Metabolic characterization of a strain (BM90) of Delftia tsuruhatensis showing highly diversified capacity to degrade low molecular weight phenols

Activation of stress reactions in the dinophyte microalga Prorocentrum cordatum as a consequence of the toxic effect of ZnO nanoparticles and zinc sulfate

According to the results of the experimental study, the main regularities of changes in morphological, structural-functional and fluorescent indices of P. cordatum were established when zinc oxide nanoparticles ZnO NPs (0.3-6.4 mg L-1) and Zn in form of salt (0.09-0.4 mg L-1) were added to the medium. The studied pollutants have cytotoxic (growth inhibition, development of oxidative stress, destruction of cytoplasmic organelles, disorganization of mitochondria) and genotoxic (changes in the morphology of nuclei, chromatin condensation) effects on microalgae, affecting almost all aspects of cell functioning. Despite the similar mechanism of action of zinc sulfate and ZnO NPs on P. cordatum cells, the negative effect of ZnO NPs is also due to the inhibition of photosynthetic activity of cells (significant decrease in the maximum quantum yield of photosynthesis and electron transport rate), reduction of chlorophyll concentration from 3.5 to 1.8 pg cell-1, as well as mechanical effect on cells: deformation and damage of cell membranes, aggregation of NPs on the cell surface. Apoptosis-like signs of cell death upon exposure to zinc sulfate and ZnO NPs were identified by flow cytometry and laser scanning confocal microscopy methods: changes in cell morphology, cytoplasm retraction, development of oxidative stress, deformation of nuclei, and disorganization of mitochondria. It was shown that the first signs of cell apoptosis appear at 0.02 mg L-1 Zn and 0.6 mg L-1 ZnO NPs after 72 h of exposure. At higher concentrations of pollutants, a dose-dependent decrease in algal enzymatic activity (up to 5 times relative to control) and mitochondrial membrane potential (up to 4 times relative to control), and an increase in the production of reactive oxygen species (up to 4-5 times relative to control) were observed. The results of the presented study contribute to the disclosure of fundamental mechanisms of toxic effects of pollutants and prediction of ways of phototrophic microorganisms reaction to this impact.

Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant

Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.

Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk

Delftia tsuruhatensis is a gram-negative, aerobic bacterium mostly known as an organic pollutant degrading and growth-promoting microorganism. However, it recently emerged as an opportunistic human pathogen. To date, the source of D. tsuruhatensis infection is not clear. The majority of studies of D. tsuruhatensis have focused on environmental or clinical strains, while investigations of D. tsuruhatensis strains isolated from food sources are limited. In the present study, we report the case of D. tsuruhatensis isolation from raw bovine milk. Classical bacteriology approaches, as well as next-generation sequencing and comparative genomics, were used to characterize the features of the D. tsuruhatensis MR-6/3H strain. The MR-6/3H strain was resistant to 19 antimicrobials among 23 tested, including all aminoglycosides, phenicol, trimethoprim-sulfamethoxazole, and almost all β-lactams. Phylogenetically, the MR-6/3H was close to clinical origin strains, including those previously isolated in Russia. Comparative genomics revealed the presence of putative antimicrobial resistance genes in the MR-6/3H isolate, mostly associated with efflux systems. Notably, genus-specific OXA-926-like β-lactamase was also detected. In all, 27 putative virulence factors were predicted, the majority of which were associated with motility, adherence, stress survival, siderophore synthesis, and immunomodulation. In the MR-6/3H genome, the five prophage regions were identified, including two with intact levels. Integrons and CRISPR-Cas systems were not detected in the MR-6/3H isolate. Thus, our findings suggest that raw milk can be the potential source of and transmission route for the dissemination of multidrug-resistant D. tsuruhatensis.

The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves

Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.

