A simple strategy for investigating the diversity and hydrocarbon degradation abilities of cultivable bacteria from contaminated soil

Complete genome sequence of Pseudomonas brenneri strain JD2-26, a potential pollutant-reducing bacterium isolated from a municipal solid waste landfill facility

We report here the complete genome sequence of Pseudomonas brenneri strain JD2-26 isolated from a municipal solid waste landfill facility. The genome consists of a 6.32-Mbp chromosome and a plasmid having a total of 6,100 genes, including 5,914 coding sequences.

Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns

The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.

Influence of Bacteria of the Genus Pseudomonas on Leguminous Plants and Their Joint Application for Bioremediation of Oil Contaminated Soils

The modern approach to the creation of biological products to stimulate plant growth is based on the study of specific inter-bacterial interactions. This study describes the impact that the introduction of strains of the genus Pseudomonas has on annual and perennial leguminous plants and the ecosystem of the leguminous plant-the indigenous microbial community. The objects of research under the conditions of vegetation experiments were plants of field peas (Pisum sativum L.), white lupine (Lupinus albus L.), chickpea (Cicer arietinum L.), alfalfa (Medicago sativa subsp. varia (Martyn) Arcang.), and white sweet clover (Melilotus albus Medik.). For the treatment of plant seeds, a liquid culture of strains of growth-stimulating bacteria Pseudomonas koreensis IB-4, and P. laurentiana ANT 17 was used. The positive effect of the studied strains on the germination, growth and development of plants was established. There was no inhibitory effect of inoculants on rhizobia; on the contrary, an increase in nodule formation was observed. The possibility of recultivation of oil-contaminated soil using chickpea and alfalfa as phytomeliorants and growth-stimulating strains P. koreensis IB-4, P. laurentiana ANT 17 as inoculants was evaluated. It is proved that seed treatment improved the morphological parameters of plants, as well as the efficiency of oil destruction.

Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections

Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.

Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities

Ambient air pollution exerts deleterious effects on our environment. Continuously exposed to the atmosphere, diverse communities of microorganisms thrive on leaf surfaces, the phylloplane. The composition of these communities is dynamic, responding to many environmental factors including ambient air pollution. In this field study, over a 2 year period, we sampled Hedera helix (ivy) leaves at six locations exposed to different ambient air pollution conditions. Daily, we monitored ambient black carbon (BC), PM_2.5, PM₁₀, nitrogen dioxide, and ozone concentrations and found that ambient air pollution led to a 2–7-fold BC increase on leaves, the phylloplane BC load. Our results further indicated that the phylloplane BC load correlates with the diversity of bacterial and fungal leaf communities, impacting diversity more than seasonal effects. The bacterial genera Novosphingobium, Hymenobacter, and Methylorubrum, and the fungal genus Ampelomyces were indicators for communities exposed to the highest phylloplane BC load. Parallel to this, we present one fungal and two bacterial phylloplane strains isolated from an air-polluted environment able to degrade benzene, toluene, and/or xylene, including a genomics-based description of the degradation pathways involved. The findings of this study suggest that ambient air pollution shapes microbial leaf communities, by affecting diversity and supporting members able to degrade airborne pollutants.

Biodegradation of petroleum by bacteria isolated from fishes of Indian Ocean

In this study, oil degrading bacteria discovered from fish living near the oil ports at Karachi in Pakistan were characterized. The bacteria isolated from skin, gills, and gut in fish could consume crude oil as a source of carbon and energy. Total 36 isolates were tested using Nutrient Agar (NA) and MSA media with different crude oil concentrations (0.2%, 0.5%, 0.7%, 1%, 2%, and 5%) and 4 out of 36 isolates (two Gram positive and two Gram negative bacteria) were selected for further identification. 16S rRNA gene sequencing revealed that the isolates are related to Bacillus velezensis, Bacillus flexus, Pseudomonas brenneri and Pseudomonas azotoforman. Oil degrading potential of these bacteria was characterized by GC-MS analysis of degradation of oil components in crude oil as well as engine oil. We found that one (2, 6, 10, 14-Tetramethylpentadecane) out of 42 components in the crude oil was fully eliminated and the other oil components were reduced. In addition, 26 out of 42 oil components in the engine oil, were fully eliminated and the rest were amended. Taken together, these studies identify that B. velezensis, B. flexus, P. brenneri and P. azotoforman have high oil degrading potential, which may be useful for degradation of oil pollutants and other commercial applications.

