Microorganisms In Marine Environment Research Articles

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (−5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Accelerated degradation of cathodic protected epoxy coating by Pseudomonas aeruginosa in seawater

The combination of coatings and cathodic protection (CP) is one of the most commonly used methods for corrosion protection of metal materials. However, the protection life of this method is difficult to match the original design, which mechanism is still not well known. Previous work reports that coatings experience degradation mainly due to cathodic disbondment and microbial factors in marine environments. To further explore the possible reason for this question, we studied the degradation behavior of epoxy coatings in the co-existence of CP and Pseudomonas aeruginosa in seawater using Electrochemical impedance spectroscopy (EIS), Confocal laser scanning microscope (CLSM), Scanning electron microscope (SEM), 3D microscopy, Fourier transform infrared spectroscopy (FTIR), Thermogravimetric analyzer (TGA), and Energy disperse spectrometer (EDS). The EIS results indicate that coating resistance drops bellows 106 Ω cm2 after 35 d of immersion under the effect of P. aeruginosa alone, but the degradation rate of coatings increases in the co-existence of CP and P. aeruginosa. The coating resistance drops bellows 106 Ω cm2 after 7 d of immersion in the P. aeruginosa containing seawater at − 1.05 VCSE. This may be due to P. aeruginosa can cause benzene ring removal from the epoxy coating, and the presence of CP promotes biofilm formation on the coating surface. The thickness of biofilm is about 33.3 μm at − 1.05 VCSE, which is about 1.5 times larger than at OCP, and the diameter of microscopic defects is about 9 times larger than in sterile seawater at the same CP potential. The presence of P. aeruginosa accelerate Cl− penetrating through the coating causing pitting corrosion of the substrate steel. This study revealed that the shorter protection life of organic coating can be attributed to the combined effect of CP and microorganisms in marine environments. The findings of this study can be referenced for better understanding of the coating failure mechanism in marine environments, and provide guidance for selecting appropriate organic coatings with anti-fouling and anti-corrosive properties.

Response mechanism of microbial community during anaerobic biotransformation of marine toxin domoic acid

Domoic acid (DA) is a potent neurotoxin produced by toxigenic Pseudo-nitzschia blooms and quickly transfers to the benthic anaerobic environment by marine snow particles. DA anaerobic biotransformation is driven by microbial interactions, in which trace amounts of DA can cause physiological stress in marine microorganisms. However, the underlying response mechanisms of microbial community to DA stress remain unclear. In this study, we utilized an anaerobic marine DA-degrading consortium GLY (using glycine as co-substrate) to systematically investigate the global response mechanisms of microbial community during DA anaerobic biotransformation.16S rRNA gene sequencing and metatranscriptomic analyses were applied to measure microbial community structure, function and metabolic responses. Results showed that DA stress markedly changed the composition of main species, with increased levels of Firmicutes and decreased levels of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several genera of tolerated bacteria (Bacillus and Solibacillus) were increased, while, Stenotrophomonas, Sphingomonas and Acinetobacter were decreased. Metatranscriptomic analyses indicated that DA stimulated the expression of quorum sensing, extracellular polymeric substance (EPS) production, sporulation, membrane transporters, bacterial chemotaxis, flagellar assembly and ribosome protection in community, promoting bacterial adaptation ability under DA stress. Moreover, amino acid metabolism, carbohydrate metabolism and lipid metabolism were modulated during DA anaerobic biotransformation to reduce metabolic burden, increase metabolic demands for EPS production and DA degradation. This study provides the new insights into response of microbial community to DA stress and its potential impact on benthic microorganisms in marine environments.

Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea.

Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL−1 and 1.9 to 3.2 × 105 bacteria mL−1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.

Alternative Sigma Factor RpoX Is a Part of the RpoE Regulon and Plays Distinct Roles in Stress Responses, Motility, Biofilm Formation, and Hemolytic Activities in the Marine Pathogen Vibrio alginolyticus.

