Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

Genomic diversity and metabolic potential of marine Pseudomonadaceae

Recent changes in the taxonomy of the Pseudomonadaceae family have led to the delineation of three new genera (Atopomonas, Halopseudomonas and Stutzerimonas). However, the genus Pseudomonas remains the most densely populated and displays a broad genetic diversity. Pseudomonas are able to produce a wide variety of secondary metabolites which drives important ecological functions and have a great impact in sustaining their lifestyles. While soilborne Pseudomonas are constantly examined, we currently lack studies aiming to explore the genetic diversity and metabolic potential of marine Pseudomonas spp. In this study, 23 Pseudomonas strains were co-isolated with Vibrio strains from three marine microalgal cultures and rpoD-based phylogeny allowed their assignment to the Pseudomonas oleovorans group (Pseudomonas chengduensis, Pseudomonas toyotomiensis and one new species). We combined whole genome sequencing on three selected strains with an inventory of marine Pseudomonas genomes to assess their phylogenetic assignations and explore their metabolic potential. Our results revealed that most strains are incorrectly assigned at the species level and half of them do not belong to the genus Pseudomonas but instead to the genera Halopseudomonas or Stutzerimonas. We highlight the presence of 26 new species (Halopseudomonas (n = 5), Stutzerimonas (n = 7) and Pseudomonas (n = 14)) and describe one new species, Pseudomonas chaetocerotis sp. nov. (type strain 536^T = LMG 31766^T = DSM 111343^T). We used genome mining to identify numerous BGCs coding for the production of diverse known metabolites (i.e., osmoprotectants, photoprotectants, quorum sensing molecules, siderophores, cyclic lipopeptides) but also unknown metabolites (e.g., ARE, hybrid ARE-DAR, siderophores, orphan NRPS gene clusters) awaiting chemical characterization. Finally, this study underlines that marine environments host a huge diversity of Pseudomonadaceae that can drive the discovery of new secondary metabolites.

Microbial communities of polluted sub-surface marine sediments

Microbial communities of coastal marine sediment play a key role in degradation of petroleum contaminants. Here the bacterial and archaeal communities of sub-surface sediments (5-10 cm) of the chronically polluted Priolo Bay (eastern coast of Sicily, Italy), contaminated mainly by n-alkanes and biodegraded/weathered oils, were characterized by cultural and molecular approaches. 16S-PCR-DGGE analysis at six stations, revealed that bacterial communities are highly divergent and display lower phylogenetic diversity than the surface sediment; sub-surface communities respond to oil supplementation in microcosms with a significant reduction in biodiversity and a shift in composition; they retain high biodegradation capacities and host hydrocarbon (HC) degraders that were isolated and identified. HC-degrading Alfa, Gamma and Epsilon proteobacteria together with Clostridia and Archaea are a common feature of sub-surface communities. These assemblages show similarities with that of subsurface petroleum reservoirs also characterized by the presence of biodegraded and weathered oils where anaerobic or microaerophilic syntrophic HC metabolism has been proposed.

Screening and Molecular Identification of Pectinase Producing Microbes from Coffee Pulp

Application of enzymes in biotechnological process has expanded considerably in recent years. In food and related industry, major importance was being attached to the use of enzymes in upgrading quality, increasing yields of extractive processes, product stabilization, and improvement of flavor and byproduct utilization. Pectinases or pectinolytic enzymes are today one of the upcoming enzymes of the commercial sector. It has been reported that microbial pectinases account for 25% of the global food enzymes sales. For this reason, this study was undertaken with aims of screening microorganisms for the pectinase activity from coffee pulp samples and molecular identification of the potential pectinolytic isolates. In the present investigation, in total, ninety-five (95) isolates were identified from thirty coffee pulp samples. Based on characterization on the selective growth media, the isolates were grouped as actinomycete (21.06%), bacteria (65.26%), and fungi (13.68%). Among these, 31.58% showed colonies surrounded by clear zones which indicate the presence of pectinase activity. After rigorous screening steps, the isolates with high potential pectinase activity were identified molecularly by sequencing 16S rDNA region of the isolates. Based on the molecular identifications, about 70% of the isolates are under genus Bacillus.

Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

Isolation, identification and diesel-oil biodegradation capacities of indigenous hydrocarbon-degrading strains of Cellulosimicrobium cellulans and Acinetobacter baumannii from tarball at Terengganu beach, Malaysia

In this study, we isolated two indigenous hydrocarbon-degrading bacteria from tarball found in Rhu Sepuluh beach, Terengganu, Malaysia. These bacteria were identified based on their physiological characteristic and 16S rRNA gene sequence analysis, and they showed 99% similarity with Cellulosimicrobium cellulans DSM 43879 and Acinetobacter baumannii ATCC 19606 respectively. Their hydrocarbon-degrading capabilities were tested using diesel-oil as sole carbon source. Results analysed using GC-MS, showed diesel-oil alkanes were degraded an average 64.4% by C. cellulans and 58.1% by A. baumannii with medium optical density reaching 0.967 (C. cellulans) and 1.515 (A. baumannii) in minimal salt media at 32°C for 10days. Individual diesel-oil alkanes were degraded between 10%-95.4% by C. cellulans and 0.2%-95.9% by A. baumannii. Both strains utilized diesel-oil for growth. The study suggests both strains are part of indigenous hydrocarbon-degrading bacteria in tarball with potential for bioremediation of oil-polluted marine environment.

Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

Biosorption of Pb(II) Ions by Klebsiella sp. 3S1 Isolated from a Wastewater Treatment Plant: Kinetics and Mechanisms Studies

Lead biosorption by Klebsiella sp. 3S1 isolated from a wastewater treatment plant was investigated through a Rotatable Central Composite Experimental Design. The optimisation study indicated the following optimal values of operating variables: 0.4 g/L of biosorbent dosage, pH 5, and 34°C. According to the results of the kinetic studies, the biosorption process can be described by a two-step process, one rapid, almost instantaneous, and one slower, both contributing significantly to the overall biosorption; the model that best fits the experimental results was pseudo-second order. The equilibrium studies showed a maximum lead uptake value of 140.19 mg/g according to the Langmuir model. The mechanism study revealed that lead ions were bioaccumulated into the cytoplasm and adsorbed on the cell surface. The bacterium  Klebsiella sp. 3S1 has a good potential in the bioremoval of lead in an inexpensive and effective process.