Comparative molecular analysis of bacterial communities inhabiting pristine and polluted with polycyclic aromatic hydrocarbons Black Sea coastal sediments

Molecular analysis was applied to characterize bacterial community structure in sediment samples collected from pristine site and oil-polluted Black Sea harbor. Amplified Ribosomal DNA Restriction Analysis (ARDRA) revealed a high similarity in the restriction patterns of both samples thus not demonstrating the effect of the pollutant on the structure of the bacterial communities. Constructed 16S rRNA gene libraries gave more detailed assessment of members. Results showed that α- and γ-Proteobacteria were dominant in the oil polluted site, whereas the pristine site was characterized by prevalence of Actinobacteria. The biodegradative potential of the adapted bacterial community in the oil-polluted sediments was demonstrated by the presence of the aromatic ring hydroxylating dioxygenase genes.     

Interactive effects of hypoxia and polybrominated diphenyl ethers (PBDEs) on microbial community assembly in surface marine sediments

Hypoxia alters the oxidation–reduction balance and the biogeochemical processes in sediments, but little is known about its impacts on the microbial community that is responsible for such processes. In this study, we investigated the effects of hypoxia and the ubiquitously dispersed flame-retardant BDE47 on the bacterial communities in marine surface sediments during a 28-days microcosm experiment. Both hypoxia and BDE47 alone significantly altered the bacterial community and reduced the species and genetic diversity. UniFrac analysis revealed that BDE47 selected certain bacterial species and resulted in major community shifts, whereas hypoxia changed the relative abundances of taxa, suggesting slower but nonetheless significant community shifts. These two stressors targeted mostly different taxa, but they both favored Bacteroidetes and suppressed Gammaproteobacteria. Importantly, the impacts of BDE47 on bacterial communities were different under hypoxic and normoxic conditions, highlighting the need to consider risk assessments for BDE47 in a broader context of interaction with hypoxia.     

丹江口库区表层沉积物细菌多样性及功能预测分析

湖泊沉积物微生物是水生态系统的重要组成部分,目前关于丹江口库区沉积物细菌群落和功能研究鲜见报道.于2017年5月对丹江口库区内5个典型生态点位表层沉积物进行采集,采用高通量测序技术对表层沉积物细菌群落组成进行研究,结果表明细菌群落主要由变形菌门(Proteobacteria)、绿弯菌门(Chloroflexi)、拟杆菌门(Bacteroidetes)、疣微菌门(Verrucomicrobia)和硝化螺旋菌门(Nitrospirae)等33个门和318个属组成,具有丰富的群落组成.沉积物细菌群落和理化指标冗余分析(RDA)结果表明,pH值、总磷、有机质和铵态氮含量均能显著影响沉积物细菌群落组成.细菌属分类单元与环境因子Spearman相关分析表明,变形菌门中11个属的细菌与环境因子显著相关,为与环境因子显著相关细菌的主要组成(占47.62%).采用细菌群落功能预测软件PICRUSt(Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)对表层沉积物细菌群落进行分析,结果表明沉积物细菌功能主要涉及能量产生和转换、信号转导机制、氨基酸运输和代谢、细胞壁/细胞膜/膜结构的生物合成等24个基因功能家族,表现出功能上的丰富性.基因功能家族预测基因拷贝数表现为台子山宋岗库心渠首黑鸡嘴.     

Analysis of bacterial diversity and metals in produced water, seawater and sediments from an offshore oil and gas production platform

Produced water is one of the largest waste products routinely discharged into the ocean from offshore oil and gas platforms. This study analyzed bacterial communities and metals in the produced water, surrounding seawater, and sediment around the Thebaud platform. The bacterial community within the produced water was different from the seawater (SAB = 13.3), but the discharge had no detectable effect on the bacterial communities in the seawater (SAB > 97). In contrast, genomic analysis of sediments revealed that the bacterial community from 250 m was different (SAB = 70) from other locations further from the discharge, suggesting that the produced water had a detectable effect on the bacterial community in the sediment closest to the discharge. These near-field sediments contained elevated concentrations of manganese and iron that are associated with the produced water effluent. The results suggested that the discharge of produced water has influenced the bacterial community structure of sediments adjacent to the platform.     

