Genome sequence of Roseomonas sp. strain B5, a quorum-quenching N-acylhomoserine lactone-degrading bacterium isolated from Malaysian tropical soil

Isolation of Bacteria Capable of Degrading Various AHLs for Biofouling Control in Membrane Bioreactors

Membrane bioreactors (MBRs) are widely used to treat wastewater, mainly due to the production of high-quality effluent. However, biofilm forming on the surface of membranes can cause many problems, which remains one of the major limitations of this technique. Bacterial quorum quenching (QQ) has been proven to be a successful strategy to control biofouling in MBRs. However, for many QQ bacterial isolates, the detailed degradation rates of acyl homoserine lactones (AHLs) have rarely been reported. Therefore, this study aimed to isolate potential QQ bacteria and investigate their degradation rates against eight different AHLs. Results showed that four isolates (A9, A12, B11, and D3) exhibited consistent C8-HSL–(N-octanoyl-L-homoserine lactone) removal capabilities. These four isolates removed at least 70% of all AHLs tested within 180 min. They might have different QQ enzymes, based on our observation that the locations of enzyme activities differed. The bacteria most closely related to A9, A12, and B11 were Brucella anthropic, Bacillus cereus, and Bacillus toyonensis, respectively. Bacillus species have shown QQ activity in many studies, but AHL-reducing Brucella species have not been previously reported. Overall, this study extends our current knowledge of QQ bacteria that could be used to mitigate biofilm formation on MBR membranes.

Metagenomic analysis of the dust particles collected from the suction tube and the suction funnel of a dermatological laser smoke evacuator system

In the last few decades, there has essentially been an explosion in the use of lasers in medicine, especially in the area of cosmetic dermatology. Potentially harmful substances are liberated when tissues are vaporized with laser. This creates numerous risks, including the spread of infectious disease. Smoke evacuators are devices that capture and filter laser plume, thereby maintaining a safe environment for the surgical team and patient. Our aim was to characterize the microbial community structure within the suction tube and funnel of the smoke evacuator system, identify their origin, and evaluate pathogenicity. Dust particles were collected from the instruments with a cotton swab. DNA was extracted from the swabs and the transport media, and sequencing was performed using the Illumina HiSeq Xplatform. Metagenomic analysis was conducted using the Empowering the Development of Genomics Expertise (EDGE) Bioinformatics pipeline and custom Python scripts. The most abundant bacterial species were Micrococcus luteus and Brevibacterium casei in the suction tube, and Dermacoccus sp. Ellin 185 and Janibacter hoylei in the suction funnel. A total of 15 medium- to high-quality metagenome-assembled genomes (MAGs) were constructed where we found 104 antibiotic-resistant genes (ARGs) and 741 virulence factors. Findings indicate that the suction tube and funnel are likely a reservoir of virulence factor genes and ARGs, which can possibly be passed on to other bacteria via horizontal gene transfer. We would like to emphasize the health risk these microorganisms pose and the need to reevaluate the current hygiene standards with regard to the smoke evacuator system.

Characterization of Distinct CyanoHABs-Related Modules in Microbial Recurrent Association Network

To elucidate the interspecies connectivity between cyanobacteria and other bacteria (non-cyanobacteria) during cyanobacterial harmful algal blooms (cyanoHABs), samples were collected from the Nakdong River, Korea, from June 2016 to August 2017, and microbial recurrent association network (MRAN) analysis was performed to overcome the limitations of conventional network analysis. Microcystis blooms were tightly linked with Pseudanabaena in summer and were accompanied by significant changes in the non-cyanobacterial community composition (nCCC) compared to non-bloom period. Riverine bacterial communities could be clearly separated into modules that were involved in the formation, maintenance, and decomposition of cyanoHABs. Roseomonas and Herbaspirillum were directly linked with major cyanobacteria and assigned to connector and module hub in cyanoHABs-related modules, respectively. The functional profiles of the cyanoHABs-related modules suggested that nitrate reduction, aerobic ammonia oxidation, fermentation, and hydrocarbon degradation could be increased during the Microcystis bloom periods. In conclusion, MRAN analysis revealed that specific bacteria belonging to cyanoHABs-related module, including connectors and module hubs, appeared to contribute to the development and collapse of cyanoHABs. Therefore, to understand cyanoHABs, a modular microbial perspective may be more helpful than a single bacterial species perspective.

