Mangrove sediments are environmental hotspots for pathogenic protists

Mangrove sediments are unique ecosystems providing habitats for diverse organisms, especially microbial communities. However, little is known about the diversity and environmental risk of a critical group of microorganisms, the protists. To address this gap, we employed metagenome sequencing technologies to provide the first comprehensive view of the protistan community in the mangrove sediment. Our results surprisingly showed that parasitic protists dominated the protistan community in mangrove sediments, with an average abundance of 59.67%, one of the highest in all ecosystems on Earth. We also found that the relative abundance of protists decreased significantly (R = -0.21, p = 0.045) with latitude but increased with depths (R = 0.7099, p < 0.001). The parasitic communities were positively influenced by microbial (bacteria, fungi, and archaea) communities, including horizontal-scale and vertical-scale. In addition, sulfate and salinity had the most significant influence on the protistan community. Our findings provide new insights into our understanding of protistan variation in mangrove sediments, including abundance, composition, and possible functions, and indicate that mangrove sediments are hotspots for environmental pathogens, posing a potential risk to human health.

Microplastics strengthen nitrogen retention by intensifying nitrogen limitation in mangrove ecosystem sediments

Mangrove wetlands are hotspots of the global nitrogen (N) cycle and important sinks of microplastics (MPs) due to their ecotone location between terrestrial and marine ecosystems. However, the effects of MPs on N cycle processes in mangrove ecosystems are still poorly understood. Thus, the present study assessed the impacts by adding MPs to mangrove sediments in a microcosm incubation experiment. The results showed that MPs increased dissolved organic carbon and nitrate but reduced ammonium contents in the sediments. MPs increased C:N stoichiometric and N:C-acquiring enzymatic ratios, indicating an intensified N limitation in mangrove sediments following exposure of MPs. MPs decreased microbial community diversity and shifted sediment microbial communities from r- to K-strategists, consistent with the intensified N limitation. In response, dissimilatory nitrate reduction to ammonium (DNRA) rates increased while nitrous oxide (N2O) production reduced suggesting more efficient N utilization in MPs treatments. The MPs with heteroatoms such as PLA- and PVC-MPs, increased DNRA rates by 67.5-78.7%, exhibiting a stronger impact than PE-MPs. The variation partitioning analysis revealed that the variances of DNRA rates and N2O production could be attributed to synergistic effects of physicochemical properties, nutrient limitation, and microbial community in mangrove sediments. Overall, this study provides pertinent insights into the impacts of MPs as a new carbon source on nutrient limitation and N turnover in mangrove ecosystems.

Coupling isotopic signatures and partial extraction method to examine lead pollution in mangrove sediments

Elevated lead (Pb) has been widely observed in mangrove sediments due to human activities, yet understanding the sources of Pb in these sediments and the factors influencing Pb accumulation is challenging. Here, we combined Pb isotopes with partial extraction methods to study Pb contamination levels in mangrove sediments from the eastern and western parts of the Maowei Sea, China. Our results showed that the Pb in the leachate and residual fraction was mainly from anthropogenic and natural sources, respectively. The use of 204Pb isotope analysis can reveal some overlooked differences between anthropogenic and natural sources. Calculation by Bayesian mixing model showed no significant difference in the total anthropogenic contribution between the two sites, but the relative contribution of each end member differed. The contribution of Pb/Zn ores was much higher in the eastern sites (30.9 ± 5.1%) than in the west (18.4 ± 5.5%), while that of agricultural activities was much lower in the east (5.2 ± 3.1%) than in the west (13.5 ± 4.6%). The elevated anthropogenic Pb accumulation in mangrove sediments was ascribed to organic matter. This study provides more data on Pb isotopic composition and new insights into Pb biogeochemistry in the mangrove environment.

Spatial and temporal change of tetrabromobisphenol A and hexabromocyclododecane in mangrove sediments from the Pearl River Estuary, South China

Spatial and temporal trends of tetrabromobisphenol (TBBPA) and hexabromocyclododecane (HBCD) in mangrove sediments from the Pearl River Estuary (PRE) in South China were evaluated. Concentrations of TBBPA and HBCD in mangrove sediments ranged from 0.23 to 13.3 and 0.36 to 54.7 ng g-1 dry weight. The highest TBBPA concentration was seen in Guangzhou mangrove wetland near a dockyard and a ferry terminal where TBBPA is utilized in the coatings for the shipbuilding industry. The rapid development of building might elucidate the higher concentrations of HBCD in Shenzhen mangrove sediments. γ-HBCD and α-HBCD was the two main diastereoisomer of HBCD in mangrove sediments with contributions of 56.1 % and 34.0 %. Sediments from the three PRE mangrove ecosystems were selectively enriched for (-)-γ-HBCD. TBBPA concentrations in mangrove sediments from Guangzhou rose during 2012-2015 and declined from 2015 to 2021. HBCD concentrations in the PRE mangrove sediments exhibited an increasing trend from 2012 to 2021.

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments

BACKGROUND

Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.

RESULTS

Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.

CONCLUSIONS

The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.

Isotopic signatures unveil the lead sources and migration in surface mangrove sediments

Mangrove sediments act as both sinks and secondary sources for lead (Pb), yet the sources, migration, and transformations of Pb in mangrove environments are poorly understood. In this study, Pb concentration in three mangrove sediments adjacent to different land-use types was evaluated. The Pb sources were quantitatively identified using Pb isotopes. Our data indicated minor Pb contamination in the mangrove sediments, possibly due to the relative lack of developed industry in this region. The Pb isotopic ratios suggested, on average, natural sources, coal combustion, agricultural activities, and traffic-related emissions respectively contributed approximately 61.4 %, 18.8 %, 14.0 %, and 5.8 % of the Pb accumulation in the mangrove sediments, suggesting that coal combustion and agriculture were important anthropogenic Pb sources. Significant relationships were observed between the ²⁰⁶Pb/²⁰⁷Pb ratios and total organic content (TOC) in mangrove sediments, which implied contrasting Pb cycling in two mangrove environments. We further suggested that organic matter and sulfur content significantly reduced Pb mobility and bioavailability in mangrove sediments. Our study provides isotopic method to investigate the Pb sources and migration in the mangrove environment.

