scholarly journals Highly Contaminated Marine Sediments Can Host Rare Bacterial Taxa Potentially Useful for Bioremediation

2021 ◽  
Vol 12 ◽  
Author(s):  
Filippo Dell’Anno ◽  
Eugenio Rastelli ◽  
Michael Tangherlini ◽  
Cinzia Corinaldesi ◽  
Clementina Sansone ◽  
...  
Keyword(s):  
Marine Sediments ◽  
High Throughput Sequencing ◽  
Integrated Approach ◽  
Aliphatic Hydrocarbons ◽  
Chemical Contamination ◽  
Bacterial Strains ◽  
Anthropogenic Pressures ◽  
Sediment Grain Size ◽  
Gulf Of Naples ◽  
Mixed Contaminants

Coastal areas impacted by high anthropogenic pressures typically display sediment contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs). Microbial-based bioremediation represents a promising strategy for sediment reclamation, yet it frequently fails due to poor knowledge of the diversity and dynamics of the autochthonous microbial assemblages and to the inhibition of the target microbes in the contaminated matrix. In the present study, we used an integrated approach including a detailed environmental characterization, high-throughput sequencing and culturing to identify autochthonous bacteria with bioremediation potential in the sediments of Bagnoli-Coroglio (Gulf of Naples, Mediterranean Sea), a coastal area highly contaminated by PAHs, aliphatic hydrocarbons and HMs. The analysis of the benthic prokaryotic diversity showed that the distribution of the dominant taxon (Gammaproteobacteria) was mainly influenced by PAHs, As, and Cd concentrations. The other abundant taxa (including Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, NB1-j, Desulfobacterota, and Myxococcota) were mainly driven by sediment grain size and by Cu and Cr concentrations, while the rare taxa (i.e., each contributing <1%) by As and aliphatic hydrocarbons concentrations and by sediment redox potential. These results suggest a differential response of bacterial taxa to environmental features and chemical contamination and those different bacterial groups may be inhibited or promoted by different contaminants. This hypothesis was confirmed by culturing and isolating 80 bacterial strains using media highly enriched in PAHs, only nine of which were contextually resistant to high HM concentrations. Such resistant isolates represented novel Gammaproteobacteria strains affiliated to Vibrio, Pseudoalteromonas, and Agarivorans, which were only scarcely represented in their original assemblages. These findings suggest that rare but culturable bacterial strains resistant/tolerant to high levels of mixed contaminants can be promising candidates useful for the reclamation by bioaugmentation strategies of marine sediments that are highly contaminated with PAHs and HMs.

scholarly journals Assessing Chemical Contamination in the Marine Sediments of the Southwest Portuguese Continental Shelf, the CSS Project: Preliminary Results

2020 ◽  
Author(s):  
Mário Mil-Homens ◽  
Miguel Santos ◽  
Marisa de Almeida ◽  
Pedro Brito ◽  
Mafalda Freitas ◽  
...  
Keyword(s):  
Continental Shelf ◽  
Marine Sediments ◽  
Chemical Contamination ◽  
Preliminary Results

scholarly journals Selection of Macroinvertebrate Indices and Metrics for Assessing Sediment Quality in the St. Lawrence River (QC, Canada)

Water ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3335
Author(s):  
Mélanie Desrosiers ◽  
Bernadette Pinel-Alloul ◽  
Charlotte Spilmont
Keyword(s):  
Grain Size ◽  
Organic Contaminants ◽  
Sediment Quality ◽  
Macroinvertebrate Community ◽  
Habitat Characteristics ◽  
Anthropogenic Pressure ◽  
Chemical Contamination ◽  
Sediment Grain Size ◽  
Selection Of ◽  
St Lawrence River

This study aims to evaluate the anthropogenic pressure in the St. Lawrence River by assessing the relationships between composition and chemical contamination of sediments and macroinvertebrate community structure using a selection of indices and metrics. The aims of this study are to (i) determine the composition of macroinvertebrate community in sediments across a gradient of disturbance, (ii) select relevant macroinvertebrate indices and metrics for the assessment of sediment quality, (iii) investigate whether responses of selected indices and metrics differ across habitats and/or sediment quality classes, and finally, (iv) determine the thresholds for critical contaminants related to significant changes in the most relevant indices and metrics. Organic and inorganic contaminants as well as other sediment variables (sediment grain size, total organic carbon, nutrients, etc.) and macroinvertebrate assemblages were determined in 59 sites along the river. Fourteen macroinvertebrate indices and metrics, on the 264 initially selected, were shown to be the most effective to be used in bioassessment for the St. Lawrence River. However, the variation in macroinvertebrate indices and metrics remains strongly explained by habitat characteristics, such as sediment grain size or the level of nutrients. There is also an influence of metals and, to a lesser extent, organic contaminants such as petroleum hydrocarbons. The 14 selected indices and metrics are promising bioassessment tools that are easy to use and interpret in an environmental assessment of sediment quality in the St. Lawrence River.