Novel N-Acyl Homoserine Lactone-Degrading Bacteria Isolated From Penicillin-Contaminated Environments and Their Quorum-Quenching Activities

N-Acyl homoserine lactones (AHLs) are signaling molecules used in the quorum sensing (QS) of Gram-negative bacteria. Some bacteria interfere with the QS system using AHL-inactivating enzymes, commonly known as quorum-quenching (QQ) enzymes. We have recently isolated a new QQ bacterium showing high resistance to multiple β-lactam antibiotics, and its QQ enzyme (MacQ) confers β-lactam antibiotic resistance and exhibits QQ activities. This observation suggests the possibility of isolating novel QQ bacteria from β-lactam antibiotic-resistant bacteria. In this direction, we attempted to isolate penicillin G (PENG)-resistant bacteria from penicillin-contaminated river sediments and activated sludge treating penicillin-containing wastewater and characterize their QQ activities. Of 19 PENG-resistant isolates, six isolates showed high QQ activity toward a broad range of AHLs, including AHLs with 3-oxo substituents. Five of the six AHL-degraders showed AHL-acylase activity and hydrolyzed the amide bond of AHLs, whereas the remaining one strain did not show AHL-acylase activity, suggesting that this isolate may likely possess alternative degradation mechanism such as AHL-lactonase activity hydrolyzing the lactone ring of AHLs. The 16S rRNA gene sequence analysis results categorized these six AHL-degrading isolates into at least five genera, namely, Sphingomonas (Alphaproteobacteria), Diaphorobacter (Betaproteobacteria), Acidovorax (Betaproteobacteria), Stenotrophomonas (Gammaproteobacteria), and Mycobacterium (Actinobacteria); of these, Mycobacterium sp. M1 has never been known as QQ bacteria. Moreover, multiple β-lactam antibiotics showed high minimum inhibitory concentrations (MICs) when tested against all of isolates. These results strongly demonstrate that a wide variety of β-lactam antibiotic-resistant bacteria possess QQ activities. Although the genetic and enzymatic elements are yet unclear, this study may infer the functional and evolutionary correlation between β-lactam antibiotic resistance and QQ activities.

Quorum sensing system and influence on food spoilage in Pseudomonas fluorescens from turbot

The spoilage of aquatic products is mainly caused by the bacterial growth, and the specific spoilage organism (SSO) plays an important role. Quorum sensing (QS) is a microbial cell-cell communication system which is coordinated with the population density, and is controlled by N-acyl-homoserine lactone (AHLs) as the Gram-negative bacteria communication signals. In this study, the SSO was Pseudomonas fluorescens (PF-04), isolated from the turbot (Scophthalmus maximus L.) during aerobically refrigerated storage. The supernatant extract of PF-04 tested the AHLs activities utilizing biosensor Chromobacterium violaceum CV026. AHL production was influenced by the environment temperature, and AHL production reduced obviously at 10 °C compare with 25 °C. In Luria-Bertani (LB) supplemented with 0.5-1.0% NaCl, AHL production reached the maximum. The AHL production was also regulated by pH of culture medium, acidic condition was conducive to persistent existence of the AHL molecules, but the alkaline environment would cause chemically unstable of AHL molecules. QS system in P. flurosecens played an imperative role in biofilm formation, protease and siderophore production. AHLs could regulate above three factors in PF-04. In summary, this study showed that (1) the influence of different environmental conditions (temperature, NaCl and pH) on AHL production revealed the correlation of QS in foods and (2) that proved the effect of external AHLs to regulate the biofilm formation, protease and siderophore production in PF-04.

Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia

Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation.