A micro-dilution method for detecting oxytetracycline-resistant bacteria in marine sediments from salmon and mussel aquaculture sites and an urbanized harbour in Atlantic Canada

A micro-dilution technique with changes in optical density (OD) used to measure bacterial growth over 72 h in culture media containing 0, 5, 10, 20, 40, 80 and 160 microg OTC (oxytetracycline)ml(-1) was applied to determine growth inhibition (GI) in mixed bacterial strains cultured from samples of marine sediments and salmon feed pellets. Growth of control cultures (Aeromonas salmonicida) was inhibited at all OTC concentrations. Some feed pellet samples and under-cage sediments from salmon aquaculture sites in the Bay of Fundy showed GI up to > or = 160 microg OTCml(-1). Lower values (40 to 80 microg OTC ml(-1)) occurred in subsurface (5-18 cm) sediments, > 100 m from salmon pens and adjacent to sewage outfalls in Halifax Harbour. GI values < 20 microg OTC ml(-1) in sediment from reference locations in Halifax Harbour and mussel aquaculture sites are considered to reflect natural background levels for OTC resistance.     

Influence of bioturbation by Hediste diversicolor on mercury fluxes from estuarine sediments: a mesocosms laboratory experiment

Mercury, with its reactive forms being the most deleterious for the trophic chains, has been identified as a major pollutant in a few confined bodies of the coastal zone. Due to feeding, burrowing, and bioirrigation activities, infauna are known to play a crucial role in the biogeochemical processes of contaminants. The main goal of the present study is to evaluate the effects of Hediste diversicolor bioturbation on mercury fluxes from estuarine sediments in a mesocosms laboratory experiment. Additionally, an attempt was made to establish a relationship between the amount of remobilised mercury to the water column and the degree of contamination of the sediments using a mercury contamination gradient. The present experiment demonstrated that the bioturbation activity caused by the gallery-diffuser H. diversicolor did not influence the remobilisation of mercury (in dissolved reactive forms) from the sediment to the water column. The concentration of dissolved reactive mercury in the water column also did not reflect the degree of contamination in the sediments. The results obtained were in accordance with the sediment characteristics of the Mondego Estuary and Ria de Aveiro (Portugal), since they are very rich in organic matter content, iron/manganese total and hydrous oxides. These physicochemical characteristics of the sediments may partially justify the retention of mercury by these systems, even when they are subjected to bioturbation. In conclusion, sediments with high organic matter content and a high concentration of iron/manganese hydrous oxides allowed for efficient retention of mercury, and the bioturbation process did not seem to affect the system. Another conclusion from this study is that the remobilisation of mercury by bioturbation to the water column is not a fast process, requiring more than 24h. This study constitutes an important work in the area of the effects of bioturbation on mercury remobilisation. Considering the toxicity of mercury for the biota, it is essential to evaluate the real magnitude of mercury processes occurring in estuarine systems in order to obtain essential information on metal behaviour.     

Clostridium perfringens as a potential indicator for the presence of sewage solids in marine sediments

Marine sediment cores collected from several depths of water and distances from a California sewage outfall were tested to see if sediments influenced by sewage solids were a reservoir of enteric pathogens, and if concentrations of indicator bacteria were related to the presence of sewage solids. Vertical distributions of microorganisms in marine sediments were determined; there was a decrease of indicator bacteria with increasing sediment depth. Aeromonas was randomly isolated, but none of the enteric bacterial pathogens or viruses were detected. While classic indicator bacteria were of little value in predicting the presence of pathogens, or relative amounts of sewage solids, Clostridium perfringens may be a suitable indicator. Clostridium perfringens concentrations were not related to the presence of pathogens in sediments.     