Characteristics and provenances of rare earth elements and Nd isotopes in surface sediments of mangrove wetlands in the Jiulong River Estuary, China

Rare earth elements (REEs) and Nd isotopes are frequently employed to determine provenance, although their characteristics and provenances in the surface sediments of mangrove wetlands are rarely analyzed. In this study, a thorough analysis of the characteristics and provenances of REEs and Nd isotopes in the surface sediments of mangrove wetland in the Jiulong River Estuary was carried out. According to the results, the mean concentration of REEs in the surface sediments was 290.9 mg·kg-1, which was greater than the background value. Unpolluted to moderately polluted for La and Ce, as well as a moderate ecological risk for Lu, were indicated by the geoaccumulation index (Igeo) and potential ecological risk of individual factors ([Formula: see text]), respectively. The surface sediments showed substantial negative Eu anomalies but no significant Ce anomalies. The enrichments in LREE and flat HREE patterns are visible in the chondrite-normalized REE patterns. REEs in the surface sediments might be attributed to both natural sources (granite and magmatic rocks) and anthropogenic activities, including coal combustion, vehicle exhaust, steel smelting, and fertilizer, based on the (La/Yb)N-∑REE and ternary (La/Yb)N-(La/Sm)N-(Gd/Yb)N plots. The three-dimensional ∑LREE/∑HREE-Eu/Eu*-εNd(0) plot, when combined with the Nd isotope, further demonstrated that the REEs in the surface sediments appeared to have come from additional nonlocal potential sources.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

BACKGROUND

Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH₄), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS

Our results showed that the metabolic pathways involved in CH₄, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N₂O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH₄ oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS

In addition to offering a perspective on the vertical distribution of microbially driven CH₄, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N₂O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.

Vertical distribution, accumulation, and characteristics of microplastics in mangrove sediment in China

Mangroves in tropical and subtropical regions worldwide are recognized as important sinks for microplastics (MPs). However, recent studies have focused on surface sediments, and in China, the vertical distribution and characteristics of MPs in mangrove sediments remain poorly understood. In this study, sediment cores of 100 cm depth were collected from six representative mangroves in China to investigate MPs via chronological analysis. Futian had the highest abundance of MPs (0-3123 n/kg), followed by Dongfang, Yunxiao, Zhanjiang, Dongzhaigang and Fangchenggang. The earliest MPs occurring in mangroves were dated back to 1955, and their abundance increased exponentially from bottom to surface sediments. MPs were mainly white in color, fiber-shaped, 1000-5000 μm in size, and of polypropylene/polyethylene polymer types. Furthermore, the MPs in the urban mangrove also showed a higher diversity in color. The results showed that the MP stocks in the urbanized Futian mangrove reached 1828 mg/m³, an order of magnitude higher than in other areas (251 ± 180 mg/m³), contributing to 0.0057 % of the carbon storage of the sediment. The abundance of MPs in mangrove sediments is expected to increase by 2.38-9.54 times by 2030, and therefore deserve further attention.

Distribution, characteristics, and human exposure to microplastics in mangroves within the Guangdong-Hong Kong-Macao Greater Bay Area

In this study, three mangroves in the Guangdong-Hong Kong-Macao Greater Bay Area- Qi'ao Island in Zhuhai, Nansha in Guangzhou, and Futian in Shenzhen-were selected for investigating the distribution of microplastics and their characteristics The average microplastic abundance in each descended in the order: Futian (1600 n/kg) > Nansha (1100 n/kg) > Qi'ao Island (440 n/kg), with values from the forest fringe being significantly higher than those in the forest interior. The microplastics were mainly fibers, 1-5 mm in size, and white/black in color; they consisted of polypropylene and polyethylene, with foam and polystyrene accounting for a high proportion in Nansha. The exposure of humans to microplastics in the Futian forest fringe reached 35.95 ng/d·kg; it was one order of magnitude higher than the exposures in Qi'ao Island and Nansha. Furthermore, ingestion accounted for approximately 74% of the total exposure to the human body, dermal contact constitutes 25%, and sediment inhalation accounted for less than 1%.

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.

Effects of different order spiking on bioavailability and ecological risk of phenanthrene in mangrove sediment-biochar system

Biochar shows unique advantage in decreasing the bioavailability of phenanthrene and has huge potential into the in-situ remediation of contaminated sediment. The different order spiking influences the bioavailability and ecological risk of phenanthrene, this study provides a comprehensive investigation of biochar (derived from mangrove Kandelia obovata -sediment system under three conditions: I) co-addition of biochar and sediment; II) biochar and subsequently sediment addition (after biochar adsorption reached equilibrium); III) sediment and subsequently biochar addition (after sediment adsorption reached equilibrium). It was observed that the adsorption capability under model I and III was much smaller than that under model II (p < 0.05). Regardless of time, K. obovate - biochar significantly (p < 0.05) increase the sorption of phenanthrene in sediment -water system. The results provide valuable studies for further in-situ remediation of phenanthrene and engineering applications.

