Stable Isotope Probing Identifies Novel m-Xylene Degraders in Soil Microcosms from Contaminated and Uncontaminated Sites

2010 ◽  
Vol 212 (1-4) ◽  
pp. 113-122 ◽  
Author(s):  
Shuguang Xie ◽  
Weimin Sun ◽  
Chunling Luo ◽  
Alison M. Cupples
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Soil Microcosms

scholarly journals Identification of Benzo[a]pyrene-Metabolizing Bacteria in Forest Soils by Using DNA-Based Stable-Isotope Probing

2015 ◽  
Vol 81 (21) ◽  
pp. 7368-7376 ◽  
Author(s):  
Mengke Song ◽  
Chunling Luo ◽  
Longfei Jiang ◽  
Dayi Zhang ◽  
Yujie Wang ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Forest Soils ◽  
Contaminated Soils ◽  
Stable Isotope Probing ◽  
Soil Microcosms ◽  
Content Type ◽  
The Family ◽  
Polycyclic Aromatic ◽  
Uncultivated Bacteria ◽  
Different Soils

ABSTRACTDNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[a]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genusTerrimonas(familyChitinophagaceae, orderSphingobacteriales), whereasBurkholderiaspp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the familyOxalobacteraceae(genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP13C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated soils.

scholarly journals Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Kriti Sharma ◽  
Márton Palatinszky ◽  
Georgi Nikolov ◽  
David Berry ◽  
Elizabeth A Shank
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Three Dimensions ◽  
Bacterial Survival ◽  
Soil Microcosms ◽  
Transparent Soil ◽  
Dry Down ◽  
Destructive Measurement ◽  
The Impact ◽  
Non Destructive

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

scholarly journals Phylogeny of Acetate-Utilizing Microorganisms in Soils along a Nutrient Gradient in the Florida Everglades

2006 ◽  
Vol 72 (10) ◽  
pp. 6837-6840 ◽  
Author(s):  
Ashvini Chauhan ◽  
Andrew Ogram
Keyword(s):  
Stable Isotope ◽  
16S Rrna ◽  
Stable Isotope Probing ◽  
Florida Everglades ◽  
Gene Clone ◽  
Rrna Gene ◽  
Acetate Oxidation ◽  
Soil Microcosms ◽  
Nutrient Gradient ◽  
Syntrophic Acetate Oxidation

ABSTRACT The consumption of acetate in soils taken from a nutrient gradient in the northern Florida Everglades was studied by stable isotope probing. Bacterial and archaeal 16S rRNA gene clone libraries from eutrophic and oligotrophic soil microcosms strongly suggest that a significant amount of acetate is consumed by syntrophic acetate oxidation in nutrient-enriched soil.

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