Effects of deposition of heavy-metal-polluted harbor mud on microbial diversity and metal resistance in sandy marine sediments

Co-pollution risk of petroleum hydrocarbons and heavy metals in typically polluted estuarine wetlands: Insights from the Xiaoqing River

Excessive accumulation of total petroleum hydrocarbons (TPH) and heavy metals (HMs) in sediments poses a significant threat to the estuarine ecosystem. In this study, the spatial and temporal distribution, ecological risks, sources, and their impacts on the microbial communities of TPH and nine HMs in the estuarine sediments of the Xiaoqing River were determined. Results showed that the spatial distribution of TPH and HMs were similar but opposite in temporal. Ni, Cr, Pb, and Co concentrations were similar to the reference values (RVs). However, the other five HMs (Cu, Zn, Cd, As, and Hg) and TPH concentrations were 2.00-763.44 times higher than RVs; hence, this deserves attention, particularly for Hg. Owing to the water content of the sediments, Hg was mainly concentrated on the surface during the wet season and on the bottom during the dry season. Moreover, because of weak hydrodynamics and upstream pollutant sinks, TPH-HMs in the river were higher than those in the estuary. TPH and HM concentrations were negatively correlated with microbial diversity. Structural equation modeling showed that HMs (path coefficient = -0.50, p < 0.001) had a negative direct effect on microbial community structure and a positive indirect effect on TPH. The microbial community (path coefficient = 0.31, 0.01 < p < 0.05) was significantly correlated with TPH. In summary, this study explores both the chemical analysis of pollutants and their interaction with microbial communities, providing a better understanding of the co-pollution of TPH and HMs in estuarine sediments.

Study on the effectiveness of membrane separation + N2 deoxidation process for the treatment of bacteria in ballast water

Effects of the membrane separation + N₂ deoxidation process on the abundance and activity of bacteria were examined under two salinity conditions at Yangshan Port, Shanghai, China. Sequencing of 16S rRNA gene amplicons demonstrated a decrease in the diversity and activity of bacteria in fresh water and marine water, with a total removal rate of approximately 63 % and 69 %, respectively. Indicator bacteria decreased to 10 CFU·100 mL^-1, which met the IMO D-2 standard. A total of 13 potential pathogens were detected after treatment, indicating that there is still a risk of pathogenic bacteria invasion in the discharge water, particularly marine bacteria, and that the D-2 standard may be insufficient as a preventive measure against pathogenic bacteria transfer. The results will provide reference for government supervision, and will also be important for monitoring foreign bacteria and technology development.

Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.

Nutrients and heavy metals mediate the distribution of microbial community in the marine sediments of the Bohai Sea, China

The Bohai Sea, one of the largest marginal seas in China, is extensively influenced by human and industrial activities. The pollutant loads from anthropogenic activities have induced severe ecological problems. The study investigates the physicochemical characteristics of seawater and sediments in Bohai Bay and Laizhou Bay of the Bohai Sea. The diversity and composition of microbial community in sediments are analyzed by 16S rRNA gene amplicon sequencing. The sequencing results present 16 phyla and 31 classes from the samples. Proteobacteria constituted a dominant phylum, of which the classes of Gamma-, Delta-, and Epsilon-are predominant sub-divisions. Nitrogen, phosphorus, and sulfur cycling related microbes present high abundance in both bays. The metabolism of organic matters is the main factor that influences the distribution of microbial communities in Bohai Bay, while the inflow of Yellow River is the dominant factor that influences the distribution of microbial communities in Laizhou Bay. Sulfur oxidizing process is expected to be positively influenced by heavy metals, while ammonia (NH₄⁺) oxidizing process is prone to be negatively affected by heavy metals in both bays. Microbial communities in the offshore sediments of Laizhou Bay and the majority microbial communities in Bohai Bay sediments are subject to similar predominant controlling factors. This phenomenon is likely ascribed to ocean circulation. The results of this study can provide constructive guidelines on ecosystem management of marginal seas in Bohai and elsewhere.