Fatty acid signatures of sediment microbial community in the chronically polluted mangrove ecosystem

Phospholipid fatty acid (PLFA) analysis was used to examine variation in the distribution of microbial communities in heavily polluted mangrove sediments of Thane creek, west coast of India. A total of 40 individual PLFAs representing 11 functional groups were identified in the sediment and were mainly dominated by saturated fatty acids (anaerobic prokaryotes) >50%. Significant dominance of PUFA, 16:3 ω6c (34.2%) indicators of micro-eukaryotes, in subsurface depth (p < 0.05) suggests input from the remnants of marine microalgae. Declined mean relative abundance of fungi (<6%) and actinomycetes (<1%) were detected in the sediment indicating their sensitivity to anthropic stressors. Homogenous profile of microbial diversity indicating active bioturbation. Cumulative metabolic stress evident from SAT/MUFA (>1), B/F (>1) and G⁺/G^- (<1) ratio and prolonged hypoxia to be prevalent in the creek during the study. In conclusion, PLFA signatures can thus be used as potential biomarkers of environmental monitoring and proxy for interpreting ecosystem health.

Characterization of a novel isoflavone glycoside-hydrolyzing β-glucosidase from mangrove soil metagenomic library

For the beneficial pharmacological properties of isoflavonoids and their related glycoconjugates, there is increasingly interest in their enzymatic conversion. In this study, a novel β-glucosidase gene isolated from metagenomic library of mangrove sediment was cloned and overexpressed in Escherichia coli BL21(DE3). The purified recombination β-glucosidase, designated as r-Bgl66, showed high catalytic activity for soy isoflavone glycosides. It converted soy isoflavone flour extract with the productivities of 0.87 mM/h for daidzein, 0.59 mM/h for genistein and 0.42 mM/h for glycitein. The kcat/Km values for daidzin, genistin and glycitin were 208.73, 222.37 and 288.07 mM-1 s-1, respectively. In addition, r-Bgl66 also exhibited the characteristic of glucose-tolerance, and the inhibition constant Ki was 471.4 mM. These properties make it a good candidate in the enzymatic hydrolysis of soy isoflavone glycosides. This study also highlights the utility of metagenomic approach in discovering novel β-glucosidase for soy isoflavone glycosides hydrolysis.

nov., a moderately thermophilic bacterium isolated from mangrove sediment

A novel moderately thermophilic and halophilic bacterium, designated strain M0105^T, was isolated from mangrove sediment collected in the Beibu Gulf, south China. The isolate is Gram-negative, non-motile and rod-shaped bacterium with smooth colonies of pale-yellow appearance. Growth occurs at 15-46 °C (optimum 37-40 °C) and pH range of 6.0-10.0 (optimum pH 8.0-9.0). It required 1-7% NaCl (optimum 3-5%) for growth. Strain M0105^T was affiliated to the family 'Rhodobacteraceae', sharing the highest 16S rRNA gene sequence similarity with Limibaculum halophilum CAU 1123^T (96.8%). The major menaquinone Q-10 and the dominant unsaturated fatty acid (C_18:1ω7) in this family were also detected in the strain M0105^T. The genome sequence possesses a circular 4.1 Mb chromosome with a G + C content of 67.9%. Strain M0105^T encoded many genes for cellular stress resistance and nutrient utilization, which could improve its adaptive capacity to the mangrove environment. Values of conserved proteins (POCP), average nucleotide identity, average amino acid identity (AAI) and DNA-DNA hybridization (dDDH) between the isolate and closely related species were below the proposed threshold for species discrimination. Information from phenotypic, chemotaxonomic and phylogenetic analyses proposed that strain M0105^T should be assigned to a novel genus within the family 'Rhodobacteraceae'. Thus, we suggested that the strain M0105^T represents a novel species in a new genus, for which the name Thermohalobaculum xanthum gen. nov., sp. nov. is proposed. The type strain of the type species is M0105^T (= BGMRC 2019^T = KCTC 52118^T = MCCC 1K03767^T = NBRC 112057^T).

Aegicerativicinus sediminis gen. nov., sp. nov., a novel carotenoid-producing marine bacterium in the family Flavobacteriaceae

A novel bright-yellow pigmented bacterial strain SM2-F^T was isolated from a mangrove sediment collected at the mangrove coast of Luoyang estuary, Quanzhou, China. Strain SM2-F^T was Gram-stain-negative, catalase-weak positive, oxidase-positive, rod-shaped, non-flagellated and non-motile. Growth of strain SM2-F^T was observed at 20-40 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 1.0-4.0% NaCl (optimum, 2.0% NaCl). Flexirubin-pigment was absent, and carotenoid-pigment was present. Phylogenetic analysis of 16S rRNA gene sequence placed strain SM2-F^T into the family Flavobacteriaceae and shared the maximum sequence similarity with Aequorivita soesokkakensis RSSK-12 ^T of 92.5%. Whole genomic comparison between strain SM2-F^T and close relatives suggested a novel species of a novel genus. The predominant quinone of strain SM2-F^T was menaquinone (MK)-6. The major fatty acids (> 10%) comprised iso-C_15:1 G (32.4%) and iso-C_15:0 (29.1%). The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids. The complete genome size was 4,094,245 bp with DNA G + C content of 36.0 mol%. Based on the data of polyphasic study, strain SM2-F^T was considered to represent a novel species of a novel genus, for which the name Aegicerativicinus sediminis gen. nov., sp. nov., was proposed. The type strain was SM2-F^T (= MCCC 1K04383^T = KCTC 82361 ^T).

