scholarly journals Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste

2019 ◽  
Vol 6 (3) ◽  
pp. 180748 ◽  
Author(s):  
Stephanie L. Mathews ◽  
Mary Jane Epps ◽  
R. Kevin Blackburn ◽  
Michael B. Goshe ◽  
Amy M. Grunden ◽  
...  
Keyword(s):  
Industrial Waste ◽  
Bacterial Species ◽  
Black Liquor ◽  
Waste Product ◽  
Value Added ◽  
Bacterial Strains ◽  
Guided Discovery ◽  
Public Response ◽  
Degrading Bacteria ◽  
Citizen Science Project

A citizen science project found that the greenhouse camel cricket ( Diestrammena asynamora ) is common in North American homes. Public response was to wonder ‘what good are they anyway?’ and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle ( Dermestes maculatus ) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms.

scholarly journals Isolation of Adherent Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Bacteria Using PAH-Sorbing Carriers

2000 ◽  
Vol 66 (5) ◽  
pp. 1834-1843 ◽  
Author(s):  
Leen Bastiaens ◽  
Dirk Springael ◽  
Pierre Wattiau ◽  
Hauke Harms ◽  
Rupert deWachter ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Bacterial Species ◽  
Sole Source ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
High Adhesion ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic ◽  
Adhesion Efficiency

ABSTRACT Two different procedures were compared to isolate polycyclic aromatic hydrocarbon (PAH)-utilizing bacteria from PAH-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which PAHs were supplied as crystals and (ii) a new method in which PAH degraders were enriched on and recovered from hydrophobic membranes containing sorbed PAHs. Both techniques were successful, but selected from the same source different bacterial strains able to grow on PAHs as the sole source of carbon and energy. The liquid enrichment mainly selected for Sphingomonasspp., whereas the membrane method exclusively led to the selection ofMycobacterium spp. Furthermore, in separate membrane enrichment set-ups with different membrane types, three repetitive extragenic palindromic PCR-related Mycobacterium strains were recovered. The new Mycobacterium isolates were strongly hydrophobic and displayed the capacity to adhere strongly to different surfaces. One strain, Mycobacterium sp. LB501T, displayed an unusual combination of high adhesion efficiency and an extremely high negative charge. This strain may represent a new bacterial species as suggested by 16S rRNA gene sequence analysis. These results indicate that the provision of hydrophobic sorbents containing sorbed PAHs in the enrichment procedure discriminated in favor of certain bacterial characteristics. The new isolation method is appropriate to select for adherent PAH-degrading bacteria, which might be useful to biodegrade sorbed PAHs in soils and sludge.

scholarly journals Degradation and polymerization of black liquor lignin using Bacillus sp. isolated from a pulp mill

BioResources ◽  
2018 ◽  
Vol 14 (1) ◽  
pp. 1049-1076 ◽  
Author(s):  
Nipatcharaporn Sapapporn ◽  
Sirilux Chaijamrus ◽  
Wassana Chatdumrong ◽  
Tochampa
Keyword(s):  
Paper Industry ◽  
Black Liquor ◽  
Waste Product ◽  
Pulp Mill ◽  
Growth Conditions ◽  
Toxic Waste ◽  
Bacterial Strains ◽  
Industrial Utilization ◽  
Growing Conditions ◽  
First Time

A strain of Bacillus bacteria, which was able to increase the molecular weight (M) of black liquor (BL) lignin through polymerization, enabling the subsequent industrial use of lignin, was isolated and characterized. This study is believed to be the first time that actual bacteria cells, rather than pure laccase, have been used to polymerize BL lignin. Black liquor is a toxic waste product from the pulp and paper industry that contains lignin. However, the M of lignin is too low for commercial use. The bacteria performed two processes. First, the bacteria produced laccase, which degraded lignin into low M aromatic compounds (LMWACs). Second, the laccase transformed the LMWACs into quinone intermediates, which polymerized and became high M lignin. Five bacterial strains were isolated from a pulp mill, and the best strain was selected. The optimum growing conditions and BL concentration were determined. The optimum growth conditions when using pure lignin were 1 g/L lignin, 5 g/L urea, and 35 °C. When using BL instead of pure lignin, the optimum concentration was 2% BL (v/v). This information could help develop effective industrial utilization of BL lignin.