Hebei Spirit oil spill monitored on site by fluorometric detection of residual oil in coastal waters off Taean, Korea

The spatiotemporal distributions of dissolved and/or dispersed oil in seawater and pore water were monitored on site by fluorometric detection method after the Hebei Spirit oil spill. The oil concentrations in intertidal seawater, 15 days after the spill, were as high as 16,600 μg/L and appeared to decrease below the Korean marine water quality standard of 10 μg/L at most sites 10 months after the spill. Fluorometric detection of oil in pore water was introduced to eliminate the effects of grain size for the quantification of oil in sediments and to better explain spatial and temporal distribution of oil pollution at sandy beaches. The fluorescence detection method was compared with the conventional laboratory technique of total petroleum hydrocarbon analysis using gas chromatography. The method of fluorescence detection of oil was capable of generating results much faster and more cost-effectively than the traditional GC technique.     

Long-term effects of crude oil on microbial processes in subarctic marine sediments: Studies on sediments amended with organic nutrients

Subarctic marine sediments amended with various organic compounds were exposed to fresh Cook Inlet crude oil at a concentration of 50 ppt for either 6 or 8 months. After the sediments were initially treated, they were returned to the approximate location where they were collected and left to be exposed to natural environmental conditions until they were retrieved for analysis. As a result of crude oil treatment, the activities of the enzymes that hydrolyse structural polysaccharides were reduced and the activities of the enzymes that hydrolyse storage polysaccharides were stimulated. In addition to these changes, we observed changes in phosphatase activity, nitrogen fixation rates, potential denitrification rates, methane concentrations, CO₂ production rates, and the glucose uptake and mineralization rates. The effect of the crude oil perturbation was different depending on the organic compound used in the amended sediments. Many of these differences could be explained by the effect of crude oil on the hydrolases which were responsible for degrading the compound in question. The results of this study suggest the effect of crude oil on microbial processes may be affected by the type of organic material present in the impacted marine sediment. This study also illustrates the value of measuring hydrolase activity in studies designed to determine the effects of this or any other pollutant on microbial processes in marine sediments.     

海底天然气渗漏的地球物理特征及识别方法

海底天然气渗漏是在海洋环境中广泛分布的自然现象.海底天然气渗漏可以指示沉积层中的烃类聚集带,渗漏出的大量气体（主要是甲烷）可能影响全球的气候变化,此外,与海底渗漏相关的浅层气改变了海底沉积物的土工性质,可能对海底工程构成威胁.因此海底渗漏研究意义重大.海底天然气渗漏不仅影响海底沉积物的物理性质,而且还极大地改变海底地形地貌,它能在海底形成麻坑、泥火山、冷泉碳酸盐岩以及化学自养生物群落等现象.在海底渗漏发生的地方,地形地貌特征可以在海洋测深和逆向散射数据上得到反映;沉积物的声学特征可以在地震剖面上得到反映,如形成声混浊、声空白、亮点、多次波、速度下拉等;有些渗漏在海面形成油渍膜,油渍膜可以在合成孔径雷达图像上得到反映.根据海底渗漏的上述地球物理特征,可以识别出可能渗漏区域,海底渗漏的证实需要用到海底观测和取样分析资料.     

Temporal changes in Sphingomonas and Mycobacterium populations in mangrove sediments contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs)

The change in community diversity and structure of the indigenous, dominant, polycyclic aromatic hydrocarbon (PAH)-degrading bacterial genera, Sphingomonas and Mycobacterium, due to contamination in the environment is not very well known. A combination of PCR-DGGE with specific primers and a cultivation-dependent microbiological method was used to detect different populations of Sphingomonas and Mycobacterium in mangrove sediments. The structure of the entire bacterial community (including Sphingomonas) did not show a shift due to environmental contamination, whereas the diversity of Mycobacterium populations in mangrove sediments with higher PAH contamination increased from exposure between Day 0 and Day 30. The isolated Mycobacterium strains migrated to the same position as the major bands of the bacterial communities in Mycobacterium-specific DGGE. A dioxygenase gene system, nidA, which is commonly found in PAH-degrading Mycobacterium strains, was also detected in the more highly contaminated sediment slurries. The present study revealed that Mycobacterium species were the dominant PAH-degraders and played an important role in degrading PAHs in contaminated mangrove sediments.     