Vibrio alginolyticus is one of the most abundant microorganisms in marine environments and is also an opportunistic pathogen mediating high-mortality vibriosis in marine animals. Alternative sigma factors play essential roles in bacterial pathogens in the adaptation to environmental changes during infection and the adaptation to various niches, but little is known about them for V. alginolyticus Our previous investigation indicated that the transcript level of the gene rpoX significantly decreased in an RpoE mutant. Here, we found that rpoX was highly expressed in response to high temperature and low osmotic stress and was under the direct control of the alternative sigma factor RpoE and its own product RpoX. Moreover, transcriptome sequencing (RNA-seq) results showed that RpoE and RpoX had different regulons, although they coregulated 105 genes at high temperature (42°C), including genes associated with biofilm formation, motility, virulence, regulatory factors, and the stress response. RNA-seq and chromatin immunoprecipitation sequencing (ChIP-seq) analyses as well as electrophoretic mobility shift assays (EMSAs) revealed the distinct binding motifs of RpoE and RpoX proteins. Furthermore, quantitative real-time reverse transcription-PCR (qRT-PCR) analysis also confirmed that RpoX can upregulate genes associated with flagella, biofilm formation, and hemolytic activities at higher temperatures. rpoX abrogation does not appear to attenuate virulence toward model fish at normal temperature. Collectively, data from this study demonstrated the regulatory cascades of RpoE and an alternative sigma factor, RpoX, in response to heat and osmotic stresses and their distinct and overlapping roles in pathogenesis and stress responses in the marine bacterium V. alginolyticusIMPORTANCE The alternative sigma factor RpoE is essential for the virulence of Vibrio alginolyticus toward marine fish, coral, and other animals in response to sea surface temperature increases. In this study, we characterized another alternative sigma factor, RpoX, which is induced at high temperatures and under low-osmotic-stress conditions. The expression of rpoX is under the tight control of RpoE and RpoX. Although RpoE and RpoX coregulate 105 genes, they are programming different regulatory functions in stress responses and virulence in V. alginolyticus These findings illuminated the RpoE-RpoX-centered regulatory cascades and their distinct and overlapping regulatory roles in V. alginolyticus, which facilitates unraveling of the mechanisms by which the bacterium causes diseases in various sea animals in response to temperature fluctuations as well as the development of appropriate strategies to tackle infections by this bacterium.

Bifunctional CuO/TiO2 nanocomposite as nanofiller for improved corrosion resistance and antibacterial protection

Abstract The capability to improve the performance of polymer coatings with the inclusion of nanomaterial is a vital factor for mitigating corrosion and reducing bacterial growth caused by micro-organisms in marine environment. Herein, we report the usage of TiO 2 -CuO nanocomposite as nanofillers for epoxy coatings to protect the surface of steel against corrosion and bacterial growth. A novel TiO 2 -CuO nanocomposite was synthesized using oxalate method and the composite was characterized for its phase composition and morphology using different techniques such as X-Ray diffraction, Raman spectral studies and scanning electron microscopy with energy dispersive X-ray (EDX) analysis. Surface characterization of synthesized nanocomposite revealed the shape and uniform distribution of CuO and TiO 2 nanoparticles. The results of electrochemical measurements conducted in 3.5% NaCl solution exhibited enhanced corrosion-protective properties of epoxy coatings with synthesized TiO 2 -CuO nanocomposites compared with the pure epoxy coating. In addition, the coated mild steel (MS) substrates tested for their antibacterial performance against the Gram-negative bacterium, Escherichia coli, showed that the nanocomposite coatings presented strong antimicrobial activity against Escherichia coli.

Biodegradation of N,N-bis(carboxymethyl)-L-glutamate and its utilization as sole source of carbon, nitrogen, and energy by a Rhizobium radiobacter strain in seawater

Biodegradation of N,N-bis(carboxymethyl)-L-glutamate and its utilization by micro-organisms in marine environments were studied in Organization of Economic Development and Cooperation (OECD) screening tests and with pure bacterial cultures. Biodegradation in excess of 60% was achieved in closed bottle tests in less than 60 days, suggesting complete degradation. The bacterial strain isolated from marine sandy sediment and utilizing N,N-bis(carboxymethyl)-L-glutamate as sole source of carbon, nitrogen, and energy was identified as Rhizobium radiobacter. The strain was capable to mineralize N,N-bis(carboxymethyl)-L-glutamate in seawater and in synthetic media containing 0–60 g L−1 sea salts. Growth and adaptation studies indicated that N-carboxymethyl-L-glutamate and L-glutamate are main metabolites.

An experimental study on the effects of nutrient enrichment on organic carbon persistence in the western Pacific oligotrophic gyre

Abstract. Carbon sequestration in the ocean is of great concern with respect to the mitigation of global warming. How to hold the fixed organic carbon in the presence of tremendous numbers of heterotrophic microorganisms in marine environments is the central issue. We previously hypothesized that excessive nutrients would ultimately decrease the storage of organic carbon in marine environments. To test this, a series of in situ nutrient enrichment incubation experiments were conducted at a site (17.59° N, 127.00° E) within the western Pacific oligotrophic gyre. Five treatments were employed: glucose (Glu), algal exudation organic material (EOM), nitrate (N) and phosphate (P), N and P in combination with glucose and a control with no added nutrients. The results showed that the dissolved organic carbon consumption rates and bacterial community specific growth rates were enhanced by inorganic nutrient enrichment treatments during the initial 48 h incubation. At the end of 14 days of incubation, about one-third (average 3.3 μmol C kg−1) more organic carbon was respired in the glucose-enriched incubation with the addition of inorganic nutrients compared to that without. In contrast, when nutrients were limiting, glucose could not be efficiently used by the bacteria and thus it remained in the environment. These results suggest that repletion of inorganic nutrients could facilitate microbial consumption of organic carbon and thus has a significant impact on carbon cycling in the environment.