Biorefinery implementation for recovery debottlenecking at existing pulp mills- Part II: Techno-economic evaluation

TAPPI Journal ◽  
2012 ◽  
Vol 11 (8) ◽  
pp. 17-24 ◽  
Author(s):  
HAKIM GHEZZAZ ◽  
LUC PELLETIER ◽  
PAUL R. STUART
Keyword(s):  
Cost Estimation ◽  
Process Model ◽  
Black Liquor ◽  
Pulp Mill ◽  
Value Added ◽  
Economic Assessment ◽  
Extraction Process ◽  
Estimation Methods ◽  
Precipitation Process

The evaluation and process risk assessment of (a) lignin precipitation from black liquor, and (b) the near-neutral hemicellulose pre-extraction for recovery boiler debottlenecking in an existing pulp mill is presented in Part I of this paper, which was published in the July 2012 issue of TAPPI Journal. In Part II, the economic assessment of the two biorefinery process options is presented and interpreted. A mill process model was developed using WinGEMS software and used for calculating the mass and energy balances. Investment costs, operating costs, and profitability of the two biorefinery options have been calculated using standard cost estimation methods. The results show that the two biorefinery options are profitable for the case study mill and effective at process debottlenecking. The after-tax internal rate of return (IRR) of the lignin precipitation process option was estimated to be 95%, while that of the hemicellulose pre-extraction process option was 28%. Sensitivity analysis showed that the after tax-IRR of the lignin precipitation process remains higher than that of the hemicellulose pre-extraction process option, for all changes in the selected sensitivity parameters. If we consider the after-tax IRR, as well as capital cost, as selection criteria, the results show that for the case study mill, the lignin precipitation process is more promising than the near-neutral hemicellulose pre-extraction process. However, the comparison between the two biorefinery options should include long-term evaluation criteria. The potential of high value-added products that could be produced from lignin in the case of the lignin precipitation process, or from ethanol and acetic acid in the case of the hemicellulose pre-extraction process, should also be considered in the selection of the most promising process option.

Biodegradation of organophosphorus Pollutants by Soil Bacteria: Biochemical Aspects and Unsolved Problems

2020 ◽  
Vol 36 (4) ◽  
pp. 126-135
Author(s):  
T.V. Shushkova ◽  
D.O. Epiktetov ◽  
S.V. Tarlachkov ◽  
I.T. Ermakova ◽  
A.A. Leontievskii
Keyword(s):  
Genome Sequencing ◽  
Soil Bacteria ◽  
Activity Regulation ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Russian Science ◽  
Degrading Bacteria ◽  
Phosphorus Source ◽  
Glyphosate Herbicide ◽  
Enzymatic Pathways

The degradation of persistent organophosphorus pollutants have been studied in 6 soil bacterial isolates and in 3 bacterial strains adapted for utilization of glyphosate herbicide (GP) under laboratory conditions. Significant differences in the uptake of organophosphonates were found in taxonomically close strains possessing similar enzymatic pathways of catabolism of these compounds, which indicates the existence of unknown mechanisms of activity regulation of these enzymes. The effect of adaptation for GP utilization as a sole phosphorus source on assimilation rates of several other phosphonates was observed in studied bacteria. The newly found efficient stains provided up to 56% of GP decomposition after application to the soil in the laboratory. The unresolved problems of microbial GP metabolism and the trends for further research on the creation of reliable biologicals capable of decomposing organophosphonates in the environment are discussed. organophosphonates, glyphosate, biodegradation, bioremediation, C-P lyase, phosphonatase, degrading bacteria Investigation of phosphonatase and genome sequencing were supported by Russian Science Foundation Grant no. 18-074-00021.

