Biofilm-degrading enzymes from Lysobacter gummosus

Microbiologically induced calcite precipitation (MICP) in situ remediated heavy metal contamination in sludge nutrient soil

Microbiologically induced calcite precipitation (MICP), as a newly developing bioremediation technology, could redeem heavy metal contamination in diverse scenarios. In this study, MICP bacterium Sporosarcina ureilytica ML-2 was employed to suppress the pollution of Pb, Cd and Zn in municipal sludge nutrient soil. After MICP remediation, the exchangeable Cd and Zn in sludge nutrient soil were correspondingly reduced by 31.02 % and 6.09 %, while the carbonate-bound Pb, Cd and Zn as well as the residual fractions were increased by 16.12 %, 6.63 %, 13.09 % and 6.10 %, 45.70 %, 3.86 %, respectively. In addition, the extractable Pb, Cd and Zn either by diethylenetriaminepentaacetic acid (DTPA) or toxicity characteristic leaching procedure (TCLP) in sludge nutrient soil were significantly reduced. These results demonstrated that the bio-calcite generated via MICP helped to immobilize heavy metals. Furthermore, MICP treatment improved the abundance of functional microorganisms related to urea cycle, while reduced the overall abundance of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). This work confirmed the feasibility of MICP in remediation of heavy metal in sludge nutrient soil, which expanded the application field of MICP and provided a promising way for heavy metal pollution management.

Deciphering the core bacterial community structure and function and their response to environmental factors in activated sludge from pharmaceutical wastewater treatment plants

Pharmaceutical wastewater is recognized for its heightened concentrations of organic pollutants, and biological treatment stands out as an effective technology to remove these organic pollution. Therefore, a comprehensive exploration of core bacterial community compositions, functions, and their responses to environmental factors in pharmaceutical wastewater treatment plants (PWWTPs) is important for understanding the removal mechanism of these organic pollutants. This study comprehensively investigated 36 activated sludge (AS) samples from 15 PWWTPs in China. The results revealed that Proteobacteria (45.41%) was the dominant phylum in AS samples, followed by Bacteroidetes (19.54%) and Chloroflexi (4.13%). While the dominant genera were similar in both aerobic and anaerobic treatment processes, their relative abundances exhibited significant variations. Genera like HA73, Kosmotoga, and Desulfovibrio were more abundant during anaerobic treatment, while Rhodoplanes, Bdellovibrio, and Hyphomicrobium dominated during aerobic treatment. 13 and 10 core operational taxonomic units (OTUs) were identified in aerobic and anaerobic sludge, respectively. Further analysis revealed that core OTUs belonging to genera Kosmotoga, Desulfovibrio, Thauera, Hyphomicrobium, and Chelativorans, were associated with key functions, including sulfur metabolism, methane metabolism, amino acid metabolism, carbohydrate metabolism, toluene degradation, and nitrogen metabolism. Furthermore, this study highlighted the crucial roles of environmental factors, such as COD, NH4+-N, SO42-, and TP, in shaping both the structure and core functions of bacterial communities within AS of PWWTPs. Notably, these factors indirectly affect functional attributes by modulating the bacterial community composition and structure in pharmaceutical wastewater. These findings provide valuable insights for optimizing the efficiency of biochemical treatment processes in PWWTPs.

Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system

This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.

Lysobacter gummosus 10.1.1, a Producer of Antimicrobial Agents

This work investigated the antimicrobial potential of Lysobacter gummosus 10.1.1. The culture fluid of the strain was found to contain antimicrobial agents active against Staphylococcus aureus, Micrococcus luteus, and Bacillus cereus. L. gummosus was first shown to be capable of forming outer membrane vesicles, which have a bacteriolytic effect against not only Gram-positive bacteria but also against the Gram-negative pathogen Pseudomonas aeruginosa. Transcriptomic analysis revealed the genes of almost all known bacteriolytic enzymes of Lysobacter, as well as the genes of enzymes with putative bacteriolytic activity. Also identified were genes involved in the biosynthesis of a number of secondary metabolites for which antimicrobial activities are known. This research is indicative of the relevance of isolating and studying L. gummosus antimicrobial agents.

