Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

Abstract Background Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. Results Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. Conclusions The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.

Download Full-text

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

Microorganisms ◽

10.3390/microorganisms8071002 ◽

2020 ◽

Vol 8 (7) ◽

pp. 1002

Author(s):

Mikhail Kulyashov ◽

Sergey E. Peltek ◽

Ilya R. Akberdin

Keyword(s):

Citrate Synthase ◽

Thermophilic Bacteria ◽

Carbon Sources ◽

Metabolic Model ◽

Biofuel Production ◽

Biotechnological Applications ◽

Metabolic Potential ◽

A Genome ◽

Wide Range ◽

Genome Scale

The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus. The developed model provides new insights into thermophilic bacterial metabolism and highlights new strategies for biotechnological applications of the strain. Our analysis suggests that Geobacillus icigianus has a potential for 2,3-butanediol production from a variety of utilized carbon sources, including glycerine, a common byproduct of biofuel production. We identified a set of solutions for enhancing 2,3-BTD production, including cultivation under anaerobic or microaerophilic conditions and decreasing the TCA flux to succinate via reducing citrate synthase activity. Both in silico predicted metabolic alternatives have been previously experimentally verified for closely related strains including the genus Bacillus.

Download Full-text

Biochemical properties of CumA multicopper oxidase from plant pathogen, Pseudomonas syringae

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbab123 ◽

2021 ◽

Author(s):

Konan Ishida ◽

Yuya Tsukamoto ◽

Masaki Horitani ◽

Tomohisa Ogawa ◽

Yoshikazu Tanaka

Keyword(s):

Pseudomonas Syringae ◽

Plant Cell ◽

Plant Pathogens ◽

Plant Cell Wall ◽

Copper Ions ◽

Multicopper Oxidase ◽

Type I ◽

Multicopper Oxidases ◽

Oxidation Activity ◽

Wide Range

Abstract Multicopper oxidases have a wide range of substrate specificity to be involved in various physiological reactions. Pseudomonas syringae, a plant pathogenic bacterium, has a multicopper oxidase, CumA. Multicopper oxidases have ability to degrade plant cell wall component, lignin. Once P. syringae enter apoplast and colonize, they start to disrupt plant immunity. Therefore, deeper understanding of multicopper oxidases from plant pathogens, help to invent measures to prevent invasion into plant cell, which bring agricultural benefits. Several biochemical studies have reported lower activity of CumA compared with other multicopper oxidase called CotA. However, the mechanisms underlying the difference in activity have not yet been revealed. In order to acquire insight into them, we conducted a biophysical characterization of PsCumA. Our results show that PsCumA has weak type I copper EPR signal, which is essential for oxidation activity. We propose that difference in the coordination of copper ions may decrease reaction frequency.

Download Full-text

Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

Scientific Reports ◽

10.1038/s41598-021-85100-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Syed A. K. Shifat Ahmed ◽

Michelle Rudden ◽

Sabrina M. Elias ◽

Thomas J. Smyth ◽

Roger Marchant ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Quorum Sensing ◽

Virulence Factors ◽

Genomic Islands ◽

Clinical Strain ◽

Whole Genome ◽

Synonymous Mutations ◽

Wide Range

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.

Download Full-text

Future trends in diagnosis using laboratory-on-a-chip technologies

Parasitology ◽

10.1017/s0031182099004126 ◽

1999 ◽

Vol 117 (7) ◽

pp. 191-203 ◽

Cited By ~ 16

Author(s):

M. S. TALARY ◽

J. P. H. BURT ◽

R. PETHIG

Keyword(s):

