Marine bacteria: potential candidates for enhanced bioremediation

XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes

Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141 200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38 000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.

Mechanisms Driving Seasonal Succession and Community Assembly in Sediment Microbial Communities Across the Dali River Basin, the Loess Plateau, China

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used high-throughput sequencing technology (16S and ITS) and the neutral community model to analyze seasonal succession and the assembly processes associated with microbial communities in the Dali River, a tributary of the Yellow River on the Loess Plateau. The results showed that sediment bacterial and fungal community diversity indexes in non-flood season were 1.03-3.15 times greater than those in flood season. There were obvious variations between non-flood and flood seasons in sediment microorganisms. The similarities among all, abundant, and rare microbial communities decreased as geographical distance increased. Proteobacteria (52.5-99.6%) and Ascomycota (22.0-34.2%) were the primary microbial phyla in all, abundant, and rare microbial communities. Sediment ammonia nitrogen, water temperature, and sediment organic carbon significantly affected (p < 0.05) the structure of all, abundant, and rare sediment microorganism communities. The ecological networks for the bacterial community of non-flood season and fungal community of flood season had complex topological parameters. The bacterial community in river sediments was driven by deterministic processes, while the fungal community was dominated by stochastic processes. These results expanded understanding about sediment microbial community characteristics in rivers on the Loess Plateau and provided insights into the assembly processes and the factors driving microbial communities in river networks.

Spatial distribution of bacteria in response to phytoplankton community and multiple environmental factors in surface waters in Sanggou Bay

Coastal bays link terrestrial and oceanic carbon reservoirs and play important roles in marine carbon cycles. Particulate organic carbon (POC) produced by phytoplankton is a major autochthonous carbon source in coastal bays. Previous studies on the fate of POC produced by phytoplankton mainly focused on the relationship between phytoplankton and zooplankton in classic food webs, while our knowledge on the roles of bacterioplankton is still limited, particularly in bays under highly intensive aquaculture activities. Here, we investigated bacterial community structure, and the influence of environmental factors and phytoplankton biomass and community structure based on samples collected in August 2022 from Sanggou Bay, a typical aquaculture bay in northern China. Environmental conditions, phytoplankton and bacterial community structure differed significantly between different aquaculture areas, showing higher relative abundance of Synechococcus sp. in the mixing area of shellfish and kelp culture (Area II) than the shellfish culture area (Area I). In contrast, Marivita cryptomonadis was more abundant in Area I, associated with elevated dissolved inorganic nitrogen (DIN), POC, POC/PN (the molar ratio of POC to particulate nitrogen) and sterol-derived total phytoplankton biomass. The strong correlation between total phytoplankton biomass and particle-associated bacteria indicated the important role of this bacterial fraction in processing organic compounds produced by phytoplankton. Significant correlations between bacterial community composition and POC/PN suggested more organic carbon potentially entering detrital biomass pools in Area I compared to Area II. Our results suggest that spatial distribution patterns of bacterial community structure were regulated by multiple abiotic and biotic factors and had a profound impact on the fate of organic carbon under highly intensive aquaculture activities in Sanggou Bay.

Genetic Adaptations and Mechanistic Insights Into Bacterial Bioremediation in Ecosystems

Metal pollution poses significant threats to the ecosystem and human health, demanding effective remediation strategies. Bioremediation, which leverages the unique metal-resistant genes found in bacteria, offers a cost-effective and efficient solution to heavy metal contamination. Genes such as Cad, Chr, Cop, and others provide pathways to improve the detoxification of the ecosystem. Through multiple techniques, genetic engineering makes bacterial genomes more capable of improving metal detoxification; nonetheless, there are still unanswered questions regarding the nature of new metal-resistant genes. This article examines bacteria's complex processes to detoxify toxic metals, including biosorption, bioaccumulation, bio-precipitation, and bioleaching. It also explores essential genes, proteins, signaling mechanisms, and bacterial biomarkers involved in breaking toxic metals.

Deciphering the molecular interaction of extracellular polymeric substances of a marine bacterium Pseudomonas furukawaii PPS-19 with petroleum hydrocarbons and development of bioadsorbent

Petroleum hydrocarbon contamination is a serious hazard to marine environments, affecting ecosystems and marine life. However, extracellular polymeric substances (EPS) of marine bacteria constituting various hydrophilic and hydrophobic functional groups sequester petroleum hydrocarbons (PHs). In this study, interaction of EPS of Pseudomonas furukawaii PPS-19 with PHs such as crude oil, n-dodecane, and pyrene and its impact on PHs adsorption was investigated. Protein component of EPS was increased after treatment with PHs. Red shift of UV-Vis spectra implied change in molecular structure of EPS. Functional groups of proteins (CO, NH2) and polysaccharides (C-C, C-OH, C-O-C) predominantly interacted with PHs. Interaction with PHs affected secondary structure of EPS. Change in binding energies of corresponding functionalities of C 1s, O 1s, and N 1s confirmed the interaction. Disruption of crystalline peaks led to increased pore size in EPS primarily due to the increase in surface electronegativity. Static quenching mechanism unveils formation of complex between fulvic acid of EPS and PHs. Relative expression of alg8 gene was significantly increased in the presence of n-dodecane (6.31 fold) (P < 0.05; One way ANOVA). n-dodecane and pyrene adsorption capacity of Immobilized EPS was significantly higher (356.5 and 338.2 mg g-1, respectively) (P < 0.001; One way ANOVA) than control. Adsorption rate fits into the pseudo-second-order kinetic model. This study establishes that interaction of PHs causes structural and physical changes in EPS and EPS could be used as an adsorbent material for the sequestration of PHs pollution.

Evaluation of antibiofilm activity of metal oxides nanoparticles and carbon nanotubes coated styrofoam on the bacterium Jeotgalicoccus huakuii

The co-existence of metal oxide nanoparticles (MONPs), carbon-based nanomaterials and microplastics (MPs) in the natural environment are expected to be of growing global concern due to their increasing abundance and persistence in the environment worldwide. Knowledge of the interaction of the above compounds particularly under light irradiation in water remains limited. In the present study, the possible individual and combined toxic effects of MONPs, carbon nanotubes (CNTs) through styrofoam (SF) on the environmental bacterium Jeotaglicoccus huakuii were systematically investigated. The fabricated MONPs and CNTs were characterized using the following techniques: FT-IR (functional groups), XRD (crystallinity), SEM, and EDX (topological morphology). The objective of this study was to investigate and identify naturally occurring bacteria capable of mitigating and detoxifying toxic pollutants under adverse conditions. Moreover, the assessment of minimum inhibitory concentration (MIC) was made through an agar well plate method, resazurin (ELISA measurement), growth kinetics and bacterial viability were assessed employing live and dead assay and biofilm combating ability was analyzed using an antibiofilm assay. Further, the biotransformation of f-MWCNTs by J. huakuii was evaluated employing RT-PCR and SEM analysis. The results demonstrated that the toxicity of Pb3O4@f-MWCNTs was comparatively higher than the remaining Pb3O4 NPs and SF coated NPs.. Interestingly, J. huakuii showed resistance against f-MWCNTs at very high concentrations and able to utilize f-MWCNTs as a sole carbon source suggesting J. huakuii as a suitable aquatic bioremediation tool for both MONPs and CNTs transfer via MPs. The results also enhanced our understanding of the affinity of MPs towards MONPs and CNTs under extreme environmental conditions.