Analysis of petroleum biodegradation by a bacterial consortium isolated from worms of the polychaeta class (Annelida): Implications for NPK fertilizer supplementation

Degradation of petroleum hydrocarbons using bacterial consortia may be a means of optimizing bioremediation techniques. In this study, bacterial strains were isolated from the digestive tract of polychaete worms and evaluated concerning the potential of the bacteria to degrade petroleum compounds (Acinetobacter sp., Bacillus sp., Pantoea sp. and Enterobacter sp.). The strains were separately screened regarding their potential to degrade oil after 24 h. The main experiment was carried out for 30 days with the addition of nitrogen, phosphorus and potassium (NPK) after 15 days (Bact-NPK15) and 28 days (Bact-NPK28) and without NPK (Bact). The Bact treatment biomass remained stable until the 20th day of the experiment. C13-C40 n-alkanes were degraded with all treatments in the following order: Bact>Bact-NPK28>Bact-NPK15. Significant differences were observed between the controls and all treatments (p = 0.00031). Measurement of polycyclic aromatic hydrocarbons (PAHs) indicates a lower contribution of these compounds in the Bact-NPK28 treatment, although no significant difference between groups was observed. Bact-NPK28 was able to remove 40% of naphthalene, while Bact-NPK15 removed 20%; this effect was not observed in Bact. Higher hopane degradation levels were observed in Bact and, to a lesser extent, in Bact-NPK28. NPK application for 28 days mainly favored PAH degradation. The evaluated consortium thus exhibits potential in the bioremediation of petroleum-contaminated areas.

Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas

Urban green areas are highly valued by citizens for their contribution to the quality of life in cities. Plants play an important role in mitigating airborne pollutants and are assisted in this role by the metabolic capacities of the millions of microbial cells that colonize leaf surfaces (phyllosphere). Many factors influence phyllosphere microbial community composition and function, but to what extent does airborne pollution in cities impact the composition of microbial communities and their functional degradation genes? Here we describe the characterization of the phyllospheric bacterial communities of Carpinus betulus L. trees (hornbeam) across three locations: the city center of Warsaw (Poland), a forest in a UNESCO World Heritage Site (Białowieża), and a forest in one of the world’s oldest operational oil fields (Bóbrka). C. betulus contained higher particulate matter (PM) concentrations, with higher concentrations of palladium and radon in the PM, on leaves in Warsaw than in the forests. Volatile organic compound (VOC) analyses of sampled air revealed higher concentrations of butanone methyl propanal, butylbenzene, and cyclohexane in Bóbrka than Warsaw and Białowieża, while in Warsaw, xylene and toluene were higher. Shotgun microbiome sequencing uncovered a dominance of Gammaproteobacteria (71%), mainly Pseudomonas spp., Actinobacteria, Alpha- and Betaproteobacteria, and Firmicutes. Community composition and function differed significantly between the forests and Warsaw city center. Statistically more hydrocarbon degradation genes were found in Białowieża compared to Warsaw and Bóbrka, and in vitro tests of diesel degradation and plant growth promotion traits of culturable representatives revealed that Białowieża held the highest number of bacteria with plant beneficial properties and degradation genes. This study provides the first detailed insights into the microbiome of C. betulus and sets the stage for developing to a more integrated understanding of phyllosphere microbiota in cities, and their relationships with human health.

Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

Production of rhamnolipids and diesel oil degradation by bacteria isolated from soil contaminated by petroleum

