Assessment on Pollution by Heavy Metals and Arsenic Based on Surficial and Core Sediments in the Cam River Mouth,Haiphong Province,Vietnam

The Cam River mouth (Haiphong Province) is one of the main river mouths of the Red River System, which is one of the most important water resources in Northern Vietnam. Over the past 50 years, the strong socio-economic development in the area has caused a considerable contamination with heavy metals (Co, Cr, Cu, Mn, Ni, Pb, and Zn) and arsenic. In this study, the vertical and horizontal distributions of heavy metals and arsenic in sediments from the Cam River mouth were investigated. In addition, the history, origin, and degree of contamination were assessed. Normalized (with respect to Al) heavy metal and arsenic concentrations in sediment cores and absolute dates obtained from the ¹³⁷Cs analysis were used to reconstruct the pollution history of the river mouth. As, Cu, Mn, Pb, and Zn concentrations increase rapidly by approximately two times or more from 1954 to 1975, and then remain nearly unchanged from 1975 until 2008, whereas Co, Cr, and Ni concentrations slightly increase from 1954 until 2008. In addition, background values for heavy metals and arsenic have also been determined with regard to the period before 1954. In the study area, Co, Cr, Cu, Ni, Mn, and Zn are evaluated as minorly enriched, whereas As and Pb are classified as moderately enriched. Generally, the anthropogenic activities in the Haiphong harbor and industrial zone locally contribute to the contamination by heavy metals and arsenic in the Cam River mouth.     

Application of Semipermeable Membrane Devices (SPMDs) and Benthic Mussels to Evaluate the Bioavailability of Sediment-associated DDTs

Bioavailability of dichlorodiphenyltrichloroethanes (DDTs) in surface sediments was evaluated with semipermeable membrane devices (SPMDs) and two different sediment-dwelling benthic mussels, Bellamya aeruginosa (B. aeruginosa) and Corbicula fluminea (C. fluminea). After 28d laboratory exposure, the positive correlations of DDT concentrations between both SPMDs and benthic mussels with sediments documented that the bioavailability of DDTs was mainly affected by surrounding sediments, while the observed differences of DDT concentrations and congener proportions between B. aeruginosa and C. fluminea were due to the specific physiological characteristics of organisms and different physico-chemical properties of contaminants. Comparisons between SPMDs and benthic mussels showed higher values of biota-sediment accumulation factors (BSAF, 0.63-3.61 for B. aeruginosa and 2.19-17.08 for C. fluminea) than device accumulation factors (DAF, 1.00-1.74). This indicated that living organisms bioaccumulated much more DDTs from sediments than SPMDs due to the different exposure and uptake routes. Strong positive associations between DDTs in SPMDs and benthic mussels indicated SPMDs could mimic the bioaccumulation of DDTs, especially in C. fluminea. However, given the distinct differences observed for both concentrations and congener proportions of DDTs in SPMDs and B. aeruginosa, future study should be directed to develop reliable models with various sediment-dwelling organisms before SPMDs are routinely used in field study.     

Detrital diversity influences estuarine ecosystem performance

Global losses of seagrasses and mangroves, eutrophication‐driven increases in ephemeral algae, and macrophyte invasions have impacted estuarine detrital resources. To understand the implications of these changes on benthic ecosystem processes, we tested the hypotheses that detrital source richness, mix identity, and biomass influence benthic primary production, metabolism, and nutrient fluxes. On an estuarine muddy sandflat, we manipulated the availability of eight detrital sources, including mangrove, seagrass, and invasive and native algal species that have undergone substantial changes in distribution. Mixes of these detrital sources were randomly assigned to one of 12 treatments and dried detrital material was added to seventy‐two 0.25 m² plots (n = 6 plots). The treatments included combinations of either two or four detrital sources and high (60 g) or low (40 g) levels of enrichments. After 2 months, the dark, light, and net uptake of NH₄⁺, dissolved inorganic nitrogen, and the dark efflux of dissolved organic nitrogen were each significantly influenced by the identity of detrital mixes, rather than detrital source richness or biomass. However, gross and net primary productivity, average oxygen flux, and net NO_X and dissolved inorganic phosphorous fluxes were significantly greater in treatments with low than with high detrital source richness. These results demonstrate that changes in detrital source richness and mix identity may be important drivers of estuarine ecosystem performance. Continued impacts to estuarine macrophytes may, therefore, further alter detritus‐fueled productivity and processes in estuaries. Specific tests that address predicted future changes to detrital resources are required to determine the consequences of this significant environmental problem.     