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan

BACKGROUND

Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

RESULTS

The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

CONCLUSION

Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

Physiology and comparative genomics of the haloalkalitolerant and hydrocarbonoclastic marine strain Rhodococcus ruber MSA14

Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L- 1), and efficient degradation of pyrene (0.2 g L- 1) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group.

Environmental stressor assessment of hydrocarbonoclastic bacteria biofilms from a marine oil spill

The environmental and economic impact of an oil spill can be significant. Biotechnologies applied during a marine oil spill involve bioaugmentation with immobilised or encapsulated indigenous hydrocarbonoclastic species selected under laboratory conditions to improve degradation rates. The environmental factors that act as stressors and impact the effectiveness of hydrocarbon removal are one of the challenges associated with these applications. Understanding how native microbes react to environmental stresses is necessary for effective bioaugmentation. Herein, Micrococcus luteus and M. yunnanensis isolated from a marine oil spill mooring system showed hydrocarbonoclastic activity on Maya crude oil in a short time by means of total petroleum hydrocarbons (TPH) at 144 h: M. luteus up to 98.79 % and M. yunnanensis 97.77 % removal. The assessment of Micrococcus biofilms at different temperature (30 °C and 50 °C), pH (5, 6, 7, 8, 9), salinity (30, 50, 60, 70, 80 g/L), and crude oil concentration (1, 5, 15, 25, 35 %) showed different response to the stressors depending on the strain. According to response surface analysis, the main effect was temperature > salinity > hydrocarbon concentration. The hydrocarbonoclastic biofilm architecture was characterised using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Subtle but significant differences were observed: pili in M. luteus by SEM and the topographical differences measured by AFM Power Spectral Density (PSD) analysis, roughness was higher in M. luteus than in M. yunnanensis. In all three domains of life, the Universal Stress Protein (Usp) is crucial for stress adaptation. Herein, the uspA gene expression was analysed in Micrococcus biofilm under environmental stressors. The uspA expression increased up to 2.5-fold in M. luteus biofilms at 30 °C, and 1.3-fold at 50 °C. The highest uspA expression was recorded in M. yunnanensis biofilms at 50 °C with 2.5 and 3-fold with salinities of 50, 60, and 80 g/L at hydrocarbon concentrations of 15, 25, and 35 %. M. yunnanensis biofilms showed greater resilience than M. luteus biofilms when exposed to harsh environmental stressors. M. yunnanensis biofilms were thicker than M. luteus biofilms. Both biofilm responses to environmental stressors through uspA gene expression were consistent with the behaviours observed in the response surface analyses. The uspA gene is a suitable biomarker for assessing environmental stressors of potential microorganisms for bioremediation of marine oil spills and for biosensing the ecophysiological status of native microbiota in a marine petroleum environment.

Functional amyloid fibrils of biofilm-forming marine bacterium Pseudomonas aeruginosa PFL-P1 interact spontaneously with pyrene and augment the biodegradation

Bacteria thrive in biofilms embedding in the three-dimensional extracellular polymeric substances (EPS). Functional Amyloid in Pseudomonas (Fap), a protein in EPS, efficiently sequesters polycyclic aromatic hydrocarbons (PAHs). Present study reports the characterization of Fap fibrils from Pseudomonas aeruginosa PFL-P1 and describes the interaction with pyrene to assess the impact on pyrene degradation. Overexpression of fap in E. coli BL21(DE3) cells significantly enhances biofilm formation (p < 0.0001) and amyloid production (p = 0.0002), particularly with pyrene. Defibrillated Fap analysis reveals FapC monomers and increased fibrillation with pyrene. Circular Dichroism (CD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) unveil characteristic amyloid peaks and structural changes in Fap fibrils upon pyrene exposure. 3D-EEM analysis identifies a protein-like fluorophore in Fap fibrils, exhibiting pyrene-induced fluorescence quenching. Binding constants range from 5.23 to 7.78 M-1, with ΔG of -5.10 kJ mol-1 at 298 K, indicating spontaneous and exothermic interaction driven by hydrophobic forces. Exogenous Fap fibrils substantially increased the biofilm growth and pyrene degradation by P. aeruginosa PFL-P1 from 46 % to 64 % within 7 days (p = 0.0236). GC-MS identifies diverse metabolites, implying phthalic acid pathway in pyrene degradation. This study deepens insights into structural dynamics of Fap fibrils when exposed to pyrene, offering potential application in environmental bioremediation.

Biosorption of Heavy Metal (Mn2+) by Thermophilic Bacterial Strains Isolated from Surya Kund Hot Spring, Yamunotri, Uttarakhand

This investigation aimed to identify the bioremediation potential of Mn2+-resistant bacterial strains cultured from the Surya Kund hot spring, Yamunotri, Uttarakhand. In this study, eight heavy metal-resistant isolates belonging to two phyla, i.e., Firmicutes and Proteobacteria, were investigated for their Mn2+ biosorption potential. The metal tolerance potential of all the thermophilic bacterial strains was determined by MIC. Bioremediation assay of these metal-resistant strains was performed for Mn2+ through the live and dead biomass of the bacterial cell. The evaluation of the bioremediation rate of metal ions through bacteria was done by AAS. All the selected bacterial strains were evaluated with effective biosorption rates for Mn2+. Acinetobacter sp. LSN-10 (YII-1) has been showing the highest potential for the removal of Mn2+ in both live (41.202%) and dead biomass (64.721%) conditions. The bioremediation rate of dead biomass was observed quite higher in comparison to bioremediation through live bacterial cells in the maximum number of isolates. This study may provide a new eco-friendly and cost-effective approach to dealing with metal toxicity. However, further investigation is needed to identify the most effective applications and potential limitations of this method.