Predatory bacteria as potential biofilm control and eradication agents in the food industry

Biofilms are a major concern within the food industry since they have the potential to reduce productivity in situ (within the field), impact food stability and storage, and cause downstream food poisoning. Within this review, predatory bacteria as potential biofilm control and eradication agents are discussed, with a particular emphasis on the intraperiplasmic Bdellovibrio-and-like organism (BALO) grouping. After providing a brief overview of predatory bacteria and their activities, focus is given to how BALOs fulfill four attributes that are essential for biocontrol agents to be successful in the food industry: (1) Broad spectrum activity against pathogens, both plant and human; (2) Activity against biofilms; (3) Safety towards humans and animals; and (4) Compatibility with food. As predatory bacteria possess all of these characteristics, they represent a novel form of biofilm biocontrol that is ripe for use within the food industry.

Microbiologically induced calcite precipitation for in situ stabilization of heavy metals contributes to land application of sewage sludge

Microbiologically induced calcite precipitation (MICP) has shed new light on solving the problem of in situ stabilization of heavy metals (HMs) in sewage sludge before land disposal. In this study, we examined whether MICP treatment can be integrated into a sewage sludge anaerobic digestion-land application process. Our results showed that MICP treatment not only prevented the transfer of ionic-state Cd from the sludge to the supernatant (98.46 % immobilization efficiency) but also reduced the soluble exchangeable Pb and Cd fractions by up to 100 % and 48.54 % and increased the residual fractions by 22.54 % and 81.77 %, respectively. In addition, the analysis of the stability of HMs in MICP-treated sludge revealed maximum reductions of 100 % and 89.56 % for TCLP-extractable Pb and Cd, respectively. Three-dimensional fluorescence, scanning electron microscopy-energy-dispersive X-ray spectroscopy, X-ray diffraction, and Fourier-transform infrared spectroscopy analyses confirmed the excellent performance of the ureolytic bacteria Sporosarcina ureilytica ML-2 in the sludge system. High-throughput sequencing showed that the relative abundance of Sporosarcina sp. reached 53.18 % in MICP-treated sludge, and the urease metabolism functional genes unit increased by a maximum of 239.3 %. The MICP technology may be a feasible method for permanently stabilizing HMs in sewage sludge before land disposal.

Comparative genomics provides insights into the potential biocontrol mechanism of two Lysobacter enzymogenes strains with distinct antagonistic activities

Lysobacter enzymogenes has been applied as an abundant beneficial microorganism to control plant disease; however, most L. enzymogenes strains have been mainly reported to control fungal diseases, not bacterial diseases. In this study, two L. enzymogenes strains were characterized, of which CX03 displayed a broad spectrum of antagonistic activities toward multiple bacteria, while CX06 exhibited a broad spectrum of antagonistic activities toward diverse fungi and oomycete, and the whole genomes of the two strains were sequenced and compared. The genome annotation showed that the CX03 genome comprised a 5,947,018 bp circular chromosome, while strain CX06 comprised a circular 6,206,196 bp chromosome. Phylogenetic analysis revealed that CX03 had a closer genetic relationship with L. enzymogenes ATCC29487T and M497-1, while CX06 was highly similar to L. enzymogenes C3. Functional gene annotation analyses of the two L. enzymogenes strains showed that many genes or gene clusters associated with the biosynthesis of different secondary metabolites were found in strains CX03 and CX06, which may be responsible for the different antagonistic activities against diverse plant pathogens. Moreover, comparative genomic analysis revealed the difference in bacterial secretory systems between L. enzymogenes strains CX03 and CX06. In addition, numerous conserved genes related to siderophore biosynthesis, quorum sensing, two-component systems, flagellar biosynthesis and chemotaxis were also identified in the genomes of strains CX03 and CX06. Most reported L. enzymogenes strains were proven mainly to suppress fungi, while CX03 exhibited direct inhibitory activities toward plant bacterial pathogens and showed an obvious role in managing bacterial disease. This study provides a novel understanding of the biocontrol mechanisms of L. enzymogenes, and reveals great potential for its application in plant disease control.