scholarly journals Integrated Genomic and Metabolomic Approach to the Discovery of Potential Anti-Quorum Sensing Natural Products from Microbes Associated with Marine Samples from Singapore

Marine Drugs ◽  
2019 ◽  
Vol 17 (1) ◽  
pp. 72 ◽  
Author(s):  
Ji Ong ◽  
Hui Goh ◽  
Swee Lim ◽  
Li Pang ◽  
Joyce Chin ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Quorum Sensing ◽  
Large Scale ◽  
Marine Ecosystem ◽  
Gene Clusters ◽  
Integrated Approach ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Bacterial Strains ◽  
Reporter System

With 70% of the Earth’s surface covered in water, the marine ecosystem offers immense opportunities for drug discovery and development. Due to the decreasing rate of novel natural product discovery from terrestrial sources in recent years, many researchers are beginning to look seaward for breakthroughs in new therapeutic agents. As part of an ongoing marine drug discovery programme in Singapore, an integrated approach of combining metabolomic and genomic techniques were initiated for uncovering novel anti-quorum sensing molecules from bacteria associated with subtidal samples collected in the Singapore Strait. Based on the culture-dependent method, a total of 102 marine bacteria strains were isolated and the identities of selected strains were established based on their 16S rRNA gene sequences. About 5% of the marine bacterial organic extracts showed quorum sensing inhibitory (QSI) activity in a dose-dependent manner based on the Pseudomonas aeruginosa QS reporter system. In addition, the extracts were subjected to mass spectrometry-based molecular networking and the genome of selected strains were analysed for known as well as new biosynthetic gene clusters. This study revealed that using integrated techniques, coupled with biological assays, can provide an effective and rapid prioritization of marine bacterial strains for downstream large-scale culturing for the purpose of isolation and structural elucidation of novel bioactive compounds.

scholarly journals Metagenome-Assembled Genome (MAG) of Oceancaulis alexandrii NP7 isolated from Mediterranean Sea polluted marine sediments and its bioremediation potential

2021 ◽  
Author(s):  
Filippo Dell’Anno ◽  
Leonardo Joaquim van Zyl ◽  
Marla Trindade ◽  
Christophe Brunet ◽  
Antonio Dell’Anno ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Marine Sediments ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Hydrocarbon Degradation ◽  
Coding Sequences ◽  
Gulf Of Naples ◽  
Polycyclic Aromatic ◽  
First Time ◽  
Encoding Genes

Abstract Oceanicaulis alexandrii strain NP7 is a marine bacterium which belongs to the Hyphomonadaceae family and was isolated from sediments highly contaminated with metals and polycyclic aromatic hydrocarbons released for decades by industrial activities in the Gulf of Naples (Mediterranean Sea). Here, we report the partial genome sequence and annotation of Oceanicaulis alexandrii strain NP7 that contains a chromosome of 2,954,327 bp and encodes for 2914 predicted coding sequences and 44 RNA- encoding genes. Although the presence of some coding sequences for genes involved in hydrocarbon degradation processes (e.g., alkB) have already been described in the literature associated with the Oceanicaulis, this is the first time that more than 100 genes involved in metal detoxification processes and hydrocarbon degradation are reported belonging to this genus. The presence of a heterogeneous set of genes involved in stress response, hydrocarbon degradation, heavy metal resistance and detoxification suggests a possible role for Oceanicaulis alexandrii NP7 in the bioremediation of these highly contaminated marine sediments.

scholarly journals Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments

2020 ◽  
Vol 8 (9) ◽  
pp. 1402
Author(s):  
Filippo Dell’Anno ◽  
Christophe Brunet ◽  
Leonardo Joaquim van Zyl ◽  
Marla Trindade ◽  
Peter N. Golyshin ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Removal Rate ◽  
Microbial Consortia ◽  
Bacterial Strains ◽  
Gulf Of Naples ◽  
Lead And Cadmium ◽  
Polluted Sediments ◽  
Polycyclic Aromatic