scholarly journals β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization

2020 ◽  
Vol 9 (1) ◽  
pp. 55
Author(s):  
María Florencia Eberhardt ◽  
José Matías Irazoqui ◽  
Ariel Fernando Amadio
Keyword(s):  
Bacterial Species ◽  
Value Added ◽  
Raw Material ◽  
Activity Levels ◽  
Treatment Technology ◽  
Catalytic Domains ◽  
Stabilization Ponds ◽  
Cazy Database ◽  
Genes Encoding ◽  
Value Added Products

Stabilization ponds are a common treatment technology for wastewater generated by dairy industries. Large proportions of cheese whey are thrown into these ponds, creating an environmental problem because of the large volume produced and the high biological and chemical oxygen demands. Due to its composition, mainly lactose and proteins, it can be considered as a raw material for value-added products, through physicochemical or enzymatic treatments. β-Galactosidases (EC 3.2.1.23) are lactose modifying enzymes that can transform lactose in free monomers, glucose and galactose, or galactooligosacharides. Here, the identification of novel genes encoding β-galactosidases, identified via whole-genome shotgun sequencing of the metagenome of dairy industries stabilization ponds is reported. The genes were selected based on the conservation of catalytic domains, comparing against the CAZy database, and focusing on families with β-galactosidases activity (GH1, GH2 and GH42). A total of 394 candidate genes were found, all belonging to bacterial species. From these candidates, 12 were selected to be cloned and expressed. A total of six enzymes were expressed, and five cleaved efficiently ortho-nitrophenyl-β-galactoside and lactose. The activity levels of one of these novel β-galactosidase was higher than other enzymes reported from functional metagenomics screening and higher than the only enzyme reported from sequence-based metagenomics. A group of novel mesophilic β-galactosidases from diary stabilization ponds’ metagenomes was successfully identified, cloned and expressed. These novel enzymes provide alternatives for the production of value-added products from dairy industries’ by-products.

scholarly journals The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 451
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Subcellular Location ◽  
Low Complexity ◽  
Extracellular Proteins ◽  
Bacterial Strains ◽  
Bacterial Proteins ◽  
Protein Subcellular Location

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of two strains per species. We calculated all orthologous pairs for each of the 20 strain pairs. Per orthologous pair, we computed the conservation of two types of LCRs: compositionally biased regions (CBRs) and homorepeats (polyX). Our results show that, in bacteria, Q-rich CBRs are the most conserved, while A-rich CBRs and polyA are the most variable. LCRs have generally higher conservation when comparing pathogenic strains. However, this result depends on protein subcellular location: LCRs accumulate in extracellular and outer membrane proteins, with conservation increased in the extracellular proteins of pathogens, and decreased for polyX in the outer membrane proteins of pathogens. We conclude that these dependencies support the functional importance of LCRs in host–pathogen interactions.

scholarly journals Isolation and efficacy of two bacterial strains antagonists of Erwinia amylovora and Pectobacterium carotovorum

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
M’hamed BENADA ◽  
Boualem BOUMAAZA ◽  
Sofiane BOUDALIA ◽  
Omar KHALADI
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Bacterial Species ◽  
Crop Protection ◽  
Soft Rot ◽  
Causal Agent ◽  
Plant Diseases ◽  
Ecological Niches ◽  
Pectobacterium Carotovorum ◽  
Bacterial Strains

Abstract Background The development of ecofriendly tools against plant diseases is an important issue in crop protection. Screening and selection process of bacterial strains antagonists of 2 pathogenic bacterial species that limit very important crops, Erwinia amylovora, the causal agent of the fire blight disease, and Pectobacterium carotovorum, the causal agent of bacterial potato soft rot, were reported. Bacterial colonies were isolated from different ecological niches, where both pathogens were found: rhizosphere of potato tubers and fruits and leaves of pear trees from the northwest region of Algeria. Direct and indirect confrontation tests against strains of E. amylovora and P. carotovorum were performed. Results Results showed a significant antagonistic activity against both phytopathogenic species, using direct confrontation method and supernatants of cultures (p<0.005). In vitro assays showed growth inhibitions of both phytopathogenic species. Furthermore, results revealed that the strains of S. plymuthica had a better inhibitory effect than the strains of P. fluorescens against both pathogens. In vivo results on immature pear fruits showed a significant decrease in the progression of the fire blight symptoms, with a variation in the infection index from one antagonistic strain to another between 31.3 and 50%, and slice of potato showed total inhibition of the pathogen (P. carotovorum) by the antagonistic strains of Serratia plymuthica (p<0.005). Conclusion This study highlighted that the effective bacteria did not show any infection signs towards plant tissue, and considered as a potential strategy to limit the fire blight and soft rot diseases.