Photolytic quorum quenching effects on the microbial communities and functional gene expressions in membrane bioreactors

Photolytic quorum quenching by ultraviolet A (UVA) irradiation is an effective strategy for controlling membrane bioreactor (MBR) biofouling; however, its effects on MBR microbial communities and functional genes have not yet been explored. Here, we report on the effects of the UVA irradiation, which mitigates membrane biofouling, on the microbial community structures, alpha and beta diversities, and functional gene expressions in the MBR mixed liquor and biocake (membrane fouling layer) for the first time. The results show that the microbial communities become less diversified when alternating UVA is applied to the MBRs. The changes in the community structure are highly influenced by spatiotemporal factors, such as microbial habitats (mixed liquor and biocake) and reactor operation time, although UVA irradiation also has some impacts on the community. The relative abundance of the Sphingomonadaceae family, which can decompose the furan ring of autoinducer-2 (AI-2) signal molecules, becomes greater with continuous UVA irradiation. Xanthomonadaceae, which produces biofilm-degrading enzymes, is also more abundant with UVA photolysis than without it. Copies of monooxygenase and hydroxylase enzyme-related genes increase in the MBR with longer UVA exposures (i.e., continuous UVA). These enzymes seem to be inducible by UVA, enhancing the AI-2 inactivation. In conclusion, UVA irradiation alters the microbial community and the metabolism in the MBR, contributing to the membrane biofouling mitigation.

Expression of Biofilm-Degrading Enzymes in Plants and Automated High-Throughput Activity Screening Using Experimental Bacillus subtilis Biofilms

Biofilm-forming bacteria are sources of infections because they are often resistant to antibiotics and chemical removal. Recombinant biofilm-degrading enzymes have the potential to remove biofilms gently, but they can be toxic toward microbial hosts and are therefore difficult to produce in bacteria. Here, we investigated Nicotiana species for the production of such enzymes using the dispersin B-like enzyme Lysobacter gummosus glyco 2 (Lg2) as a model. We first optimized transient Lg2 expression in plant cell packs using different subcellular targeting methods. We found that expression levels were transferable to differentiated plants, facilitating the scale-up of production. Our process yielded 20 mg kg⁻¹ Lg2 in extracts but 0.3 mg kg⁻¹ after purification, limited by losses during depth filtration. Next, we established an experimental biofilm assay to screen enzymes for degrading activity using different Bacillus subtilis strains. We then tested complex and chemically defined growth media for reproducible biofilm formation before converting the assay to an automated high-throughput screening format. Finally, we quantified the biofilm-degrading activity of Lg2 in comparison with commercial enzymes against our experimental biofilms, indicating that crude extracts can be screened directly. This ability will allow us to combine high-throughput expression in plant cell packs with automated activity screening.

Extracellular riboflavin induces anaerobic biofilm formation in Shewanella oneidensis

BACKGROUND

Some microorganisms can respire with extracellular electron acceptors using an extended electron transport chain to the cell surface. This process can be applied in bioelectrochemical systems in which the organisms produce an electrical current by respiring with an anode as electron acceptor. These organisms apply flavin molecules as cofactors to facilitate one-electron transfer catalyzed by the terminal reductases and in some cases as endogenous electron shuttles.

RESULTS

In the model organism Shewanella oneidensis, riboflavin production and excretion trigger a specific biofilm formation response that is initiated at a specific threshold concentration, similar to canonical quorum-sensing molecules. Riboflavin-mediated messaging is based on the overexpression of the gene encoding the putrescine decarboxylase speC which leads to posttranscriptional overproduction of proteins involved in biofilm formation. Using a model of growth-dependent riboflavin production under batch and biofilm growth conditions, the number of cells necessary to produce the threshold concentration per time was deduced. Furthermore, our results indicate that specific retention of riboflavin in the biofilm matrix leads to localized concentrations, which by far exceed the necessary threshold value.