Securing a port's future through Circular Economy: Experiences from the Port of Gävle in contributing to sustainability

Ports are an important player in the world, due to their role in global production and distributions systems. They are major intermodal transport hubs, linking the sea to the land. For all ports, a key requirement for commercial and economic viability is to retain ships using them and to remain accessible to those ships. Ports need to find approaches to help them remain open. They must ensure their continued economic viability. At the same time, they face increasing pressure to become more environmentally and socially conscious. This paper examines the approach taken by the Port of Gävle, Sweden, which used contaminated dredged materials to create new land using principles of Circular Economy. The paper demonstrates that using Circular Economy principles can be a viable way of securing a port's future and contributing to its sustainability, and that of the city/region where it operates.

Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident

A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core

In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community.

Impact of sludge deposition on biodiversity

Sludge deposition in the environment is carried out in several countries. It encompasses the dispersion of treated or untreated sludge in forests, marsh lands, open waters as well as estuarine systems resulting in the gradual accumulation of toxins and persistent organic compounds in the environment. Studies on the life cycle of compounds from sludge deposition and the consequences of deposition are few. Most reports focus rather on treatment-methods and approaches, legislative aspects as well as analytical evaluations of the chemical profiles of sludge. This paper reviews recent as well as some older studies on sludge deposition in forests and other ecosystems. From the literature covered it can be concluded that sludge deposition induces two detrimental effects on the environment: (1) raising of the levels of persistent toxins in soil, vegetation and wild life and (2) slow and long-termed biodiversity-reduction through the fertilizing nutrient pollution operating on the vegetation. Since recent studies show that eutrophication of the environment is a major threat to global biodiversity supplying additional nutrients through sludge-based fertilization seems imprudent. Toxins that accumulate in the vegetation are transferred to feeding herbivores and their predators, resulting in a reduced long-term survival chance of exposed species. We briefly review current legislation for sludge deposition and suggest alternative routes to handling this difficult class of waste.

Distinct microbial populations are tightly linked to the profile of dissolved iron in the methanic sediments of the Helgoland mud area, North Sea

Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here, we used quantitative PCR-based 16S rRNA gene copy numbers and pyrosequencing-based relative abundances of bacteria and archaea to investigate covariance between distinct microbial populations and specific geochemical profiles in the top 5 m of sediment cores from the Helgoland mud area, North Sea. We found that gene copy numbers of bacteria and archaea were specifically higher around the peak of dissolved iron in the methanic zone (250–350 cm). The higher copy numbers at these depths were also reflected by the relative sequence abundances of members of the candidate division JS1, methanogenic and Methanohalobium/ANME-3 related archaea. The distribution of these populations was strongly correlated to the profile of pore-water Fe²⁺ while that of Desulfobacteraceae corresponded to the pore-water sulfate profile. Furthermore, specific JS1 populations also strongly co-varied with the distribution of Methanosaetaceae in the methanic zone. Our data suggest that the interplay among JS1 bacteria, methanogenic archaea and Methanohalobium/ANME-3-related archaea may be important for iron reduction and methane cycling in deep methanic sediments of the Helgoland mud area and perhaps in other methane-rich depositional environments.

Environmental management for dredging sediments - the requirement of developing nations

Scientific research has characterized the effects of dredging, an underwater excavation process for navigational purposes or material extraction, and has shown its association with a number of chemical, physical and biological impacts. Due to this, much environmental management has been applied in the dredging industry in order to manage its detrimental effects. However, developing nations may have different approaches towards their dredging environmental management to compare to their companions with higher economic strength. Moreover, scientific evidence to make an informed decision is often lacking, hence affecting the number of research executed at these nations, limiting their efforts to preserve the environment. This paper reviews the dredging environmental impacts and its two important factors, dredging technology and sediment characteristic, that determine the magnitude of impacts through literature review, and discusses the need for a more integrated dredging environmental management to be developed for developing nations.