Bacterial screening in Indian coastal regions for efficient polypropylene microplastics biodegradation

Polypropylene based medical devices significantly increased production and usage in COVID-19 pandemic states, and this material is very resilient in the environment. Thus, more than ever, rapid action is needed to reduce this pollution. This study focuses on the degradation of polypropylene microplastics (PP MPs) by unique marine bacterial strains obtained from the Thoundi (Bacillus tropicus, Bacillus cereus, Stenotrophomonas acidaminiphila, and Brucella pseudintermedia) and Rameshwaram coasts (Bacillus cereus). Those above five bacterial strains were chosen after preliminary screening of their hydrophobicity, biofilm-forming capabilities, and responsiveness to the zone of clearance technique. During the biodegradation process (28 days), the growth, metabolic activity, and viability of these five isolates were all raised. After the post-biodegradation process, the weight loss percentages of the mentioned bacterial strains treated with PP MPs gradually decreased, with values of 51.5 ± 0.5 %, 47.5 ± 0.5 %, 33 ± 1 %, 28.5 ± 0.5 and 35.5 ± 0.5 %, respectively. UV-Vis DRS and SEM analysis confirmed that bacterial strains adhering to MPs cause cracks and cavities on their surface. The degradation of PP MPs can be inferred from alterations in the FT-IR spectrum, specifically in the carbonyl group range of 1100-1700 cm-1, as well as changes in the 1H NMR spectrum, including chemical shift and proton peak pattern alterations. Bacterial strains facilitated the degradation of PP MPs through the secretion of hydrolase-categorized enzymes of protease, lipase, and esterase. The findings of this study indicate that marine bacteria may possess distinctive characteristics that facilitate the degradation of plastic waste and contribute to environmental conservation.

A review: Marine aquaculture impacts marine microbial communities

Marine aquaculture is key for protein production but disrupts marine ecosystems by releasing excess feed and pharmaceuticals, thus affecting marine microbes. Though vital, its environmental impact often remains overlooked. This article delves into mariculture's effects on marine microbes, including bacteria, fungi, viruses, and antibiotic-resistance genes in seawater and sediments. It highlights how different mariculture practices-open, pond, and cage culture-affect these microbial communities. Mariculture's release of nutrients, antibiotics, and heavy metals alters the microbial composition, diversity, and functions. Integrated multi-trophic aquaculture, a promising sustainable approach, is still developing and needs refinement. A deep understanding of mariculture's impact on microbial ecosystems is crucial to minimize pollution and foster sustainable practices, paving the way for the industry's sustainable advancement.

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

IMPORTANCE

Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.

Insight on recently discovered PET polyester-degrading enzymes, thermostability and activity analyses

The flexibility and the low production costs offered by plastics have made them crucial to society. Unfortunately, due to their resistance to biological degradation, plastics remain in the environment for an extended period of time, posing a growing risk to life on earth. Synthetic treatments of plastic waste damage the environment and may cause damage to human health. Bacterial and fungal isolates have been reported to degrade plastic polymers in a logistic safe approach with the help of their microbial cell enzymes. Recently, the bacterial strain Ideonella sakaiensis (201-F6) was discovered to break down and assimilate polyethylene terephthalate (PET) plastic via metabolic processes at 30 °C to 37 °C. PETase and MHETase enzymes help the bacterium to accomplish such tremendous action at lower temperatures than previously discovered enzymes. In addition to functioning at low temperatures, the noble bacterium's enzymes have amazing qualities over pH and PET plastic degradation, including a shorter period of degradation. It has been proven that using the enzyme PETase, this bacterium hydrolyzes the ester linkages of PET plastic, resulting in production of terephthalic acid (TPA), nontoxic compound and mono-2-hydroxyethyl (MHET), along with further depolymerization of MHET to release ethylene glycogen (EG) and terephthalic acid (TPA) by the second enzyme MHETase. Enzymatic plastic degradation has been proposed as an environmentally friendly and long-term solution to plastic waste in the environment. As a result, this review focuses on the enzymes involved in hydrolyzing PET plastic polymers, as well as some of the other microorganisms involved in plastic degradation.

Significance of Herbaspirillum sp. in biodegradation and biodetoxification of herbicides, pesticides, hydrocarbons and heavy metals - A review

In today's industrialized world, contamination of soil and water with various substances has emerged as a pressing concern. Bioremediation, with its advantages of degradation or detoxification, non-polluting nature, and cost-effectiveness, has become a promising method due to technological advancements. Among the bioremediation agents, bacteria have been highly explored and documented as a productive organism. Recently, few studies have reported on the significance of Herbaspirillum sp., a Gram-negative bacterium, in bioremediating herbicides, pesticides, polycyclic aromatic hydrocarbons, metalloids, and heavy metals, as well as its role in augmenting phytoremediation efforts. Herbaspirillum sp. GW103 leached 66% of Cu from ore materials and significantly enhanced the phytoaccumulation of Pb and Zn in plumule and radical tissues of Zea mays L. plants. Additionally, Herbaspirillum sp. WT00C reduced Se6+ into Se0, resulting in an increased Se0 content in tea plants. Also, Herbaspirillum sp. proved effective in degrading 0.6 mM of 4-chlorophenol, 92.8% of pyrene, 77.4% of fluoranthene, and 16.4% of trifluralin from aqueous solution and soil-water system. Considering these findings, this review underscores the need for further exploration into the pathways of pollutant degradation, the enzymes pivotal in the degradation or detoxification processes, the influence of abiotic factors and pollutants on crucial gene expression, and the potential toxicity of intermediate products generated during the degradation process. This perspective reframes the numerical data to underscore the underutilized potential of Herbaspirillum sp. within the broader context of addressing a significant research gap. This shift in emphasis aligns more closely with the problem-necessity for solution-existing unexplored solution framework.

Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms

Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus-prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus-host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction-modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes, which may result in the blooming of defence strategists in biofilms. The detachment of bloomed defence strategists may reduce the infectivity of viruses in seawater and result in the emergence of a novel role of marine biofilms.

Biofilm-Mediated Heavy Metal Removal from Aqueous System by Multi-Metal-Resistant Bacterial Strain Bacillus sp. GH-s29

Worldwide ever-augmenting urbanization, modernization, and industrialization have contributed to the release of pernicious compounds and a variety of pollutants into the environment. The pollutants discharged due to industrialization are of global concern. Industrial waste and effluent are comprised of hazardous organic and inorganic chemicals including heavy metals which pose a significant threat to the environment and may bring about numerous diseases or abnormalities in human beings. This brings on greater urgency for remediation of these polluted soil and water using sustainable approaches and mechanisms. In the present research, a multi-metal-resistant, gram-positive, non-virulent bacterial strain Bacillus sp. GH-s29 was isolated from contaminated groundwater of Bhojpur district, Bihar, India. The strain had the potential to develop a biofilm that was able to remediate different heavy metals [arsenic, cadmium, and chromium] from individual and multi-heavy metal solutions. Maximum removal for As (V), Cd (II), and Cr (VI) from individual-metal and the multi-metal solution was observed to be 73.65%, 57.37%, 61.62%, and 48.92%, 28.7%, and 35.46%, respectively. SEM-EDX analysis revealed the sequestration of multi-heavy metals by bacterial biofilm. Further characterization by FTIR analysis ensured that the presence of negatively charged functional groups on the biofilm-EPS such as hydroxyl, phosphate, sulfate, and carboxyl helps in binding to the positively charged metal ions. Thus, Bacillus sp. GH-s29 proved to be an effective and economical alternative for different heavy metal remediation from contaminated sites.