CONCLUSION

This study describes a new quorum-sensing mechanism in S. oneidensis. Biofilm formation of S. oneidensis is induced by low concentrations of riboflavin resulting in an upregulation of the ornithine-decarboxylase speC. The results can be applied for the development of strains catalyzing increased current densities in bioelectrochemical systems.

Characterization of Lysobacter spp. strains and their potential use as biocontrol agents against pear anthracnose

Colletotrichum fructicola, is an important fungal pathogen that has been reported to cause pear (Pyrus) anthracnose in China, resulting in substantial economic losses due to severe defoliation and decreased fruit quality and yield. In the search for novel strategies to control pear anthracnose, Lysobacter strains have drawn a great deal of attention due to their high-level production of extracellular enzymes and bioactive metabolites. In the present study, we compared four Lysobacter strains including Lysobacter enzymogenes OH11, Lysobacter antibioticus OH13, Lysobacter gummosus OH17 and Lysobacter brunescens OH23 with respect to their characteristics and activity against pear anthracnose caused by C. fructicola. The results showed that the evaluated Lysobacter species presented various colony morphologies when cultured on different media and were proficient in producing protease, chitinase, cellulase and glucanase, with L. enzymogenes OH11 showing typical twitching motility. L. enzymogenes OH11 and L. gummosus OH17 showed potent activity against the tested fungi and oomycetes. L. gummosus OH17 produced HSAF (heat-stable antifungal factor) which was demonstrated to be a major antifungal factor in L. enzymogenes OH11 and C3. Furthermore, L. antibioticus OH13 and L. brunescens OH23 exhibited strong antibacterial activity, especially against Xanthomonas species. Cultures of L. enzymogenes OH11 protected pear against anthracnose caused by C. fructicola, and the in vivo results indicated that treatment with an L. enzymogenes OH11 culture could decrease the diameter of lesions in pears by 35 % and reduce the severity of rot symptoms compared to that observed in the control. In the present study, we systemically compared four Lysobacter strains and demonstrated that they have strong antagonistic activity against a range of pathogens, demonstrating their promise in the development of biological control agents.

Lytic potential of Lysobacter capsici VKM B-2533T: bacteriolytic enzymes and outer membrane vesicles

Recent recurrent outbreaks of bacterial resistance to antibiotics have shown the critical need to identify new lytic agents to combat them. The species Lysobacter capsici VKM B-2533^T possesses a potent antimicrobial action against a number of bacteria, fungi and yeasts. Its activity can be due to the impact of bacteriolytic enzymes, antibiotics and peptides. This work isolated four homogeneous bacteriolytic enzymes and a mixture of two proteins, which also had a bacteriolytic activity. The isolates included proteins identical to L. enzymogenes α- and β-lytic proteases and lysine-specific protease. The proteases of 26 kDa and 29 kDa and a protein identified as N-acetylglycosaminidase had not been isolated in Lysobacter earlier. The isolated β-lytic protease digested live methicillin-resistant staphylococcal cells with high efficiency (minimal inhibitory concentration, 2.85 μg/mL). This property makes the enzyme deserving special attention. A recombinant β-lytic protease was produced. The antimicrobial potential of the bacterium was contributed to by outer membrane vesicles (OMVs). L. capsici cells were found to form a group of OMVs responsible for antifungal activity. The data are indicative of a significant antimicrobial potential of this bacterium that requires thorough research.

