Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms

AbstractChain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.

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Changes in Denitrifier Abundance, Denitrification Gene mRNA Levels, Nitrous Oxide Emissions, and Denitrification in Anoxic Soil Microcosms Amended with Glucose and Plant Residues

Applied and Environmental Microbiology ◽

10.1128/aem.02993-09 ◽

2010 ◽

Vol 76 (7) ◽

pp. 2155-2164 ◽

Cited By ~ 129

Author(s):

Sherri L. Henderson ◽

Catherine E. Dandie ◽

Cheryl L. Patten ◽

Bernie J. Zebarth ◽

David L. Burton ◽

...

Keyword(s):

Nitrous Oxide ◽

Organic Carbon ◽

Plant Residue ◽

Plant Residues ◽

Barley Plant ◽

Mrna Levels ◽

Soil Microcosms ◽

Denitrification Gene ◽

Gene Mrna ◽

Amended Soil

ABSTRACT In agricultural cropping systems, crop residues are sources of organic carbon (C), an important factor influencing denitrification. The effects of red clover, soybean, and barley plant residues and of glucose on denitrifier abundance, denitrification gene mRNA levels, nitrous oxide (N2O) emissions, and denitrification rates were quantified in anoxic soil microcosms for 72 h. nosZ gene abundances and mRNA levels significantly increased in response to all organic carbon treatments over time. In contrast, the abundance and mRNA levels of Pseudomonas mandelii and closely related species (nirS P) increased only in glucose-amended soil: the nirS P guild abundance increased 5-fold over the 72-h incubation period (P < 0.001), while the mRNA level significantly increased more than 15-fold at 12 h (P < 0.001) and then subsequently decreased. The nosZ gene abundance was greater in plant residue-amended soil than in glucose-amended soil. Although plant residue carbon-to-nitrogen (C:N) ratios varied from 15:1 to 30:1, nosZ gene and mRNA levels were not significantly different among plant residue treatments, with an average of 3.5 Ã¯Â¿Â½ 107 gene copies and 6.9 Ã¯Â¿Â½ 107 transcripts g−1 dry soil. Cumulative N2O emissions and denitrification rates increased over 72 h in both glucose- and plant-tissue-C-treated soil. The nirS P and nosZ communities responded differently to glucose and plant residue amendments. However, the targeted denitrifier communities responded similarly to the different plant residues under the conditions tested despite changes in the quality of organic C and different C:N ratios.

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Microbial Degradation in Soil Microcosms of Fuel Oil Hydrocarbons from Drilling Cuttings

Environmental Science & Technology ◽

10.1021/es00006a027 ◽

1995 ◽

Vol 29 (6) ◽

pp. 1615-1621 ◽

Cited By ~ 95

Author(s):

Claude-Henri. ChaIneau ◽

Jean-Louis. Morel ◽

Jean. Oudot

Keyword(s):

Microbial Degradation ◽

Fuel Oil ◽

Soil Microcosms ◽

Oil Hydrocarbons ◽

Degradation In Soil

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The fate of a genetically modifiedPseudomonasstrain and its transgene during the composting of poultry manure

Canadian Journal of Microbiology ◽

10.1139/w04-030 ◽

2004 ◽

Vol 50 (6) ◽

pp. 415-421 ◽

Cited By ~ 9

Author(s):

J Guan ◽

J L Spencer ◽

M Sampath ◽

J Devenish

Keyword(s):