Investigations on the ability of bacteria to enhance removal of hydrocarbons and reduce heavy metal toxicity in sediments are necessary to design more effective bioremediation strategies. In this study, five bacterial strains, Halomonas sp. SZN1, Alcanivorax sp. SZN2, Pseudoalteromonas sp. SZN3, Epibacterium sp. SZN4, and Virgibacillus sp. SZN7, were isolated from polluted sediments from an abandoned industrial site in the Gulf of Naples, Mediterranean Sea, and tested for their bioremediation efficiency on sediment samples collected from the same site. These bacteria were added as consortia or as individual cultures into polluted sediments to assess biodegradation efficiency of polycyclic aromatic hydrocarbons and heavy metal immobilisation capacity. Our results indicate that these bacteria were able to remove polycyclic aromatic hydrocarbons, with a removal rate up to ca. 80% for dibenzo-anthracene. In addition, these bacteria reduced arsenic, lead, and cadmium mobility by promoting their partitioning into less mobile and bioavailable fractions. Microbial consortia generally showed higher performance toward pollutants as compared with pure isolates, suggesting potential synergistic interactions able to enhance bioremediation capacity. Overall, our findings suggest that highly polluted sediments select for bacteria efficient at reducing the toxicity of hazardous compounds, paving the way for scaled-up bioremediation trials.

Calcareous dinoflagellate cysts in marine sediments of the Gulf of Naples (Mediterranean Sea)

1994 ◽  
Vol 84 (1-2) ◽  
pp. 45-56 ◽  
Author(s):  
Marina Montresor ◽  
Elvira Montesarchio ◽  
Donato Marino ◽  
Adriana Zingone
Keyword(s):  
Mediterranean Sea ◽  
Marine Sediments ◽  
Dinoflagellate Cysts ◽  
Gulf Of Naples ◽  
Calcareous Dinoflagellate Cysts

scholarly journals Analysis of Sea Storm Events in the Mediterranean Sea: The Case Study of 28 December 2020 Sea Storm in the Gulf of Naples, Italy

2021 ◽  
Vol 11 (23) ◽  
pp. 11460
Author(s):  
Alberto Fortelli ◽  
Alessandro Fedele ◽  
Giuseppe De Natale ◽  
Fabio Matano ◽  
Marco Sacchi ◽  
...  
Keyword(s):  
Urban Areas ◽  
Integrated Approach ◽  
Wave System ◽  
Storm Events ◽  
Sea Waves ◽  
Coastal System ◽  
Gulf Of Naples ◽  
Tidal Change ◽  
Sea Storm

The coastline of the Gulf of Naples, Italy, is characterized by a series of infrastructures of strategic importance, including touristic and commercial ports between Pozzuoli to Sorrento, main roads, railways, and urban areas. Furthermore, the Gulf of Naples hosts an intense traffic of touristic and commercial maritime routes. The risk associated with extreme marine events is hence very significant over this marine and coastal area. On 28 December 2020, the Gulf of Naples was hit by an extreme sea storm, with severe consequences. This study focuses on the waterfront area of Via Partenope, where the waves overrun the roadway, causing massive damage on coastal seawall, road edges, and touristic structures (primarily restaurants). Based on the analysis of the meteorological evolution of the sea storm and its effects on the waterfront, we suggest that reflective processes induced on the sea waves by the tuff cliffs at the base of Castel dell’Ovo had an impact in enhancing the local-scale waves magnitude. This caused in turn severe flooding of the roadway and produced widespread damage along the coast. The analysis of the event of 28 December 2020, also suggests the need of an effective mitigation policy in the management of coastal issues induced by extreme sea storm events. Wind-based analysis and prediction of the sea wave conditions are currently discussed in the literature; however, critical information on wave height is often missing or not sufficient for reliable forecasting. In order to improve our ability to forecast the effects of sea storm events on the coastline, it is necessary to analyze all the components of the coastal wave system, including wave diffraction and reflection phenomena and the tidal change. Our results suggest in fact that only an integrated approach to the analysis of all the physical and anthropic components of coastal system may provide a correct base of information for the stakeholders to address coastal zone planning and protection.

scholarly journals Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10060
Author(s):  
Meng Wang ◽  
Samina Noor ◽  
Ran Huan ◽  
Congling Liu ◽  
JiaYi Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Culture Collection ◽  
Medium Composition ◽  
Microbial Culture ◽  
Bacterial Strains ◽  
Marine Microbes ◽  
Natural Systems ◽  
Operational Taxonomic Units ◽  
The Impact ◽  
Culture Dependent

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.

scholarly journals Culture-independent analysis of the bacterial communities in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

2021 ◽  
Author(s):  
Jianming Zhang ◽  
Hye Seon Song ◽  
Chengcheng Zhang ◽  
Yeon Bee Kim ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Whole Genome Analysis ◽  
Sequencing Platform ◽  
Tuber Mustard ◽  
Fermented Vegetables

Abstract Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial communities using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from six samples. Firmicutes and Proteobacteria were the main phyla in all of samples. Meanwhile, Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated there were clear differences between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole genome analysis of Lactobacillus suantsaii, Lactobacillus sakei subsp. sakei, and Weissella cibaria showed they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.

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