nov., a moderately halopilic bacterium isolated from mangrove sediment

A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, named NBU-8HK146^T. Strain NBU-8HK146^T was able to grow at temperatures of 10-40 °C, at salinities of 0-11% (w/v) and at pH 5.5-9.5. Veoges-Proskauer, methyl red reaction and hydrolysis of Tween 20 were negative. Catalase and oxidase activities, H₂S production, hydrolysis of starch, casein, Tweens 40, 60 and 80 were positive. The major cellular fatty acids were C_16:0, iso-C_15:0 and summed feature 9. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified glycolipids. According to 16S rRNA gene sequence similarities, strain NBU-8HK146^T shared 98.0%, 97.9%, 97.7%, 97.6% and 97.3% similarities to the species with validated name Microbulbifer taiwanensis CC-LN1-12^T, Microbulbifer rhizosphaerae Cs16b^T, Microbulbifer marinus Y215^T, Microbulbifer donghaiensis CN85^T and Microbulbifer aggregans CCB-MM1^T, respectively. Phylogenetic analyses indicated that strain NBU-8HK146^T formed a distinct lineage with strains Microbulbifer taiwanensis CC-LN1-12^T and Microbulbifer marinus Y215^T. Both digital DNA-DNA hybridization values (19.5-22.7%) and average nucleotide identity values (73.2-78.9%) between strain NBU-8HK146^T and related species of genus Microbulbifer were below the species delineation cutoffs. The DNA G+C content was 58.9 mol%. Many proteins involving in the adaption of osmotic stress in the salt environment of mangrove were predicted in genome of strain NBU-8HK146^T. From phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain NBU-8HK146^T can be regarded as a new Microbulbifer species for which the name Microbulbifer hainanensis. The type strain is NBU-8HK146^T (= KCTC 82226^T = MCCC 1K04737^T).

Spatial distributions, source apportionment and ecological risks of C9-C17 chlorinated paraffins in mangrove sediments from Dongzhai Harbor, Hainan Island

The spatial distributions, possible sources of C₉-C₁₇ chlorinated paraffins (CPs), and the ecological risks posed in mangrove sediment in Dongzhai Harbor (Hainan Island, China) were investigated. Comprehensive two-dimensional gas chromatography combined with electron capture negative ionization mass spectrometry was used to determine 50 C₉-C₁₇ CP congener groups. The concentrations of C₉-CPs, short-chain CPs (SCCPs), and medium-chain CPs (MCCPs) in the mangrove sediment samples were 8.28-79.7, 89.2-931, and 58.8-834 ng g^-1 dry weight, respectively. The CPs concentrations in the mangrove sediment samples were moderate compared with those found in other regions worldwide. The spatial distributions and congener patterns of the CPs indicated that the CP concentrations were mainly controlled by local emissions and that wastewater discharged from livestock and shrimp breeding facilities and domestic sewage were the main sources of CPs in mangrove sediment in Dongzhai Harbor. C₁₀Cl_6-7 and C₁₄Cl_7-8 were the dominant SCCP and MCCP congener groups, respectively. The MCCP concentrations and total organic carbon contents significantly correlated (R² = 0.607, P < 0.05). Hierarchical cluster analysis and principal component analysis indicated that the SCCP and MCCP congeners were from different commercial CP formulations and sources. Risk assessments suggested that SCCPs and MCCPs in mangrove sediment in Dongzhai Harbor do not currently pose marked risks to sediment-dwelling organisms.

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

BACKGROUND

Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood.

RESULTS

Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H₂-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production.

CONCLUSIONS

Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.

Distribution of mercury in sediments, plant and animal tissues in Matang Mangrove Forest Reserve, Malaysia

Charcoal production activities at the Matang Mangrove Forest Reserve (MMFR) in Peninsular Malaysia have a potential to emit volatile compounds such as Hg back into the ambient environment, raising concerns on the public health and safety. The present study was aimed at analyzing Hg concentration from different plant/animal tissues and sediment samples (in total 786 samples) to understand clearly the Hg distribution at the MMFR. Leaves of Rhizophora spp. showed higher Hg concentration with an increasing trend from young, to mature, to senescent and decomposing stages, which was possibly due to accumulation of Hg over time. The low Hg concentration in Rhizophora roots and bark suggests a limited absorption from the sediments and a meagre accumulation/partitioning by the plant tissue, respectively. In the case of mangrove cockles the concentration of Hg was lower than the permissible limits for seafood consumption. Although the mangrove gastropod - Cassidula aurisfelis Bruguière had rather elevated Hg in the muscle tissue, it is still less than the environmental safely limit. Beside the chances of atmospheric deposition for Hg, the sediment samples were found to be unpolluted in nature, indicating that in general the MMFR is still safe in terms of Hg pollution.

Development of a digestion method for determining microplastic pollution in vegetal-rich clayey mangrove sediments

Microplastics are ubiquitous pollutants found in environments. Mangrove sediments containing vegetal litter are different from other environmental matrices such as river and marine sediments. The presence of vegetal litter leads to an under-estimation of microplastic pollution, particularly classical digestion methods are not suitable for removing this type of organic matter. The present study aims to develop a digestion method to remove vegetal litter and improve the determination of microplastic pollution in mangrove sediments. Results showed that our three-stage method with repeatedly addition of hydrogen peroxide had the highest efficiency in removing mangrove vegetal litter when compared with the three classical digestion methods. The high match scores of Fourier Transform Infrared Spectroscopy proved that the developed method had little impacts on the integrity of five polymer types of microplastics. The developed method also achieved high efficiency in extracting microplastics from mangrove sediments containing different content of vegetal litter. CAPSULE: A digestion method was developed for extracting microplastics in clayey mangrove sediments rich in vegetal litter.