Feasibility of isolated novel facultative quorum quenching consortiums for fouling control in an AnMBR

Anaerobic membrane bioreactor (AnMBR) technology is being recognized as an appealing strategy for wastewater treatment, however, severity of membrane fouling inhibits its widespread implementations. This study engineered novel facultative quorum quenching consortiums (FQQs) coping with membrane fouling in AnMBRs with preliminary analysis for their quorum quenching (QQ) performances. Herein, Acyl-homoserine lactones (AHLs)-based quorum sensing (QS) in a lab-scale AnMBR initially revealed that N-Hexanoyl-dl-homoserine lactone (C6-HSL), N-Octanoyl-dl-homoserine lactone (C8-HSL) and N-Decanoyl-dl-homoserine lactone (C10-HSL) were the dominant AHLs in AnMBRs in this study. Three FQQs, namely, FQQ-C6, FQQ-C8 and FQQ-C10, were harvested after anaerobic screening of aerobic QQ consortiums (AeQQs) which were isolated by enrichment culture, aiming to degrade C6-HSL, C8-HSL and C10-HSL, respectively. Growth of FQQ-C6 and FQQ-C10 using AHLs as carbon source under anaerobic condition was significantly faster than those using acetate, congruously suggesting that their QQ performance will not be compromised in AnMBRs. All FQQs degraded a wide range of AHLs pinpointing their extensive QQ ability. FQQ-C6, FQQ-C8 and FQQ-C10 remarkably alleviated extracellular polymeric substances (EPS) production in a lab-scale AnMBR by 72.46%, 35.89% and 65.88%, respectively, and FQQ-C6 retarded membrane fouling of the AnMBR by 2 times. Bioinformatics analysis indicated that there was a major shift in dominant species from AeQQs to FQQs where Comamonas sp., Klebsiella sp., Stenotrophomonas sp. and Ochrobactrum sp. survived after anaerobic screening and were the majority in FQQs. High growth rate utilizing AHLs under anaerobic condition and enormous EPS retardation efficiency in FQQ-C6 and FQQ-C10 could be attributed to Comamonas sp.. These findings demonstrated that FQQs could be leveraged for QQ under anaerobic systems. We believe that this was the first work proposing a bacterial pool of facultative QQ candidates holding biotechnological promises for membrane fouling control in AnMBRs.

Phage-Derived Antibacterials: Harnessing the Simplicity, Plasticity, and Diversity of Phages

Despite the successful use of antibacterials, the emergence of multidrug-resistant bacteria has become a serious threat to global healthcare. In this era of antibacterial crisis, bacteriophages (phages) are being explored as an antibacterial treatment option since they possess a number of advantages over conventional antibacterials, especially in terms of specificity and biosafety; phages specifically lyse target bacteria while not affecting normal and/or beneficial bacteria and display little or no toxicity in that they are mainly composed of proteins and nucleic acids, which consequently significantly reduces the time and cost involved in antibacterial development. However, these benefits also create potential issues regarding antibacterial spectra and host immunity; the antibacterial spectra being very narrow when compared to those of chemicals, with the phage materials making it possible to trigger host immune responses, which ultimately disarm antibacterial efficacy upon successive treatments. In addition, phages play a major role in horizontal gene transfer between bacterial populations, which poses serious concerns for the potential of disastrous consequences regarding antibiotic resistance. Fortunately, however, recent advancements in synthetic biology tools and the speedy development of phage genome resources have allowed for research on methods to circumvent the potentially disadvantageous aspects of phages. These novel developments empower research which goes far beyond traditional phage therapy approaches, opening up a new chapter for phage applications with new antibacterial platforms. Herein, we not only highlight the most recent synthetic phage engineering and phage product engineering studies, but also discuss a new proof-of-concept for phage-inspired antibacterial design based on the studies undertaken by our group.

Differential effects of coral-giant clam assemblages on biofouling formation

To prevent the settlement and/or the growth of fouling organisms (i.e. bacteria, fungi or microalgae), benthic sessile species have developed various defense mechanisms among which the production of chemical molecules. While studies have mostly focused on the release of chemical compounds by single species, there exist limited data on multi-species assemblages. We used an integrative approach to explore the potential interactive effects of distinct assemblages of two corals species and one giant clam species on biofouling appearance and composition. Remarkably, we found distinct biofouling communities suggesting the importance of benthic sessile assemblages in biofouling control. Moreover, the assemblage of 3 species led to an inhibition of biofouling, likely through a complex of secondary metabolites. Our results highlight that through their different effect on their near environment, species assemblages might be of upmost importance for their survival and therefore, should now be taken into account for sustainable management of coral reefs.