Novel quorum quenching enzymes identified from draft genome of Roseomonas sp. TAS13

Roseomonas sp. strain TAS13 isolated from an activated sludge sample degrades N-acylhomoserine lactones (AHLs) that are widely utilized as a signal in bacterial quorum sensing systems. The draft genome of Roseomonas sp. TAS13 contains 816 contigs (total 5,078,941 bp) which carries 4760 protein-coding genes and 52 tRNA genes (DDBJ/EMBL/GenBank accession numbers BDLP01000001 through BDLP01000816).

Genome Anatomy of Streptococcus parasanguinis Strain C1A, Isolated from a Patient with Acute Exacerbation of Chronic Obstructive Pulmonary Disease, Reveals Unusual Genomic Features

Streptococcus parasanguinis causes invasive diseases. However, the mechanism by which it causes disease remains unclear. Here, we describe the complete genome sequence of S. parasanguinis C1A, isolated from a patient diagnosed with an acute exacerbation of chronic obstructive pulmonary disease. Several genes that might be associated with pathogenesis are also described.

Pantoea sp. isolated from tropical fresh water exhibiting N-acyl homoserine lactone production

N-Acyl homoserine lactone (AHL) serves as signaling molecule for quorum sensing (QS) in Gram-negative bacteria to regulate various physiological activities including pathogenicity. With the aim of isolating freshwater-borne bacteria that can cause outbreak of disease in plants and portrayed QS properties, environmental water sampling was conducted. Here we report the preliminary screening of AHL production using Chromobacterium violaceum CV026 and Escherichia coli [pSB401] as AHL biosensors. The 16S rDNA gene sequence of isolate M009 showed the highest sequence similarity to Pantoea stewartii S9-116, which is a plant pathogen. The isolated Pantoea sp. was confirmed to produce N-3-oxohexanoyl-L-HSL (3-oxo-C6-HSL) through analysis of high resolution mass tandem mass spectrometry.

Pseudomonas cremoricolorata strain ND07 produces N-acyl homoserine lactones as quorum sensing molecules

Quorum sensing (QS) is a bacterial cell-to-cell communication system controlling QS-mediated genes which is synchronized with the population density. The regulation of specific gene activity is dependent on the signaling molecules produced, namely N-acyl homoserine lactones (AHLs). We report here the identification and characterization of AHLs produced by bacterial strain ND07 isolated from a Malaysian fresh water sample. Molecular identification showed that strain ND07 is clustered closely to Pseudomonas cremoricolorata. Spent culture supernatant extract of P. cremoricolorata strain ND07 activated the AHL biosensor Chromobacterium violaceum CV026. Using high resolution triple quadrupole liquid chromatography-mass spectrometry, it was confirmed that P. cremoricolorata strain ND07 produced N-octanoyl-l-homoserine lactone (C8-HSL) and N-decanoyl-l-homoserine lactone (C10-HSL). To the best of our knowledge, this is the first documentation on the production of C10-HSL in P. cremoricolorata strain ND07.

Degradation of bacterial quorum sensing signaling molecules by the microscopic yeast Trichosporon loubieri isolated from tropical wetland waters

Proteobacteria produce N-acylhomoserine lactones as signaling molecules, which will bind to their cognate receptor and activate quorum sensing-mediated phenotypes in a population-dependent manner. Although quorum sensing signaling molecules can be degraded by bacteria or fungi, there is no reported work on the degradation of such molecules by basidiomycetous yeast. By using a minimal growth medium containing N-3-oxohexanoylhomoserine lactone as the sole source of carbon, a wetland water sample from Malaysia was enriched for microbial strains that can degrade N-acylhomoserine lactones, and consequently, a basidiomycetous yeast strain WW1C was isolated. Morphological phenotype and molecular analyses confirmed that WW1C was a strain of Trichosporon loubieri. We showed that WW1C degraded AHLs with N-acyl side chains ranging from 4 to 10 carbons in length, with or without oxo group substitutions at the C3 position. Re-lactonisation bioassays revealed that WW1C degraded AHLs via a lactonase activity. To the best of our knowledge, this is the first report of degradation of N-acyl-homoserine lactones and utilization of N-3-oxohexanoylhomoserine as carbon and nitrogen source for growth by basidiomycetous yeast from tropical wetland water; and the degradation of bacterial quorum sensing molecules by an eukaryotic yeast.