Mercury concentration data from Matang Mangrove Forest Reserve, Malaysia

This paper presents the results of mercury analysis on 786 abiotic (surface sediments) and biotic (plant and animal tissues) samples collected from 10 sites at Matang Mangrove Forest Reserve in Peninsular Malaysia. Sediment samples were collected at the surface level from both river bank and forest understory. Whereas plant tissues obtained from Rhizophora apiculata Blume and Rhizophora mucronata L. consisted of leaves (in four stages namely young, mature, senescent and decomposing), bark and roots (divided into xylem, cortex and epidermis), the animal samples were represented by muscle tissue of the gastropod Cassidula aurisfelis Bruguière and the cockle Tegillarca granosa L. The mercury concentration measurements were obtained through a cold vapor atomic absorption spectrometer. The core data have been analysed and interpreted in the paper "Distribution of mercury in sediments, plant and animal tissues in Matang Mangrove Forest Reserve, Malaysia" [1].

Operationally defined mercury (Hg) species can delineate Hg bioaccumulation in mangrove sediment systems: A case study

This study investigated the linkage between mercury (Hg) speciation in the surficial sediments from a mangrove ecosystem of the Zuari Estuary, west coast of India, with Hg bioaccumulation in gastropods collected from the same area. Multiple operationally defined protocols and methods were used for determination of Hg speciation study in the mangrove sediments. Moderately low concentrations of Hg were observed in the sediments, ranging from 37.3 ± 1.9 to 79.6 ± 4.0 µg/kg. Geochemical fractionation showed that a significant part of sedimentary Hg was present within the structure of the sediment (residual fraction) and not bioavailable. Non-residual Hg was primarily associated with oxidizable (sedimentary organic matter (SOM) or sulfide) binding phase of the sediments, and ranged from 9.2 ± 0.3 to 78.5 ± 3.9 µg/kg. Concentration of methylmercury (MeHg) (a neurotoxin) in the sediments varied from 1.7 ± 0.1 to 4.4 ± 0.1 µg/kg. l-Cysteine, a suitable complexing ligand, extractable Hg concentration in the sediments ranged from 4.3 ± 0.1 to 15.9 ± 0.3 µg/kg. Statistical analysis suggested that MeHg was adsorbed on Fe/Mn oxyhydroxide phases in the sediments. l-Cysteine was found to extract sedimentary MeHg and thermodynamically less stable Hg-SOM complexes from the sediments. Concentrations of bioaccumulated Hg in soft tissues of the gastropod, Pirenella cingulata, ranged from 57.6 ± 4.4 to 224.4 ± 7.2 µg/kg. Positive correlations existed between the concentration of bioaccumulated Hg in the gastropods and the concentrations of Hg associated with the oxidizable phase, sedimentary MeHg and l-Cysteine extracted Hg in the sediments. This study indicated that operationally defined Hg species can be useful in estimating bioavailable Hg to obligatory deposit feeder in tropical mangrove systems.

Polybrominated diphenyl ethers and polychlorinated biphenyls in mangrove sediments of Shantou, China: Occurrence, profiles, depth-distribution, and risk assessment

Surface and columnar sediments were collected from four mangrove Wetlands in Shantou coastal areas of South China to investigate the level, distribution, possible sources and ecotoxicological risks of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs). Total concentration of 14 PBDEs (∑₁₄PBDEs) and 41 PCBs (∑₄₁PCBs) varied from 0.61 to 180 ng/g and 42-636 pg/g dry weight (dw) in surface sediments, respectively. The concentration of PBDEs was much higher than that of PCBs. Compared with other mangrove Wetlands around the world, PCBs levels in the studied area were relatively low, while the concentrations of PBDE were at higher level. Decabromodiphenyl ether (BDE-209) was the predominant PBDEs homologue in all sediment samples, indicating the extensive use of deca-BDE in this area. Penta-CBs and hexa-CBs were the main homologues of PCBs. Spatial variations showed that the concentration of PBDEs might be mainly affected by anthropogenic activities in specific sites of this region, whereas dry and wet deposition might be an important input source of PCBs in this area. Although accurate sediment chronology was not available, higher concentrations of PBDEs and PCBs were still found in some deeper sediment layers, suggesting that new input quantity tends to decrease with the increase of control. Risk assessment showed that penta-BDEs and deca-BDE may have potential negative ecological effects on the ecological of Shantou mangrove sediments, while the effects of PCBs can be neglected.

Spatial variation and ecological risk assessment of heavy metals in mangrove sediments across China

The spatial variations of nine heavy metals in the surface sediments of six Avicennia marina mangrove wetlands across China were investigated. These were Yunxiao, Futian (FT), Zhanjiang, Fangchenggang (FCG), Dongfang (DF), and Dongzhaigang (DZG). Results showed that environmental factors, such as organic matter and sediment grain size, affected heavy metal distribution. The high heavy metal levels in mangrove sediments may be due to their large retention capacity. The dominant heavy metals were Zn, Cr, Pb, Cu, and Cd. Pollution was highest at FT and lowest at FCG. The principal component analysis indicated that Zn, Cd, Cu, Ni, Cr, and Pb were mainly derived from anthropogenic activities. Ecological risk assessments showed that FT was the most polluted area with considerable ecological risk, whereas pollution levels were lowest at FCG, DF, and DZG. This study provides the first integrated analysis of heavy metal pollution of sediments across China.