Structural and functional properties of antimicrobial protein L5 of Lysоbacter sp. XL1

The Gram-negative bacterium Lysobacter sp. XL1 secretes into the extracellular space five bacteriolytic enzymes that lyse the cell walls of competing microorganisms. Of special interest are homologous lytic proteases L1 and L5. This work found protein L5 to possess Gly-Gly endopeptidase and N-acetylmuramoyl-L-Ala amidase activities with respect to staphylococcal peptidoglycan. Protein L5 was found to be capable of aggregating into amyloid-like fibril structures. The crystal structure of protein L5 was determined at a 1.60-Å resolution. Protein L5 was shown to have a rather high structural identity with bacteriolytic protease L1 of Lysobacter sp. XL1 and α-lytic protease of Lysobacter enzymogenes at a rather low identity of their amino acid sequences. Still, the structure of protein L5 was revealed to have regions that differed from their equivalents in the homologs. The revealed structural distinctions in L5 are suggested to be of importance in exhibiting its unique properties.

The impact of the omics era on the knowledge and use of Lysobacter species to control phytopathogenic micro-organisms

Omics technologies have had a tremendous impact on underinvestigated genera of plant disease biocontrol agents such as Lysobacter. Strong evidence of the association between Lysobacter spp. and the rhizosphere has been obtained through culture-independent methods, which has also contributed towards highlighting the relationship between Lysobacter abundance and soil suppressiveness. It is conceivable that the role played by Lysobacter spp. in soil suppressiveness is related to their ability to produce an impressive array of lytic enzymes and antibiotics. Indeed, genomics has revealed that biocontrol Lysobacter strains share a vast number of genes involved in antagonism activities, and the molecular pathways underlying how Lysobacter spp. interact with the environment and other micro-organisms have been depicted through transcriptomic analysis. Furthermore, omics technologies shed light on the regulatory pathways governing cell motility and the biosynthesis of antibiotics. Overall, the results achieved so far through omics technologies confirm that the genus Lysobacter is a valuable source of novel biocontrol agents, paving the way for studies aimed at making their application in field conditions more reliable.

Growth media affect the volatilome and antimicrobial activity against Phytophthora infestans in four Lysobacter type strains

Bacterial volatile organic compounds (VOCs) play important ecological roles in soil microbial interactions. Lysobacter spp. are key determinants of soil suppressiveness against phytopathogens and the production of non-volatile antimicrobial metabolites has been extensively characterised. However, the chemical composition and antagonistic properties of the Lysobacter volatilome have been poorly investigated. In this work, VOC emission profiles of four Lysobacter type strains grown on a sugar-rich and a protein-rich medium were analysed using solid-phase microextraction gas chromatography-mass spectrometry and proton transfer reaction-time of flight-mass spectrometry. Lysobacter antibioticus, L. capsici, L. enzymogenes and L. gummosus type strains were recognised according to their volatilome assessed using both headspace mass spectrometry methods Moreover, the chemical profiles and functional properties of the Lysobacter volatilome differed according to the growth medium, and a protein-rich substrate maximised the toxic effect of the four Lysobacter type strains against Phytophthora infestans. Antagonistic (pyrazines, pyrrole and decanal) and non-antagonistic (delta-hexalactone and ethanol) VOCs against Ph. infestans or putative plant growth stimulator compounds (acetoin and indole) were mainly emitted by Lysobacter type strains grown on protein- and sugar-rich media respectively. Thus nutrient availability under soil conditions could affect the aggressiveness of Lysobacter spp. and possibly optimise interactions of these bacterial species with the other soil inhabitants.