Flow Cytometric Investigation of Salinicola halophilus S28 Physiological Response Provides Solid Evidence for Its Uncommon and High Ability to Face Salt-Stress Conditions

In a previous work, some bacterial strains isolated from the Saline di Tarquinia marine salterns (Viterbo, Italy) showed very unusual growth profiles in relation to temperature and salinity variations when grown in solid media. In particular, Salinicola halophilus S28 showed optimal or suboptimal growth in a very wide range of NaCl concentrations, suggesting a great coping ability with salinity variations. These intriguing outcomes did not fit with the general Salinicola halophilus description as a moderately halophilic species. Therefore, this study profiles the actual physiological status of S28 cells subjected to different NaCl concentrations to provide evidence for the actual coping ability of strain S28 with broad salinity variations. Flow cytometry was selected as the evaluation method to study the physiological status of bacterial cells subjected to different salinity levels, monitoring the strain response at different growth phases over 72 h. Strain S28 showed maximal growth at 8% NaCl; however, it grew very well with no statistically significant differences at all salinity conditions (4–24% NaCl). Flow cytometric results provided clear evidence of its actual and strong ability to face increasing salinity, revealing a good physiological response up to 24% of NaCl. In addition, strain S28 showed very similar cell physiological status at all salinity levels, as also indicated by the flat growth profile revealed in the range of 4–24% NaCl. This is the first study regarding the physiological response during the growth of halophilic bacteria under different conditions of salinity via flow cytometry. This technique represents an effective tool for the investigation of the physiological status of each cell, even if it is somehow underrated and underused by microbiologists for this purpose.

Treatment of High-Polyphenol-Content Waters Using Biotechnological Approaches: The Latest Update

Polyphenols and their intermediate metabolites are natural compounds that are spread worldwide. Polyphenols are antioxidant agents beneficial for human health, but exposure to some of these compounds can be harmful to humans and the environment. A number of industries produce and discharge polyphenols in water effluents. These emissions pose serious environmental issues, causing the pollution of surface or groundwater (which are used to provide drinking water) or harming wildlife in the receiving ecosystems. The treatment of high-polyphenol-content waters is mandatory for many industries. Nowadays, biotechnological approaches are gaining relevance for their low footprint, high efficiency, low cost, and versatility in pollutant removal. Biotreatments exploit the diversity of microbial metabolisms in relation to the different characteristics of the polluted water, modifying the design and the operational conditions of the technologies. Microbial metabolic features have been used for full or partial polyphenol degradation since several decades ago. Nowadays, the comprehensive use of biotreatments combined with physical-chemical treatments has enhanced the removal rates to provide safe and high-quality effluents. In this review, the evolution of the biotechnological processes for treating high-polyphenol-content water is described. A particular emphasis is given to providing a general concept, indicating which bioprocess might be adopted considering the water composition and the economic/environmental requirements. The use of effective technologies for environmental phenol removal could help in reducing/avoiding the detrimental effects of these chemicals. In addition, some of them could be employed for the recovery of beneficial ones.

Time of Day for Harvest Affects the Fermentation Parameters, Bacterial Community, and Metabolic Characteristics of Sorghum-Sudangrass Hybrid Silage