Polymerase Chain Reaction ◽

Incubation Temperature ◽

Genetically Modified ◽

Chicken Manure ◽

Detection Sensitivity ◽

Plate Count ◽

Chain Reaction ◽

Nested Polymerase Chain Reaction ◽

Soil Microcosms ◽

Polymerase Chain

The fate of the genetically modified (GM) Pseudomonas chlororaphis strain 3732 RN-L11 and its transgene (lacZ insert) during composting of chicken manure was studied using plate count and nested polymerase chain reaction (PCR) methods. The detection sensitivity of the nested PCR method was 165 copies of the modified gene per gram of moist compost or soil. Compost microcosms consisted of a 100-g mixture of chicken manure and peat, whereas soil microcosms were 100-g samples of sandy clay loam. Each microcosm was inoculated with 4 × 1010CFU of P. chlororaphis RN-L11. In controlled temperature studies, neither P. chlororaphis RN-L11 nor its transgene could be detected in compost microcosms after incubation temperature was elevated to 45 °C or above for one or more days. In contrast, in the compost microcosms incubated at 23 °C, the target organism was not detected by the plate count method after 6 days, but its transgene was detectable for at least 45 days. In compost bins, the target organism was not recovered from compost microcosms or soil microcosms at different levels in the bins for 29 days. However, the transgene was detected in 8 of the 9 soil microcosms and in only 1 of the 9 compost microcosms. The compost microcosm in which transgene was detected was at the lower level of the bin where temperatures remained below 45 °C. The findings indicated that composting of organic wastes could be used to reduce or degrade heat sensitive GM microorganisms and their transgenes.Key words: composting, genetically modified Pseudomonas strain, transgene, polymerase chain reaction.

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Response of soil enzymes to Linear Alkylbenzene Sulfonate (LAS) addition in soil microcosms

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2008.09.019 ◽

2009 ◽

Vol 41 (1) ◽

pp. 69-76 ◽

Cited By ~ 8

Author(s):

María del Mar Sánchez-Peinado ◽

Belén Rodelas ◽

María Victoria Martínez-Toledo ◽

Jesús González-López ◽

Clementina Pozo

Keyword(s):

Soil Enzymes ◽

Linear Alkylbenzene Sulfonate ◽

Soil Microcosms ◽

Linear Alkylbenzene ◽

Alkylbenzene Sulfonate

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Survival of enterococci and Tn916-like conjugative transposons in soil

Canadian Journal of Microbiology ◽

10.1139/w04-090 ◽

2004 ◽

Vol 50 (11) ◽

pp. 957-966 ◽

Cited By ~ 16

Author(s):

Robert E Andrews Jr. ◽

Wesley S Johnson ◽

Abby R Guard ◽

Jonathan D Marvin

Keyword(s):

Enterococcus Faecalis ◽

Denaturing Gradient Gel Electrophoresis ◽

Soil Microflora ◽

Swine Waste ◽

Soil System ◽

Soil Microcosms ◽

Conjugative Transposons ◽

Native Soil ◽

Gradient Gel Electrophoresis ◽

Normal Soil

The persistence of Enterococcus faecalis, fecal enterococci from swine waste, and Tn916-like elements was determined following inoculation into autoclaved and native soil microcosms. When cells of E. faecalis CG110 (Tn916) were inoculated into native microcosms, enterococcal viability in the soil decreased approximately 5 orders of magnitude (4.8 × 105CFU/g soil to < 10 CFU/g) after 5 weeks. In autoclaved microcosms, the viability of E. faecalis decreased by only 20% in 5 weeks. In contrast, the content of Tn916, based on PCR of DNA extracts from soil microcosms, decreased by about 20% in both native and autoclaved microcosms. Similar results were obtained when the source of fecal enterococci and Tn916-like elements was swine waste. Because the concentration of Tn916-independent E. faecalis DNA (the D-alanine D-alanine ligase gene), based on PCR, decreased to nearly undetectable levels (at least 3 orders of magnitude) after 5 weeks in the native microcosms, the evidence suggests Tn916 stability in the soil results from en masse transfer of the transposon to the normal soil microflora and not survival of E. faecalis DNA in the soil system. Results from denaturing gradient gel electrophoresis suggest that multiple forms of Tn916 occur in swine waste, but only forms most like Tn916 exhibit stability in the soil.Key words: Tn916, Enterococcus faecalis, soil, antibiotic resistance, conjugation, transposon.

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