Complete genome sequence of Desulfocapsa sulfexigens,a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds

Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial family Desulfobulbaceae and is one of two validly described members of its genus. This strain was selected for genome sequencing, because it is the first marine bacterium reported to thrive on the disproportionation of elemental sulfur, a process with a unresolved enzymatic pathway in which elemental sulfur serves both as electron donor and electron acceptor. Furthermore, in contrast to its phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D. sulfexigens is unable to grow by sulfate reduction and appears metabolically specialized in growing by disproportionating elemental sulfur, sulfite or thiosulfate with CO₂ as the sole carbon source. The genome of D. sulfexigens contains the set of genes that is required for nitrogen fixation. In an acetylene assay it could be shown that the strain reduces acetylene to ethylene, which is indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1 comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a predicted function based on auto-annotation. The chromosome furthermore encodes 46 tRNA genes and 3 rRNA operons.     

AN ASSESSMENT OF THE POTENTIAL IMPACT OF ALIEN INVASIVE VEGETATION ON THE GEOMORPHOLOGY OF RIVER CHANNELS IN SOUTH AFRICA

Summary

Invasion of the riparian zone by alien vegetation is recognised as a serious problem in many areas of South Africa. Vegetation is a dynamic component of river channels. It is an important control variable affecting channel form whereas the flow and sediment regime influences vegetation growth. Wherever alien vegetation invades the riparian zone it can be expected that there will be some impact on the physical structure of the riparian habitat. This paper reviews the effect of riparian vegetation on channel processes and channel form and discusses the implications of the invasion of riparian zones by alien vegetation. Woody species in particular are seen as having a significant potential for inducing channel modification, whilst their removal could lead to significant channel instability and mobilisation of sediment. The need for further research into the impact of alien vegetation on the geomorphology of South African river channels is stressed.     

Resting Stages of Skeletonema marinoi Assimilate Nitrogen From the Ambient Environment Under Dark,Anoxic Conditions

The planktonic marine diatom Skeletonema marinoi forms resting stages, which can survive for decades buried in aphotic, anoxic sediments and resume growth when re-exposed to light, oxygen, and nutrients. The mechanisms by which they maintain cell viability during dormancy are poorly known. Here, we investigated cell-specific nitrogen (N) and carbon (C) assimilation and survival rate in resting stages of three S. marinoi strains. Resting stages were incubated with stable isotopes of dissolved inorganic N (DIN), in the form of ¹⁵N-ammonium (NH₄⁺) or -nitrate (NO₃⁻) and dissolved inorganic C (DIC) as ¹³C-bicarbonate (HCO₃⁻) under dark and anoxic conditions for 2 months. Particulate C and N concentration remained close to the Redfield ratio (6.6) during the experiment, indicating viable diatoms. However, survival varied between <0.1% and 47.6% among the three different S. marinoi strains, and overall survival was higher when NO₃⁻ was available. One strain did not survive in the NH₄⁺ treatment. Using secondary ion mass spectrometry (SIMS), we quantified assimilation of labeled DIC and DIN from the ambient environment within the resting stages. Dark fixation of DIC was insignificant across all strains. Significant assimilation of ¹⁵N-NO₃⁻ and ¹⁵N-NH₄⁺ occurred in all S. marinoi strains at rates that would double the nitrogenous biomass over 77–380 years depending on strain and treatment. Hence, resting stages of S. marinoi assimilate N from the ambient environment at slow rates during darkness and anoxia. This activity may explain their well-documented long survival and swift resumption of vegetative growth after dormancy in dark and anoxic sediments.     

