The diversity changes of soil microbial communities stimulated by climate, soil type and vegetation type analyzed via a functional gene array

2015 ◽  
Vol 31 (11) ◽  
pp. 1755-1763 ◽  
Author(s):  
Fu Chen ◽  
Min Tan ◽  
Yongjun Yang ◽  
Jing Ma ◽  
Shaoliang Zhang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Type ◽  
Vegetation Type ◽  
Gene Array ◽  
Soil Microbial Communities ◽  
Functional Gene ◽  
Soil Microbial

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 Detection of irradiation induced changes on the activity and diversity of soil microbial communities: The effect of soil type

2005 ◽  
Vol 40 ◽  
pp. S939-S944 ◽  
Author(s):  
N. R. Parekh ◽  
E. D. Potter ◽  
J. S. Poskitt ◽  
B. A. Dodd ◽  
N. A. Beresford
Keyword(s):  
Microbial Communities ◽  
Soil Type ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Induced Changes

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

Soil microbial communities are shaped by vegetation type and park age in cities under cold climate

2017 ◽  
Vol 19 (3) ◽  
pp. 1281-1295 ◽  
Author(s):  
Nan Hui ◽  
Ari Jumpponen ◽  
Gaia Francini ◽  
D. Johan Kotze ◽  
Xinxin Liu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Vegetation Type ◽  
Soil Microbial Communities ◽  
Cold Climate ◽  
Soil Microbial

scholarly journals Effects of vegetation type, fine and coarse roots on soil microbial communities and enzyme activities in eastern Tibetan plateau

CATENA ◽  
2020 ◽  
Vol 194 ◽  
pp. 104694 ◽  
Author(s):  
Lixia Wang ◽  
Xueyong Pang ◽  
Na Li ◽  
Kaibin Qi ◽  
Junsheng Huang ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Microbial Communities ◽  
Enzyme Activities ◽  
Vegetation Type ◽  
Soil Microbial Communities ◽  
Eastern Tibetan Plateau ◽  
Coarse Roots ◽  
Soil Microbial

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.

Effect of vegetation type on the diversity of soil microbial communities at the new stage Volcanic Lava Platform, Wudalianchi area, Northeast China

2019 ◽  
Vol 39 (21) ◽  
Author(s):  
曹宏杰 CAO Hongjie ◽  
王立民 WANG Limin ◽  
徐明怡 XU Mingyi ◽  
黄庆阳 HUANG Qingyang ◽  
谢立红 XIE Lihong ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Northeast China ◽  
Vegetation Type ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Volcanic Lava

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.

Sign in / Sign up

Export Citation Format

Share Document