PAHs contamination and bacterial communities in mangrove surface sediments of the Jiulong River Estuary, China

Enhancement of benzo[a]pyrene mineralization: symbiotic biodegradation by Acinetobacter sp. strain HAP1 in Association with Cyanobacteriota sp. S66

The ability of Acinetobacter sp. strain HAP1, isolated from petroleum refinery effluent, to eliminate different concentrations (20, 40, 60, 80 and 100 mg/L) of Benzo[a]Pyrene degradation (BaP) was studied. A test to improve this degradation capacity was carried out by culturing the bacterial strain in association with a cyanobacteria. The results show a highly significant effect of the concentration of (BaP) and a very highly significant effect of the symbiosis between the bacterial strain and the cyanobacteria. This combination was able to significantly improve the (BaP) degradation rate by up to 18%. This degradation and especially in association leads to a complete mineralization of (BaP) and there is a difference in yield that can go up to 15%. Through molecular identification based on 16S rRNA gene sequence analysis, strains HAP1 and S66 were recognized as Acinetobacter sp. strain HAP1 and Cyanobacteriota sp. S66, respectively. Comparison of the retrieved sequences with the NCBI GenBank database was done, and the closest matches were found to be Acinetobacter pittii strain JD-10 for bacteria and Pseudochroococcus couteii strain PMC 885.14 for cyanobacteria.

Deep relationships between bacterial community and polycyclic aromatic hydrocarbons in soil profiles near typical coking plants

Bacterial communities play an important role in maintaining the normal functioning of ecosystems; therefore, it is important to understand the effects of polycyclic aromatic hydrocarbons (PAHs) on the bacterial community. In addition, understanding the metabolic potential of bacterial communities for PAHs is important for the remediation of PAH-contaminated soils. However, the deep relationship between PAHs and bacterial community in coking plants is not clear. In this study, we determined the bacterial community and the concentration of PAHs in three soil profiles contaminated by coke plants in Xiaoyi Coking Park, Shanxi, China, using 16S rRNA and gas chromatography coupled with mass spectrometry, respectively. The results show that 2 ~ 3 rings PAHs are the main PAHs and Acidobacteria (23.76%) was the dominant bacterial community in three soil profiles. Statistical analysis showed that there were significant differences in the composition of bacterial communities at different depths and different sites. Redundancy analysis (RDA) and variance partitioning analysis (VPA) illustrate the influence of environmental factors (including PAHs, soil organic matter (SOM), and pH) on the vertical distribution of soil bacterial community, and PAHs were the main factors affecting the bacterial community in this study. The co-occurrence networks further indicated correlations between bacterial community and PAHs and found that Nap has the greatest effect on bacterial community compared with other PAHs. In addition, some operational taxonomic units (OTUs, OTU2, and OTU37) have the potential to degrade PAHs. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for further study on the potential of microbial PAHs degradation from a genetic perspective, which showed that different PAH metabolism genes were present in the genomes of bacterial communities in the three soil profiles, and a total of 12 PAH degradation-related genes were isolated, mainly dioxygenase and dehydrogenase genes.

Impact of petroleum refinery on aquatic ecosystem of Skikda Bay (Algeria): Diversity and abundance of viable bacterial strains

This paper reports a study on the impact of petroleum refinery effluents on the bacterial load and diversity of the aquatic ecosystem in Skikda Bay (Algeria). The results showed a large spatiotemporal variation in the isolated bacterial species. This difference between stations and seasons could be attributed to environmental factors and to the pollution rate at the different sampling sites. Statistical analysis results showed that physicochemical parameters such as pH, electrical conductivity and salinity have a very significant effect on the microbial load (p < 0.001), while hydrocarbon pollution has a significant effect on the diversity of bacterial species (p < 0.05). In total 75 bacteria were isolated from six sampling sites during the four seasons. A significant spatiotemporal richness and diversity was observed in water samples. A total of 42 strains belonging to 18 bacterial genera were identified. Most of these genera belong to the class of Proteobacteria.

Salipiger pentaromativorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from mangrove sediment

Polycyclic aromatic hydrocarbons (PAHs) have been recognized as a potential health risk and are widespread in nature due to their intrinsic chemical stability and high recalcitrance to degradation. A taxonomic study was carried out on strain P9^T, which was isolated from a PAH-degrading consortium, enriched from the mangrove sediment from Zhangzhou, PR China. The isolate was chemoheterotrophic, aerobic, Gram-stain-negative, short-rod shaped, and motile by one polar flagellum. Growth was observed at salinities from 0.5-6.0 % (optimum, 3 %), at pH 4-9 (optimum, pH 7) and at 10-41 °C (optimum, 25-30 °C). It did not synthesize bacteriochlorophyll a. Catalase and oxidase activities were positive. Acid was produced from starch, amygdalin, arbutin, cellobiose, d-fructose, maltose, d-mannitol, melezitose, melibiose, raffinose, d-ribose, sucrose, trehalose, d-xylose, aesculin ferric citrate, gentiobiose, glycogen, l-arabinose, l-rhamnose, methyl α-d-glucopyranoside, methyl β-d-xylopyranoside, N-acetylglucosamine and salicin, and weakly positive for d-arabitol, d-galactose, lactose, turanose and glycerol. Phylogenetic analysis revealed that strain P9^T fell within the clade comprising the type strains of Salipiger species and formed an independent cluster with Salipiger profundus, which was distinct from other members of the family Rhodobacteraceae. The 16S rRNA gene sequence comparisons showed that strain P9^T was most closely related to Salipiger bermudensis HTCC 260^T (96.7 %), and other species of the genus Salipiger (95.7-94.2 %). Strain P9^T had the highest digital DNA-DNA hybridization value with S. profundus CGMCC 1.12377^T (25.0 %) and the highest average nucleotide identity (ANIb and ANIm) values with S. profundus CGMCC 1.12377^T(80.3 and 85.8 %, respectively). The sole respiratory quinone was quinone 10. The dominant fatty acids were C_18 : 1  ω7c (61.4 %), C_16 : 0 (17.5 %) and C_19 : 0  ω8c cyclo (7.6 %). The G+C content of the chromosomal DNA was 65.8 mol%. In the polar lipid profile, phospholipid, phosphatidylglycerol, aminolipid, glycolipid and phosphatidylethanolamine were the major compounds. Based on the phenotypic and phylogenetic data, strain P9^T represents a novel species of the genus Salipiger, for which the name Salipiger pentaromativorans sp. nov. is proposed. The type strain is P9^T (=CCTCC AB 209290^T=LMG 25701^T=MCCC 1F01055^T).

Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds

Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V₃-V₄). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations

Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg^-1), moderate (600 mg kg^-1), and high (1200 mg kg^-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg^-1 sediment day^-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg^-1 sediment day^-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Influence of polycyclic aromatic hydrocarbon pollution on the diversity and function of bacterial communities in urban wetlands

Human disturbance has become the primary driving factor behind declining urban wetland ecological health due to rapid urbanization. Sediment microbial communities are critical for wetland ecosystem functioning but experience a range of natural and anthropogenic stressors due to rapid urbanization and land use changes, especially in developing countries. Polycyclic aromatic hydrocarbons (PAHs) released into the environment primarily come from anthropogenic sources like industrial activities and traffic emissions. Environmental PAH contamination is accelerating due to rapid urbanization, which also increases potential PAH-related dangers to human health. However, PAHs are widely distributed and not easy to centrally control. Microorganisms are the primary mediators of wetland purification, with most PAH-degrading microorganisms being bacteria. To better understand the influence of PAH contamination on urban wetland microbial communities, bacterial community compositions within sediments of urban wetlands in three land use types were investigated using high-throughput DNA sequencing and bioinformatics analyses. Statistical analyses revealed significant differences in overall microbial compositions among the three land use types, although γ-proteobacteria was the dominant phyla across all samples. Among the potential PAH-degrading bacterial taxa in sediments, Sphingomonas was the most prevalent. The distributions of PAH-degrading taxa were primarily affected by variance in organic compound abundances in addition to various physico-chemical variables, among which high-ring PAH content was a key parameter associated with bacterial distributions, except in the riverine wetlands. Functional inference via phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that 30 of the 43 genes related to PAH metabolism were predicted to be present within the genomes of bacteria among the three land use type. In particular, dioxygenase and dehydrogenase genes involved in PAH degradation were inferred to be prevalent, indicating that the host urban wetlands exhibited strong potential for organic pollutant degradation.

Effect of pyrene and phenanthrene in shaping bacterial communities in seagrass meadows sediments

Polycyclic aromatic hydrocarbons (PAHs), originating from anthropogenic and natural sources, are highly concerned environmental pollutants. This study investigated the impact of two model PAHs (pyrene and phenanthrene) on bacterial community succession in the seagrass meadows sediment in a lab-scale microcosm. Halophila ovalis sediment slurry microcosms were established, one group was placed as a control, and the other two were treated with pyrene and phenanthrene. Bacterial community succession in response to respective PAHs was investigated by 16S rRNA amplicon sequencing. The results demonstrated that bacterial diversity decrease in each microcosm during the incubation process; however, the composition of bacterial communities in each microcosm was significantly different. Proteobacteria (37-89%), Firmicutes (9-41%), and Bacteroides (7-21%) were the predominant group at the phylum levels. Their abundance varies during the incubation process. Several previously reported hydrocarbon-degrading genera, such as Pseudomonas, Spinghobium, Sphingobacterium, Mycobacterium, Pseudoxanthomonas, Idiomarina, Stenotrophomonas, were detected in higher abundance in pyrene- and phenanthrene-treated microcosms. However, these genera were distinctly distributed in the pyrene and phenanthrene treatments, suggesting that certain bacterial groups favorably degrade different PAHs. Statistical analyses, such as ANOSIM and PERMANOVA, also revealed that significant differences existed among the treatments' bacterial consortia (P < 0.05). This work showed that polycyclic aromatic hydrocarbon significantly affects bacterial community succession, and different PAHs might influence the bacterial community succession differently.

Parent and alkylated polycyclic aromatic hydrocarbons in surface sediments of mangrove wetlands across Taiwan Strait, China: Characteristics, sources and ecological risk assessment

The characteristics, distributions and sources of parent polycyclic aromatic hydrocarbons (PAHs) and alkyl-PAHs (A-PAHs) as well as their ecological risk were explored in six mangrove wetlands across the Taiwan Strait, China. A-PAHs fingerprinting information, combined with PAHs diagnostic ratios and a positive matrix factorization model, were used to identify the sources of PAHs in the mangrove wetland surface sediment samples. The results showed that the total concentration of the 36 PAHs in the sediment samples varied from 186.2 to 2469.2 ng⸱g^-1. Furthermore, the total concentration of PAHs would be underestimated about 37.1%-80.6% when only the concentrations of 16 priority PAHs were examined in the sediment samples. Coal combustion (32.7%) and petroleum combustion (24.6%) were identified as important contributing sources in the Yunxiao, Fugong, and Quanzhou mangrove wetlands, whereas the main source was mainly petroleum combustion (49.1%) in the Guandu, Zhuwei and Waziwei mangrove wetlands. In addition, the guidelines for assessing the ecological risk of individual A-PAHs need to be developed due to lack of criteria for most individual A-PAHs.

Protein molecular responses of field-collected oysters Crassostrea hongkongensis with greatly varying Cu and Zn body burdens

The oyster Crassostrea hongkongensis is an ideal biomonitor due to its widespread distribution along the coast of Southern China and the ability to hyperaccumulate metals including Cu and Zn. In this study, we conducted the first investigation of the molecular responses to metal hyperaccumulation based on quantitative shotgun proteomics technique and genome information. Gill tissue of oysters collected from the uncontaminated environment (Site 1, 59.6 μg/g and 670 μg/g dry weight for Cu and Zn) displayed significant protein profile differentiation compared to those from a moderately contaminated (Site 2, 1,465 μg/g and 10,170 μg/g for Cu and Zn) and a severely contaminated environment (Site 3, 3,899 μg/g and 39,170 μg/g for Cu and Zn). There were 626 proteins identified to be differentially expressed at Site 3 but only 247 proteins at Site 2. Oysters from a moderately contaminated estuary (Site 2) displayed fewer effects as compared to oysters under severe contamination, with fluctuated small molecule metabolism and enhanced translation process. At Site 3, the induction of reactive oxygen species (ROS) was the main toxicity under the extremely high level of metal stress, which resulted in protein damage. Additionally, the impaired structure of cytoskeleton and modified membrane tracking process at Site 3 oysters led to the blockage or less efficient protein or macromolecule distribution within cells. Nonetheless, proteomic analysis in this study revealed that oysters could partly alleviate the adverse metal effects by boosting the translation process, enhancing the ability to recycle the misfolded proteins, and enhancing the potential to eliminate the excess ROS. Our study demonstrated an adaptive potential of oysters at the protein level to survive under conditions of metal hyper-accumulation.

