array to analyze soil microbial communities, and the results demonstrated that the variation of signal intensities among replicates based on the CORS method was significantly lower than the total intensity normalization method. The developed CORS provides a useful approach for microarray data normalization and comparison for studies of complex microbial communities.

scholarly journals Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

2014 ◽  
Vol 23 (12) ◽  
pp. 2988-2999 ◽  
Author(s):  
Fabiana S. Paula ◽  
Jorge L. M. Rodrigues ◽  
Jizhong Zhou ◽  
Liyou Wu ◽  
Rebecca C. Mueller ◽  
...  
Keyword(s):  
Land Use ◽  
Land Use Change ◽  
Microbial Communities ◽  
Forest Soil ◽  
Gene Diversity ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Amazon Forest ◽  
Soil Microbial ◽  
Functional Gene Diversity

Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil

Chemosphere ◽  
2009 ◽  
Vol 75 (2) ◽  
pp. 193-199 ◽  
Author(s):  
Yuting Liang ◽  
Joy D. Van Nostrand ◽  
Jian Wang ◽  
Xu Zhang ◽  
Jizhong Zhou ◽  
...  
Keyword(s):  
Crude Oil ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Gene Analysis ◽  
Soil Microbial ◽  
Functional Gene Analysis

scholarly journals Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

2012 ◽  
Vol 79 (4) ◽  
pp. 1284-1292 ◽  
Author(s):  
Kai Xue ◽  
Liyou Wu ◽  
Ye Deng ◽  
Zhili He ◽  
Joy Van Nostrand ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Agricultural Research ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Functional Genes ◽  
N Availability ◽  
Low Input ◽  
Soil Microbial ◽  
Denitrification Genes

ABSTRACTVarious agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3−concentration and denitrification genes, NH4+concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

scholarly journals Development of an Environmental Functional Gene Microarray for Soil Microbial Communities

2010 ◽  
Vol 76 (21) ◽  
pp. 7161-7170 ◽  
Author(s):  
Ken C. McGrath ◽  
Rhiannon Mondav ◽  
Regina Sintrajaya ◽  
Bill Slattery ◽  
Susanne Schmidt ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Environmental Samples ◽  
Agricultural Soils ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Gene Microarray ◽  
Independent Manner ◽  
Soil Microbial ◽  
Functional Attributes ◽  
Culture Independent

ABSTRACT Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N2O. A total of 109 genes displayed expression that differed significantly between soils with low and high N2O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.

scholarly journals Functional Molecular Ecological Networks

mBio ◽  
2010 ◽  
Vol 1 (4) ◽  
Author(s):  
Jizhong Zhou ◽  
Ye Deng ◽  
Feng Luo ◽  
Zhili He ◽  
Qichao Tu ◽  
...  
Keyword(s):  
Conceptual Framework ◽  
Microbial Communities ◽  
Environmental Changes ◽  
Gene Array ◽  
Soil Microbial Communities ◽  
Ecological Networks ◽  
Functional Gene ◽  
Soil Microbial ◽  
Hybridization Data ◽  
Array Hybridization

ABSTRACT Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. IMPORTANCE Microorganisms are the foundation of the Earth's biosphere and play integral and unique roles in various ecosystem processes and functions. In an ecosystem, various microorganisms interact with each other to form complicated networks. Elucidating network interactions and their responses to environmental changes is difficult due to the lack of appropriate experimental data and an appropriate theoretical framework. This study provides a conceptual framework to construct interaction networks in microbial communities based on high-throughput functional gene array hybridization data. It also first documents that elevated carbon dioxide in the atmosphere dramatically alters the network interactions in soil microbial communities, which could have important implications in assessing the responses of ecosystems to climate change. The conceptual framework developed allows microbiologists to address research questions unapproachable previously by focusing on network interactions beyond the listing of, e.g., the number and abundance of species. Thus, this study could represent transformative research and a paradigm shift in microbial ecology.

scholarly journals Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

2010 ◽  
Vol 5 (3) ◽  
pp. 403-413 ◽  
Author(s):  
Yuting Liang ◽  
Joy D Van Nostrand ◽  
Ye Deng ◽  
Zhili He ◽  
Liyou Wu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Gene Diversity ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Soil Microbial ◽  
Functional Gene Diversity

scholarly journals Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Hao Yu ◽  
Zhili He ◽  
Aijie Wang ◽  
Jianping Xie ◽  
Liyou Wu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Forest Soil ◽  
Forest Ecosystem ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Total Carbon ◽  
Functional Genes ◽  
Functional Markers ◽  
Soil Microbial

ABSTRACTNumerous studies have shown that the continuous increase of atmosphere CO2concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2(eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2at both soil depths, although the stimulation effect of eCO2on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO2increases.IMPORTANCEThe concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2(eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.

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