Gene Expression ◽

Lower Cost ◽

Building Blocks ◽

Cancer Diagnostics ◽

Future Trends ◽

Biotechnological Applications ◽

Environmental Testing ◽

Current State ◽

Microelectronic Fabrication ◽

Wide Range

There has been an enormous growth in the development of biotechnological applications, where advances in the techniques of microelectronic fabrication and the technologies of miniaturization and integration in semiconductor industries are being applied to the production of Laboratory-on-a-Chip devices. The aim of this development is to create devices that will perform the same processes that are currently carried out in the laboratory in reduced timescales, at a lower cost, requiring less reagents, and with a greater resolution of detection and specificity. The expectations of this Laboratory-on-a-Chip revolution is that this technology will facilitate rapid advances in gene discovery, genetic mapping and gene expression with broader applications ranging from infectious diseases and cancer diagnostics to food quality and environmental testing. A review of the current state of development in this field reveals the scale of the ongoing revolution and serves to highlight the advances that can be perceived in the development of Laboratory-on-a-Chip technologies. Since miniaturization can be applied to such a wide range of laboratory processes, some of the sub-units that can be used as building blocks in these devices are described, with a brief description of some of the fabrication processes that can be used to create them.

Download Full-text

Improving Habitat Quality at the Local and Landscape Scales Increases Wild Bee Assemblages and Associated Pollination Services in Apple Orchards in China

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.621469 ◽

2021 ◽

Vol 9 ◽

Author(s):

Panlong Wu ◽

Piaopiao Dai ◽

Meina Wang ◽

Sijie Feng ◽

Aruhan Olhnuud ◽

...

Keyword(s):

Management Practices ◽

Ground Cover ◽

Agricultural Landscapes ◽

Wild Bees ◽

Natural Habitats ◽

Pollination Services ◽

Wild Bee ◽

Wide Range ◽

Bee Diversity ◽

Landscape Scales

Bees provide key pollination services for a wide range of crops. Accumulating evidence shows the effect of semi-natural habitats at the landscape level and local management practices on bee diversity in fields. However, most of the evidence is derived from studies in North America and Europe. Whether this paradigm is applicable in China, which is characterized by smallholder-dominated agricultural landscapes, has rarely been studied. In this study, we aimed to investigate how bee diversity affected apple production, and how landscape and local variables affected bee diversity and species composition on the Northern China Plain. The results showed that bees significantly increased apple fruit set compared to bagged controls. Wild bee diversity was positively related to apple seed numbers. Higher seed numbers reduced the proportion of deformed apples and thus increased fruit quality. Wild bee abundance was positively correlated with flowering ground cover, and both the abundance and species richness of wild bees were positively affected by the percentage of semi-natural habitats. We conclude that apple quality can benefit from ecological intensification comprising the augmentation of wild bees by semi-natural habitats and flowering ground cover. Future pollination management should therefore reduce the intensification level of management at both the local and landscape scales.

Download Full-text

Biosynthesis, purification, characterization and immobilization of laccase from Lithothelium sp.

Chemija ◽

10.6001/chemija.v31i3.4292 ◽

2020 ◽

Vol 31 (3) ◽

Author(s):

Ingrida Radveikienė ◽

Ingrida Pilotaitė ◽

Rimgailė Dainytė ◽

Regina Vidžiūnaitė

Keyword(s):

Residual Activity ◽

Catalytic Efficiency ◽

Hydrophobic Interaction Chromatography ◽

Metal Salts ◽

Biotechnological Applications ◽

Affinity Constants ◽

Sds Page ◽

Wide Range ◽

Optimum Ph ◽

Sulphate Salts

Novel fungal laccase isoenzymes (namely L95-1 and L95-2) produced by the Ascomycete Lithothelium sp. isolated from the forest soil were purified. However, only one of them was characterized, because the other isoenzyme lost its activity during purification. Extracellular L95-1 laccase was purified 30-fold using ion-exchange and hydrophobic interaction chromatography, with an overall yield of 88%. The molecular mass of purified L95-1 was estimated to be 85 kDa by SDS-PAGE analysis. L95-1 laccase was stable at temperature 4–22°C and pH 6.0–6.5. The substrate specificity of L95-1 laccase was examined with various compounds. Determined affinity constants (KM) varied in a wide range of 3.7–2020.0 µM, whereas catalytic efficiency constants (kcat/KM) covered a range of 0.008–1.9 µM–1 s–1. The optimum pH for most substrates varied in a range from pH 5.0 to 6.0. Sodium azide and fluoride strongly inhibited L95-1 activity, whereas sulphate salts inhibited weakly. The laccase was immobilized on the Fe3O4 nanoparticles and characterized. Residual activity remained at 20% after ten cycles of ABTS oxidation reaction. The immobilized laccase showed higher tolerance to various metal salts. The properties of L95-1 laccase make it potentially useful in the biotechnological applications.