Abundance and characteristics of microplastics in the mangrove sediment of the semi-enclosed Maowei Sea of the south China sea: New implications for location, rhizosphere, and sediment compositions

Microplastic pollution of intertidal mangrove ecosystems is receiving growing attention, and scientists suspect that the microplastic pollution of semi-enclosed seas is significantly different from that of other coastal types because of their unique geographical features. However, data on the distributions and characteristics of microplastics in the mangrove sediment of semi-enclosed seas are very limited. This study selected the Maowei Sea, a typical semi-enclosed sea, as its representative study site. The analysis revealed that the microplastic abundances in the river estuaries were much lower than those at the oceanic entrance zones, with values ranging from 520 ± 8 to 940 ± 17 items/kg. Polyethylene (PE)/polypropylene (PP)/polystyrene (PS), white/transparent, and <1 mm were the dominant type, colour, and size of the microplastics, respectively, in the observed mangrove sediments. Moreover, some other factors, including the rhizosphere/non-rhizosphere and the proportion of organic matter, codetermined the distribution and characteristics of microplastics. Specifically: (1) the percentage of colorful microplastics were higher in the rhizosphere due to the microbial activities and (2) positive linear relationships were found between the pore volume (PV) values of the free particulate organic matter (FPOM), occluded particulate organic matter (OPOM) (1.6-2.0 g/cm³ and >2.0 g/cm³), and the abundance of very small microplastics (<1 mm).

Anaerobic degradation of sulfamethoxazole in mangrove sediments

The effects of sucrose and electron acceptors on the anaerobic degradation of sulfamethoxazole (SMX) in mangrove sediments were investigated in this study. Among three sulfonamides, sulfamethoxazole, sulfadimethoxine and sulfamethazine, only SMX could be completely degraded in mangrove sediments. Degradation of SMX was enhanced by the addition of sucrose to the sediments. The degradation rates of SMX were increased in bioreactor experiments with sucrose. The addition of electron acceptors (sodium hydrogen carbonate, sodium sulfate, and sodium nitrate) could further enhance SMX degradation. The order of anaerobic SMX degradation rates under three different conditions was as follows: sulfate-reducing conditions > methanogenic conditions > nitrate-reducing conditions. Methanolobus, Desulfuromonas, and Thauera were found in the highest proportions among methanogens, sulfate-reducing bacteria and denitrifying bacteria, respectively. Achromobacter, Brevundimonas, Delftia, Idiomarina, Pseudomonas, and Rhodopirellula were the major bacterial communities responsible for SMX degradation in the sediment. Overall, 16 bacterial and archaeal genera were identified as the core microbial community facilitating anaerobic SMX degradation for all methanogenic, sulfate-reducing and nitrate-reducing conditions. The results of this study provide feasible methods for the removal of SMX from mangrove sediments.

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.

Effect of pH on transport and transformation of Cu-sediment complexes in mangrove systems

Impact of pH variation of overlying water column on transport and transformation of Cu-sediment complexes in the bottom mangrove sediments was investigated by using different metal extraction studies. The total Cu concentration in the studied sediments varied from ~64 ± 1 to 78 ± 2 mg·kg^-1. The sequential extraction study showed that a major part of the sedimentary Cu (85-90% of the total sedimentary Cu) was present within the structure of the sediments with minimum mobility and bioavailability. The redistribution of non-residual Cu among the different binding phases of the sediments was observed at different pH. It was found that Cu shifted from the different non-residual binding phases to the organic binding phase of the sediments at higher pH. Partial leaching of sedimentary Cu-SOM complexes (with increasing stability as determined by kinetic extraction study) was observed at higher pH. This study infers that increase in pH of overlying water column may release Cu-SOM complexes and increase the mobility of Cu-complexes in mangrove systems.

The implications of water extractable organic matter (WEOM) on the sorption of typical parent, alkyl and N/O/S-containing polycyclic aromatic hydrocarbons (PAHs) by microplastics

Microplastics sorption of persistent organic pollutants (POPs) was the core processes that cause negative effects to biota, and their influencing factors and related mechanisms are poorly understood. In this study, we explored the impacts of water extractable organic matter (WEOM), an important source of endogenous dissolved organic matter in mangrove sediment, on the sorption coefficients of typical parent, alkyl and N/O/S-containing polycyclic aromatic hydrocarbons (PAHs) by microplastics. The presence of L-WEOM (D) impeded the PAHs sorption as the coefficients (K_f) decreased to 10.17 (μg/kg)/(μg/L)ⁿ and to 8.39 (μg/kg)/(μg/L)ⁿ for fluorene (Flu) and 1-methyl-fluorene (1-M-Flu), respectively. The K_f exhibited good linear relationships with the aliphaticity of L-WEOM (p < 0.05) rather than the aromatic carbon/alkyl carbon content (p > 0.05). Under the presences of L-WEOM (D), (S) and (K), the lone pair electrons of N/O/S-containing PAHs was the dominant factor contributing to the obvious difference of the K_f values from the other groups. Moreover, the largest impact of L-WEOM (D) on the Flu sorption was in the case of PVC microplastics, while almost no effect was in the case of PS microplastics. The findings of our work may be helpful in improving our understanding of the role of WEOM on the sorption of PAHs to microplastics in the field mangrove sediment.

Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment

Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.

Fungi extracellular enzyme-containing microcapsules enhance degradation of sulfonamide antibiotics in mangrove sediments

Mangroves represent a special coastal vegetation along the coastlines of tropical and subtropical regions. Sulfonamide antibiotics (SAs) are the most commonly used antibiotics. The application of white-rot fungi extracellular enzyme-containing microcapsules (MC) for aerobic degradation of SAs in mangrove sediments was investigated in this study. Degradation of three SAs, sulfamethoxazole (SMX), sulfadimethoxine (SDM), and sulfamethazine (SMZ), was enhanced by adding MC to the sediments. The order of SA degradation in batch experiments was SMX > SDM > SMZ. Bioreactor experiments revealed that SA removal rates were higher with than without MC. The enhanced SA removal rates with MC persisted with three re-additions of SAs. Thirteen bacteria genera (Achromobacter, Acinetobacter, Alcaligenes, Aquamicrobium, Arthrobacter, Brevundimonas, Flavobacterium, Methylobacterium, Microbacterium, Oligotropha, Paracoccus, Pseudomonas, and Rhodococcus) were identified to be associated with SA degradation in mangrove sediments by combination of next-generation sequencing, bacterial strain isolation, and literature search results. Results of this study suggest that MC could be used for SA removal in mangrove sediments.