Microbial biochemical pathways of arsenic biotransformation and their application for bioremediation

Arsenic is a ubiquitous toxic metalloid, the concentration of which is beyond WHO safe drinking water standards in many areas of the world, owing to many natural and anthropogenic activities. Long-term exposure to arsenic proves lethal for plants, humans, animals, and even microbial communities in the environment. Various sustainable strategies have been developed to mitigate the harmful effects of arsenic which include several chemical and physical methods, however, bioremediation has proved to be an eco-friendly and inexpensive technique with promising results. Many microbes and plant species are known for arsenic biotransformation and detoxification. Arsenic bioremediation involves different pathways such as uptake, accumulation, reduction, oxidation, methylation, and demethylation. Each of these pathways has a certain set of genes and proteins to carry out the mechanism of arsenic biotransformation. Based on these mechanisms, various studies have been conducted for arsenic detoxification and removal. Genes specific for these pathways have also been cloned in several microorganisms to enhance arsenic bioremediation. This review discusses different biochemical pathways and the associated genes which play important roles in arsenic redox reactions, resistance, methylation/demethylation, and accumulation. Based on these mechanisms, new methods can be developed for effective arsenic bioremediation.

Dye degradation by early colonizing marine bacteria from the Arabian Sea, India

Malachite green dye belongs to the triphenylmethane group and is a common environmental pollutant that threatens non-target organisms. We report the potential of the early colonizing marine bacterium Pseudomonas sp. ESPS40 isolated from the Arabian Sea, India, to decolorize malachite green (MG). The bacterium ESPS40 exhibited a higher ability for MG degradation (86-88%) at varying NaCl concentrations (1-3%). The highest MG degradation (~ 88%) was observed at 1% NaCl. The bacterial strain ESPS40 showed degradation up to 800 mg L^-1 MG. Further, enzyme activities such as tyrosinase (63.48-526.52 U L^-1) and laccase (3.62-28.20 U L^-1) were also analyzed with varying concentrations (100 mg L^-1-1000 mg L^-1) of MG during the degradation process. The dye degradation was confirmed by Fourier transform infrared spectroscopy (FTIR) and high-performance liquid chromatography (HPLC). The outcome of the present study demonstrated Pseudomonas sp. ESPS40 as a potential strain for the efficient degradation of MG at higher concentrations. Thus, Pseudomonas sp. ESPS40 can be utilized as a potential candidate for the biodegradation of MG in wastewater treatment.

Enhancement of soil high-molecular-weight polycyclic aromatic hydrocarbon degradation by Fusarium sp. ZH-H2 using different carbon sources

High-molecular-weight PAHs (HMW-PAHs) in soil cannot be easily degraded. However, nutrient supplementation could stimulate the growth of exogenously added strains to enhance the degradation of HMW-PAHs in polluted soil. This study evaluated the applicability of Fusarium sp. ZH-H2, a polycyclic aromatic hydrocarbon (PAH)-degrading strain isolated by our research group, for the bioremediation of contaminated soil from the Hebei coal mining area in China. A soil incubation experiment was conducted to investigate the effect of two carbon sources and different carbon, nitrogen, and phosphorus (C:N:P) ratios on the remediation of high-molecular-weight PAHs (HMW-PAHs) in soil by Fusarium sp. ZH-H2, as well as the induction of lignin peroxidase activity. Our findings indicated that the HDF2 treatment (equal parts of humic acid and starch as carbon sources at a 50:1:0.5 C:N:P ratio) enhanced the removal rate of total HMW-PAHs from soil, reaching a maximum removal rate of 37.15 %. The removal rates of Pyr (a 4-ring PAH), BaP (a 5-ring PAH), and BghiP (a 6-ring PAH) were the highest in HDF2 treatment, and the removal rates were 39.51 %, 54.63 %, and 38.60 %, respectively. Compared with the ZH-H2 treatment, different carbon sources and C:N:P ratios significantly induced soil lignin peroxidase activity and the HDF2 treatment also resulted in the highest enzyme activity (up to 34.68 U/L). Furthermore, there was a significant or highly significant linear positive correlation between the removal rate of HMW-PAHs and enzyme activity in all cases. Our findings suggest that the optimal HMW-PAH degradation performance and enhancement of lignin peroxidase activity by ZH-H2 were achieved when both starch and humic acid were used as carbon sources at a C:N:P ratio of 50:1:0.5.

Plastic-microbe interaction in the marine environment: Research methods and opportunities

Approximately 9 million metric tons of plastics enters the ocean annually, and once in the marine environment, plastic surfaces can be quickly colonised by marine microorganisms, forming a biofilm. Studies on plastic debris-biofilm associations, known as plastisphere, have increased exponentially within the last few years. In this review, we first briefly summarise methods and techniques used in exploring plastic-microbe interactions. Then we highlight research gaps and provide future research opportunities for marine plastisphere studies, especially, on plastic characterisation and standardised biodegradation tests, the fate of "environmentally friendly" plastics, and plastisphere of coastal habitats. Located in the tropics, Southeast Asian (SEA) countries are significant contributors to marine plastic debris. However, plastisphere studies in this region are lacking and therefore, we discuss how the unique environmental conditions in the SEA seas may affect plastic-microbe interaction and why there is an imperative need to conduct plastisphere studies in SEA marine environments. Finally, we also highlight the lack of understanding of the pathogenicity and ecotoxicological effects of plastisphere on marine ecosystems.

Bacterial Communities in Effluents Rich in Phenol and Their Potential in Bioremediation: Kinetic Modeling

Phenol is used in the manufacturing process of phenolic resins from which residues remain that must be sent for confinement. For that reason, in this study, the wastewater of a resin factory was analyzed to isolate the bacteria present, identify them by molecular methods and finally evaluate their impact on bioremediation treatment. A total of 15 bacteria were isolated, of these, eight belong to the genus Bacillus spp. All bacteria were individually multiplied and inoculated in clusters in 15 L reactors which were carefully monitored for pH, electrical conductivity, chemical oxygen demand and temperature. The acquired data were analyzed using ANOVA with repeated measurements. The first test revealed that native bacterial communities reduce the phenol content by up to 20% and COD by 49%, which is significant with respect to the reactor not being inoculated with bacteria. Furthermore, when a mathematical model was applied to the reactors, it was shown that the bacteria require an adaptation time of approximately 100 h. A second test where the inoculation was interspersed with the addition of lime as a flocculant showed that, even though the reduction in phenol and COD was lower than in the previous test, the difference between treatments and control is statistically significant (α ≤ 0.05).

