Abstract:
:Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than 100 years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modeled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.
journal_name
J Ind Microbiol Biotechnoljournal_title
Journal of industrial microbiology & biotechnologyauthors
Araujo-Granda P,Gras A,Ginovart M,Moulton Vdoi
10.1007/s10295-019-02245-8subject
Has Abstractpub_date
2020-01-01 00:00:00pages
1-20issue
1eissn
1367-5435issn
1476-5535pii
10.1007/s10295-019-02245-8journal_volume
47pub_type
杂志文章abstract::The valorization of lignin is critical for the economic viability of the bioeconomy. Microbial metabolism is advantageous for handling the myriad of aromatic compounds resulting from lignin chemical or enzymatic depolymerization. Coupling aromatic metabolism to fatty acid biosynthesis makes possible the production of ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-020-02269-5
更新日期:2020-10-01 00:00:00
abstract::The economic viability of the biorefinery concept is limited by the valorization of lignin. One possible method of lignin valorization is biological upgrading with aromatic-catabolic microbes. In conjunction, lignin monomers can be produced by fast pyrolysis and fractionation. However, biological upgrading of these li...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-019-02208-z
更新日期:2019-11-01 00:00:00
abstract::Corynebacterium glutamicum SNK 118 was metabolically engineered with improved L-arginine titer. Considering the crucial role of NADPH level in L-arginine production, pntAB (membrane-bound transhydrogenase) and ppnK (NAD+ kinase) were co-expressed to increase the intracellular NADPH pool. Expression of pntAB exhibited ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-018-2103-8
更新日期:2019-01-01 00:00:00
abstract::Pentose sugars are increasingly being used in industrial applications of Saccharomyces cerevisiae. Although L-arabinose is a highlighted pentose that has been identified as next-generation biomass, arabinose fermentation has not yet undergone extensive development for industrial utilization. In this study, we integrat...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-019-02233-y
更新日期:2019-12-01 00:00:00
abstract::Industrial applications for lactate, such as the production of chemicals, has led to interest in producing this organic acid by metabolically engineered a yeast such as Saccharomyces cerevisiae, which is more acid tolerant than lactic acid bacteria. This paper deals with lactate production by S. cerevisiae K1-LDH, in ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-004-0138-5
更新日期:2004-06-01 00:00:00
abstract::The operation of bioreactors and the metabolism of microorganisms in biofilms or soil/sediment systems are strongly dictated by the transport processes therein. Nuclear magnetic resonance (NMR) spectroscopy or magnetic resonance imaging (MRI) allow nondestructive and noninvasive quantification and visualisation (in ca...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1038/sj/jim/7000087
更新日期:2001-01-01 00:00:00
abstract::We have found a novel fungal genus that produces extremely bioactive volatile organic compounds (VOCs). This fungal isolate was initially discovered as an endophyte in Cinnamomum zeylanicum in a botanical garden in Honduras. This endophytic fungus, Muscodor albus, produces a mixture of VOCs that are lethal to a wide v...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1007/s10295-006-0090-7
更新日期:2006-07-01 00:00:00
abstract::Microbial diversity is fundamental to maintenance and conservation of global genetic resources. As extreme environments are explored, the richness of microbial diversity is increasingly evident. Measures must be taken to estimate, record, and conserve microbial diversity, not only to sustain human health but also to e...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1038/sj.jim.2900390
更新日期:1997-05-01 00:00:00
abstract::Brevundimonas diminuta is a small Gram-negative bacterium used for validation of membranes and filters used in the pharmaceutical and drinking water treatment industries. Current assays are time consuming, nonselective, and may be subject to interference by competing indigenous microorganisms. The focus of this study ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-010-0738-1
更新日期:2010-09-01 00:00:00
abstract::Plant cell walls are comprised of cellulose, hemicellulose and other polymers that are intertwined. This complex structure acts as a barrier to degradation by single enzyme. Thus, a cocktail consisting of bi and multifunctional xylanases and xylan debranching enzymes is most desired combination for the efficient utili...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1007/s10295-008-0342-9
更新日期:2008-07-01 00:00:00
abstract::Recycling of office waste paper (photocopy, inkjet, and laser prints) is a major problem due to difficulty in removal of nonimpact ink. Biological deinking of office waste paper is reported using several microorganisms and their enzymes. We report here deinking and decolorization of the dislodged ink particles from in...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-005-0017-8
更新日期:2005-09-01 00:00:00
abstract::A superoxide dismutase (SOD) gene was cloned from the thermophilic bacterium Rhodothermus sp. XMH10 for the first time and highly expressed in Escherichia coli. The Rhodothermus sp. XMH10 SOD (RhSOD) gene encodes 209 amino acids with a putative molecular weight of 23.6 kDa and a pI value of 5.53. The recombinant RhSOD...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-007-0274-9
更新日期:2008-02-01 00:00:00
abstract::The catechol meta cleavage pathway is one of the central metabolic pathways for the degradation of aromatic compounds. A novel organization of the pathway genes, different from that of classical soil microorganisms, has been observed in Sphingomonas sp HV3 and Pseudomonas sp. DJ77. In a Comamonas sp. JS765, cdoE encod...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-006-0170-8
更新日期:2007-02-01 00:00:00
abstract::During the biotransformation of castor oil into gamma-decalactone, R. aurantiaca produced both the lactone form and its precursor (4-hydroxydecanoic acid). After six days of culture, a maximum yield of gamma-decalactone of 6.5 g/l was obtained. The parameters of gamma-decalactone adsorption on three Macronet resins (M...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-009-0659-z
更新日期:2010-02-01 00:00:00