Effects of decabromodiphenyl ether and planting on the abundance and community composition of nitrogen-fixing bacteria and ammonia oxidizers in mangrove sediments: A laboratory microcosm study

While nitrogen (N) fixation and ammonia oxidation by microorganisms are two important N cycling processes, little is known about how the microbes that drive these two processes respond when sediments are contaminated with persistent organic pollutants. In this study, we carried out a laboratory microcosm experiment to examine the effects of decabromodiphenyl ether (BDE-209), either on its own or combined with a common mangrove species, Avicennia marina, on the abundance, diversity, and community composition of N-fixing bacteria (NFB) and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in mangrove sediments. The sediments were very N-limited after one year. The rates of N fixation and NFB abundance were significantly higher in the sediments that contaminated by BDE-209, especially in the planted sediment, indicating that both BDE-209 and planting stimulated N fixation in N-limited mangrove sediments. In contrast, the potential nitrification rate and abundance of AOA and AOB decreased significantly under BDE-209 and planting, and the inhibitory effects were stronger in the sediment with both planting and BDE-209 than in the sediments with either BDE-209 or planting. The results from pyrosequencing showed that the richness and diversity of NFB increased, while those of AOA and AOB decreased, in the sediments treated with BDE-209 only and with BDE-209 combined with planting. The community compositions of NFB, AOA, and AOB in the sediments shifted significantly because of BDE-209, either alone or particularly when combined with planting, as shown by the increases in some NFB from the Proteobacteria phylum and decreases in AOA in the Nitrosopumilus genus and AOB in the Nitrosospira genus, respectively.

Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium

A pyrene-degrading microbial consortium was obtained after enrichment with mangrove sediment collected from Thailand. Five cultivable bacteria (Mycobacterium spp. PO1 and PO2, Novosphingobium pentaromativorans PY1, Ochrobactrum sp. PW1, and Bacillus sp. FW1) were successfully isolated from the consortium. Draft genomes of them showed that two different morphotypes of Mycobacterium (PO1 and PO2), possessed a complete gene set for pyrene degradation. PY1 contained genes for phthalate assimilation via protocatechuate, a central intermediate, by meta-cleavage pathway, and PW1 possessed genes for protocatechuate degradation via ortho-cleavage pathway. The occurrence of biosurfactant-producing genes in FW1 suggests the involvement in enhancing the pyrene bioavailability. Biotransformation experiments revealed that Mycobacterium completely degraded 100mgL^-1 pyrene within six days, whereas no significant degradation was observed with the others. Notably, PY1 and PW1 exhibited higher activity for protocatechuate degradation than the others. The artificially reconstructed consortia containing Mycobacterium with the other three strains (PY1, PW1 and FW1) showed three-fold higher degradation rate for pyrene than the individual Mycobacterium. The enhanced pyrene biodegradation achieved in the consortium was due to the cooperative interaction of bacterial mixture. Our findings showing that synergistic degradation of pyrene in the consortium will facilitate the application of the defined bacterial consortium in bioremediation.

Bacterial communities associated with anaerobic debromination of decabromodiphenyl ether from mangrove sediment

This study evaluated decabromodiphenyl ether (BDE-209) anaerobic debromination and bacterial community changes in mangrove sediment. BDE-209 debromination rates were enhanced with zerovalent iron compared to without zerovalent iron in the sediment. BDE-209 debromination rates in microcosms constructed with sediments collected in autumn were higher than in microcosms constructed with sediments collected in spring and were higher at the Bali sampling site than the Guandu sampling site. The intermediate products resulting from the reductive debromination of BDE-209 in sediment were nona-BDE (BDE-206, BDE-207), octa-BDEs (BDE-196, BDE-197), hepta-BDEs (BDE-183, BDE-184, BDE-191), hexa-BDEs (BDE-137, BDE-138, BDE-154, BDE-157), penta-BDEs (BDE-85, BDE-99, BDE-100, BDE-126), tetra-BDEs (BDE-47, BDE-49, BDE-66, BDE-77), tri-BDEs (BDE-17, BDE-28), and di-BDEs (BDE-15). Fifty bacterial genera associated with BDE-209 debromination were identified. Overall, 12 of the 50 bacterial genera were reported to be involved in dehalogenation of aromatic compounds. These bacteria have high potential to be BDE-209 debromination bacteria. Different combinations of bacterial community composition exhibit different abilities for BDE-209 anaerobic debromination.

In situ visualization and quantitative investigation of the distribution of polycyclic aromatic hydrocarbons in the micro-zones of mangrove sediment

The distribution of polycyclic aromatic hydrocarbons (PAHs) in the micro-zones of mangrove sediment is a predominant factors determining PAH bioavailability. In this study, a novel method for the in situ visualization (via microscope) and quantitative investigation of the PAH distribution in the micro-zones of mangrove sediment was established using microscopic fluorescence spectral analysis combined with derivative synchronous fluorescence spectroscopy (MFSA-DSFS). The MFSA-DSFS method significantly suppressed the background fluorescence signal of the sediment (the S/N values increased by over two orders of magnitude). The proportion of the nonpolar organic carbon content in the particulate organic matter (POM) rather than its content in the total organic matter (TOM) showed a significantly positive correlation with the uneven PAH distribution (Relative DC-M values) evaluated using the established method (p < 0.05). The extent of the uneven PAH distribution in the micro-zones of aged sediment was higher than that in the spiked sediment. Moreover, the distribution pattern of the PAHs within the mangrove sediment changed to become more homogeneous in the presence of low-molecular-weight organic acids (LMWOAs), which primarily contribute to increasing the POM content.