Risk-based decision-making framework for the selection of sediment dredging option

The aim of this study was to develop a risk-based decision-making framework for the selection of sediment dredging option. Descriptions using case studies of the newly integrated, holistic and staged framework were followed. The first stage utilized the historical dredging monitoring data and the contamination level in media data into Ecological Risk Assessment phases, which have been altered for benefits in cost, time and simplicity. How Multi-Criteria Decision Analysis (MCDA) can be used to analyze and prioritize dredging areas based on environmental, socio-economic and managerial criteria was described for the next stage. The results from MCDA will be integrated into Ecological Risk Assessment to characterize the degree of contamination in the prioritized areas. The last stage was later described using these findings and analyzed using MCDA, in order to identify the best sediment dredging option, accounting for the economic, environmental and technical aspects of dredging, which is beneficial for dredging and sediment management industries.

Distinct diversity of the czcA gene in two sedimentary horizons from a contaminated estuarine core

In estuarine ecosystems, trace metals are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediments accumulate and are then transformed by diagenetic processes, recording the history of the estuary's chemical contamination. In such a specific environment, we investigated to what extent a chronic exposure to contaminants could affect metal-resistant sedimentary bacteria in subsurface sediments. The occurrence and diversity of cadmium resistance genes (cadA, czcA) was investigated in 5- and 33-year-old sediments from a highly contaminated estuary (Seine France). Primers were designed to detect a 252-bp fragment of the czcA gene, specifically targeting a transmembrane helice domain (TMH IV) involved in the proton substrate antiport of this efflux pump. Although the cadA gene was not detected, the highest diversity of the sequence of the czcA gene was observed in the 5-year-old sediment. According to the percentage of identity at the amino acid level, the closest CzcA relatives were identified among Proteobacteria (α, β, γ, and δ), Verrucomicrobia, Nitrospirae, and Bacteroidetes. The most abundant sequences were affiliated with Stenotrophomonas. In contrast, in the 33-year-old sediment, CzcA sequences were mainly related to Rhodanobacter thiooxydans and Stenotrophomonas, suggesting a shaping of the metal-resistant microbial communities over time by both diagenetic processes and trace metal contamination.

Environmental Screening Method for Dredging in Contaminated River

Dredging in a contaminated river has been widely accepted to have an impact on the environment; however environmental risk assessment analysis could be costly, time-consuming and difficult to perform. Therefore, a screening method acting as a preliminary risk assessment analysis to screen potential contaminated areas is necessary. The aim of this study is to demonstrate a new screening method for risk assessment analysis in a scenario where economy, time and simplicity factors had been a concern. The development of this method is based on a variation of standard Ecological Risk Assessment. An analysis will be performed on two elements. Firstly, the level of contaminants in the water, groundwater and air (known as the media) and, secondly the behavior of environmental indicators during monitoring of historical dredging. This analysis is performed in order to establish the degree of contamination in an area that is about to be dredged, in where the publicly accessible contamination level in the media and the historical dredging monitoring data will be utilized. Eight dredged sites in Peninsular Malaysia are selected as the case studies of this research. This research showed that Sungai Perlis has a very high total risk value, which could have a fatal impact on its biodiversity if dredging is performed with negligence at this location. This research could provide an opportunity for Malaysia to increase its efforts to avoid dredging impacts without being constrained on time, cost and simplicity factors.