Bacterial and organic matter distribution in the sediments of the Thracian Sea (NE Aegean Sea)

Recently, black carbon has been introduced as the form of carbon that may be separated from the biologically mediated carbon cycle thereby representing the non-bioavailable fraction of the estimated organic carbon. It has been speculated that the bioavailability of organic matter may be a limiting factor for the presence of active bacteria within the sediments. In order to address this question, marine sediments were collected from the Thracian Sea (Eastern Mediterranean), a complex system impacted by riverine inputs and Black Sea water masses. In addition to counts of total bacteria, we estimated the fraction of active bacteria by using a destaining step to the DAPI staining method. Black carbon was also estimated following the thermal oxidation method in order to determine the fraction of the refractory organic matter. The fraction of black carbon to total organic carbon varied from 16% to 53% indicating that black carbon constitutes a significant pool of sedimentary organic carbon in the Thracian sea. A fraction ranging from 18% to 97% was scored as nucleoid containing cells. We did not record any significant differences in the fraction of nucleoid-containing bacteria among sediment depths (P<0.05) indicating that there was no accumulation of dead bacterial cells with depth. The same was observed for the fraction of black carbon and bioavailable organic carbon with sediment depth (P<0.05) indicating that benthic consumers are not the key regulators of the organic matter pool in these sediments but have a minor effect. A possible reason for these observations and for the uncoupling between the active bacterial fraction and the bioavailability of organic matter could be (i) the presence of refractory components in the estimated bioavailable organic matter and (ii) the hydrological and geological complexity of the study area. The North Aegean marginal slopes are highly unstable experiencing frequent seismic events. These events are capable of inducing sediment transport from the upper slopes thus altering the entire sediment profile. On the other hand, the significant correlations that were recorded between nucleoid-containing cells and phytopigments (chlorophyll a, phaeopigments, chloroplastic pigment equivalents) at all sediment depths indicate that bacterial communities respond immediately to the deposited phytodetritus, using it as a primary source of carbon and energy. Our data suggests that the Thracian Sea sediments are by no means homogeneous and can best be described as a mosaic controlled by numerous local and regional environmental factors.     

Heavy metal contamination from gold mining recorded in Porites lobata skeletons, Buyat-Ratototok district, North Sulawesi, Indonesia

Shallow marine sediments and fringing coral reefs of the Buyat-Ratototok district of North Sulawesi, Indonesia, are affected by submarine disposal of tailings from industrial gold mining and by small-scale gold mining using mercury amalgamation. Between-site variation in heavy metal concentrations in shallow marine sediments was partially reflected by trace element concentrations in reef coral skeletons from adjacent reefs. Corals skeletons recorded silicon, manganese, iron, copper, chromium, cobalt, antimony, thallium, and lead in different concentrations according to proximity to sources, but arsenic concentrations in corals were not significantly different among sites. Temporal analysis found that peak concentrations of arsenic and chromium generally coincided with peak concentrations of silica and/or copper, suggesting that most trace elements in the coral skeleton were incorporated into detrital siliciclastic sediments, rather than impurities within skeletal aragonite.     