scholarly journals Investigating Lignin-Derived Monomers and Oligomers in Low-Molecular-Weight Fractions Separated from Depolymerized Black Liquor Retentate by Membrane Filtration

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2887
Author(s):  
Kena Li ◽  
Jens Prothmann ◽  
Margareta Sandahl ◽  
Sara Blomberg ◽  
Charlotta Turner ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Performance ◽  
Membrane Filtration ◽  
Black Liquor ◽  
Complex Mixture ◽  
Value Added ◽  
Kraft Pulping ◽  
Classification Model ◽  
Low Molecular Weight ◽  
Chemical Complexity

Base-catalyzed depolymerization of black liquor retentate (BLR) from the kraft pulping process, followed by ultrafiltration, has been suggested as a means of obtaining low-molecular-weight (LMW) compounds. The chemical complexity of BLR, which consists of a mixture of softwood and hardwood lignin that has undergone several kinds of treatment, leads to a complex mixture of LMW compounds, making the separation of components for the formation of value-added chemicals more difficult. Identifying the phenolic compounds in the LMW fractions obtained under different depolymerization conditions is essential for the upgrading process. In this study, a state-of-the-art nontargeted analysis method using ultra-high-performance supercritical fluid chromatography coupled to high-resolution multiple-stage tandem mass spectrometry (UHPSFC/HRMSn) combined with a Kendrick mass defect-based classification model was applied to analyze the monomers and oligomers in the LMW fractions separated from BLR samples depolymerized at 170–210 °C. The most common phenolic compound types were dimers, followed by monomers. A second round of depolymerization yielded low amounts of monomers and dimers, while a high number of trimers were formed, thought to be the result of repolymerization.

In vitro evaluation of the effect of nicotine, cotinine, and caffeine on oral microorganisms

2008 ◽  
Vol 54 (6) ◽  
pp. 501-508 ◽  
Author(s):  
Karina Cogo ◽  
Michelle Franz Montan ◽  
Cristiane de Cássia Bergamaschi ◽  
Eduardo D. Andrade ◽  
Pedro Luiz Rosalen ◽  
...  
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
Culture Media ◽  
Bacterial Species ◽  
In Vitro Study ◽  
Bacterial Strains ◽  
Planktonic Cells ◽  
Susceptibility Tests

The aim of this in vitro study was to evaluate the effects of nicotine, cotinine, and caffeine on the viability of some oral bacterial species. It also evaluated the ability of these bacteria to metabolize those substances. Single-species biofilms of Streptococcus gordonii , Porphyromonas gingivalis , or Fusobacterium nucleatum and dual-species biofilms of S. gordonii – F. nucleatum and F. nucleatum – P. gingivalis were grown on hydroxyapatite discs. Seven species were studied as planktonic cells, including Streptococcus oralis , Streptococcus mitis , Propionibacterium acnes , Actinomyces naeslundii , and the species mentioned above. The viability of planktonic cells and biofilms was analyzed by susceptibility tests and time-kill assays, respectively, against different concentrations of nicotine, cotinine, and caffeine. High-performance liquid chromatography was performed to quantify nicotine, cotinine, and caffeine concentrations in the culture media after the assays. Susceptibility tests and viability assays showed that nicotine, cotinine, and caffeine cannot reduce or stimulate bacterial growth. High-performance liquid chromatography results showed that nicotine, cotinine, and caffeine concentrations were not altered after bacteria exposure. These findings indicate that nicotine, cotinine, and caffeine, in the concentrations used, cannot affect significantly the growth of these oral bacterial strains. Moreover, these species do not seem to metabolize these substances.

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