abstract::Bacterial biofilms of Pseudomonas aeruginosa selectively labeled by introduction of 2-13C-glycerol was studied by solid-state and high-resolution nuclear magnetic resonance. The 13C nuclei were mainly integrated into mannuronate and guluronate, the two monomer units forming the bacterial alginate. The signal for the C...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:
更新日期:2001-01-01 00:00:00
abstract::Utilization of renewable feedstocks for the production of bio-based bulk chemicals, such as 2,3-butanediol (2,3-BDO), by engineered strains of the non-pathogenic yeast, Saccharomyces cerevisiae, has recently become an attractive option. In this study, to realize rapid production of 2,3-BDO, a flocculent, 2,3-BDO-produ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-018-2033-5
更新日期:2018-05-01 00:00:00
abstract::Study of the distribution of the oxygen mass transfer coefficient, k (l) a, for a stirred bioreactor and simulated (pseudoplastic solutions of carboxymethylcellulose sodium salt) bacterial (P. shermanii), yeast (S. cerevisiae), and fungal (P. chrysogenum free mycelia) broths indicated significant variation of transfer...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-010-0930-3
更新日期:2011-09-01 00:00:00
abstract::A closed-circuit microbial fuel cell (C-MFC) was operated to investigate the electron flux under fed-batch mode, and the results were compared to those of open-circuit MFC (O-MFC) and a fermentation reactor (F-reactor). The current was the largest electron sink (52.7% of influent SCOD) in C-MFC, whereas biomass and me...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-015-1629-2
更新日期:2015-07-01 00:00:00
abstract::L-DOPA is a key pharmaceutical agent for treating Parkinson's, and market demand has exploded due to the aging population. There are several challenges associated with the chemical synthesis of L-DOPA, including complicated operation, harsh conditions, and serious pollution. A biocatalysis route for L-DOPA production ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-019-02237-8
更新日期:2019-12-01 00:00:00
abstract::Chalcones, the central precursor of flavonoids, are synthesized exclusively in plants from tyrosine and phenylalanine via the sequential reaction of phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate:coenzyme A ligase (4CL) and chalcone synthase (CHS). Chalcones are converted into the corres...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1007/s10295-003-0061-1
更新日期:2003-08-01 00:00:00
abstract::An assay has been developed to accurately quantify the growth and release behaviour of bacterial biofilms on several test reference materials and coatings, using the marine bacterium Cobetia marina as a model organism. The assay can be used to investigate the inhibition of bacterial growth and release properties of ma...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-009-0681-1
更新日期:2010-04-01 00:00:00
abstract::Over 100 bacteria from pulp and slime samples in a Canadian paper mill were identified by partial sequencing of their 16S rDNAs. Seventy-one percent of the isolates could be assigned to a bacterial genus with a high level of confidence. Another 12% exhibited at least 95% similarity within their 16S rDNA sequence with ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-002-0017-x
更新日期:2003-03-01 00:00:00
abstract::Production of recombinant proteins is an industrially important technique in the biopharmaceutical sector. Many recombinant proteins are problematic to generate in a soluble form in bacteria as they readily form insoluble inclusion bodies. Recombinant protein solubility can be enhanced by minimising stress imposed on ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-014-1489-1
更新日期:2014-09-01 00:00:00
abstract::Acid blue-15, a complex and resonance-stabilized triphenylmethane (TPM) textile dye, resistant to transformation, was decolorized/degraded in an up-flow immobilized cell bioreactor. A consortium comprised of isolates belonging to Bacillus sp., Alcaligenes sp. and Aeromonas sp. formed a multispecies biofilm on refracto...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-004-0121-1
更新日期:2004-03-01 00:00:00
abstract::Amyris is a fermentation product company that leverages synthetic biology and has been bringing novel fermentation products to the market since 2009. Driven by breakthroughs in genome editing, strain construction and testing, analytics, automation, data science, and process development, Amyris has commercialized nine ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-020-02314-3
更新日期:2020-11-01 00:00:00
abstract::For decades, microbial natural products have been one of the major sources of novel drugs for pharmaceutical companies, and today all evidence suggests that novel molecules with potential therapeutic applications are still waiting to be discovered from these natural sources, especially from actinomycetes. Any appropri...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1007/s10295-010-0882-7
更新日期:2011-03-01 00:00:00
abstract::Tolerance to various stresses is a key phenotype for cell catalysts, which are used widely in bioproduction of diverse valuable chemicals. Using the Rhodococcus ruber TH strain, which exhibits high nitrile hydratase activity, as the target cell catalyst for acrylamide production, we established a method to improve cel...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-012-1146-5
更新日期:2012-10-01 00:00:00
abstract::There have been numerous developments in ethanol fermentation technology since the beginning of the new millennium as ethanol has become an immediate viable alternative to fast-depleting crude reserves as well as increasing concerns over environmental pollution. Nowadays, although most research efforts are focused on ...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1007/s10295-011-0999-3
更新日期:2011-09-01 00:00:00
abstract::Twenty years ago, the first complete gene cluster encoding the actinorhodin biosynthetic pathway was cloned and characterized. Subsequently, the gene clusters encoding the biosynthetic pathways for many antibiotics were isolated. In the past decade, breakthroughs in technology brought that generation of rationally des...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章,评审
doi:10.1007/s10295-004-0131-z
更新日期:2004-03-01 00:00:00
abstract::The overall objective of this study is to evaluate the morphological [scanning electron microscopy (SEM)], physicochemical [differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), chemical composition analysis, Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR)], and bi...
journal_title:Journal of industrial microbiology & biotechnology
pub_type: 杂志文章
doi:10.1007/s10295-011-1027-3
更新日期:2012-02-01 00:00:00