Discovery of Three 22-Membered Macrolides by Deciphering the Streamlined Genome of Mangrove-Derived Streptomyces sp. HM190

Strain HM190, a moderate halophile, was isolated from rhizosphere soil of the mangrove Kandelia obovata in Fugong village, China. The 16S ribosomal RNA (rRNA) gene sequence and the results of phylogenetic analysis revealed that strain HM190 belonged to the genus Streptomyces and had the highest sequence similarity of 99.79% to Streptomyces heilongjiangensis NEAU-W2^T. The complete genome of strain HM190 comprised 7,762,826 bp in a linear chromosome with 71.97% G + C content. According to antiSMASH analysis, a total of 30 biosynthetic gene clusters (BGCs) were predicted to be involved in secondary metabolism, 12 of which were responsible for the production of polyketide- and non-ribosomal peptide-derived secondary metabolites. Gene cluster 5 was responsible for macrolide biosynthesis in a strain-specific 126,331-bp genomic island belonging to the left-arm region. Combined genomics–metabolomics analysis led to the discovery of three 22-membered macrolides (compounds 1–3). Their structures were elucidated by using spectroscopic techniques including high-resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR). The absolute configurations of compounds 1–3 were determined by the X-ray single crystal diffraction and NMR data analysis. All three compounds displayed moderate cytotoxic activities toward tumor cell lines HepG2, A549, and HCT116.

Polycyclic Aromatic Hydrocarbons in Surface Sediments and Fish Tissues Collected from a Protected Lagoon Region

Polycyclic aromatic hydrocarbons (PAHs) were detected and quantified in sediment and edible fish (Megalops atlanticus) from Caleta lagoon (Lagoon of Terminos, Mexico) in order to assess their potential health impact on consumers. Sum PAH concentrations in sediment and fish muscle tissues were dominated by high molecular weight PAH compound (46.4%-93.1%) relative to low molecular weight compounds (6.9%-42.9%). Contamination was associated with local industrial activities and urbanization. The effective range low (ERL: 4022 ng g^-1) value were lower suggested adverse biological effect would be rarely observed. While the analysis of PAHs in muscle of M. atlanticus suggests a minimum impact to consumers according to the permitted limits of dibenzo (a, h) anthracene (10 ng g^-1) and benzo [a] pyrene (0.1-1.2 μg kg^-1). It is advisable to propose environmental strategies to mitigate future environmental damage in the ecosystem.

Biodegradation of aged polycyclic aromatic hydrocarbons in agricultural soil by Paracoccus sp. LXC combined with humic acid and spent mushroom substrate

Paracoccus sp. LXC combined with humic acid (HA) and spent mushroom substrate (SMS) obtained from Auricularia auricular and Sarcomyxa edulis was tested for the remediation of agricultural soil contaminated with aged polycyclic aromatic hydrocarbons (PAHs). The biomass and diversity of bacteria and fungi and the soil enzyme activity were analyzed. PAH removal and dissipation kinetics were examined. The highest degradation rate of PAHs was 56.5% when soil was amended with Paracoccus sp. LXC combined with HA and unsterilized SMS from A. auricular. The half-life of PAHs decreased from 2323.3 days in natural attenuation to 66.6-277.2 days in amended treatments. Soil treated with Paracoccus sp. LXC combined with HA and SMS from A. auricular acquired high contents of organic matter and nutrients. HA and SMS aided the growth of PAH-degrading bacteria and promoted the diversity of bacteria but not of fungi. The degradation rate of PAHs was mainly correlated positively with soil laccase activity. Low- and middle-molecular-weight PAHs were significantly removed by Paracoccus sp. LXC, HA and SMS. High-molecular-weight PAHs were removed by SMS but not by Paracoccus sp. LXC. Biodegradation by Paracoccus sp. LXC combined with HA and SMS is a promising choice for remediating aged PAH-contaminated agricultural soils.

Distribution and sources of organic contaminants in surface sediments of Hooghly river estuary and Sundarban mangrove, eastern coast of India

This study investigated polycyclic aromatic hydrocarbons (PAHs) and organochlorine compounds such as polychlorinated biphenyls (PCBs) and DDT-related pesticides in surface sediments of Hooghly estuary and the Sundarban mangrove wetlands. Concentrations of ∑₁₇PAH, ∑₁₈₂PCB and ∑₆DDT ranged from 15.4 to 1731, not detected (nd) to 13.5 and nd to 8.97 ng g^-1 dry weight, respectively. Low levels of PCBs and low to moderate concentrations of DDTs and PAHs reflected recent development in West Bengal, which was dominated by agriculture and multifarious industries in the past. Diagnostic ratios suggested that major sources of PAHs are combustion processes, DDTs are input by agriculture, antifouling paints and public health campaigns, and organochlorines are predominantly from industrial origin. Heavier PCB congeners suggest local sources and short-range transport of such chemicals. Decision makers may use these findings for managing the Hooghly River watershed in order to promote a sustainable development on the eastern coast of India.

Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment

The bacterial community from estuarine sediment undertakes the bioremediation and energy transformation of anthropogenic pollutants especially polycyclic aromatic hydrocarbons (PAHs). However, information and studies on bacterial synergism and related metabolic profiles under the stress of PAHs are limited. In this study, sediments from estuarine were collected and co-incubated with a classical PAH, pyrene. The results showed that Alpha- and Gammaproteobacteria became abundant at the late domesticating phase with the dominant genus of ZD0117, the uncultivated bacteria affiliated into Gammaproteobacteria. Functional gene analysis based on metagenomic sequencing showed that quantitatively changes of genes directly related to the degradation of aromatic hydrocarbon coordinated with genes involved into various metabolic pathways such as acylglycerol degradation, nitrogen fixation, sulfate transport system, Arnon-Buchanan cycle, and Calvin cycle (P < 0.01 and |ρ| > 0.8). Fifty-six metagenome-assembled genomes (MAGs) were reconstructed, which were primarily composed by Alpha- and Gammaproteobacteria. Bacteria belonging to the phylum Proteobacteria were found to be abundant in MAGs and contained genes encoding for dehydrogenase, which are key enzymes for pyrene degradation. In addition, genomes of uncultivated bacteria were successfully reconstructed and were proven to carry genes of synergistically metabolizing pyrene. Based on analysis of typical MAGs, the metabolic pathways involved in syntrophic associations of a pyrene-degrading consortium were reconstructed. The results in this study could make us fully understand the metabolic patterns of pyrene-degrading consortium from the estuarine sediment and widen the scope of functional bacteria.

Characteristics of microbial community indicate anthropogenic impact on the sediments along the Yangtze Estuary and its coastal area, China

In the contaminated coastal sediments, variations of microbial community can reflect the impact of anthropogenic activities. The identification, evaluation and monitoring of the potential bio-indicator species and biomarker communities are vital for the ecological studies in sedimentary environments. Based on the high-throughput sequencing, the microbial communities were characterized in the sediments along the Yangtze Estuary and its coastal area. The results showed that the structure and composition of microbial communities varied greatly among different sampling sites at the phyla level, especially for Euryarchaeota. Metabolic pathway and quantitative PCR analyses suggested that the methane metabolism-related microbes were mainly included in the phylum of Euryarchaeota. Elevated abundances of methane metabolism-related microbes were found at Shidongkou (SDK) and Wusongkou (WSK), where microbes were seriously impacted by the wastewater treatment plant (WWTP) effluent and urban runoff. By comparing with the Euryarchaeota in WWTP sludge, the relatively high abundance of Euryarchaeota in sediment at SDK may be mainly related to the massive growth of indigenous species, promoted by anthropogenic nutrients. Moreover, redundancy discriminant analysis and correlation analysis revealed that methanogens and methanotrophs mainly respond to the nutrients and metals, such as total organic carbon, total phosphorus, total nitrogen, SO₄^2-, NO₂^-, NH₄⁺, Cr, and Zn, which were often related to human activities. Network analyses showed that the species related to the metabolism of methane may play a vital role in the interassociation among different microbial communities. Therefore, methanogens, methanotrophs and their community compositions could be considered as potential bio-indicator species and biomarker communities, indicating anthropogenic activities in the sediments along the Yangtze Estuary and its coastal area.

Effects of Organic Pollutants on Bacterial Communities Under Future Climate Change Scenarios

Coastal ecosystems are highly dynamic and can be strongly influenced by climate change, anthropogenic activities (e.g., pollution), and a combination of the two pressures. As a result of climate change, the northern hemisphere is predicted to undergo an increased precipitation regime, leading in turn to higher terrestrial runoff and increased river inflow. This increased runoff will transfer terrestrial dissolved organic matter (tDOM) and anthropogenic contaminants to coastal waters. Such changes can directly influence the resident biology, particularly at the base of the food web, and can influence the partitioning of contaminants and thus their potential impact on the food web. Bacteria have been shown to respond to high tDOM concentration and organic pollutants loads, and could represent the entry of some pollutants into coastal food webs. We carried out a mesocosm experiment to determine the effects of: (1) increased tDOM concentration, (2) organic pollutant exposure, and (3) the combined effect of these two factors, on pelagic bacterial communities. This study showed significant responses in bacterial community composition under the three environmental perturbations tested. The addition of tDOM increased bacterial activity and diversity, while the addition of organic pollutants led to an overall reduction of these parameters, particularly under concurrent elevated tDOM concentration. Furthermore, we identified 33 bacterial taxa contributing to the significant differences observed in community composition, as well as 35 bacterial taxa which responded differently to extended exposure to organic pollutants. These findings point to the potential impact of organic pollutants under future climate change conditions on the basal coastal ecosystem, as well as to the potential utility of natural bacterial communities as efficient indicators of environmental disturbance.

Temporal trends and transport of perfluoroalkyl substances (PFASs) in a subtropical estuary: Jiulong River Estuary, Fujian, China

The seasonal variations and spatial distributions of fifteen perfluoroalkyl substances (PFASs) were investigated in the water of the subtropical Jiulong River Estuary (JRE) in Fujian, China. The concentrations and composition profiles of PFASs showed significant seasonal variations. ∑PFASs concentrations ranged from 4.8 to 37.6 ng L^-1, 12.2 to 110 ng L^-1 and 3.3 to 43.0 ng L^-1 in the dry, medium and wet seasons, respectively. Perfluorooctane sulfonate (PFOS) was found to be the most abundant PFAS in the dry season, with a composition of 33% ± 5%, Perfluorohexanoic acid PFHxA (47% ± 13%) and perfluoropentanoic acid (PFPeA) (52% ± 15%) were the dominant compounds in the medium and wet seasons, respectively. Seasonal and spatial distributions of ∑PFASs were different in the upstream and downstream sections. High concentration of PFHxA occurred in the medium season, and showed a linear decreasing trend from upstream to downstream. The majority of other PFASs did not show clear seasonal variation. Composition profiles indicated that the JRE was mainly contaminated by short-chain perfluoroalkyl carboxylic acids (PFCAs), shipbuilding industry, multiple wastewater and river runoff were identified as major potential sources.

Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis

Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg^-1 sediment day^-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.

Shift in the microbial community composition of surface water and sediment along an urban river

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P < 0.05). The bacterial diversity in sediments was significantly higher than their corresponding water samples. Additionally, archaeal communities showed obvious spatial variability in the surface water. The construction of the hydropower station resulted in increased Cyanobacteria abundance in the upstream (32.2%) compared to its downstream (10.3%). Several taxonomic groups of potential fecal indicator bacteria, like Flavobacteria and Bacteroidia, showed an increasing trend in the urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P < 0.01) and NO₃^- (P < 0.05), and metals (Zn, Fe) (P < 0.05) were the most significant drivers determining the microbial community composition in the urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations.