Vertical variations and associated ecological function of bacterial communities from Sphagnum to underlying sediments in Dajiuhu Peatland

To investigate vertical changes of bacterial communities from living plants to the associated sediments and bacterial biogeochemical roles in peatland ecosystem,samples of different part of individual Sphagnum palustre and the different layers of the underlying sediments were collected from Dajiuhu Peatland in central China.All samples were subject to 16S rRNA gene clone libraries and quantitative PCR analysis.Even though bacteria vary in abundance at the same order of magnitude in all samples,they show great profile difference in composition from the top part of S.palustre to the low layer of the sediments.Cyanobacteria and alpha-Proteobacteria dominate at the top part whereas Acidobacteria at the middle part of S.palustre.Alpha-Proteobacteria and Acidobacteria are the dominant phyla at the bottom part of S.palustre and in the surface peat sediment.In contrast,bacterial communities in the subsurface sediments are dominated by Acidobacteria.These profile distributions of different bacterial communities are closely related to their ecological functions in the peatland ecosystem.Specifically,most Cyanobacteria were observed at the top green part of S.palustre,a horizon where the active photosynthesis of the moss occurs,which infers their endosymbiosis.In contrast,Acidobacteria,dominant in the subsurface sediments,are able to decompose the specific compounds on the cell wall of Sphagnum moss and thus might play an important role in the formation of the peatland,including the acidic condition.Methane oxidizing process might have been underestimated in Sphagnum peatland due to the identification of Methylocystaceae in all parts of the moss investigated here.The vertical difference in bacterial composition and bacterial ecological functions presented here sheds light on the understanding of biogeochemical processes,in particular the CH4 flux,in peat ecosystems.     

Spatial distribution and ecotoxicity of petroleum hydrocarbons in sediments from the Galicia continental shelf (NW Spain) after the Prestige oil spill

The distribution of aliphatic and aromatic hydrocarbons was determined in surface sediments collected at 36 stations along the Galicia continental shelf (NW Spain), following the Prestige oil spill. Sampling was performed in December 2002, just after the accident, and in February and September 2003. Concentrations of PAHs (summation operator 13 parent components) were in the range of 0.9-422 microg/kgdw, the highest values being close to coastal urban areas (e.g. Pontevedra and A Coru?a), whereas in the stations of the area most heavily impacted by the spill (off Costa da Morte) concentrations were in the range of 14.8-89.6 microg/kgdw, with a certain predominance of alkylated compounds, which may suggest a mixture of petrogenic and pyrolytic sources. The detailed study of petrogenic molecular markers (e.g. steranes and triterpanes) showed the occurrence of an old (weathered) petrogenic chronic pollution in the shelf sediments but not of the Prestige oil, with the possible exception of few stations in the area of Costa da Morte. This was attributed to the heavy nature of the spilled oil that was barely dispersed in the water column and mainly stranded on the coast or sedimented in the form of oil patches. The addition of increasing amounts of fuel oil to a representative sediment sample showed that the molecular indices were indicative of the presence of the Prestige oil when the amount was above 1g/kg of sediment. The toxicity of selected samples (showing the higher PAH concentrations) was tested using the bivalve embryogenesis bioassay. Embryogenesis success reached high values in all cases (80-88%, with 86% in the control), indicating a lack of toxicity in the sediments and supporting the conclusion that the patchiness of the fuel eventually reaching the seafloor reduced its impact on the benthic communities of the Galician shelf.     

Benthic marine pollution around McMurdo Station, Antarctica: A summary of findings

McMurdo Station is the United States Antarctic Research Program's (USARP) centre for scientific and logistical support for most of the continent and is the largest settlement in Antarctica. Over 30 years of human presence with shipping, air-transport, scientific, and municipal activities have resulted in severe but localized nearshore marine benthic pollution. This review will summarize the results of 3 years of research which has documented concentrations of chemical contaminants, changes in community patterns, and the toxicity of sediments to invertebrate species and infaunal communities. The primary contaminants are petroleum hydrocarbons in the sediments of Winter Quarters Bay, the site of shipping activities and a former dumpsite. Total hydrocarbon levels in sediments in Winter Quarters Bay were comparable to the most polluted harbours in temperate latitudes. However, a steep gradient of pollution existed: stations less than 1 km away were nearly pristine. Benthic invertebrate communities changed dramatically along this contamination gradient. The results of both field and laboratory bioassay experiments with contaminated sediments found that biological changes observed in benthic communities around McMurdo Station were most likely caused by hydrocarbons, PCBs, and PCTs. A primary goal of polar pollution research is to determine the response and tolerance of Antarctic biota to physical and chemical anthropogenic disturbance, and the mitigation of negative effects. To this end, future work should include continued monitoring of changes in chemical and community patterns, studies of the physiological responses of Antarctic invertebrates to chemical contamination, and further comparisons of anthropogenic and natural disturbances to benthic communities.     