To characterize the effects of time of day for harvest on the fermentation parameters, bacterial community, and metabolic characteristics of sorghum-sudangrass hybrid (SSG) silage, SSG (vegetative stage) harvested at 7:00 (AM), 12:00 (M), and 17:00 (PM) on three sunny days were ensiled for 1, 3, 7, 14, 30, and 60 days. Compared to AM silage, M and PM silages were characterized by delayed fermentation, unnormal lower final pH, and lower acetic acid production. In addition, PM silage contained higher residual water-soluble carbohydrates than other silages. After 60 days of ensiling, AM silage was dominated by Lactobacillus, whereas the bacterial communities of M and PM silages were complex and mainly composed of bacteria such as Delftia, Methylobacterium-Methylorubrum, Enhydrobacter, Acinetobacter, and Bacillus. The harvest time affected a wide range of metabolic pathways including "Metabolism" and "Cellular Processes" and "Organismal Systems" in SSG silage. Particularly, at the late stage of ensiling M silage exhibited highest relative abundances of amino acid metabolisms including "glycine, serine, and threonine metabolism," "phenylalanine metabolism," and lowest relative abundances of "lysine biosynthesis." These results suggest that the time of day for harvest could affect the fermentation parameters, bacterial community, and metabolic characteristics of SSG silage. Better SSG silage characteristics could be achieved through morning harvest. IMPORTANCE Ensiling is a common way for preserving green forages worldwide. Silage fermentation quality can vary greatly depending on the chemical and microbial characteristics of forage crop being ensiled. It is well documented that forages exhibit considerable variations in chemical composition and epiphytic microbiota during daylight. However, the effects of the time of day for harvest on silage fermentation is less investigated. Our results demonstrate that the time of day for harvest could affect the fermentation parameters, bacterial community, and metabolic characteristics of SSG hybrid silage. Harvesting SSG late in the day delayed fermentation process, lowered acetic acid production and final pH, and increased the residual water-soluble carbohydrates content in silage. Moreover, the delayed harvest time increased the relative abundances of bacteria such as Delftia, Methylobacterium-Methylorubrum, Acinetobacter, Enhydrobacter, and Bacillus, and amino acid metabolisms at the late stage of SSG ensiling. This study highlights the importance of diurnal changes in forage to fermentation characteristics, providing a strategy to improve silage quality through optimizing the harvest time.

Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species

Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective.

IMPORTANCED. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.

Synergetic suppression effects upon the combination of UV-C irradiation and berberine on Microcystis aeruginosa and Scenedesmus obliquus in reclaimed water: Effectiveness and mechanisms

The risk of harmful algal blooms (HABs) in the water recharged with reclaimed water is a bottleneck for water reuse. The suppression effects and mechanisms of the combination of UV-C and berberine on Microcystis aeruginosa and Scenedesmus obliquus in reclaimed water were investigated. Mono UV-C irradiation at 75 mJ cm^-2 could suppress the growth of M. aeruginosa for 7 d and that at 90 mJ cm^-2 could suppress the growth of S. obliquus for 5 d. UV-C irradiation combined with 0.2-2 mg L^-1 berberine lengthened the inhibition period of M. aeruginosa to 10- > 22 d and that of S. obliquus to 7- > 22 d and induced more rapid lethal effects on the harmful microalgal cells, in significant synergetic patterns. The combination of UV-C and berberine suppressed total, intracellular and extracellular microcystin-LR (MC-LR) more effectively and decreased the MC-LR quota significantly, which further reduced the risks of microcystin production and release. Furthermore, synergetic mechanisms of the combined treatments were systematically investigated from the aspects of photosynthetic system (photosynthetic activity and pigments), metabolic activity (ATP and membrane potential), oxidation stress (reactive oxygen species (ROS) and glutathione (GSH)), and apoptosis-like cell death (phosphatidylserine (PS) ectropion, caspase-3 activity and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) positive rate). The combination treatment provided a joint attack of UV-C and berberine on photosynthetic transport chain of photosynthetic system II (PS II), and a synergetic pathway to achieve more severe disruptions in energy metabolism as well as aggravated oxidative stress. The accumulated ROS enhanced increases in programmed cell death (PCD) indicators of both microalgal species, which contributed to the enhancement effects on growth suppression. The results showed that the combination treatment achieved lower dose requirements of both UV-C irradiation and berberine for inducing the same inhibition effects on microalgal cells, which was promising to be applied in the HABs control of reclaimed water.