Phylogeny and polycyclic aromatic hydrocarbons degradation potential of bacteria isolated from crude oil-contaminated site

This study employed the use of 16S rRNA gene sequence analysis to identify three of four native bacterial strains isolated from crude oil-contaminated site in Poza Rica, Veracruz, Mexico. The identified bacteria were Ochrobactrum intermedium, Pandoraea pnomenusa and Ochrobactrum sp., but SA2-09 strain was not identified. The ability of the isolates to degrade polycyclic aromatic hydrocarbons (PAHs) was evaluated at 31.61 and 54.52 mg/kg PAHs in soil, when used as crude oil in soil microcosm during 80 days of incubation at 30°C. The results demonstrated that O. intermedium biodegraded many PAHs, including the high molecular weight (HMW) PAHs fluoranthene (100% equivalent 0.24 mg/kg), benzo [b] fluoranthene (81.8% equal 0.18 mg/kg), Benzo[a]pyrene (87.0%, 0.20 mg/kg) and Benzo[g,h,i]perylene (52.7%, 0.39 mg/kg). P. pnomenusa had a degradation profile of HMW PAHs, which was similar to O. intermedium, while Ochrobactrum sp. and the strain SA-09 exhibited lower degradation rates of HMW.

Polybrominated diphenyl ethers, organochlorine pesticides, and polycyclic aromatic hydrocarbons in water from the Jiulong River Estuary, China: levels, distributions, influencing factors, and risk assessment

Estuarine systems play an important role in the transportation and transformation of organic pollutants from rivers. Polybrominated diphenyl ether (PBDE), organochlorine pesticide (OCP), and polycyclic aromatic hydrocarbon (PAH) concentrations in water of the Jiulong River Estuary (JRE), China, were investigated to characterize their distribution, possible source, and potential ecological risk as well as the influencing factors. The total concentrations of PBDEs, OCPs, and PAHs varied from 5.2 to 12.3 pg L^-1, from 29.1 to 96.4 ng L^-1, and from 28.6 to 48.5 ng L^-1, respectively. Their compositions were all consistent at different stations; even the input pathways were multifarious. A source analysis showed that PBDEs may come from the flame retardant usages of penta-BDE and deca-BDE; hexachlorocyclohexane isomers (HCHs) were from the use of technical HCHs, while DDTs were attributed to early residuals of industrial sources, and PAHs were mainly from pyrolytic sources. The spatial distributions of PBDEs and OCPs were quite similar with their concentrations, decreasing along the estuary and then increasing when passing the Xiamen Harbor. PAH concentrations were similar along the whole estuary, suggesting that local sources and hydrological conditions might be the influencing factors. The concentrations of these pollutants changed with tidal conditions and were positively correlated with SPM, DOC, and chlorophyll a but negatively correlated with salinity. The ecological risk assessment revealed that OCPs and PAHs posed slightly higher potential risks to aquatic organism in the study area.

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water

The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river.

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing

This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (p<0.05). Despite explaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

Phylogenetic analysis of bacterial community composition in sediments with organic contaminants from the Jiaojiang estuary in China

The aim of this study was to investigate the bacterial community composition, the concentration of organic contaminants, and their relationship in the sediments of Jiaojiang estuary. Sediments were collected from seven stations and the environmental parameters were analyzed. The results showed that the site closest to the chemical industry zone was the most polluted. Bacterial communities were determined using 16S rRNA clone libraries and phylogenetic analysis. These results revealed that there were 13 known bacterial phyla in the sediments and that Proteobacteria were the dominant group. Using these data, we assessed the correlation between bacterial communities and organic contaminants using cluster, multidimensional scaling, and redundancy analyses. These showed that there was no simple relationship between organic contaminants and bacterial community diversity in the sediments, but polycyclic aromatic hydrocarbons were more influential than the other pollutants and negatively affected Chloroflexi.

Pyrosequencing analysis of bacterial communities in Lake Bosten, a large brackish inland lake in the arid northwest of China

The bacteria inhabiting brackish lake environments are poorly known, and there are few studies on the microbial diversity of these environments. Lake Bosten, a large brackish inland lake, is the largest lake in Xinjiang Province in northwestern China. Because sediments record past limnic changes, the analysis of sedimentary bacteria in Lake Bosten may help elucidate bacterial responses to environmental change. We employed 454 pyrosequencing to investigate the diversity and bacterial community composition in Lake Bosten. A total of 48 230 high-quality sequence reads with 16 314 operational taxonomic units were successfully obtained from the 4 selected samples, and they were numerically dominated by members of the Deltaproteobacteria (17.1%), Chloroflexi (16.1%), Betaproteobacteria (12.6%), Bacteroidetes (6.6%), and Firmicutes (5.7%) groups, accounting for more than 58.1% of the bacterial sequences. The sediment bacterial communities and diversity were consistently different along the 2 geographic environmental gradients: (i) freshwater–brackish water gradient and (ii) oligotrophic–mesotrophic habitat gradient. Deltaproteobacteria, Chloroflexi, and Betaproteobacteria were amplified throughout all of the sampling sites. More Bacteroidetes and Firmicutes were found near the Kaidu River estuary (site 14). Our investigation showed that Proteobacteria did not display any systematic change along the salinity gradient, and numerous 16S rRNA sequences could not be identified at the genus level. Our data will provide a better understanding of the diversity and distribution of bacteria in arid region brackish lakes.

Effects of flooding and aging on phytoremediation of typical polycyclic aromatic hydrocarbons in mangrove sediments by Kandelia obovata seedlings

A laboratory experiment was conducted to evaluate the effects of flooding and aging on the phytoremediation of naphthalene (Nap), anthracene (Ant) and benzo[a]pyrene (B[a]P) in mangrove sediment by Kandelia obovata (K. obovata) Druce seedlings. Flooding increased dissipation efficiency in the rhizosphere zone from 69.47% to 82.45%, 64.27% to 80.41%, and 61.55% to 78.31% for Nap, Ant and B[a]P, respectively. Aging decreased dissipation efficiency significantly. Further investigation demonstrated that increased enzyme activity was one of important factors for increasing PAHs dissipation rates in flooded mangrove sediments. Moreover, a novel method for in situ quantitative investigation of PAHs distribution in root tissues was established using microscopic fluorescence spectra analysis. Subsequently, the effects of flooding and aging on the distribution of PAHs in root tissues were evaluated using this established method. The order of bioavailable fractions of PAHs after phytoremediation was as follows: non-aging/non-flooding>flooding>aging.