Biosurfactants are microbial secondary metabolites. The most studied are rhamnolipids, which decrease the surface tension and have emulsifying capacity. In this study, the production of biosurfactants, with emphasis on rhamnolipids, and diesel oil degradation by 18 strains of bacteria isolated from waste landfill soil contaminated by petroleum was analyzed. Among the studied bacteria, gram-positive endospore forming rods (39%), gram positive rods without endospores (17%), and gram-negative rods (44%) were found. The following methods were used to test for biosurfactant production: oil spreading, emulsification, and hemolytic activity. All strains showed the ability to disperse the diesel oil, while 77% and 44% of the strains showed hemolysis and emulsification of diesel oil, respectively. Rhamnolipids production was observed in four strains that were classified on the basis of the 16S rRNA sequences as Pseudomonas aeruginosa. Only those strains showed the rhlAB gene involved in rhamnolipids synthesis, and antibacterial activity against Escherichia coli, P. aeruginosa, Staphylococcus aureus, Bacillus cereus, Erwinia carotovora, and Ralstonia solanacearum. The highest production of rhamnolipids was 565.7 mg/L observed in mineral medium containing olive oil (pH 8). With regard to the capacity to degrade diesel oil, it was observed that 7 strains were positive in reduction of the dye 2,6-dichlorophenolindophenol (2,6-DCPIP) while 16 had the gene alkane mono-oxygenase (alkB), and the producers of rhamnolipids were positive in both tests. Several bacterial strains have shown high potential to be explored further for bioremediation purposes due to their simultaneous ability to emulsify, disperse, and degrade diesel oil. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 32:262-270, 2016.

Pseudomonads Rule Degradation of Polyaromatic Hydrocarbons in Aerated Sediment

Given that the degradation of aromatic pollutants in anaerobic environments such as sediment is generally very slow, aeration could be an efficient bioremediation option. Using stable isotope probing (SIP) coupled with pyrosequencing analysis of 16S rRNA genes, we identified naphthalene-utilizing populations in aerated polyaromatic hydrocarbon (PAH)-polluted sediment. The results showed that naphthalene was metabolized at both 10 and 20°C following oxygen delivery, with increased degradation at 20°C as compared to 10°C—a temperature more similar to that found in situ. Naphthalene-derived ¹³C was primarily assimilated by pseudomonads. Additionally, Stenotrophomonas, Acidovorax, Comamonas, and other minor taxa were determined to incorporate ¹³C throughout the measured time course. The majority of SIP-detected bacteria were also isolated in pure cultures, which facilitated more reliable identification of naphthalene-utilizing populations as well as proper differentiation between primary consumers and cross-feeders. The pseudomonads acquiring the majority of carbon were identified as Pseudomonas veronii and Pseudomonas gessardii. Stenotrophomonads and Acidovorax defluvii, however, were identified as cross-feeders unable to directly utilize naphthalene as a growth substrate. PAH degradation assays with the isolated bacteria revealed that all pseudomonads as well as Comamonas testosteroni degraded acenaphthene, fluorene, and phenanthrene in addition to naphthalene. Furthermore, P. veronii and C. testosteroni were capable of transforming anthracene, fluoranthene, and pyrene. Screening of isolates for naphthalene dioxygenase genes using a set of in-house designed primers for Gram-negative bacteria revealed the presence of such genes in pseudomonads and C. testosteroni. Overall, our results indicated an apparent dominance of pseudomonads in the sequestration of carbon from naphthalene and potential degradation of other PAHs upon aeration of the sediment at both 20 and 10°C.

Halophilic bacteria are colonizing the exhibition areas of the Capuchin Catacombs in Palermo, Italy

The Capuchin Catacombs of Palermo, Italy, contain over 1800 mummies dating from the 16th to 20th centuries AD. Their environment is not conducive to the conservation of the remains due to, among other factors, water infiltration, which is producing salt efflorescences on the walls. A multiphasic approach was applied to investigate the halophilic microbiota present in the Catacombs. Enrichment cultures were conducted on media containing different NaCl concentrations, ranging from 3 to 20 %. For screening of the strains, the following two PCR-based methods were used and compared: fluorescence internal transcribed spacer PCR (f-ITS) and random amplification of polymorphic DNA (RAPD) analyses. Results derived from RAPD profiles were shown to be slightly more discriminative than those derived from f-ITS. In addition, the proteolytic and cellulolytic abilities were screened through the use of plate assays, gelatin agar and Ostazin Brilliant Red H-3B (OBR-HEC), respectively. Many of the strains isolated from the wall samples displayed proteolytic activities, such as all strains belonging to the genera Bacillus, Virgibacillus and Arthrobacter, as well as some strains related to the genera Oceanobacillus, Halobacillus and Idiomarina. In addition, many of the strains isolated from materials employed to stuff the mummies showed cellulolytic activities, such as those related to species of the genera Chromohalobacter and Nesterenkonia, as well as those identified as Staphylococcus equorum and Halomonas sp. Furthermore, many of the strains were pigmented ranging from yellow to a strong pink color, being directly related to the discoloration displayed by the materials.