Soil Microbial Ecology

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

by Alexandre Jousset

The Pressurized Porous Surface Model: An Improved Tool to Study Bacterial Behavior Under a Wide Range of Environmentally Relevant Matric Potentials

by Gamze Gulez

J Microbiol Methods. 2010 Sep;82(3):324-6

Hydration-Controlled Bacterial Motility and Dispersal on Surfaces

by Gamze Gulez

Proc. Natl. Acad. Sci. USA 107: 14369-14372

Soil Ecosystem Functioning Under Climate Change: Plant Species and Community Effects

by Paul Kardol

Feedbacks of terrestrial ecosystems to atmospheric and climate change depend on soil ecosystem dynamics. Soil... more Feedbacks of terrestrial ecosystems to atmospheric and climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate
change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering
the soil communities that depend on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant
community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and precipitation in Tennessee (USA). Specifically, we collected soils at the plot level (plant community soils) and beneath dominant plant species (plant-specific soils). We used
microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: (1) Overall, while there were some interactions,
water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activity, and soil nematodes. Multiple climate-change factors can interact to shape ecosystems, but in our study, those interactions were largely driven by changes in water. (2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning, and this impact was not obvious when
looking at plant community soils. Climate-change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. These results indicate that accurate assessments of climate-change impacts on soil
ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate-change-induced shifts in plant community composition
will likely modify or counteract the direct impact of atmospheric and climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting the manner in which global change will alter ecosystem functioning.

High beta diversity of bacteria in the shallow terrestrial subsurface

by jianjun wang

Wang, Jianjun. Wu, Yucheng. Jiang, Hongcheng. Li, Chunhai. Dong, Hailiang. Wu, Qinglong. Soininen, Janne. (2008) High beta diversity of bacteria in the shallow terrestrial subsurface. Environmental Microbiology 10:2537-2549.

While there have been a vast number of studies on bacterial alpha diversity in the shallow terrestrial subsurface,... more While there have been a vast number of studies on bacterial alpha diversity in the shallow terrestrial subsurface, beta diversity – how the bacterial community composition changes with spatial distance – has received surprisingly limited attention. Here, bacterial beta diversity and its controlling factors are investigated by denaturing gradient gel electrophoresis and cloning of samples from a 700-cm-long sediment core, the lower half of which consisted of marine-originated sediments. According to canonical correspondence analysis with variation partitioning, contemporary environmental variables explain beta diversity in a greater proportion than depth. However, we also found that community similarity decayed significantly with spatial distance and the slopes of the distance–decay relationships are relatively high. The high beta diversity indicates that the bacterial distribution patterns are not only controlled by contemporary environments, but also related to historical events, that is, dispersal or depositional history. This is highlighted by the different beta diversity patterns among studied sediment layers. We thus conclude that the high beta diversity in the shallow terrestrial subsurface is a trade-off between historical events and environmental heterogeneity. Furthermore, we suggest that the high beta diversity of bacteria is likely to be recapitulated in other terrestrial sites because of the great frequency of high geochemical and/or historical variations along depth.