Using in situ bacterial communities to monitor contaminants in river sediments

Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments.

Effects of Temperature Stress and Aquarium Conditions on the Red Macroalga Delisea pulchra and its Associated Microbial Community

In recent years, there has been an increase in the rate and severity of diseases affecting habitat-forming marine organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a temperate red macroalga that suffers from a bleaching disease that is more frequent during summer, when seawater temperatures are elevated and the alga's chemical defense is weakened. A bacterial cause for the disease is implied by previous studies showing that some isolated strains can cause bleaching in vitro and that host-associated microbial communities are distinct between diseased and healthy individuals. However, nothing is known about the successional events in the microbial community that occur during the development of the disease. To study this aspect in the future, we aimed here to develop an experimental setup to study the bleaching disease in a controllable aquarium environment. Application of a temperature stress (up to 27°C) did not cause a clear and consistent pattern of bleaching, suggesting that temperature alone might not be the only or main factor to cause the disease. The results also showed that the aquarium conditions alone are sufficient to produce bleaching symptoms. Microbial community analysis based on 16S rRNA gene fingerprinting and sequencing showed significant changes after 15 days in the aquarium, indicating that the native microbial associates of D. pulchra are not stably maintained. Microbial taxa that were enriched in the aquarium-held D. pulchra thalli, however, did not match on a taxonomic level those that have been found to be enriched in natural bleaching events. Together our observations indicate that environmental factors, other than the ones investigated here, might drive the bleaching disease in D. pulchra and that the aquarium conditions have substantial impact on the alga-associated microbiome.

Effect of enhanced reactive nitrogen availability on plant-sediment mediated degradation of polycyclic aromatic hydrocarbons in contaminated mangrove sediment

As land-ocean interaction zones, mangrove systems receive substantial polycyclic aromatic hydrocarbons (PAHs) from sewage and combustion of fossil fuel. In this study, we investigated the relationship between dissolved inorganic nitrogen (DIN) availability and degradation rate of phenanthrene, a typical PAH compound, in mangrove plant-sediment systems, using Avicennia marina as a model plant. After 50 day incubation, phenanthrene removal ratios in sediments ranged from 53.8% to 97.2%. In non-rhizosphere sediment, increasing DIN accessibility increased microbial biomass and total microbial activity, while enhancements in population size of phenanthrene degradation bacteria (PDB) and phenanthrene degradation rates were insignificant. In contrast, the presence of excessive DIN in rhizosphere sediment resulted in a significantly large number of PDB, leading to a rapid dissipation rate of phenanthrene. The differences in degradation rates and abundances of degrader in sediment may be explained by the enhanced root activity due to the elevation in DIN accessibility.

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition

Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils.

Biodegradation, Biosorption of Phenanthrene and Its Trans-Membrane Transport by Massilia sp. WF1 and Phanerochaete chrysosporium

Reducing phenanthrene (PHE) in the environment is critical to ecosystem and human health. Biodegradation, biosorption, and the trans-membrane transport mechanism of PHE by a novel strain, Massilia sp. WF1, and an extensively researched model fungus, Phanerochaete chrysosporium were investigated in aqueous solutions. Results showed that the PHE residual concentration decreased with incubation time and the data fitted well to a first-order kinetic equation, and the t_1/2 of PHE degradation by WF1, spores, and mycelial pellets of P. chrysosporium were about 2 h, 87 days, and 87 days, respectively. The biosorbed PHE was higher in P. Chrysosporium than that in WF1, and it increased after microorganisms were inactivated and inhibited, especially in mycelial pellets. The detected intracellular auto-fluorescence of PHE by two-photon excitation microscopy also proved that PHE indeed entered into the cells. Based on regression, the intracellular (K_din) and extracellular (K_dout) dissipation rate constants of PHE by WF1 were higher than those by spores and mycelial pellets. In addition, the transport rate constant of PHE from outside solution into cells (K_inS/V_out) for WF1 were higher than the efflux rate constant of PHE from cells to outside solution (K_outS/V_in), while the opposite phenomena were observed for spores and mycelial pellets. The amount of PHE that transported from outside solution into cells was attributed to the rapid degradation and active PHE efflux in the cells of WF1 and P. Chrysosporium, respectively. Besides, the results under the inhibition treatments of 4°C, and the presence of sodium azide, colchicine, and cytochalasin B demonstrated that a passive trans-membrane transport mechanism was involved in PHE entering into the cells of WF1 and P. Chrysosporium.

Isolation and characterization of heavy polycyclic aromatic hydrocarbon-degrading bacteria adapted to electrokinetic conditions

Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria capable of growing under electrokinetic conditions were isolated using an adjusted acclimation and enrichment procedure based on soil contaminated with heavy PAHs in the presence of an electric field. Their ability to degrade heavy PAHs under an electric field was individually investigated in artificially contaminated soils. The results showed that strains PB4 (Pseudomonas fluorescens) and FB6 (Kocuria sp.) were the most efficient heavy PAH degraders under electrokinetic conditions. They were re-inoculated into a polluted soil from an industrial site with a PAH concentration of 184.95 mg kg(-1). Compared to the experiments without an electric field, the degradation capability of Pseudomonas fluorescens and Kocuria sp. was enhanced in the industrially polluted soil under electrokinetic conditions. The degradation extents of total PAHs were increased by 15.4 and 14.0% in the electrokinetic PB4 and FB6 experiments (PB4 + EK and FB6 + EK) relative to the PB4 and FB6 experiments without electrokinetic conditions (PB4 and FB6), respectively. These results indicated that P. fluorescens and Kocuria sp. could efficiently degrade heavy PAHs under electrokinetic conditions and have the potential to be used for the electro-bioremediation of PAH-contaminated soil, especially if the soil is contaminated with heavy PAHs.