Epilithic and endolithic microorganisms and deterioration on stone church facades subject to urban pollution in a sub-tropical climate

Weathering of two church facades in Rio de Janeiro was caused substantially by salts, mainly halite and gypsum, detected by SEM and chemical analyses, which cause physical stresses by deposition within the rock. Biofilm populations, determined by SEM and as operational taxonomic units (OTUs), degraded stone by penetration, solubilization and redeposition of minerals on their surfaces. Endolithic cyanobacteria were associated with gypsum deposits. Microbiomes were typical for high-stress environments, high salt, intense insolation, low water and low nutrients (eg halophilic Rubrobacter, Salinicola, Sterigmatomyces). The main colonizers on the church most affected by traffic (Nossa Senhora da Candelária - CA) were Actinobacteria; Gammaproteobacteria (chiefly Pseudomonas) were predominant on the site situated in a leafy square (São Francisco de Paula - SF). Major Gammaproteobacteria on CA were halophilic Halomonas and Rhodobacteriaceae. Fungal OTUs on both churches were principally dimorphic, yeast-like basidiomycetes. Many OTUs of thermophilic microorganisms (eg the Thermomicrobia class, Chloroflexi) were present. This is the first use of next generation sequencing (NGS) to study microbial biofilm interactions with metamorphic and granite buildings in an intensely urban, sub-tropical climate.

Effects of biocide treatments on the biofilm community in Domitilla's catacombs in Rome

Different types of biofilms are widespread on lithic faces of the Catacombs of Domitilla (Rome, Italy) due to the favorable microclimatic conditions (temperature, high RH% and low irradiance). The biofilm, once established, becomes particularly dangerous due to the coverage of valuable surfaces causing spoilage, softening of materials and mineral precipitation. It is common practice to treat these surfaces with biocides in order to eradicate the microorganisms present. The aim of the present research was to compare the changes occurring to the microbial community present in the biofilm in one site of the Catacombs of Domitilla (CD15) before and after a biocide treatment (a mixture of quaternary ammonium compounds and octylisothiazolone, OIT), applied for a one month period. A multistep approach was followed, based on microscopy, cultural methods and molecular techniques (f-ITS and 16S rDNA sequencing), for the phenotypic and genetic analysis of the culturable microbial population. Our results highlighted that the biocide treatments had little effect against cyanobacteria, while the bacterial population increased in numbers but changed drastically in terms of diversity. In fact, some bacteria proliferate at the expense of the organic matter released by dead microorganisms as demonstrated by laboratory tests. Further, our data describe how the microbial interaction can have different responses depending on the favorable conditions for one kind of microorganism in respect to the others. This study exemplifies the real risks of applying biocide treatments on complex microbial communities and pinpoints the necessity of subjecting treatments to monitoring and reassessment. Moreover, the work showed the potential of bacteria isolated after the treatment for use, under controlled conditions, in combatting unwanted microbial growth in that they possess a positive tropism toward stressed microorganisms and high hydrolytic enzymatic activity against cell components (e.g. cellulose, chitin and pectin). A tentative protocol is proposed.

The Lysobacter capsici AZ78 Genome Has a Gene Pool Enabling it to Interact Successfully with Phytopathogenic Microorganisms and Environmental Factors

Lysobacter capsici AZ78 has considerable potential for biocontrol of phytopathogenic microorganisms. However, lack of information about genetic cues regarding its biological characteristics may slow down its exploitation as a biofungicide. In order to obtain a comprehensive overview of genetic features, the L. capsici AZ78 genome was sequenced, annotated and compared with the phylogenetically related pathogens Stenotrophomonas malthophilia K729a and Xanthomonas campestris pv. campestris ATCC 33913. Whole genome comparison, supported by functional analysis, indicated that L. capsici AZ78 has a larger number of genes responsible for interaction with phytopathogens and environmental stress than S. malthophilia K729a and X. c. pv. campestris ATCC 33913. Genes involved in the production of antibiotics, lytic enzymes and siderophores were specific for L. capsici AZ78, as well as genes involved in resistance to antibiotics, environmental stressors, fungicides and heavy metals. The L. capsici AZ78 genome did not encompass genes involved in infection of humans and plants included in the S. malthophilia K729a and X. c. pv. campestris ATCC 33913 genomes, respectively. The L. capsici AZ78 genome provides a genetic framework for detailed analysis of other L. capsici members and the development of novel biofungicides based on this bacterial strain.

