Comparison of two field systems for determination of crude oil biodegradation in cold seawater.

Marine oil spills have devastating environmental impacts and extrapolation of experimental fate and impact data from the lab to the field remains challenging due to the lack of comparable field data. In this work we compared two field systems used to study in situ oil depletion with emphasis on biodegradation and associated microbial communities. The systems were based on (i) oil impregnated clay beads and (ii) hydrophobic Fluortex adsorbents coated with thin oil films. The bacterial communities associated with the two systems displayed similar compositions of dominant bacterial taxa. Initial abundances of Oceanospirillales were observed in both systems with later emergences of Flavobacteriales, Alteromonadales and Rhodobacterales. Depletion of oil compounds was significantly faster in the Fluortex system and most likely related to the greater bioavailability of oil compounds as compared to the clay bead system.

The fate of conventional and potentially degradable gillnets in a seawater-sediment system.

Abandoned gillnets in the marine environment represent a global environmental risk due to the ghost fishing caused by the nets. Degradation of conventional nylon gillnets was compared to that of nets made of polybutylene succinate co-adipate-co-terephthalate (PBSAT) that are designed to degrade more readily in the environment. Gillnet filaments were incubated in microcosms of natural seawater (SW) and marine sediments at 20 °C over a period of 36 months. Tensile strength tests and scanning electron microscopy analyses showed weakening and degradation of the PBSAT filaments over time, while nylon filaments remained unchanged. Pyrolysis-gas chromatography/mass spectrometry revealed potential PBSAT degradation products associated with the filament surfaces, while nylon degradation products were not detected by these analyses. Microbial communities differed significantly between the biofilms on the nylon and PBSAT filaments. The slow deterioration of the PBSAT gillnet filaments shown here may be beneficial and reduce the ghost fishing periods of these gillnets.

Developing a Riboswitch-Mediated Regulatory System for Metabolic Flux Control in Thermophilic Bacillus methanolicus.

Genome-wide transcriptomic data obtained in RNA-seq experiments can serve as a reliable source for identification of novel regulatory elements such as riboswitches and promoters. Riboswitches are parts of the 5' untranslated region of mRNA molecules that can specifically bind various metabolites and control gene expression. For that reason, they have become an attractive tool for engineering biological systems, especially for the regulation of metabolic fluxes in industrial microorganisms. Promoters in the genomes of prokaryotes are located upstream of transcription start sites and their sequences are easily identifiable based on the primary transcriptome data. Bacillus methanolicus MGA3 is a candidate for use as an industrial workhorse in methanol-based bioprocesses and its metabolism has been studied in systems biology approaches in recent years, including transcriptome characterization through RNA-seq. Here, we identify a putative lysine riboswitch in B. methanolicus, and test and characterize it. We also select and experimentally verify 10 putative B. methanolicus-derived promoters differing in their predicted strength and present their functionality in combination with the lysine riboswitch. We further explore the potential of a B. subtilis-derived purine riboswitch for regulation of gene expression in the thermophilic B. methanolicus, establishing a novel tool for inducible gene expression in this bacterium.

Establishment of a functional system for recombinant production of secreted proteins at 50 °C in the thermophilic Bacillus methanolicus.

BACKGROUND: The suitability of bacteria as microbial cell factories is dependent on several factors such as price of feedstock, product range, production yield and ease of downstream processing. The facultative methylotroph Bacillus methanolicus is gaining interest as a thermophilic cell factory for production of value-added products from methanol. The aim of this study was to expand the capabilities of B. methanolicus as a microbial cell factory by establishing a system for secretion of recombinant proteins. RESULTS: Native and heterologous signal peptides were tested for secretion of α-amylases and proteases, and we have established the use of the thermostable superfolder green fluorescent protein (sfGFP) as a valuable reporter protein in B. methanolicus. We demonstrated functional production and secretion of recombinant proteases, α-amylases and sfGFP in B. methanolicus MGA3 at 50 °C and showed that the choice of signal peptide for optimal secretion efficiency varies between proteins. In addition, we showed that heterologous production and secretion of α-amylase from Geobacillus stearothermophilus enables B. methanolicus to grow in minimal medium with starch as the sole carbon source. An in silico signal peptide library consisting of 169 predicted peptides from B. methanolicus was generated and will be useful for future studies, but was not experimentally investigated any further here. CONCLUSION: A functional system for recombinant production of secreted proteins at 50 °C has been established in the thermophilic B. methanolicus. In addition, an in silico signal peptide library has been generated, that together with the tools and knowledge presented in this work will be useful for further development of B. methanolicus as a host for recombinant protein production and secretion at 50 °C.

Production of Value-Added Chemicals by Bacillus methanolicus Strains Cultivated on Mannitol and Extracts of Seaweed Saccharina latissima at 50°C.