Temporal-spatial variation of bacterial diversity in estuary sediments in the south of Zhejiang Province, China

The winter and summer microbial community structure in sediment samples obtained from the estuaries of the wastewater-polluted River Ou (DO and XO), River Feiyun (DF and XF), and River Ao (DA and XA) in the south of Zhejiang Province in China was determined using 454 pyrosequencing. Sediment samples (DD and XD) were also correspondingly collected near the shore far from the estuaries for comparison. For the above sediments, 294,870 effective sequences were obtained to do the bacterial diversity and abundance determination. In total, 1924, 1517, 2071, 1956, 1995, 1800, 2261, and 2097 operational taxonomic units were obtained at 3 % distance cutoff in the DO, XO, DF, XF, DA, XA, DD, and XD sediments, respectively. Bacterial phylotype richness in DD was higher than the other sediments, and XO had the least richness. The most dominant class in the DA, DD, DF, DO, and XA sediments is Gammaproteobacteria. Deltaproteobacteria is the most dominant one in XD, XO, and XF. Circa 14.4 % sequences in XD were found to be affiliated with the Flavobacteriales order. Characterization of the estuarine sediment bacterial communities indicated that chemical pollution has the potential to decrease the natural variability that exists among estuary ecosystems. However, chemical pollutants did not cause clear bio-homogenization in these estuaries.

Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing

Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere.

Diversity change of microbial communities responding to zinc and arsenic pollution in a river of northeastern China

Pollution discharge disturbs the natural functions of water systems. The environmental microbial community composition and diversity are sensitive key indicators to the impact of water pollutant on the microbial ecology system over time. It is meaningful to develop a way to identify the microbial diversity related to heavy metal effects in evaluating river pollution. Water and sediment samples were collected from eight sections along the Tiaozi River where wastewater and sewage were discharged from Siping City in northeastern China. The main pollutants contents and microbial communities were analyzed. As the primary metal pollutants, zinc (Zn) and arsenic (As) were recorded at the maximum concentrations of 420 and 5.72 μg/L in the water, and 1704 and 1.92 mg/kg in the sediment, respectively. These pollutants posed a threat to the microbial community diversity as only a few species of bacteria and eukaryotes with strong resistance were detected through denaturing gradient gel electrophoresis (DGGE). Acinetobacter johnsonii, Clostridium cellulovorans, and Trichococcus pasteurii were the dominant bacteria in the severely polluted areas. The massive reproduction of Limnodrilus hoffmeisteri almost depleted the dissolved oxygen (DO) and resulted in the decline of the aerobic bacteria. It was noted that the pollution reduced the microbial diversity but the L. hoffmeisteri mass increased as the dominant community, which led to the overconsuming of DO and anaerobic stinking water bodies. Water quality, concentrations of heavy metals, and the spatial distribution of microbial populations have obvious consistencies, which mean that the heavy metals in the river pose a serious stress on the microorganisms.

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

Heavy metal and organic contaminants in mangrove ecosystems of China: a review

China's rapid economic growth has been accompanied by increasing environmental pollution. Mangrove ecosystems are now facing greater pollution pressures due to elevated chemical discharges from various land-based sources. Data on the levels of heavy metals and organic pollutants in mangrove compartments (sediments, plants, zoobenthos, and fish) in China over the past 20 years have been summarized to evaluate the current pollution status of the mangrove ecosystem. Overall, the Pearl River and Jiulong River estuaries were severely polluted spots. Concentrations of Cu, Zn, Cd, and Pb in mangrove sediments of Guangdong, Fujian, and Hong Kong were higher than those from Guangxi and Hainan. The pollution status was closely linked to industrialization and urbanization. The highest concentrations of polycyclic aromatic hydrocarbons (PAHs) were found in mangrove sediments from Hong Kong, followed by Fujian and Guangdong. Mangrove plants tend to have low-enriched ability for heavy metals and organic pollutants. Much higher levels of Pb, Cd, and Hg were observed in mollusks.

Application of binary diagnostic ratios of polycyclic aromatic hydrocarbons for identification of Tsunami 2004 backwash sediments in Khao Lak, Thailand

Identification of Tsunami deposits has long been a controversial issue among geologists. Although there are many identification criteria based on the sedimentary characteristics of unequivocal Tsunami deposits, the concept still remains ambiguous. Apart from relying on some conventional geological, sedimentological, and geoscientific records, geologists need some alternative “proxies” to identify the existence of Tsunami backwash in core sediments. Polycyclic aromatic hydrocarbons (PAHs) are a class of very stable organic molecules, which can usually be presented as complex mixtures of several hundred congeners; one can assume that the “Tsunami backwash deposits” possess different fingerprints of PAHs apart from those of “typical marine sediments.” In this study, three-dimensional plots of PAH binary ratios successfully identify the Tsunami backwash deposits in comparison with those of global marine sediments. The applications of binary ratios of PAHs coupled with HCA are the basis for developing site-specific Tsunami deposit identification criteria that can be applied in paleotsunami deposits investigations.

Interactive effects of cadmium and pyrene on contaminant removal from co-contaminated sediment planted with mangrove Kandelia obovata (S., L.) Yong seedlings

The interactive effects of cadmium (Cd) and pyrene (Pyr) on contaminant removal from co-contaminated sediment planted with Kandelia obovata were investigated by a pot experiment. We found that dry weight of plant was significantly decreased under high level of Cd-Pyr combined stress. High Pyr caused the increase of Cd toxicity to K. obovata under high Cd stress because more Cd translocated to the plant tissues. Cd toxicity inhibited Pyr degradation in co-contaminated sediments and higher Pyr degradation was found in the rhizosphere than that in the non-rhizosphere sediment under high Cd treatment. The total number of microorganisms in sediments tended to decrease with increasing Cd under Cd-Pyr combined stress and more amount existed in the rhizosphere sediment. In conclusion, Cd and Pyr removal by K. obovata can influence interactions between these two pollutants in co-contaminated sediment. This suggests that this mangrove can effectively remedy sites co-contaminated with these two types of contamination.

Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB

We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al., 2010). In that study, samples were collected from three different islands: Eleanor Island (EL107), Knight Island (KN114A), and Smith Island (SM006B), and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA). The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with that of the overall polycyclic aromatic hydrocarbons (PAHs).

Effects of fomesafen on soil enzyme activity, microbial population, and bacterial community composition

Fomesafen is a diphenyl ether herbicide that has an important role in the removal of broadleaf weeds in bean and fruit tree fields. However, very little information is known about the effects of this herbicide on soil microbial community structure and activities. In the present study, laboratory experiments were conducted to examine the effects of different concentrations of fomesafen (0, 10, 100, and 500 μg/kg) on microbial community structure and activities during an exposure period of 60 days, using soil enzyme assays, plate counting, and denaturing gradient gel electrophoresis (DGGE). The results of enzymatic activity experiments showed that fomesafen had different stimulating effects on the activities of acid phosphatase, alkaline phosphatase, and dehydrogenase, with dehydrogenase being most sensitive to fomesafen. On the tenth day, urease activity was inhibited significantly after treatment of different concentrations of fomesafen; this inhibiting effect then gradually disappeared and returned to the control level after 30 days. Plate counting experiments indicated that the number of bacteria and actinomycetes increased in fomesafen-spiked soil relative to the control after 30 days of incubation, while fungal number decreased significantly after only 10 days. The DGGE results revealed that the bacterial community varied in response to the addition of fomesafen, and the intensity of these six bands was greater on day 10. Sequencing and phylogenetic analyses indicated that the six excised DGGE bands were closely related to Emticicia, Bacillus, and uncultured bacteria. After 10 days, the bacterial community exhibited no obvious change compared with the control. Throughout the experiment, we concluded that 0-500 μg/kg of fomesafen could not produce significant toxic effects on soil microbial community structure and activities.

Concentrations and sources of polycyclic aromatic hydrocarbons in surface coastal sediments of the northern Gulf of Mexico

BACKGROUND

Coastal sediments in the northern Gulf of Mexico have a high potential of being contaminated by petroleum hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), due to extensive petroleum exploration and transportation activities. In this study we evaluated the spatial distribution and contamination sources of PAHs, as well as the bioavailable fraction in the bulk PAH pool, in surface marsh and shelf sediments (top 5 cm) of the northern Gulf of Mexico.

RESULTS

PAH concentrations in this region ranged from 100 to 856 ng g-1, with the highest concentrations in Mississippi River mouth sediments followed by marsh sediments and then the lowest concentrations in shelf sediments. The PAH concentrations correlated positively with atomic C/N ratios of sedimentary organic matter (OM), suggesting that terrestrial OM preferentially sorbs PAHs relative to marine OM. PAHs with 2 rings were more abundant than those with 5-6 rings in continental shelf sediments, while the opposite was found in marsh sediments. This distribution pattern suggests different contamination sources between shelf and marsh sediments. Based on diagnostic ratios of PAH isomers and principal component analysis, shelf sediment PAHs were petrogenic and those from marsh sediments were pyrogenic. The proportions of bioavailable PAHs in total PAHs were low, ranging from 0.02% to 0.06%, with higher fractions found in marsh than shelf sediments.

CONCLUSION

PAH distribution and composition differences between marsh and shelf sediments were influenced by grain size, contamination sources, and the types of organic matter associated with PAHs. Concentrations of PAHs in the study area were below effects low-range, suggesting a low risk to organisms and limited transfer of PAHs into food web. From the source analysis, PAHs in shelf sediments mainly originated from direct petroleum contamination, while those in marsh sediments were from combustion of fossil fuels.

Impacts of mariculture on the diversity of bacterial communities within intertidal sediments in the Northeast of China

Mariculture is one of the major seafood supplies worldwide and has caused serious environmental concerns on the coastal zone. Its rapid development has been shown to disrupt the sediment ecosystems and thus influence the benthic bacterial communities. Bacterial diversity and community structure within both adjacent farms and non-cultured zones intertidal sediments along the coasts of Qinhuangdao and Dalian, China, were investigated using full-length 16S rRNA gene-based T-RFLP analyses and clone library construction. Richness and Shannon-Wiener index were significantly increased at sites adjacent the mariculture farm with mean values of 29 and 2.97 from peak profiles of T-RFLP result. Clustering analyses suggested that impacts of mariculture on bacterial diversity of sediment were significantly larger than those resulted from temporal and spatial scales. Upon comparisons of RFLP patterns from 602 clones from libraries of the selected five samples, 137 OTUs were retrieved. Members of γ- and δ-Proteobacteria, Bacilli, Flavobacteria, and Actinobacteria were recorded in all libraries. In addition, γ-Proteobacteria were dominant in all samples (21.7~45.0 %). Redundancy analysis revealed that the distribution of bacterial composition seemed to be determined by the variables of salinity, PO4 (3-)-P, NH4 (+)-N, and Chlorophyll a content. The phyla of γ-Proteobacteria, Clostridia, Flavobacteria, Bacilli, and Planctomycetes were principal components to contribute to the bacterial differences of clone libraries. Our finding demonstrated that these phyla could display variations of bacterial composition linked to environmental disturbance resulted from mariculture.

An innovative bioremediation strategy using a bacterial consortium entrapped in chitosan beads

This aim of this work was to develop a bioremediation strategy for oil-contaminated mangrove sediments using chitosan beads containing an immobilised hydrocarbonoclastic bacterial consortium. The consortium composed of 17 isolates was obtained from an enrichment culture. The isolates were identified by 16S rDNA sequencing, which revealed 12 different genera. Thirteen isolates showed resistance to chitosan and were thus able to be trapped in chitosan beads for microcosm evaluation. The data revealed that entrapped consortium grew in the microcosms until day 15, which is when the beads disintegrated and released their biomass into the sediments. Bacterial bioaugmentation within the sediments was confirmed by cell counts; additionally, the dynamics of the bacterial populations were analysed through denaturing gradient gel electrophoresis. The chitosan showed a prebiotic effect on the autochthonous bacterial communities. Therefore, chitosan beads containing selected immobilised bacteria attain two bioremediation purposes, bioaugmentation and biostimulation, and thus represent an emergent approach.