DNA-Sequenzierung in der mikrobiellen Diversitätsforschung

Microorganisms hold key roles in food webs and biogeochemical cycles. The identification of these organisms, their diversity and distribution patterns are, therefore, central topics in microbial ecology. The introduction of sequencing strategies has revolutionized the field of microbial ecology and paved the road for in-depth molecular diversity studies. Here we describe the application of DNA-sequencing strategies to study the diversity, evolution and ecological function of microorganisms in marine environments.

Diversity and distribution of proteorhodopsin-containing microorganisms in marine environments

Proteorhodopsin (PR) is a recently discovered protein involved in the utilization of light energy. Several studies have shown that PR-containing microorganisms are widespread and compose a large proportion of the biomass in marine ecosystems. A better understanding of the ecological role of PR will help clarify the effect of the global flow of energy and the carbon cycle on marine communities. In this study, a bioinformatical database of PR codon sequences, the Global Distribution Database of Proteorhodopsin (GDDP), as a tool for analyzing the diversity and distribution of PR-containing microorganisms in marine environments throughout the world was designed. The community structure of PR microorganisms were also compared using PCR assays and UniFrac analyses of 12 samples collected from three water layers (0, 75, and 200 m) at four representative sites in the Pacific, Atlantic, and Indian Oceans. The results indicate that PRcontaining microorganisms can be grouped into two distribution types: widespread and location-specific. Representative cases of the former include SAR11-PR and HOT2C01-PR. Interestingly, PR communities cluster by geographic locale but not by water depth.

The FeL model of iron acquisition: Nondissociative reduction of ferric complexes in the marine environment

Recently there has been recognition of the importance of reductive processes in the acquisition of iron by microorganisms in marine environments with Fe(III) reduction induced by either membrane‐bound reductases or by superoxide, a powerful Fe(III) reducing agent generated either by photochemical or biological means. We have measured the relative rates of iron uptake achieved by the cyanobacterium L. majuscula in the presence of a variety of model‐ and naturally‐derived organic ligands exhibiting a broad range of conditional ferric and ferrous stability constants. Additionally, we have investigated the effect upon iron uptake rate of varying the concentration of both iron and the iron‐binding ligands. We have reconciled this data with previous work in which we measured rates of reduction by exogenous superoxide of Fe(III) bound to these same complexes. We show that the rate of formation of ferrous iron and the rate of uptake of iron by Lyngbya majuscula are each independent of the concentration of Fe' and demonstrate that this is consistent with our previous finding that this organism acquires iron via nondissociative reduction of ferric complexes. We also show that the rate of reoxidation of organically complexed Fe(II) is a critical determinant of the subsequent bioavailability of iron, a feature not previously addressed in the literature. In view of the central importance of the complexation and redox behavior of the iron‐ organic complexes to iron uptake rate, we propose a new kinetic model of iron acquisition, termed the FeL model, that is consistent with presented and previously published data and which describes processes both in natural and artificial conditions.

Trophic Interactions among Marine Microbes in Oil-contaminated Seawater on a Mesocosmic Scale

We studied the effects of oil spills on the trophic interactions among microorganisms in marine environments on a mesocosmic scale. When Bunker-A oil or kerosene was introduced into the mesocosm, bacterial numbers increased for the first 3 days, then decreased with a concomitant propagation of either heterotrophic nanoflagellates (HNFs) or viruses. We hypothesized that the sensitivity of HNFs to each oil resulted in this trophic relationship. To test this hypothesis, the rates at which HNFs grazed on bacteria were examined by conducting microcosm experiments in the presence of one of these oils. The rates were markedly reduced by kerosene but slightly increased by Bunker-A oil. The removal of HNFs by filtration led to a fluctuation in the numbers of bacteria and viruses that was quite similar to that in the mesocosm with kerosene. We conclude that the inhibitory effect of oil components on unicellular microorganisms is one of the key factors controlling the microbial food-web in oil-contaminated seawater.

Life under Nutrient Limitation in Oligotrophic Marine Environments: An Eco/Physiological Perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis)

The oceans of the world are nutrient-limited environments that support a dynamic diversity of microbial life. Heterotrophic prokaryotes proliferate in oligotrophic regions and affect nutrient transformation and remineralization thereby impacting directly on the all marine biota. An important challenge in studying the microbial ecology of oligotrophic environments has been the isolation of ecologically important species. This goal has been recognized not only for its relevance in defining the dynamics of community composition, but for enabling physiological studies of competitive species and inferring their impact on the microbial food web. This review describes the successful isolation attempts of the ultramicrobacterium, Sphingopyxis alaskensis (formerly described as Sphingomonas alaskensis) using extinction dilution culturing methods. It then provides a comprehensive perspective of the unique physiological and genetic properties that have been identified that distinguish it from typical copiotrophic species. These properties are described through studies of the growth phase and growth rate control of macromolecular synthesis, stress resistance and global gene expression (proteomics). We also discuss the importance of integrating ecological and physiological approaches for studying microorganisms in marine environments.