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.

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.

Geochemical partitioning of Cu and Ni in mangrove sediments: relationships with their bioavailability

Sequential extraction study was performed to determine the concentrations of non-residual metal-complexes in the mangrove sediments from the Divar Island, (west coast of India). Accumulation of metal in the mangrove roots (from the same location) was determined and used as an indicator of bioavailability of metal. An attempt was made to establish a mechanistic linkage between the non-residual metal complexes and their bioavailability in the mangrove system. The non-residual fractions of Cu and Ni were mainly associated with Fe/Mn oxyhydroxide and organic phases in the sediments. A part of these metal fractions were bioavailable in the system. These two phases were the major controlling factors for Ni speciation and their bioavailability in the studied sediments. However, Cu was found to interact more strongly with the organic phases than Ni in the mangrove sediments. Organic phases in the mangrove sediments acted as buffer to control the speciation and bioavailability of Cu in the system.

Cataloguing the bacterial diversity of the Sundarbans mangrove, India in the light of metagenomics

In this present study we report the profile of bacterial community at variable depth of soil sediment in the world's largest tropical mangrove sediments of Sundarbans, India using 16S rRNA gene amplicon sequencing. Metagenome of three samples consisted of 61301 sequences with 32.0 Mbp and 55.6% G + C content. Metagenome data of this study are available at NCBI under the Biosample data base accession no. SRX883521. The taxonomic analysis of 2746 species belonged to 33 different phyla revealing the dominance of Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Acidobacteria, Nitrospirae and Actinobacteria respectively. Remarkably less than 5.0% sequences belong to a poorly characterized group. Our pyrosequencing data report unfolds the bacterial community profile at different depth of soil sediment indicating the changing community pattern, in the light of specific chronology.

Anaerobic biodegradation of PAHs in mangrove sediment with amendment of NaHCO3

Mangrove sediment is unique in chemical and biological properties. Many of them suffer polycyclic aromatic hydrocarbon (PAH) contamination. However, the study on PAH biological remediation for mangrove sediment is deficient. Enriched PAH-degrading microbial consortium and electron acceptor amendment are considered as two effective measures. Compared to other electron acceptors, the study on CO2, which is used by methanogens, is still seldom. This study investigated the effect of NaHCO3 amendment on the anaerobic biodegradation of four mixed PAHs, namely fluorene (Fl), phenanthrene (Phe), fluoranthene (Flua) and pyrene (Pyr), with or without enriched PAH-degrading microbial consortium in mangrove sediment slurry. The trends of various parameters, including PAH concentrations, microbial population size, electron-transport system activities, electron acceptor and anaerobic gas production were monitored. The results revealed that the inoculation of enriched PAH-degrading consortium had a significant effect with half lives shortened by 7-13 days for 3-ring PAHs and 11-24 days for 4-ring PAHs. While NaHCO3 amendment did not have a significant effect on the biodegradation of PAHs and other parameters, except that CO2 gas in the headspace of experimental flasks was increased. One of the possible reasons is that mangrove sediment contains high concentrations of other electron acceptors which are easier to be utilized by anaerobic bacteria, the other one is that the anaerobes in mangrove sediment can produce enough CO2 gas even without adding NaHCO3.

Kinetic speciation and bioavailability of copper and nickel in mangrove sediments

An attempt was made to establish a mechanistic linkage between chemical speciation of copper and nickel, and their bioavailability in mangrove ecosystem. Kinetic speciation study was performed to determine the concentrations of labile metal-complexes and their dissociation rate constants in mangrove sediments. Concentrations of copper and nickel in the mangrove roots were used as indicators of their bioavailability. It was found that the bioaccumulation of both the metals gradually increased with the increasing concentrations of the labile metal complexes and their dissociation rate constants in the mangrove sediments. This study shows that concentration of labile metal (copper and nickel) complexes and their dissociation rate constants in mangrove sediment can be a good indicator of their bioavailability.

Abilities and genes for PAH biodegradation of bacteria isolated from mangrove sediments from the central of Thailand

PAH-degrading bacteria, including Novosphingobium sp. PCY, Microbacterium sp. BPW, Ralstonia sp. BPH, Alcaligenes sp. SSK1B, and Achromobacter sp. SSK4, were isolated from mangrove sediments. These isolates degraded 50-76% of 100 mg/l phenanthrene within 2 weeks. Strains PCY and BPW also degraded pyrene at 98% and 71%, respectively. Furthermore, all of them probably produced biosurfactants in the presence of hydrocarbons. Interestingly, PCY has a versatility to degrade various PAHs. Molecular techniques and plasmid curing remarkably revealed the presence of the alpha subunit of pyrene dioxygenase gene (nidA), involving in its pyrene/phenanthrene degrading ability, located on megaplasmid of PCY which has never before been reported in sphingomonads. Moreover, genes encoding ferredoxin, reductase, extradiol dioxygenase (bphA3A4C) and exopolysaccharide biosynthetase, which may be involved in PAH degradation and biosurfactant production, were also found in PCY. Therefore, we conclude that these isolates, especially PCY, can be the candidates for use as inoculums in the bioremediation.