Bioaugmentation of soils by increasing microbial richness: missing links

Dejonghe, Winnie; Boon, Nico; Seghers, Dave; Top, Eva M.; Verstraete, Willy

doi:10.1046/j.1462-2920.2001.00254.x

Cited by 55 publications

(64 citation statements)

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“…Species variety of soil fungi is slightly lower than that of bacteria (Bridge and Spooner 2001;Hawksworth 2001), due to their high productivity and fast growth (Hanson et al 2005). The count of bacterial species is in the order of hundreds to thousands in 1 g of soil, whereas entire species number is more than 2-3 million (Torsvik et al 1994;Dejonghe et al 2001;Prescott et al 2000).…”

Section: Role Of Soil Fauna and Microbesmentioning

confidence: 99%

Litter decomposition in forest ecosystems: a review

Krishna

Mohan

2017

Energ. Ecol. Environ.

464

215

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Litter decomposition in terrestrial ecosystems has a major role in the biogeochemical cycling of elements in the environment. Climatic features, like temperature, rainfall, humidity, and seasonal variations affect the rate of litter decomposition. This review attempts to understand the litter decomposition process in tropical forest ecosystems. It also reviews the influence of various factors on litter degradation and techniques used for assessing leaf litter decomposition. It is observed that very few studies were conducted on litter decomposition in forest ecosystems, such as tropical and temperate forests. Hence, comprehensive studies on litter degradation have to be undertaken in order to understand the turnover rate of nutrients and other elements in these sensitive ecosystems.

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Section: Role Of Soil Fauna and Microbesmentioning

confidence: 99%

Litter decomposition in forest ecosystems: a review

Krishna

Mohan

2017

Energ. Ecol. Environ.

464

215

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“…Recent studies on bacterial communities showed that changes in ecosystem functioning are associated with changes in the genetic structure of bacterial communities, suggesting that the performance of ecosystem-based processes depends on the bacterial community composition (Dejonghe et al 2001;Wittebolle et al 2005). However, it has also been shown that bacterial communities are functionally redundant, i.e.…”

Section: Introductionmentioning

confidence: 99%

Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source

Temudo

Muyzer

Kleerebezem

et al. 2008

Appl Microbiol Biotechnol

109

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Anaerobic fermentation by an open mixed culture was investigated at different pH values (4-8.5) and with three substrates (glucose, glycerol and xylose). The populations established in each condition were assessed by denaturing gradient gel electrophoresis analysis of the 16S ribosomal RNA gene fragments. The fermentation pattern and the composition of the microbial population were also evaluated when operational variations were imposed (increase of substrate concentration or introduction of a second substrate). The experimental results demonstrated that at low and high pH values, a clearly different fermentation pattern was associated with the dominance of a specialised group of clostridiae. At intermediate pH values, the product spectrum was rather variable and seemed to be sensitive to variations in the microbial community. Different substrates resulted in the establishment of different microbial communities. When fed with a mixture of two substrates, mixotrophic microorganisms (capable of degrading both substrates) were found to overgrow the originally dominant specialists. Overall, the experiments have shown that some operational variables have a clear impact on the fermentation pattern and on the population established. However, a uniform relationship between the process characteristics (associated to a metabolic response) and the microbial population present is not always possible.

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“…Its broad biocatalytic potential makes it highly suitable for applications such as bioremediation (8) and biocatalysis (7,40). Of special interest are solvent-tolerant P. putida strains.…”

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confidence: 99%

Transcriptome Analysis of a Phenol-Producing Pseudomonas putida S12 Construct: Genetic and Physiological Basis for Improved Production

et al. 2008

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The unknown genetic basis for improved phenol production by a recombinant Pseudomonas putida S12 derivative bearing the tpl (tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased biosynthesis of tryptophan caused by a mutation in the trpE gene as the genetic basis for the enhanced phenol production. In addition, several genes in degradation routes connected to the tyrosine biosynthetic pathway were upregulated. This either may be a side effect that negatively affects phenol production or may point to intracellular accumulation of tyrosine or its intermediates. A number of genes identified by the transcriptome analysis were selected for targeted disruption in P. putida S12TPL3. Physiological and biochemical examination of P. putida S12TPL3 and these mutants led to the conclusion that the metabolic flux toward tyrosine in P. putida S12TPL3 was improved to such an extent that the heterologous tyrosine-phenol lyase enzyme had become the rate-limiting step in phenol biosynthesis.Pseudomonas putida is a ubiquitous soil bacterium that has become increasingly important for a wide range of biotechnological applications (46). Its broad biocatalytic potential makes it highly suitable for applications such as bioremediation (8) and biocatalysis (7,40). Of special interest are solvent-tolerant P. putida strains. These organisms have evolved several mechanisms to deal with toxic compounds, including modifications of the inner and outer membranes and active extrusion of a broad range of compounds through membrane-associated efflux pumps (18,31,32). Solvent-tolerant bacteria are especially useful for the biosynthesis of compounds that are toxic to other microorganisms (7,39,48). They have been used to produce different aromatic compounds, such as cinnamic acid (24), p-hydroxybenzoic acid (33, 43), 3-methylcatechol (35, 50), and phenol (51).Previously, we reported the construction of a P. putida S12 strain which efficiently produces phenol from glucose as a demonstration case for the "green" production of a toxic, hydroxylated aromatic compound (51). This strain has since been converted into an efficient producer of other, value-added aromatics (43). Efficient phenol production was achieved by introduction of the tpl gene from Pantoea agglomerans, encoding the enzyme tyrosine-phenol lyase (TPL), followed by a combined approach of targeted genetic engineering, random mutagenesis, antimetabolite selection, and high-throughput screening. This approach resulted in strain P. putida S12TPL3, which was capable of converting glucose into phenol with a yield of 7% (mol/mol) (51). The optimization of phenol production was achieved mostly by random approaches. As a result, little is known about the genetic basis of the enhanced phenol production.Transcriptome analysis has been used successfully in the past to gain comprehensive insight into complex metabolic networks (12,27,29) and o...

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Bioaugmentation of soils by increasing microbial richness: missing links

Cited by 55 publications

References 0 publications

Litter decomposition in forest ecosystems: a review

Litter decomposition in forest ecosystems: a review

Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source

Transcriptome Analysis of a Phenol-Producing Pseudomonas putida S12 Construct: Genetic and Physiological Basis for Improved Production

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