Download Full-text

Embryonic and larval development of the caridean shrimp Palaemon argentinus (Decapoda, Caridea): effects of salinity and diet

Crustaceana ◽

10.1163/15685403-bja10041 ◽

2021 ◽

Vol 94 (1) ◽

pp. 45-62

Author(s):

Carolina Tropea ◽

Liane Stumpf ◽

Laura S. López Greco

Keyword(s):

Larval Development ◽

Artemia Salina ◽

Culture Conditions ◽

Nutritional Requirements ◽

Larval Performance ◽

Larval Rearing ◽

Caridean Shrimp ◽

Natural Habitats ◽

Larval Stages ◽

Wide Range

Abstract The caridean shrimp Palaemon argentinus is a species of commercial and ecological interest. Its numerous larval stages, the lack of knowledge on their nutritional requirements, and their ability to survive in a wide range of salinities raise questions on the optimum conditions for larval rearing in captivity. The present study was aimed at evaluating embryonic development under different salinities and larval development under different combinations of salinities and diet regimes, in order to define alternative, cheaper culture conditions. We tested salinities usually encountered by the species in natural habitats (0.1, 1 and 5 ppt) and a highly protein-inert diet (Tetracolor®) as a potential replacement for live food (nauplii of Artemia salina). The incubation period and fecundity were similar among salinity treatments. Overall, the number of survival days and percentage of zoeae that moulted two, three and four times were higher when embryogenesis occurred at 5 ppt and when larvae were exposed to 5 ppt. These results suggest that the conditions experienced by embryos affect the performance of the first larval stages, and probably reflect the lower energetic requirements of zoeae to osmoregulate as water and haemolymph osmolarity become closer. On the other hand, larval performance was better when fed A. salina nauplii than Tetracolor®. The latter may not cover the nutritional requirements of zoeae or may have low digestibility due to insufficient enzymes in the undeveloped larval digestive system. Based on the present results, we conclude that a salinity of 5 ppt combined with a diet consisting of Artemia sp. nauplii is optimal for larval culture at early stages.

Download Full-text

Is the Asian house gecko, Hemidactylus frenatus, really a threat to Australia’s biodiversity?

Australian Journal of Zoology ◽

10.1071/zo12077 ◽

2012 ◽

Vol 60 (6) ◽

pp. 361 ◽

Cited By ~ 10

Author(s):

E. P. Vanderduys ◽

A. S. Kutt

Keyword(s):

Current Evidence ◽

Human Influence ◽

Natural Habitats ◽

Natural Systems ◽

Wide Range ◽

Hemidactylus Frenatus

Invasive animals can have a wide range of impacts in natural systems. The introduced Asian house gecko Hemidactylus frenatus has invaded widely in Australia, but is largely restricted to human-altered landscapes. Hoskin (2011) has argued that H. frenatus has the potential to negatively impact Australian ecosystems by invading natural habitats. We examine this contention by reviewing an extensive standardised fauna survey dataset collected in northern and central Queensland during the key period of H. frenatus expansion from the 1990s to 2012. In light of these data we also re-examine data from other areas that suggest H. frenatus is a benign threat and is unlikely to become an environmental pest within Australia. On current evidence, we conclude that H. frenatus is unlikely to spread much beyond areas of human influence.