The facultative methylotroph Bacillus methanolicus MGA3 has previously been genetically engineered to overproduce the amino acids L-lysine and L-glutamate and their derivatives cadaverine and γ-aminobutyric acid (GABA) from methanol at 50°C. We here explored the potential of utilizing the sugar alcohol mannitol and seaweed extract (SWE) containing mannitol, as alternative feedstocks for production of chemicals by fermentation using B. methanolicus. Extracts of the brown algae Saccharina latissima harvested in the Trondheim Fjord in Norway were prepared and found to contain 12-13 g/l of mannitol, with conductivities corresponding to a salt content of ∼2% NaCl. Initially, 12 B. methanolicus wild type strains were tested for tolerance to various SWE concentrations, and some strains including MGA3 could grow on 50% SWE medium. Non-methylotrophic and methylotrophic growth of B. methanolicus rely on differences in regulation of metabolic pathways, and we compared production titers of GABA and cadaverine under such growth conditions. Shake flask experiments showed that recombinant MGA3 strains could produce similar and higher titers of cadaverine during growth on 50% SWE and mannitol, compared to on methanol. GABA production levels under these conditions were however low compared to growth on methanol. We present the first fed-batch mannitol fermentation of B. methanolicus and production of 6.3 g/l cadaverine. Finally, we constructed a recombinant MGA3 strain synthesizing the C30 terpenoids 4,4'-diaponeurosporene and 4,4'-diapolycopene, experimentally confirming that B. methanolicus has a functional methylerythritol phosphate (MEP) pathway. Together, our results contribute to extending the range of both the feedstocks for growth and products that can be synthesized by B. methanolicus.

Genetic Tools and Techniques for Recombinant Expression in Thermophilic Bacillaceae.

Although Escherichia coli and Bacillus subtilis are the most prominent bacterial hosts for recombinant protein production by far, additional species are being explored as alternatives for production of difficult-to-express proteins. In particular, for thermostable proteins, there is a need for hosts able to properly synthesize, fold, and excrete these in high yields, and thermophilic Bacillaceae represent one potentially interesting group of microorganisms for such purposes. A number of thermophilic Bacillaceae including B.methanolicus, B.coagulans, B.smithii, B.licheniformis, Geobacillus thermoglucosidasius, G. kaustophilus, and G. stearothermophilus are investigated concerning physiology, genomics, genetic tools, and technologies, altogether paving the way for their utilization as hosts for recombinant production of thermostable and other difficult-to-express proteins. Moreover, recent successful deployments of CRISPR/Cas9 in several of these species have accelerated the progress in their metabolic engineering, which should increase their attractiveness for future industrial-scale production of proteins. This review describes the biology of thermophilic Bacillaceae and in particular focuses on genetic tools and methods enabling use of these organisms as hosts for recombinant protein production.

Candicidin biosynthesis gene cluster is widely distributed among Streptomyces spp. isolated from the sediments and the neuston layer of the Trondheim fjord, Norway.

A large number of Streptomyces bacteria with antifungal activity isolated from samples collected in the Trondheim fjord (Norway) were found to produce polyene compounds. Investigation of polyene-containing extracts revealed that most of the isolates produced the same compound, which had an atomic mass and UV spectrum corresponding to those of candicidin D. The morphological diversity of these isolates prompted us to speculate about the involvement of a mobile genetic element in dissemination of the candicidin biosynthesis gene cluster (can). Eight candicidin-producing isolates were analyzed by performing a 16S rRNA gene-based taxonomic analysis, pulsed-field gel electrophoresis, PCR, and Southern blot hybridization with can-specific probes. These analyses revealed that most of the isolates were related, although they were morphologically diverse, and that all of them contained can genes. The majority of the isolates studied contained large plasmids, and two can-specific probes hybridized to a 250-kb plasmid in one isolate. Incubation of the latter isolate at a high temperature resulted in loss of the can genes and candicidin production, while mating of the "cured" strain with a plasmid-containing donor restored candicidin production. The latter result suggested that the 250-kb plasmid contains the complete can gene cluster and could be responsible for conjugative transfer of this cluster to other streptomycetes.

Violacein-producing Collimonas sp. from the sea surface microlayer of costal waters in Trøndelag, Norway.

A new strain belonging to the genus Collimonas was isolated from the sea surface microlayer off the coast of Trøndelag, Norway. The bacterium, designated Collimonas CT, produced an antibacterial compound active against Micrococcus luteus. Subsequent studies using LC-MS identified this antibacterial compound as violacein, known to be produced by several marine-derived bacteria. Fragments of the violacein biosynthesis genes vioA and vioB were amplified by PCR from the Collimonas CT genome and sequenced. Phylogenetic analysis of these sequences demonstrated close relatedness of the Collimonas CT violacein biosynthetic gene cluster to those in Janthinobacterium lividum and Duganella sp., suggesting relatively recent horizontal gene transfer. Considering diverse biological activities of violacein, Collimonas CT shall be further studied as a potential producer of this compound.

Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim Fjord, Norway.

The water surface microlayer is still poorly explored, although it has been shown to contain a high density of metabolically active bacteria, often called bacterioneuston. Actinomycetes from the surface microlayer in the Trondheim fjord, Norway, have been isolated and characterized. A total of 217 isolates from two separate samples morphologically resembling the genus Streptomyces have been further investigated in this study. Antimicrobial assays showed that about 80% of the isolates exhibited antagonistic activity against non-filamentous fungus, Gram-negative, and Gram-positive bacteria. Based on the macroscopic analyses and inhibition patterns from the antimicrobial assays, the sub-grouping of isolates was performed. Partial 16S rDNAs from the candidates from each subgroup were sequenced and phylogenetic analysis performed. 7 isolates with identical 16S rDNA sequences were further studied for the presence of PKS type I genes. Sequencing and phylogenetic analysis of the PKS gene fragments revealed that horizontal gene transfer between closely related species might have taken place. Identification of unique PKS genes in these isolates implies that de-replication can not be performed based solely on the 16S rDNA sequences. The results obtained in this study suggest that streptomycetes from the neuston population may be an interesting source for discovery of new antimicrobial agents.