Greenhouse gas emission potential of tropical coastal sediments in densely urbanized area inferred from metabarcoding microbial community data.

Although benthic microbial community offers crucial insights into ecosystem services, they are underestimated for coastal sediment monitoring. Sepetiba Bay (SB) in Rio de Janeiro, Brazil, holds long-term metal pollution. Currently, SB pollution is majorly driven by domestic effluents discharge. Here, functional prediction analysis inferred from 16S rRNA gene metabarcoding data reveals the energy metabolism profiles of benthic microbial assemblages along the metal pollution gradient. Methanogenesis, denitrification, and N2 fixation emerge as dominant pathways in the eutrophic/polluted internal sector (Spearman; p < 0.05). These metabolisms act in the natural attenuation of sedimentary pollutants. The methane (CH4) emission (mcr genes) potential was found more abundant in the internal sector, while the external sector exhibited higher CH4 consumption (pmo + mmo genes) potential. Methanofastidiosales and Exiguobacterium, possibly involved in CH4 emission and associated with CH4 consumers respectively, are the main taxa detected in SB. Furthermore, SB exhibits higher nitrous oxide (N2O) emission potential since the norB/C gene proportions surpass nosZ up to 4 times. Blastopirellula was identified as the main responsible for N2O emissions. This study reveals fundamental contributions of the prokaryotic community to functions involved in greenhouse gas emissions, unveiling their possible use as sentinels for ecosystem monitoring.

Microbial indicators along a metallic contamination gradient in tropical coastal sediments.

The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.

Microbial community metabolic alterations and resistance to metals and antibiotics driven by chronic exposition to multiple pollutants in a highly impacted tropical coastal bay.

Microbial communities from Sepetiba Bay (SB, Rio de Janeiro, Brazil), characterized by 16S rRNA gene (V4-V5 region) sequencing analysis, were found to be correlated with the metallic contamination factor and the Quality Ratio (QR) index. Consistently, the predicted function of microbial communities, obtained with Tax4Fun2, showed that the functional patterns in SB internal sector under the highest anthropogenic pressure were different from that observed in the external sector with the lowest contamination level. Signal transduction, cellular community, membrane transport, and energy metabolism were among the KEGG pathways favored by metallic contamination in the SB internal sector, while lipid metabolism, transcription, and translation were among the pathways favored in the SB external sector. Noteworthy, the relative proportions of KEGG pathways and genes associated with metallic homeostasis showed significant differences according to the SB sectors, consistently with the ecological risk classification (QR index) of sediments. The functional prediction approach is an economically viable alternative and presents an overview of the main pathways/genes favored in the SB microbiota exposed to long-term pollution. In contrast, the microgAMBI, ecological status index based on bacterial community composition, was not consistent with the metallic contamination of SB, suggesting that this index requires improvements to be applied in tropical areas. Our study also revealed a strong correlation between metal resistance genes (MRG) and antibiotic resistance genes (ARG), indicating that MRG and ARG are co-selected by the metallic contamination prevailing in SB.

Sterol and PAHs fingerprint analysis of organic matter at Southeast Brazilian Bay.

Southeast Brazilian bays have been increasingly degraded by untreated organic loads. Therefore, to assess fecal contamination status, sediment quality regarding polycyclic aromatic hydrocarbons (PAHs), and sources of organic matter (OM), we have determined fine-grained and total organic carbon (TOC) content and concentrations of PAHs and sterols in twenty-six surface sediment samples in Sepetiba Bay. The fine-grained (1-26 %), TOC (0.20-3.45 %), PAHs (

Applying enzymatic biomarkers of the in situ microbial community to assess the sediment risk from Sepetiba Bay (Brazil).

The Quality Ratio (QR) index was applied in Sepetiba Bay to integrate geochemical and microbiological parameters of the in situ microbial community in order to classify the ecological risk of sediments. Total concentrations (C) of Hg, Cd, As, Pb, Cr, Cu and Zn (indicators of the mixture of contaminants) were determined at 26 stations and at a background area (C0) to calculate the contamination factor (CF = C/C0) and the degree of contamination (ΣCF). Enzymatic biomarkers of energy production into cell (dehydrogenase - DHA) and hydrolase of organic matter outside the cell (esterases - EST) were determined. The QR, a function of the microbial term (DHA/EST) and the geochemical term (TOC × ΣCF/fine-grained content), was able to segregate stations into the internal sector (east of the bay with the largest continental contributions) and the external sector (west of the bay), proving its accessibility (low-cost and fast) and efficiency for assessing ecological risk.

Microbial community shift under exposure of dredged sediments from a eutrophic bay.

Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.

Microbial community activity in response to multiple contaminant exposure: a feasible tool for sediment quality assessment.

Sediments represent complex mixtures and the impacts of their physical and chemical processes on biota are important for assessing potential health risks. We aimed to rank sediment samples from Guanabara Bay by developing an algorithm (quality ratio-QR), focusing on key sediment parameters (fine grain size, total organic carbon (TOC), metal concentrations) and enzymatic activities (dehydrogenase (DHA-energy production into cell) and esterases (EST-hydrolase organic matter outside the cell membrane)) of in situ microbial communities. Our QR is supported by quantitative information and significant correlations between geochemical and microbial processes. The QR is a function of the dependent term DHA/EST and the geochemical term (TOC×∑CF)/fine-grained sediment, where ∑CF is the sum of contamination factors (ratio between actual and background metal concentrations). We could rank our sampling sites into three risk classes based on QR: low, medium, and high. Our findings suggest altered homeostasis due to the development of contamination resistance. We applied a sensitivity analysis, using Brazilian law for sediment quality assessment, to calibrate our risk index. Our QR is suitable for measuring the potential health risk of any sediment, especially in developing countries with serious technical limitations, since its evaluated parameters are cheap, fast, and easy to obtain.