Oil pollution impact on marine communities and a problem of sea water quality improvement

Sea entered pollutions, in particular oil and oil products, interact complexly with marine biota. On the one hand, oil causes disfunction of marine communities, death of some marine representatives and sometimes of the whole community. On the other hand, marine organisms and their communities transform pollutions during purification processes improving marine environment quality. It is known, that under pollution conditions the number of aquarium-inhabiting organisms is reduced and only the most resistable species are left. The study of such species opens perspectives for the creation of hydrobiological systems and their purposeful use in cleaning polluted waters and sanitation of coastal aquaria.     

Interactive effects of hypoxia and PBDE on larval settlement of a marine benthic polychaete

Marine benthic polychaete Capitella sp. I is widely known to adapt to polluted habitats; however, its response to xenobiotics under hypoxic conditions has been rarely studied. This research aimed to test the hypothesis that interactive effects of hypoxia and congener BDE-47 of polybrominated diphenyl ethers (PBDE), which is ubiquitous in marine sediments, may alter the settlement of Capitella sp. I. Our results revealed that under hypoxic condition, settlement success and growth in body length of Capitella larvae were significantly reduced compared to those under normoxia of similar BDE-47 concentration. While no significant changes in morphology of settled larvae were noted in both exposure conditions, the presence of BDE-47 could enhance polychaete growth. The present findings demonstrated that the interactive effects of hypoxia and environmentally realistic concentrations of BDE-47 in sediments could affect polychaete settlement, which, in turn, reduce its recruitment and subsequent population size in the marine benthic ecosystem.     

Implications of dredging induced changes in sediment particle size composition for the structure and function of marine benthic macrofaunal communities

A meta-analysis approach was used to assess the effect of dredging induced changes in sediment composition, under different conditions of natural physical disturbance, for the structure and function of marine benthic macrofaunal communities. Results showed the sensitivity of macrofaunal communities increased as both the proportion of gravel increased and the level of natural physical disturbance decreased. These findings may be explained by the close association of certain taxa with the gravel fraction, and the influence of natural physical disturbance which, as it increases, tends to restrict the colonisation by these species. We conclude that maintaining the gravel content of surface sediments after dredging and, where practicable, locating extraction sites in areas of higher natural disturbance will minimise the potential for long-term negative impacts on the macrofauna.     

Bacterial community in sediment from the Western Pacific "Warm Pool" and its relationship to environment

Total DNAs were extracted from different sections of deep sea sediment core sample collected from the Western Pacific "Warm Pool". The bacterial 16S ribosomal DNA (rDNA) clone libraries were constructed and analyzed by PCR-restriction fragment length polymorphism (RFLP) and DNA sequencing. The bacterial communities in these samples and their relationship to environment were analyzed consequently. The results indicated that among eight main bacterial groups found in these sediments, members of the γ-Proteobacteria were most abundant in each section of sediment core sample and the genus Colwellia belonging to γ-Proteobacteria was dominant in this area. Members of the α-Proteobacteria were found commonly existing in these samples, while members belonging to β-Proteobacteria were seldom detected. The diversity of bacterial communities from different sections of sediment core sample was δ- and ε-Proteo-bacteria and the bacterial group including genera Cytopahga, Flexibacteria and Bacteroides (CFB group)