Comparative genomics and metabolic profiling of the genus Lysobacter

Background

Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses.

Results

Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani.

Conclusions

Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2191-z) contains supplementary material, which is available to authorized users.

Diversity and Activity of Lysobacter Species from Disease Suppressive Soils

The genus Lysobacter includes several species that produce a range of extracellular enzymes and other metabolites with activity against bacteria, fungi, oomycetes, and nematodes. Lysobacter species were found to be more abundant in soil suppressive against the fungal root pathogen Rhizoctonia solani, but their actual role in disease suppression is still unclear. Here, the antifungal and plant growth-promoting activities of 18 Lysobacter strains, including 11 strains from Rhizoctonia-suppressive soils, were studied both in vitro and in vivo. Based on 16S rRNA sequencing, the Lysobacter strains from the Rhizoctonia-suppressive soil belonged to the four species Lysobacter antibioticus, Lysobacter capsici, Lysobacter enzymogenes, and Lysobacter gummosus. Most strains showed strong in vitro activity against R. solani and several other pathogens, including Pythium ultimum, Aspergillus niger, Fusarium oxysporum, and Xanthomonas campestris. When the Lysobacter strains were introduced into soil, however, no significant and consistent suppression of R. solani damping-off disease of sugar beet and cauliflower was observed. Subsequent bioassays further revealed that none of the Lysobacter strains was able to promote growth of sugar beet, cauliflower, onion, and Arabidopsis thaliana, either directly or via volatile compounds. The lack of in vivo activity is most likely attributed to poor colonization of the rhizosphere by the introduced Lysobacter strains. In conclusion, our results demonstrated that Lysobacter species have strong antagonistic activities against a range of pathogens, making them an important source for putative new enzymes and antimicrobial compounds. However, their potential role in R. solani disease suppressive soil could not be confirmed. In-depth omics'-based analyses will be needed to shed more light on the potential contribution of Lysobacter species to the collective activities of microbial consortia in disease suppressive soils.

A halotolerant thermostable lipase from the marine bacterium Oceanobacillus sp. PUMB02 with an ability to disrupt bacterial biofilms

A halotolerant thermostable lipase was purified and characterized from the marine bacterium Oceanobacillus sp. PUMB02. This lipase displayed a high degree of stability over a wide range of conditions including pH, salinity, and temperature. It was optimally active at 30 °C and pH 8.0 respectively and was stable at higher temperatures (50-70 °C) and alkaline pH. The molecular mass of the lipase was approximately 31 kDa based on SDS-PAGE and MALDI-ToF fingerprint analysis. Conditions for enhanced production of lipase by Oceanobacillus sp. PUMB02 were attained in response surface method-guided optimization with factors such as olive oil, sucrose, potassium chromate, and NaCl being evaluated, resulting in levels of 58.84 U/ml being achieved. The biofilm disruption potential of the PUMB02 lipase was evaluated and compared with a marine sponge metagenome derived halotolerant lipase Lpc53E1. Good biofilm disruption activity was observed with both lipases against potential food pathogens such as Bacillus cereus MTCC1272, Listeria sp. MTCC1143, Serratia sp. MTCC4822, Escherichia coli MTCC443, Pseudomonas fluorescens MTCC1748, and Vibrio parahemolyticus MTCC459. Phase contrast microscopy, scanning electron microscopy, and confocal laser scanning microscopy showed very effective disruption of pathogenic biofilms. This study reveals that marine derived hydrolytic enzymes such as lipases may have potential utility in inhibiting biofilm formation in a food processing environment and is the first report of the potential application of lipases from the genus Oceanobacillus in biofilm disruption strategies.