Download Full-text

Plastics recycling: challenges and opportunities

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2008.0311 ◽

2009 ◽

Vol 364 (1526) ◽

pp. 2115-2126 ◽

Cited By ~ 814

Author(s):

Jefferson Hopewell ◽

Robert Dvorak ◽

Edward Kosior

Keyword(s):

Carbon Dioxide Emissions ◽

Oil And Gas ◽

Renewable Resource ◽

Gas Production ◽

Rapid Expansion ◽

Natural Habitats ◽

Oil And Gas Production ◽

Wide Range ◽

Challenges And Opportunities ◽

Product Reuse

Plastics are inexpensive, lightweight and durable materials, which can readily be moulded into a variety of products that find use in a wide range of applications. As a consequence, the production of plastics has increased markedly over the last 60 years. However, current levels of their usage and disposal generate several environmental problems. Around 4 per cent of world oil and gas production, a non-renewable resource, is used as feedstock for plastics and a further 3–4% is expended to provide energy for their manufacture. A major portion of plastic produced each year is used to make disposable items of packaging or other short-lived products that are discarded within a year of manufacture. These two observations alone indicate that our current use of plastics is not sustainable. In addition, because of the durability of the polymers involved, substantial quantities of discarded end-of-life plastics are accumulating as debris in landfills and in natural habitats worldwide. Recycling is one of the most important actions currently available to reduce these impacts and represents one of the most dynamic areas in the plastics industry today. Recycling provides opportunities to reduce oil usage, carbon dioxide emissions and the quantities of waste requiring disposal. Here, we briefly set recycling into context against other waste-reduction strategies, namely reduction in material use through downgauging or product reuse, the use of alternative biodegradable materials and energy recovery as fuel. While plastics have been recycled since the 1970s, the quantities that are recycled vary geographically, according to plastic type and application. Recycling of packaging materials has seen rapid expansion over the last decades in a number of countries. Advances in technologies and systems for the collection, sorting and reprocessing of recyclable plastics are creating new opportunities for recycling, and with the combined actions of the public, industry and governments it may be possible to divert the majority of plastic waste from landfills to recycling over the next decades.

Download Full-text

Distribution and Antimicrobial Resistance of Salmonella Isolated from Pigs with Diarrhea in China

Microorganisms ◽

10.3390/microorganisms6040117 ◽

2018 ◽

Vol 6 (4) ◽

pp. 117 ◽

Cited By ~ 10

Author(s):

Jin-Hui Su ◽

Yao-Hong Zhu ◽

Tian-Yi Ren ◽

Liang Guo ◽

Gui-Yan Yang ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Metal Tolerance ◽

Heavy Metal Tolerance ◽

Clonal Expansion ◽

Multidrug Resistant ◽

High Similarity ◽

Enteric Diseases ◽

Antimicrobial Resistance Genes ◽

Wide Range ◽

Sequence Types

Salmonella can cause enteric diseases in humans and a wide range of animals, and even outbreaks of foodborne illness. The aim of this study was to investigate the frequency and distribution of serovars, and antimicrobial resistance in Salmonella isolates from pigs with diarrhea in 26 provinces in China from 2014 to 2016. A total of 104 Salmonella isolates were identified and the dominant serovar was S. 4,[5],12:i:- (53.9%). All Salmonella isolates were resistant to trimethoprim-sulfamethoxazole, and many were resistant to ampicillin (80.8%) and tetracycline (76.9%). Among 104 Salmonella isolates, aac(6′)-Ib-cr was the dominant plasmid-mediated quinolone resistance gene (80.8%), followed by qnrS (47.1%). The pulsed-field gel electrophoresis results suggest that the Salmonella isolates from different regions were genetically diverse, and ST34 was the most prevalent. S. 4,[5],12:i:- isolates is the widespread presence of heavy metal tolerance genes. The fact that the same sequence types were found in different regions and the high similarity coefficient of S. 4,[5],12:i:- isolates from different regions indicate the clonal expansion of the isolates, and the isolates carried various antimicrobial resistance genes. The multidrug resistant Salmonella can be widely detected in pigs, which will present a challenge for farm husbandry.

Download Full-text