Molecular analysis of bacterial diversity in mudflats along the salinity gradient of an acidified tropical Bornean estuary (South East Asia)

BACKGROUND

The Brunei River and Bay estuarine system (BES) in the northwest of Borneo is acidic and highly turbid. The system supports extensive intertidal mudflats and presents a potentially steep salinity and pH gradient along its length (45 km). Temporal variation in physical parameters is observed diurnally due to seawater flux during tidal forcing, and stochastically due to elevated freshwater inflow after rains, resulting in a salinity range between 0 and 34 psu. High velocity freshwater run-off from acid sulphate formations during monsoon seasons results in highly variable and acidic conditions (pH 4) at the upper reaches of the BES, whereas the pH is relatively stable (pH 8) at the seaward extremes, due to mixing with seawater from the South China Sea. At their surfaces, the BES mudflats present microbial ecosystems driven by oxygenic phototrophs. To study the effect of various physical parameters on the bacterial diversity of the BES mudflats, surface samples were collected from six sites stretching over 40 km for molecular and phylogentic analysis.

RESULTS

The bacterial diversity at these sites was compared by community fingerprinting analysis using 16S rRNA gene based denaturing gradient gel electrophoresis and by 16S rRNA gene sequencing and phylogenetic analyses. Results revealed functionally conserved, diatom-driven microbial mudflat communities composed of mainly novel, uncultured species. Species composition was evaluated as 50-70% unique for each site along the BES. Clustering of the sequences commonly occurred and revealed that proteobacterial diversity was related to the salinity gradient. When considering all phyla, the diversity varied consistently with physical parameters (including anthropogenic) that are expected to influence microbial composition.

CONCLUSION

The BES mudflats were found to comprise the typical functional groups of microorganisms associated with photosynthetic carbon flux, sulfur cycling (Gamma- and Deltaproteobacteria), and decomposition (Bacteroidetes). From a structural perspective, however, the mudflats constituted discretely distributed communities along the physical gradient of the BES, composed of largely novel species of Bacteria. This study provides first insights into patterns of bacterial community structure in tropical South East Asian coastal ecosystems that are potentially threatened by increasing variability in pH and salinity, in line with predicted future environmental change.

Activation of methanogenesis by cadmium in the marine archaeon Methanosarcina acetivorans

Methanosarcina acetivorans was cultured in the presence of CdCl₂ to determine the metal effect on cell growth and biogas production. With methanol as substrate, cell growth and methane synthesis were not altered by cadmium, whereas with acetate, cadmium slightly increased both, growth and methane rate synthesis. In cultures metabolically active, incubations for short-term (minutes) with 10 µM total cadmium increased the methanogenesis rate by 6 and 9 folds in methanol- and acetate-grown cells, respectively. Cobalt and zinc but not copper or iron also activated the methane production rate. Methanogenic carbonic anhydrase and acetate kinase were directly activated by cadmium. Indeed, cells cultured in 100 µM total cadmium removed 41–69% of the heavy metal from the culture and accumulated 231–539 nmol Cd/mg cell protein. This is the first report showing that (i) Cd²⁺ has an activating effect on methanogenesis, a biotechnological relevant process in the bio-fuels field; and (ii) a methanogenic archaea is able to remove a heavy metal from aquatic environments.

Characterization of soil bacterial communities in rhizospheric and nonrhizospheric soil of Panax ginseng

A culture-independent approach was used to evaluate the bacterial community in rhizospheric and nonrhizospheric soil in which Panax ginseng had grown for 3 years. For each sample, soil was randomly collected from multiple sampling points and mixed thoroughly before genomic DNA extraction. Universal primers 27f and 1492r were used to amplify 16S rRNA genes. Clone libraries were constructed using the amplified 16S rRNA genes, and 192 white clones were chosen for further sequencing. After digestion with restriction endonuclease, 44 operational taxonomic units (OTUs) were generated for rhizospheric and 21 OTUs for nonrhizospheric soils, and the clones of each OTU were sequenced. Blast analysis showed that bacillus, acidobacteria, and proteobacteria were the dominant populations in rhizospheric soil, and proteobacteria were dominant in nonrhizospheric soil. Phylogenetic results showed that bacillus and acidobacteria were clustered into the group of uncultured bacteria in rhizospheric soil; however, proteobacteria were the unique dominant in nonrhizospheric soil.

Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis

BACKGROUND

Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis.

RESULTS

The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype.

CONCLUSIONS

The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.