Microbial elimination of pyrethroids: specific strains and involved enzymes

Pyrethroids, which are synthetic organic insecticides, are widely used in agriculture and households to resist pests and control disease transmission. However, pyrethroids have inevitably caused environmental pollution, leading to concerns for food safety and human health. Bioremediation has emerged as one of the most promising methods to eliminate pyrethroids compounds. Pyrethroid-degrading microorganisms and the relevant enzymes have shown an efficient ability in degrading pyrethroids by hydrolyzing the ester linkage. In this review, a wide variety of pyrethroid-degrading strains were presented and classified from different sources, such as wastewater, soils, and oceans. In addition, the recombinant expression, enzyme identification, and molecular modification of these microbial pyrethroid-degrading enzymes were also compared and discussed in detail. Moreover, the potential applications of pyrethroid-degrading enzymes, including immobilization and biodegradation towards a series of pyrethroids, were also presented. All of the positive results obtained from this review could be a good guideline for the other research in this field. KEY POINTS: • Distribution of pyrethroid-degrading strains in different sources was summarized. • Enzymatic properties including pH, temperature, and substrate specificity were compared. • Promising molecular modification and immobilization of hydrolases were present.

Long-term fertilization has different impacts on bacterial communities and phosphorus forms in sugarcane rhizosphere and bulk soils under low-P stress

The application of phosphorus (P) fertilizer effectively improves soil P availability, but it also affects soil microbial communities. However, the responses of soil bacterial communities and P forms to long-term P fertilization, and the relationships of bacterial communities with soil P forms remain unclear in P-deficient field. In this study, the impacts of different P fertilization treatments (chemical nitrogen and potassium (NK); chemical N, P and K (NPK); and NPK plus straw (NPKS)) on the bacterial communities and P forms in sugarcane rhizosphere (RS) and bulk soils (BS) were evaluated. Compared with the NK, the NPK and NPKS treatments significantly (P<0.05) increased the yield and quality characters of sugarcane, especially under NPKS. Additionally, P fertilization significantly increased the available P (AP), soluble inorganic P (Pi) and retained Pi in both the RS and BS, but they significantly increased the Chao1 and Shannon index only in the BS; and almost all these indices were significantly higher in the RS than in the BS. The bacterial community compositions were also significantly altered by P fertilization, with major changes in the RS and minor changes in the BS. The bacterial genera that were enriched in the sugarcane rhizosphere mainly included Bradyrhizobium, Rhodanobacter, Pseudolabrys, Conexibacter, and Burkholderia-Caballeronia-Paraburkholderia, some of which potentially promote the plant growth. Compared to NK, functional groups involved in the cycling of carbon, N, and sulfur significantly increased or decreased with fertilizer P application. Moreover, the relative abundances of many bacterial species were significantly correlated with the soil P forms. In conclusion, long-term P fertilization altered bacterial structure and functions in P-deficient sugarcane soil, which could help the soil P cycling and suppling. The results provide useful information to stimulate the power of the microbes by fertilization measures to improve soil nutrients and crop production.

Heavy metal resistance of marine bacteria on the sediments of the Black Sea

The Black Sea is unfortunately globally established as a highly polluted sea, with contaminants from various sources polluting its marine sediments. This study aimed at analyzing heavy metal resistance levels by heterotrophic bacteria colonizing marine sediments across Black Sea shores within Turkey. Twenty-nine bacterial samples from marine sediments were investigated through exposure to sixteen heavy metal salts using the microdilution method. The minimum inhibitory concentration values for bacterial colonies within such marine sediment samples ranged from <0.97 mM/L to >1000 mM/L. Trough and peak minimum inhibitory concentration values were determined at <0.17 mg/mL and > 331 mg/mL. Peak tolerated and peak toxic heavy metals were identified as iron and cadmium, respectively. Resistance ratios were also obtained in this study. Bacillus wiedmannii was identified as the most resistant bacterial population when exposed to heavy metal salts. This study shows occurrence of heavy metal resistant bacteria within Black Sea sediments.

Application of Marine Microbial Natural Products in Cosmetics

As the market size of the cosmetics industry increases, the safety and effectiveness of new products face higher requirements. The marine environment selects for species of micro-organisms with metabolic pathways and adaptation mechanisms different from those of terrestrial organisms, resulting in their natural products exhibiting unique structures, high diversity, and significant biological activities. Natural products are usually safe and non-polluting. Therefore, considerable effort has been devoted to searching for cosmetic ingredients that are effective, safe, and natural for marine micro-organisms. However, marine micro-organisms can be difficult, or impossible, to culture because of their special environmental requirements. Metagenomics technology can help to solve this problem. Moreover, using marine species to produce more green and environmentally friendly products through biotransformation has become a new choice for cosmetic manufacturers. In this study, the natural products of marine micro-organisms are reviewed and evaluated with respect to various cosmetic applications.

Exploration of anti-chromium mechanism of marine Penicillium janthinellum P1 through combinatorial transcriptomic analysis and WGCNA

Fungi have a promising application prospect in the remediation of heavy-metal wastewater pollution which is a sticky global problem. New marine-derived strain Penicillium janthinellum P1 is of high chromium resistance. However, a comprehensive study of the transcriptomics in Penicillium janthinellum P1 strains is lacking. Firstly, the changing trends of a series of physiological and biochemical indices of P1 strain at 0 M and 1 M Cr concentration were investigated to track the ROS variation. Secondly, transcriptome sequencing of P1 was performed by RNA-Seq sequencing technology. The transcriptome data indicated that 12,352 coding protein regions were predicted, and 6655 differentially expressed genes were identified by DESeq2, of which 4234 genes were up-regulated, and 2421 genes down-regulated. Through further co-expression network of WGCNA analysis, the filtered unigenes were clustered into 19 modules. Combined with the physiological and biochemical findings, the three modules with the highest correlation with the six traits were selected to construct the network, and 52 hub genes were obtained. Furthermore, 10 speculative hub genes related to chromium resistance were selected and verified by real-time PCR. The results were in line with the expected experimental assumption. These results improve our understanding of the transcriptomic dimensions of the high chromium resistance of Penicillium janthinellum P1 strains.

A novel degradation mechanism of naphthenic acids by marine Pseudoalteromonas sp

Naphthenic acids (NAs) are a persistent toxic organic pollutant that occur in different environment worldwide and cause serious threat to the ecosystem and public health. However, knowledge on the behavior and fate of NAs in marine environments still remains unknown. In this study, the degradation mechanism of NAs (cyclohexylacetic acid, CHAA) was investigated using an common indigenous marine Pseudoalteromonas sp. The results showed that CHAA could be degraded completely under aerobic condition, but could not be utilized directly under anaerobic condition. Interestingly, transcriptome and key enzyme activity results showed the CHAA degradation pathway induced under aerobic condition could still work in anaerobic condition. The degradation was activated by acetyl-CoA transferase and sequentially formed the corresponding cyclohexene, alcohol, and ketone with the assistance of related enzymes, and finally cleaved by hydroxymethylglutarate-CoA lyase. Besides, there was a positive correlation between chemotaxis and aerobic degradation genes (r = 0.976, P < 0.05), the chemotaxis would enhance bacterium movement and NAs biodegradation. It is proposed that bacterium could translocate to NAs and accomplish biodegradation from aerobic to anaerobic environments, which was a new anaerobic degradation pathway of NAs. This study provides new insights into the fate of NAs and other organic contaminants in marine environment.

Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics

Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.

Deep-sea mercury resistant bacteria from the Central Indian Ocean: A potential candidate for mercury bioremediation

Deep-sea bacteria when grown in normal environmental conditions get morphologically and genetically adapted to resist the provided culture conditions for their survival, making them a possible aspirant in mercury bioremediation. In this study, seawater samples were collected from different depths of the Central Indian Ocean and seven mercury resistant bacteria (resistant to 100 mg L^-1 concentration of inorganic Hg as HgCl₂) were isolated. Based on 16S rRNA gene sequencing, the identified isolates belong to the genera Pseudomonas, Bacillus and Pseudoalteromonas. The presence of the merA gene in the isolates contributes to the effective volatilization of mercury. The Inductively Coupled Plasma Mass-Spectroscopy analysis revealed that the isolates can reduce up to >80% of inorganic mercury. Moreover, Fourier Transform Infrared spectrum analysis indicates that functional groups play a key role in the mechanism of adaptation towards Hg²⁺ reduction. Thus, the deep-sea bacteria expressed significant tolerance and reduction potential towards ionic mercury.

A key antisense sRNA modulates the oxidative stress response and virulence in Xanthomonas oryzae pv. oryzicola

Pathogens integrate multiple environmental signals to navigate the host and control the expression of virulence genes. In this process, small regulatory noncoding RNAs (sRNAs) may function in gene expression as post-transcriptional regulators. In this study, the sRNA Xonc3711 functioned in the response of the rice pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), to oxidative stress. Xonc3711 repressed production of the DNA-binding protein Xoc_3982 by binding to the xoc_3982 mRNA within the coding region. Mutational analysis showed that regulation required an antisense interaction between Xonc3711 and xoc_3982 mRNA, and RNase E was needed for degradation of the xoc_3982 transcript. Deletion of Xonc3711 resulted in a lower tolerance to oxidative stress due to the repression of flagella-associated genes and reduced biofilm formation. Furthermore, ChIP-seq and electrophoretic mobility shift assays showed that Xoc_3982 repressed the transcription of effector xopC2, which contributes to virulence in Xoc BLS256. This study describes how sRNA Xonc3711 modulates multiple traits in Xoc via signals perceived from the external environment.

Small, stable RNA species perform diverse functions in both prokaryotes and eukaryotes. In this study, the sRNA Xonc3711 decreased the production of DNA-binding protein Xoc_3982 in the bacterium Xanthomonas oryzae pv. oryzicola (Xoc) by base pairing with the xoc_3982 transcript. When Xonc3711 was mutated, Xoc was impaired in its ability to form flagella and produce biofilms, which reduced Xoc tolerance to oxidative stress. We also discovered that the DNA-binding protein Xoc_3982 represses the expression of xopC2, which encodes an effector protein, and reduces its expression. Our results show that Xonc3711 modulates and integrates multiple systems in Xoc to protect cells from oxidative damage.

Production and characterization of biodegradable polyhydroxybutyrate by Micrococcus luteus isolated from marine environment

Marine microorganisms are reported to produce polyhydroxybutyrate (PHB) that has wide range of medical and industrial applications with the advantage of biodegradability. PHBs are synthesized as an energy and carbon storage element under metabolic pressure. The scope of this work is enhancing PHB production using marine microbial isolate, Micrococcus luteus by selectively optimizing various growth conditions such as different media components and growth parameters that influence the cell growth and PHB production were sampled. Micrococcus luteus produced 7.54 g/L of PHB utilizing glucose as a carbon source and ammonium sulphate as a nitrogen source with maximum efficiency. The same optimized operational conditions were further employed in batch fermentation over a time span of 72 h. Interestingly higher cell dry weight of 21.52 g/L with PHB yield of 12.18 g/L and 56.59% polymer content was observed in batch fermentation studies at 64 h. The chemical nature of the extracted polymer was validated with physio-chemical experiments and was at par with the commercially available PHB. This study will spotlight M. luteus as a potential source for large-scale industrial production of PHB with reducing environmental pollutions.

Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal Tolerance

Heavy metal pollution is a global knotty problem and fungi hold promising potential for the remediation of wastewater containing heavy metals. Here, a new highly chromium-tolerance species, Penicillium janthinellum P1, is investigated. The genome of P1 was sequenced and assembled into 30 Mb genome size containing 10,955 predicted protein-coding genes with a GC content of 46.16% through an integrated method of Illumina short-read sequencing and single-molecule real-time Pacific Biosciences sequencing platforms. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of Penicillium janthinellum P1 and Penicillium oxalicum 114-2 was estimated to be 74 MYA. 33 secondary metabolism gene clusters were identified via antiSMASH software, mainly including non-ribosomal peptide synthase genes and T1 polyketide synthase genes. 525 genes were annotated to encode enzymes that act on carbohydrates, involving 101 glucose-degrading enzymes and 24 polysaccharide synthase. By whole-genome sequence analysis, large numbers of metal resistance genes were found in strain P1. Especially ABC transporter and Superoxide dismutase ensure that the P1 fungus can survive in a chromium-polluted environment. ChrA and ChrR were also identified as key genes for chromium resistance. Analysis of their genetic loci revealed that the specific coding-gene arrangement may account for the fungus’s chromium resistance. Genetic information and comparative analysis of Penicillium janthinellum are valuable for further understanding the mechanism of high resistance to heavy metal chromium, and gene loci analysis provides a new perspective for identifying chromium-resistant strains.

Microscopic techniques to evaluate the biofilm formation ability of a marine bacterium Pseudomonas aeruginosa PFL-P1 on different substrata

Biofilm formation in bacteria is strongly affected by the nature of substrata. Different substrata such as glass, polystyrene, steel, ceramic, and rubber were used to assess the biofilm forming ability of a marine bacterium Pseudomonas aeruginosa PFL-P1 using a scanning electron microscope (SEM), atomic force microscope (AFM), and confocal laser scanning microscope (CLSM). The bacterium formed dense biofilms with varied aggregation on different substrata. SEM study revealed small rod-shaped cells with diverse arrangements within the biofilms on all the substrata under study. The AFM study revealed the highest roughness of 545 nm on the ceramic substratum. The biofilms formed on ceramic substratum were characterized with maximum roughness (742 nm), maximum peak height (1,480 nm), and maximum arithmetic mean height (611 nm), significantly higher than all the other substrata (p < .05). AFM studies confirmed that P. aeruginosa PFL-P1 exhibited biofilm heterogeneity on all the substrata. The CLSM study indicated a higher fraction of nucleic acids to α-polysaccharides ratio in the biofilms. COMSTAT analysis revealed the highest biofilm biomass of ~18 μm³ /μm² on the ceramic substratum. The maximum biofilm thickness of ~50 μm in the native state on the ceramic substratum was significantly higher than glass (p = .0015), polystyrene (p = .0001), steel (p = .0035), and rubber substrata (p = .0001). The higher surface roughness of ceramic substratum is accountable for more area for colonization, as evident from higher biomass and thickness of the biofilm. This study provides insight into the substratum properties, which modulate the biofilm forming ability in bacteria.

Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability

The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.

Effect of C/N substrates for enhanced extracellular polymeric substances (EPS) production and Poly Cyclic Aromatic Hydrocarbons (PAHs) degradation

Extracellular Polymeric Substances (EPS) influenced Poly Cyclic Aromatic Hydrocarbons (PAHs) degrading Klebsiella pneumoniae was isolated from the marine environment. To increase the EPS production by Klebsiella pneumoniae, several physicochemical parameters were tweaked such as different carbon sources (arabinose, glucose, glycerol, lactose, lactic acid, mannitol, sodium acetate, starch, and sucrose at 20 g/L), nitrogen sources (ammonium chloride, ammonium sulphate, glycine, potassium nitrate, protease peptone and urea at 2 g/L), different pH, carbon/nitrogen ratio, temperature, and salt concentration were examined. Maximum EPS growth and biodegradation of Anthracene (74.31%), Acenaphthene (67.28%), Fluorene (62.48%), Naphthalene (57.84%), and mixed PAHs (55.85%) were obtained using optimized conditions such as glucose (10 g/L) as carbon source, potassium nitrate (2 g/L) as the nitrogen source at pH 8, growth temperature of 37 °C, 3% NaCl concentration and 72 h incubation period. The Klebsiella pneumoniae biofilm architecture was studied by confocal laser scanning microscopy (CLSM) and scanning electron microscope (SEM). The present study demonstrates the EPS influenced PAHs degradation of Klebsiella pneumoniae.

NaCl Concentration-Dependent Aminoglycoside Resistance of Halomonas socia CKY01 and Identification of Related Genes

Among various species of marine bacteria, those belonging to the genus Halomonas have several promising applications and have been studied well. However, not much information has been available on their antibiotic resistance. In our efforts to learn about the antibiotic resistance of strain Halomonas socia CKY01, which showed production of various hydrolases and growth promotion by osmolytes in previous study, we found that it exhibited resistance to multiple antibiotics including kanamycin, ampicillin, oxacillin, carbenicillin, gentamicin, apramycin, tetracycline, and spectinomycin. However, the H. socia CKY01 resistance pattern to kanamycin, gentamicin, apramycin, tetracycline, and spectinomycin differed in the presence of 10% NaCl and 1% NaCl in the culture medium. To determine the mechanism underlying this NaCl concentration-dependent antibiotic resistance, we compared four aminoglycoside resistance genes under different salt conditions while also performing time-dependent reverse transcription PCR. We found that the aph2 gene encoding aminoglycoside phosphotransferase showed increased expression under the 10% rather than 1% NaCl conditions. When these genes were overexpressed in an Escherichia coli strain, pETDuet-1::aph2 showed a smaller inhibition zone in the presence of kanamycin, gentamicin, and apramycin than the respective control, suggesting aph2 was involved in aminoglycoside resistance. Our results demonstrated a more direct link between NaCl and aminoglycoside resistance exhibited by the H. socia CKY01 strain.

The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions

Bacteria, the first organisms that appeared on Earth, continue to play a central role in ensuring life on the planet, both as biogeochemical agents and as higher organisms' symbionts. In the last decades, they have been employed both as bioremediation agents for cleaning polluted sites and as bioconversion effectors for obtaining a variety of products from wastes (including eco-friendly plastics and green energies). However, some recent reports suggest that bacterial biodiversity can be negatively affected by the present environmental crisis (global warming, soil desertification, and ocean acidification). This review analyzes the behaviors positively selected by evolution that render bacteria good models of sustainable practices (urgent in these times of climate change and scarcity of resources). Actually, bacteria display a tendency to optimize rather than maximize, to economize energy and building blocks (by using the same molecule for performing multiple functions), and to recycle and share metabolites, and these are winning strategies when dealing with sustainability. Furthermore, their ability to establish successful reciprocal relationships by means of anticipation, collective actions, and cooperation can also constitute an example highlighting how evolutionary selection favors behaviors that can be strategic to contain the present environmental crisis.

Bacterial communities as indicators of environmental pollution by POPs in marine sediments

Decades of intensive discharge from industrial activities into coastal systems has resulted in the accumulation of a variety of persistent organic pollutants (POPs) in marine waters and sediments, having detrimental impacts on aquatic ecosystems and the resident biota. POPs are among the most hazardous chemicals originating from industrial activities due to their biotoxicity and resistance to environmental degradation. Bacterial communities are known to break down many of these aromatic compounds, and different members of naturally occurring bacterial consortia have been described to work in syntrophic association to thrive in heavily contaminated waters and sediments, making them potential candidates as bioindicators of environmental pollution. In this study environmental, sampling was combined with chemical analysis of pollutants and high-resolution sequencing of bacterial communities using Next Generation Sequencing molecular biology tools. The aim of the present study was to describe the bacterial communities from marine sediments containing high loads of POPs and to identify relevant members of the resident microbial communities that may act as bioindicators of contamination. Marine sediments were collected from a coastal bay area of the Baltic Sea historically influenced by intense industrial activity, including metal smelting, oil processing, and pulp and paper production. Different types of POPs were detected at high concentrations. Fiberbank sediments, resulting from historic paper industry activity, were found to harbour a clearly distinct bacterial community including a number of bacterial taxa capable of cellulolytic and dechlorination activities. Our findings indicate that specific members of the bacterial communities thrive under increasing levels of POPs in marine sediments, and that the abundances of certain taxa correlate with specific POPs (or groups), which could potentially be employed in monitoring, status assessment and environmental management purposes.

Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus

In the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting remarkable differences among individuals. Our results showed that there is a correlation between microbiota structure and geographical location of the echinoderm collection site, highlighting over-representation of metagenomic functions related to amino acid and bioactive peptides metabolism in specimens inhabiting the nature reserve. Finally, we also described the developmental delay and aberrations exhibited by sea urchin embryos exposed to distinct bacterial isolates, and showed that these defects rely upon hydrophilic compound(s) synthesized by the bacterial strains assayed. Altogether, our findings lay the groundwork to decipher the relationships of bacteria with sea urchins in their aquatic environment, also providing an additional layer of information to understand the biological roles of the coelomic fluid.