Delftibactin-A, a Non-ribosomal Peptide With Broad Antimicrobial Activity

The rapid emergence of drug resistant bacteria is occurring worldwide, outpacing the development of new antibiotics. It is known that some of the main sources of antibiotics are the bacteria themselves, many of which are secondary metabolites of Gram positive bacteria. Siderophores, which are secondary metabolites, function as natural chelators (e.g., iron). They are produced and secreted by many bacteria and have been experimented on as "carriers" of several types of antibiotics that pass the cell membrane of challenging Gram negative bacteria. Delftibactin A is a non-ribosomal peptide (NRP), which is known to detoxify gold in Delftia spp. and form gold nuggets, and is considered to be a siderophore. In this study we demonstrate that the supernatant from novel environmental isolates of Delftia spp. have antimicrobial activity. We characterized the active fraction and identified delftibactin A as a compound with antimicrobial activity. Delftibactin A exhibits potent antimicrobial activity against Gram positive multi drug resistant (MDR) bacteria like Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin resistant Enterococcus (VRE), and also against the Gram negative pathogens Acinetobacter baumannii and Klebsiella pneumoniae. We discovered that the production of delftibactin A is greatly influenced by temperature. Furthermore, we have demonstrated the possibility of utilizing delftibactin A as a siderophore carrier of toxic metals such as gallium into Gram negative bacteria. These findings expose new opportunities of yet unexploited natural products such as delftibactin A, which have been known for other bacterial uses, as potent factors in the battle against MDR bacteria.

Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of Eruca sativa, growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as Delftia acidovorans at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (C16:1ω7c/C16:1ω6c) and C16:0) and matched that of Delftia acidovorans at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the Delftia clade and constructed a monophyletic subcluster with Delftia acidovorans NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.

Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome

Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify "core microbiome" members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with "core" taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified "core" microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.

Characterization of plant growth promoting feature of a neutromesophilic, facultatively chemolithoautotrophic, sulphur oxidizing bacterium Delftia sp. strain SR4 isolated from coal mine spoil

A new facultative chemolithoautotrophic heavy metal resistant sulfur-oxidizing bacterium was isolated from spoil sample of an open cast coal mine. FESEM demonstrated that the bacterium from Delftia genus was rod-shaped mucoid and motile. It autotrophically oxidized 20 mM thiosulfate and 1 g l^-1 elemental sulfur to 220 mg l^-1 and 203 mg l^-1 of sulfate, respectively in 7 days under oxic condition and was also able to grow heterotrophically. The strain showed many plant growth promoting properties like production of IAA (23 ug ml^-1), ammonia (6 umol ml^-1), siderophore (55% siderophore unit), and HCN (30 ppm) upon 48 hours of incubation. In Pikovskaya's agar, the strain showed phosphate solubilization index of 2.0 and solubilized tri-calcium phosphate (232 ug ml^-1) and lowered pH from 8.0 to 4.5 within 18 days. The strain yielded promising results on Brassica juncea growth and sulfur, phosphorus, and lead uptake. Where sulfur and phosphorous accumulation was 52 and 116% higher in whole treated plants (derived from microbe-coated seeds), lead accumulation were 81 and 50% higher in shoot and root of the treated plants than control plants (derived from untreated seeds) . These results point that this multifunctional strain can be proposed for phytorestoration of heavy metal contaminated sites.

Delftia tsuruhatensis, an Emergent Opportunistic Healthcare-Associated Pathogen

Delftia tsuruhatensis, which was first isolated in environmental samples, was rarely associated with human infections. We report on pneumonia caused by D. tsuruhatensis in an infant who underwent cardiac surgery. Retrospective analyses detected 9 other isolates from 8 patients. D. tsuruhatensis is an emergent pathogen, at least for immunocompromised patients.