Inhibition of Real-Time PCR in DNA Extracts from Aquifer Sediment

Variation in inhibition of real-time PCR was investigated with DNA extracts from 50 aquifer sediment core samples of 5 cm length collected through a 2.5 meter vertical profile across a landfill leachate plume. The inhibition was quantified using an internal control of the green fluorescent protein ( gfp ) gene, which was spiked into the real-time PCR reactions. The inhibition was investigated at two gfp gene concentrations: at 1.7 · 10 ⁷ gfp gene copies/g sediment (5.1 · 10 ⁴ gfp gene copies/PCR reaction) and at 1.7 · 10 ⁵ gfp gene copies/g sediment (5.1 · 10 ² gfp gene copies/PCR reaction). Despite the low TOC content of the sediment (average 0.4 mg C/g dw) the average real-time PCR response was partially inhibited, compared to a reference (pure water), at both high and low gfp concentrations. The relative amplification (reference = 1) was 0.85 ± 0.20 (high) and 0.66 ± 0.23 (low), showing significantly (P < 0.05) stronger inhibition at the lower target gene concentration. The inhibition of the real-time PCR did not show a systematic variation in the vertical profile related to plume position but variations were significant on a small scale of 5–15 cm depth intervals. One of the 50 samples failed to produce a signal with either concentration of the gfp internal control and three other samples inhibited real-time PCR at both high and low gfp concentration. These 4 samples, which were the samples with the highest inhibition, were the only DNA extracts with a visible brown colouration, indicating contents of humic-like substances. Elevated absorbance at 400 nm of these samples also indicated that humic-like substances were responsible for inhibition. However, other factors not associated with either absorbance or TOC may have contributed to the inhibition in less inhibited samples since the variation in real-time PCR response could not be sufficiently explained by absorbance or TOC. The results of this study suggest that an internal control is needed in real-time PCR reactions with DNA from environmental samples due to variation in inhibition to correctly quantify the number of target genes, especially at low target gene concentrations, when dilution of DNA extracts is not practical.     

Minireview: The Potential of Enhanced Manganese Redox Cycling for Sediment Oxidation

Both natural and anthropogenic processes are responsible for excessive organic loading of submerged soils, with detrimental environmental consequences. The often insufficient natural attenuation can be enhanced by exploiting microbial manganese cycles. This review describes how an anoxic oxidation of organic matter with concomitant reduction of MnO ₂ can link up with a reoxidation of the resulting, soluble Mn(II) in oxic layers. The potentially attainable oxidation rates through these natural cycles are of the same order as the organic carbon accumulation rates. The microbiology and physiology of the responsible organisms are discussed, as well as examples of naturally occurring manganese cycles and the possibility to engineer this natural phenomenon.     

Geochemistry and Microbial Populations in Sediments of the Northern Baffin Bay,Arctic

The Northern Baffin Bay between Greenland and Canada is a remote Arctic area restricted in primary production by seasonal ice cover, with presumably low sedimentation rates, carbon content and microbial activities in its sediments. Our aim was to study the so far unknown subseafloor geochemistry and microbial populations driving seafloor ecosystems. Shelf sediments had the highest organic carbon content, numbers of Bacteria and Archaea, and microcosms inoculated from Shelf sediments showed highest sulfate reduction and methane production rates. Sediments in the central deep area and on the southern slope contained less organic carbon and overall lower microbial numbers. Similar 16S rRNA gene copy numbers of Archaea and Bacteria were found for the majority of the sites investigated. Sulfate in pore water correlated with dsrA copy numbers of sulfate-reducing prokaryotes and differed between sites. No methane was found as free gas in the sediments, and mcrA copy numbers of methanogenic Archaea were low. Methanogenic and sulfate-reducing cultures were enriched on a variety of substrates including hydrocarbons. In summary, the Greenlandic shelf sediments contain vital microbial communities adapted to their specific environmental conditions.     

Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments

Microorganisms dwelling in sediments have a crucial role in biogeochemical cycles and are expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting major health risks for human populations. We present here a metagenomic study of the sediment from two harbours on the Mediterranean French coast, l'Estaque and St Mandrier. The first site is highly polluted with arsenic and heavy metals, while the arsenic concentration in the second site is below toxicity levels. The goal of this study was to elucidate the potential impact of the microbial community on the chemical parameters observed in complementary geochemical studies performed on the same sites. The metagenomic sequences, along with those from four publicly available metagenomes used as control data sets, were analysed with the RAMMCAP workflow. The resulting functional profiles were compared to determine the over‐represented Gene Ontology categories in the metagenomes of interest. Categories related to arsenic resistance and dissimilatory sulphate reduction were over‐represented in l'Estaque. More importantly, despite very similar profiles, the identification of specific sequence markers for sulphate‐reducing bacteria and sulphur‐oxidizing bacteria showed that sulphate reduction was significantly more associated with l'Estaque than with St Mandrier. We propose that biotic sulphate reduction, arsenate reduction and fermentation may together explain the higher mobility of arsenic observed in l'Estaque in previous physico‐chemical studies of this site. This study also demonstrates that it is possible to draw sound conclusions from comparing complex and similar unassembled metagenomes at the functional level, even with very low sequence coverage.