The Influence of pCO2-Driven Ocean Acidification on Open Ocean Bacterial Communities during A Short-Term Microcosm Experiment in the Eastern Tropical South Pacific (ETSP) off Northern Chile

Due to the increasing anthropogenic CO₂ emissions, Ocean Acidification (OA) is progressing rapidly around the world. Despite the major role that microorganisms play on the marine biogeochemical cycling and ecosystem functioning, the response of bacterial communities upon OA scenarios is still not well understood. Here, we have conducted a detailed characterization of the composition and relative abundance of bacterial communities in the water column of an open-ocean station in the Eastern Tropical South Pacific (ETSP) off northern Chile and their interactions with environmental factors. In addition, through a short-term microcosm experiment, we have assessed the effect of low pH/high pCO₂ conditions over the abundance and genetic diversity of bacterial communities. Our results evidence a clear partitioning of community composition that could be attributed mostly to dissolved oxygen. However, our experimental approach demonstrated that low pH/high pCO₂ conditions might modify the structure of the bacterial community, evidencing that small changes in pH may impact significantly the abundance and diversity of key microorganisms. This study constitutes a first step aiming to provide insight about the influence of changing carbonate chemistry conditions on natural bacterial communities and to shed light on the potential impact of OA in biogeochemical cycles on the ETSP region.

Ligninolytic enzyme involved in removal of high molecular weight polycyclic aromatic hydrocarbons by Fusarium strain ZH-H2

The capacity of Fusarium sp. strain ZH-H2 to secret lignin peroxidase (LiP), laccase (Lac), and manganese peroxidase (MnP) and degrade high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) was studied. When the fungus was grown in control mineral salt medium for 4 days, LiP and Lac activities were detected at 8871 U L^-1 and 5123 U L^-1, respectively. In the presence of HMW-PAHs as the sole carbon source, only LiP activity was detectable, and LiP activity had significantly reduced HMW-PAHs at day 7, with a maximum decrease of 85.9%. A strong correlation between LiP activity and HMW-PAHs removal efficiency could be fit into various models, with the highest correlation coefficients obtained for quadratic functions (P < 0.01). When a specific enzyme inhibitor was added, the ability of Fusarium to remove HMW-PAHs was reduced from 85.9 to 66.7%, depending on the inhibitor's concentration. Meanwhile, the determined activity of LiP was reduced from 11.4 to 48.6%. We conclude that in the presence of HMW-PAHs as the only carbon source to support growth, Fusarium ZH-H2 mainly produces LiP but not Lac or MnP for HMW-PAHs degradation. To our knowledge, it was the first time to propose a metabolic lignin peroxidase characterization of HMW-PAHs degradation by Fusarium sp. strains.

Microremediation of tannery wastewater by siderophore producing marine bacteria

The present study evaluated the microremediation potential of nine siderophore producing marine bacteria for hazardous raw tannery wastewater from common effluent treatment plant (CETP). Most of the pollutants detected in the wastewater were diminished after the bioremediation process. Further, among the three potent isolates selected for aerobic and anaerobic bioremediation study, Marinobacter hydrocarbonoclasticus demonstrated the highest bioremediation aerobically with a reduction in chromium (88%), sulphate (71%), phosphate (68%) and nitrate (57%). Notably, Nitratireductor kimnyeongensis could attack the effluent under both aerobic and anaerobic conditions as substantiated by statistically significant (p < .05) reduction in the pollutants [chromium (85%), sulphate (63%), Chemical Oxygen Demand (COD) (69%), phosphate (76%)]. From the study it is evident that the pollutant load reduction was achieved under both aerobic and anaerobic conditions, however, aerobic environment was more effective in reducing chromium, Biochemical Oxygen Demand (BOD), sulphate, nitrate and phosphate. The bioremediation efficiency was further confirmed by the bioassay experiments with plant and animal models where higher seed germination, greater plant length and biomass, as well as improved survival rate of Artemia nauplii for bioremediated wastewater was observed as compared to the untreated effluent indicating a significant reduction in toxicity. The results for simultaneous removal of multiple-toxicants thus signify effectiveness and ease of using the robust properties of these marine bacterial strains suggesting their potential application for bioremediation. Hence this could pave a promising way for an environment-friendly and economically feasible clean-up strategy for safer disposal of tannery wastewater.

Microbial prospection of communities that produce biosurfactants from the water column and sediments of the Gulf of Mexico

Microbial communities capable of hydrocarbon degradation linked to biosurfactant (BS) and bioemulsifier (BE) production are basically unexplored in the Gulf of México (GOM). In this work, the BS and BE production of culturable marine bacterial hydrocarbonoclasts consortia isolated from two sites (the Perdido Fold Belt and Coatzacoalcos area) was investigated. The prospection at different locations and depths led to the screening and isolation of a wide variety of bacterial consortia with BS and BE activities, after culture enrichment with crude oil and glycerol as the carbon sources. At least 55 isolated consortia presented reduction in surface tension (ST) and emulsifying activity (EI₂₄ ). After colony purification, bacteria were submitted to polyphasic analysis assays that resulted in the identification of different strains of cultivable Gammaproteobacteria Gram (-) Citrobacter, Enterobacter, Erwinia, Pseudomonas, Vibrio, Shewanella, Thalassospira, Idiomarina, Pseudoalteromonas, Photobacterium, and Gram (+) Staphylococcus, Bacillus, and Microbacterium. Overall, the best results for ST reduction and EI₂₄ were obtained with consortia. Individually, Pseudomonas, Bacillus, and Enterobacter strains showed the best results for the reduction of ST after 6 days, while Thalassospira and Idiomarina strains showed the best results for EI₂₄ (above 68% after 9 days). Consortia isolates from the GOM had the ability to degrade crude oil by up to 40-80% after 24 and 36 months, respectively. In all cases, biodegradation of crude oil was related to the reduction in ST and bioemulsifying activity and was independent from the depth in the water column.

Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck

Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.

Microbial diversity from the continental shelf regions of the Eastern Arabian Sea: A metagenomic approach

The marine microbiome is a complex and least-understood habitat, which play a significant role in global biogeochemical cycles. The present study reported the culture-independent assessment of microbial diversity from the Arabian Sea (AS) sediments (from Gujarat to Malabar; at 30 m depth) by using metagenome sequence analysis. Our results elucidated that bacterial communities in the Malabar coastal region are highly diverse than the Gujarat coast. Moreover, Statistical analysis (Spearman rank correlation) showed a significant correlation co-efficient value (r = P < 0.001) between microbial communities and physicochemical parameters (salinity and dissolved oxygen) in the water column. A total of 39 bacterial phyla were recorded from the eastern side of AS, of which six phyla Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Firmicutes, and Planctomycetes were found to be the most dominant group. The most dominant genus from Valapad region (Malabar Coast) was found to be Halomonas sp., while other regions were dominated with Psychrobacter pulmonis. The subsequent Principal Coordinate Analysis (PCoA) showed 99.53% variance, which suggests that, highly distinct microbial communities at Valapad (Malabar Coast) sampling location than other sites. Moreover, the microbial metabolic activity analysis revealed the important functions of microbial communities in the AS are hydrocarbon degradation, polymer degradation, nutrient oxidation and sulphate reduction (biodegradation process). Further extended studies are needed to be carried out for better understanding the functional diversity of microbial communities from the marine sediments.