Growth suppression and apoptosis-like cell death in Microcystis aeruginosa by H2O2: A new insight into extracellular and intracellular damage pathways

H₂O₂ has been suggested and applied as effective algaecide for harmful cyanobacterial bloom control, however, the transport of exogenous H₂O₂ into microalgal cells, the subsequent intracellular damage pathway and dose-response variations were little studied. We addressed these questions in a bloom-forming cyanobacterium Microcystis aeruginosa with H₂O₂ at 0.1-1.5 mM. The results showed that H₂O₂ at 0.4 mM and above significantly suppressed M. aeruginosa growth for over two weeks, and induced apoptosis-like death in terms of membrane potential dissipation, caspase-3 activation, chromatin condensation, and lysis induction. However, the dose-response effects were not monotonic. H₂O₂ at 0.7 mM resulted in the severest growth suppression among 0.1-1.5 mM treatments, including the lowest biomass for 74% loss, the highest cell lysis ratio for 79%, and the highest utilization rate of H₂O₂ for 0.101 mM d^-1. Moreover, several evidence point to severer apoptosis-like cell death in 0.7 mM treatments, involving fastest and severest cell lysis, smallest cell size and wrinkled surface and lowest membrane potential. Therefore, the apoptosis-like cell death induced by H₂O₂ at moderate dosages should be a crucial cause for the non-monotonic dose-response effects on growth suppression. Additionally, intracellular H₂O₂ level increased rapidly within 20 min after exposure at 0.4 mM and above, directly confirming the transport of exogenous H₂O₂ into M. aeruginosa cells and the intracellular damages due to subsequent elevation in intracellular oxidative stress. The study demonstrates that H₂O₂ at moderate dosages could be a promising method for the biomass control, in a fast and efficient way, on M. aeruginosa blooms.

Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1

A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic phage RG-2014 was isolated for developing phage based therapeutic approaches against Delftia tsuruhatensis strain ARB-1. The strain ARB-1 belongs to the Comamonadaceae family of the Betaproteobacteria class. RG-2014 was characterized for its type, burst size, latent and eclipse time periods of 150 ± 9 PFU/cell, 10-min, <5-min, respectively. The phage was found to be a dsDNA virus belonging to the Podoviridae family. It has an isometric icosahedrally shaped capsid with a diameter of 85 nm. The complete genome of the isolated phage was sequenced and determined to be 73.8 kbp in length with a G + C content of 59.9%. Significant similarities in gene homology and order were observed between Delftia phage RG-2014 and the E. coli phage N4 indicating that it is a member of the N4-like phage group.

Kinetic modeling of Shewanella baltica KB30 growth on different substrates through respirometry

Background

Shewanella baltica KB30 was isolated from seawater collected in Kandalaksha Bay, White Sea (Russia). This strain is known for its ability to grow on a pool of different substrates, including carbohydrates, carboxylic and amino acids, and lipids. However, no data are available on its metabolic efficiency in relation to the use of different carbon sources typologies. This work represents the first attempt to characterize S. baltica by its heterotrophic kinetic performance.

Results

Growth and substrate consumption, during the biodegradation of sodium acetate, glucose, tween 80 and peptone, were analyzed through a respirometric method. To find the model best fitting the experimental data and to obtain the kinetic parameters, the equations of Monod, Moser, Contois and Tessier were applied. The kinetic behavior of S. baltica was fitted to Monod model for sodium acetate and tween 80, while it was adjusted to Contois model for glucose and peptone. In this regard, peptone was consumed faster than the other substrates, as indicated by the highest values of substrate degradation rate, which exceeded 60 mg O₂ L⁻¹ h⁻¹.

Conclusions

Proteolytic metabolism was favored than lipidic and glucidic metabolism, which could contribute much more to mineralization and recycling of proteins than lipids and carbohydrates.

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis)

Cotton boll weevils, Anthonomus grandis, are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray-Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems.

Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from the peninsular zone of India

The biodiversity of wheat associated bacteria was deciphered from the peninsular zone of India. A total of 264 isolated bacteria were analyzed through amplified ribosomal DNA restriction analysis (ARDRA, using three restriction enzymes Alu I, Msp I and Hae III, which led to the clustering of these isolates into 12–16 groups for the different sites at >75% similarity index, adding up to 70 groups). 16S rRNA gene based phylogenetic analysis, revealed that all the bacteria belonged to three phyla Proteobacteria, Firmicutes, and Actinobacteria of 32 distinct species of 15 genera namely: Achromobacter, Alcaligenes, Arthrobacter, Bacillus, Delftia, Enterobacter, Exiguobacterium, Klebsiella, Methylobacterium, Micrococcus, Paenibacillus, Pseudomonas, Rhodobacter, Salmonella and Staphylococcus. Representative strains from each cluster were screened in vitro for plant growth promoting traits. Among plant growth promoting activities, siderophore producers were highest (15%), when compared to indole acetic acid producers (13%), Zn-solubilizers (11%), P-solubilizers (11%), ammonia (10%), hydrogen cyanide producers (9%), biocontrol (8%), N₂-fixers (7%), 1-aminocyclopropane-1-carboxylate deaminase (6%), GA producers (6%) and K-solubilizers (5%). Among 32 representative strains, Alcaligenes faecalis, Arthrobacter sp., Bacillus siamensis, Bacillus subtilis, Delftia acidovorans, Methylobacterium mesophilicum, Methylobacterium sp., Pseudomonas poae, Pseudomonas putida, and Pseudomonas stutzeri exhibited more than six different plant growth promoting activities at high temperature. Thermotolerant bacterial isolates may have application as inoculants for plant growth promotion and biocontrol agents for crops growing at high temperature conditions.

Physiologic and metabolic characterization of a new marine isolate (BM39) of Pantoea sp. producing high levels of exopolysaccharide

Background

Marine environments are the widest fonts of biodiversity representing a resource of both unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, exopolysaccharides (EPS) have many physiological functions and practical applications. Since EPS production by many bacteria is too scarce for practical use and only few species are known for their high levels of production, the search of new high EPS producers is of paramount importance. Many marine bacteria, that produce EPS to cope with strong environmental stress, could be potentially exploited at the industrial level.

Results

A novel bacterium, strain BM39, previously isolated from sediments collected in the Tyrrhenian Sea, was selected for its production of very high levels of EPS. BM39 was affiliated to Pantoea sp. (Enterobacteriaceae) by 16S rRNA gene sequencing and biochemical tests. According to the phylogenetic tree, this strain, being quite far from the closest known Pantoea species (96% identity with P. agglomerans and P. ananatis) could belong to a new species. EPS production was fast (maximum of ca. 21 g/L in 24 h on glucose medium) and mainly obtained during the exponential growth. Preliminary characterization, carried out by thin layer and gel filtration chromatography, showed that the EPS, being a glucose homopolymer with MW of ca. 830 kDa, appeared to be different from those of other bacteria of same genus. The bacterium showed a typical slightly halophilic behavior growing optimally at NaCl 40 ‰ (growing range 0-100 ‰). Flow cytometry studies indicated that good cell survival was maintained for 24 h at 120 ‰. Survival decreased dramatically with the increase of salinity being only 1 h at 280 ‰. The biochemical characterization, carried out with the Biolog system, showed that MB39 had a rather limited metabolic capacity. Its ability, rather lower than that of P. agglomerans, was almost only confined to the metabolization of simple sugars and their derivatives. Few alcohols, organic acids and nitrogen compounds were partially used too.

Conclusions

Strain BM39, probably belonging to a new species, due to its remarkable EPS production, comparable to those of known industrial bacterial producers, could be suggested as a new microorganism for industrial applications.

Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes

Sequence analysis of the 16S ribosomal RNA gene was used to study bacterial diversity of a pristine forest soil and of two cultures of the same soil enriched with cellulolytic bacteria. Our analysis revealed high bacterial diversity in the native soil sample, evidencing at least 10 phyla, in which Actinobacteria, Proteobacteria and Acidobacteria accounted for more than 76% of all sequences. In both enriched samples, members of Proteobacteria were the most frequently represented. The majority of bacterial genera in both enriched samples were identified as Brevundimonas and Caulobacter, but members of Devosia, Sphingomonas, Variovorax, Acidovorax, Pseudomonas, Xanthomonas, Stenotrophomonas, Achromobacter and Delftia were also found. In addition, it was possible to identify cellulolytic taxa such as Acidothermus, Micromonospora, Streptomyces, Paenibacillus and Pseudomonas, which indicates that this ecosystem could be an attractive source for study of novel enzymes for cellulose degradation.