An alternative approach to bioaccumulation assessment of methyl-Hg, total-Hg, Cd, Pb, Zn in bivalve Anomalocardia brasiliana from Rio de Janeiro bays.

We present an alternative approach for establishing in situ bioaccumulation assessment of methyl-Hg (MeHg), total-Hg, Cd, Pb and Zn in bivalve Anomalocardia brasiliana from four bays of Rio de Janeiro presenting varying degrees of eutrophication, acid volatile sulfides (2-55 µmol g-1), simultaneously extracted metals (SEM) and total metals (TM) in sediments. Using metal concentrations of composite samples from three size classes of bivalve and their incorporation rates (IR = metal concentration / total length), which depend on exposure time, we calculated asymptotic IR and respective consequent metal concentrations. Both IR and the metal concentration presented inverse relationships with total length (excepting MeHg) and bay contamination. Lead and zinc concentrations were above Brazilian legal criteria in the most anoxic and contaminated bay, suggesting significant metal bioavailability (SEM/TM between 8% and 63%).

Screening-level risk assessment applied to dredging of polluted sediments from Guanabara Bay, Rio de Janeiro, Brazil.

Guanabara Bay is characterized by predominant eutrophication and anoxic sediments with a mixture of pollutants. The risk prognosis associated with the dumping of its dredged sediments into the open ocean was addressed by our algorithm. Our algorithm could prioritize areas, characterize major processes related to dredging, measure the potential risk of sediments, and predict the effects of sediment mixing. The estimated risk of dredged sediment was >10-fold than that of ocean sediments. Among metals, mercury represented 50-90% of the total risk. The transfer of dredged material into the ocean or internal dumping in the bay requires a 1:10 dilution to mitigate the risk and bring the risk levels close to that in the EPA criteria, below which there is less likelihood of adverse effects to the biota, and a 1:100 dilution to maintain the original characteristics of the ocean disposal control area. Our algorithm indicator can be used in the design of both aquatic and continental disposal of dredged materials and their management.

Bioaccumulation of heavy metals by shrimp (Litopenaeus schmitti): A dose-response approach for coastal resources management.

We reveal a dose-response relationship for bioaccumulation of Zn, Cu and Cr in shrimp Litopenaeus schmitti from Sepetiba Bay, Rio de Janeiro, Brazil. Our model estimates the current risk (AD50 was 70% of the legal limit) and the daily metal uptake rate for each metal. It can also evaluate the relative reliability of predictions for tissue concentrations reaching the legal limits for human consumption (approximately 1year) and predictions related to asymptotic length, arising from (i) direct regression of the metal concentration (MeC) versus total length (TL) and age (duration of exposure), and (ii) correlation of the incorporation rate (IR=MeC/TL) with age. Metal incorporation rates (IR), i.e. a kinetic proxy for absorption during growth up to attainment of asymptotic length, decrease with age, reflecting a slow-down in metal absorption. This pattern mitigates the high initial concentrations observed for juveniles.

Copper and lead removal from aqueous solutions by bacterial consortia acting as biosorbents.

A bacterial consortium was selected in the presence of Cu from sediment samples taken from Sepetiba Bay, Brazil, which is a site historically contaminated by metals. Bacteria were exposed to 0, 1, 6, 12.5, 25 and 50µg·mL(-1) Cu, Pb and Cu+Pb for 11days of bioassay. Results showed Alcanivorax dominance (81%) and cell counts of 10(8)cells·mL(-1). However, a reduction in dehydrogenase activity was observed from the fifth day of exposure for all Cu, Pb, and Cu+Pb concentrations tested. Esterase activity tended to increase, indicating higher energy demand to complete the bacterial lifecycle. Pb concentrations in the filtered culture medium (0.2µm) were below the detection limit, indicating biosorption, whereas concentrations of Cu were close to the tested concentrations, indicative of efflux. Results suggest the need for biomarkers, such as esterase and dehydrogenase enzymatic activity, in the assessment of resistance and tolerance of communities previously exposed to stressors.

Organic matter and pyritization relationship in recent sediments from a tropical and eutrophic bay.

The degree of pyritization (DOP) and the extension of metals incorporation into pyrite was investigated at Guanabara Bay sediments. Maximum concentrations of total organic carbon (TOC), total sulfur, biopolymers and viable bacteria cells were observed in silted stations close to discharge points of sewage and minimum concentrations at sandy stations at the entrance of the bay. Pyrite iron concentrations (Fepy) was always lower than the reactive iron and Fepy were below the detection limit at sandy stations. The same trend was found to metals, which its degree of pyritization was Mn=Cu>As=Co>Ni>Cd>Zn≫Pb>Cr. The bay gathers all required factors to sulfate reduction and pyrite formation, once the C:S ratio express the reduced tendency conditions, almost half of the TOC present in its sediments is labile and both reactive sulfur and iron are available. However the degree of trace metals pyritization did not exceed 20%, consistent with the median DOP (29%).

Geomicrobiology of cores from Suruí Mangrove--Guanabara Bay--Brazil.

The aim of this work was to quantify the biopolymers associated to esterase enzymes and identify bacterial respiratory activity in four cores collected in Suruí Mangrove, Guanabara Bay - RJ. Biopolymer concentration was 1000 times lower than previously reported in the literature, indicating the need for creating and establishing eutrophication indicative rates and records compatible with tropical coastal systems. The biochemical representative relationships in the cores were equivalent to those from studies on coastal marine environments made in the Northern Hemisphere. The esterase enzymes in the sediment proved efficient in the mineralization of biopolymers, even with preferentially anaerobic metabolic physiology. Despite the lack of incipient geomicrobiological studies, the results highlighted the possible application of microbiology to a better understanding of geological processes.