Development of Tools for Genetic Analysis of Phenanthrene Degradation and Nanopod Production by Delftia sp. Cs1-4

The bacterium Delftia sp. Cs1-4 produces novel extracellular structures (nanopods) in conjunction with its growth on phenanthrene. While a full genome sequence is available for strain Cs1-4, genetic tools that could be applied to study phenanthrene degradation/nanopod production have not been reported. Thus, the objectives of this study were to establish such tools, and apply them for molecular analysis of nanopod formation or phenanthrene degradation. Three types of tools were developed or validated. First, we developed a new expression system based on a strong promoter controlling expression of a surface layer protein (NpdA) from Delftia sp. Cs1-4, which was ca. 2,500-fold stronger than the widely used lactose promoter. Second, the Cre-loxP system was validated for generation of markerless, in-frame, gene deletions, and for in-frame gene insertions. The gene deletion function was applied to examine potential roles in nanopod formation of three genes (omp32, lasI, and hcp), while the gene insertion function was used for reporter gene tagging of npdA. Lastly, pMiniHimar was modified to enhance gene recovery and mutant analysis in genome-wide transposon mutagenesis. Application of the latter to strain Cs1-4, revealed several new genes with potential roles in phenanthrene degradation or npdA expression. Collectively, the availability of these tools has opened new avenues of investigation in Delftia sp. Cs1-4 and other related genera/species with importance in environmental toxicology.

Immobilization of Delftia tsuruhatensis in macro-porous cellulose and biodegradation of phenolic compounds in repeated batch process

Delftia tsuruhatensis BM90, previously isolated from Tyrrhenian Sea and selected for its ability to degrade a wide array of phenolic compounds, was immobilized in chemically modified macro porous cellulose. The development of bacterial adhesion on the selected carrier was monitored by scanning electron microscopy. Evident colonization started already after 8h of incubation. After 72h, almost all the carrier surface was covered by the bacterial cells. Extracellular bacterial structures, such as pili or fimbriae, contributed to carrier colonization and cell attachment. Immobilized cells of D. tsuruhatensis were tested for their ability to biodegrade a pool of 20 phenols in repeated batch process. During the first activation batch (72h), 90% of phenols degradation was obtained already in 48h. In the subsequent batches (up to 360h), same degradation was obtained after 24h only. By contrast, free cells were slower: to obtain almost same degradation, 48h were needed. Thus, process productivity, achieved by the immobilized cells, was double than that of free cells. Specific activity was also higher suggesting that the use of immobilized D. tsuruhatensis BM90 could be considered very promising in order to obtain an efficient reusable biocatalyst for long-term treatment of phenols containing effluents.

Seasonal and wastewater stream variation of trace organic compounds in a dairy processing plant aerobic bioreactor

Bioreactors are often an integral part of dairy factory efforts to reduce the biological oxygen demand of their wastewater. In this study, infeed, mixed liquor and supernatant samples of an aerobic bioreactor used by a dairy factory in South-Eastern Australia were analyzed for nutrients and organic compounds using gas chromatography-mass spectrometry and physicochemical analyses. Despite different concentrations of organic inputs into the bioreactor, nutrients and trace organic compounds were reduced significantly (i.e. average concentration of trace organic compounds: infeed=1681 μg/L; mixed liquor=257 μg/L; supernatant=23 μg/L). However, during one sampling period the bioreactor was adversely affected by the organic loading. Trace organic compounds in the samples were predominantly fatty acids associated with animal products. The analyses suggest that it is possible to trace a disruptive input (i.e. infeed with high organic carbon concentrations) into an aerobic bioreactor by measuring concentrations of fatty acids or ammonia.