Further Analysis of Anammox Bacterial Community Structures Along an Anthropogenic Nitrogen-Input Gradient from the Riparian Sediments of the Pearl River Delta to the Deep-Ocean Sediments of the South China Sea

The community structures of anammox bacteria in sediments along an anthropogenic inorganic nitrogen input gradient were further delineated with the newly available information incorporated. Anammox bacterial 16S rRNA gene-amplified sequences retrieved from riparian sediments of the Pearl River, Mai Po coastal wetland, and the South China Sea (SCS) sediments were compiled, compared and analyzed. Results indicated that the community structures of anammox bacteria varied from the upstream of the Pearl River to deep-ocean sediment of the SCS along the anthropogenic input grandient. Mai Po wetland had the most diverse anammox bacteria, followed by the shallow SCS, deep SCS and the Pearl River. Genera of the anammox bacteria Kuenenia and Brocadia showed higher proportion in the riparian sediments of the Pearl River, while those of Kuenenia and Scalindua dominated the Mai Po coastal wetland. The Scalindua subclusters showed apparent segregation in coastal wetland (S. zhenghei-III and S. wagneri), shallow SCS (S. zhenghei-I and S3) and deep SCS (S. zhenghei-I, S2 and S. arabica). Pearson correlation analysis indicated nitrogen species [NH₄⁺ and ∑(NO₂^?+NO₃^? )] negatively correlated with the diversity indices of anammox bacteria. Canonical correspondence analysis (CCA) showed that salinity, inorganic nitrogen [NH₄+, ∑(NO₂^?+NO₃^?)], and ratio of NH₄⁺/∑(NO₂^? +NO₃^?) significantly affected the bacterial community compositions. Results collectively support that the community composition of anammox bacteria can serve as a bio-indicator to the anthropogenic terrestrial N input or pollution.     

Indicator value of midge larvae (Diptera: Nematocera) in shallow boreal lakes with a focus on habitat,water quality,and climate

Identification of indicator species is invaluable for lake management and long-term environmental change assessments. In this study, multi- and intralake datasets were investigated for their fossil midge assemblages (mostly Chironomidae) in the surface sediment layers representing the modern faunal composition. The aim was to examine taxon-specific responses to selected key variables and to assign indicator taxa for these environmental factors. Taxon-specific optima and tolerances were calculated and the significance of a particular environmental variable in explaining the distribution patterns was tested for each taxa. The results showed that numerous taxa had significant relationship with the environmental variables of interest. Thus, several midge indicator taxa were identified for the key variables. For the interest of palaeolimnology, the present results imply that when reconstructing long-term changes in a single environmental variable, variability in other regional, local or in-lake variables can distort the inference due to the complex taxon-specific responses to multiple environmental factors.     

Metal Speciation and Contamination in Dredged Harbor Sediments from Kaohsiung Harbor,Taiwan

The status of metal speciation and contamination of sediments in Kaohsiung Harbor, Taiwan, was evaluated by a five-step sequential extraction procedure (exchangeable, carbonate, Fe–Mn oxides, organic matter, and residual). Eleven dredged sediment samples from various locations in the harbor were characterized in terms of heavy metals, grain size, and total organic carbons. Results showed that Hg, Pb, Cd, Cr, Cu, Zn, Ni, and Mn had different species composition patterns. The degree of sediment contamination was determined for an individual contamination factor (ICF) and a global contamination factor (GCF); results showed that Kaohsiung Harbor had a high potential risk for Pb, Cd, Cr, and Cu. Based on GCF values, the results showed that those stations, located in the vicinity of the river mouth, fish port, and industrial sites, contributed high potential risk to Kaohsiung Harbor. The potential risk of heavy metals to the environment was assessed for risk using the risk assessment code (RAC) and results showed that Pb, Cd, Zn, and Mn generally created a medium to high risk, and Hg, Cr, Cu, and Ni generally created a low to medium risk.     

THE DETERMINATION OF CHLOROPHYLL a IN WATER CONTAINING SEDIMENT

SUMMARY

The presence of sediment at concentrations of 0,2% by mass in water samples significantly lowered the amount of chlorophyll a that could be measured. Two types of sediment differed in their ability to lower the chlorophyll a concentration. The chemically more active sediment had a marked depressive effect on the chlorophyll a concentration and the relationship between chlorophyll a and cell numbers in the samples was non-linear. It is recommended that the use of chlorophyll a as an indicator of biomass in water containing sediment should be approached with care.     

Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO₂) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pH_T 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pH_T 8.10). At pH_T 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pH_T declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms.     

Microphytobenthic dynamics in a Wadden Sea intertidal flat – Part II: Seasonal and spatial variability of non-diatom community components in relation to abiotic parameters

The microphytobenthos colonizing the intertidal flats forms an important component of the Wadden Sea. Ten sampling points along a 1-km transect were studied in a fringe area of the Solthörn tidal flat, southern North Sea, in order to determine seasonal differences in the microphytobenthos. An accompanying paper deals with the major component of the flora, the diatoms; here we, focus on the minor taxonomic groups. From May 2008 to May 2009 surface sediments were collected during low tide. Variation of environmental factors as well as microphytobenthic density (abundance and chlorophyll a) were monitored. The area investigated was a mixed-sediment mudflat, with a gradient from coarse to fine. Highest biomass was obtained in summer 2008 with 215.9?±?12.6?mg chlorophyll a m^–2. In late autumn the chlorophyll a concentration decreased continuously at all investigated stations. Lowest values were detected in December 2008. Species abundances varied considerably both along the transect and seasonally, depending on species-specific requirements as well as hydrodynamic conditions (tidal currents). Higher densities of benthic pro- and eukaryotic microalgae were observed in sites characterized by fine sediments. Apart from the diatoms, the most abundant microphytobenthic group was the cyanophytes. Coccoid cyanophytes, mainly Merismopedia sp., were most abundant during summer, with cell numbers up to 5.72?×?10⁶ cells cm^?2, while diatoms dominated in winter, spring and autumn. Filamentous cyanophytes, particularly Microcoleus chthonoplastes, were most abundant during autumn, while coccoid chlorophytes (spring: Chlorococcum submarinum, Crucigenia tetrapedia, Tetraselmis suecica), euglenophytes (summer: Euglena obtusa), dinophytes (autumn: Amphidinium operculatum, A. herdmanii) and cryptophytes (autumn: Hillea marina, Hemiselmis virescens) contributed to the microphytobenthos during warmer seasons. The statistical analysis confirmed that the composition of the microphytobenthos was related to sediment features and to characteristics of particular seasons.     

Calcareous dinoflagellate cyst distributions in surface sediments from upwelling areas off NW Africa, and their relationships with environmental parameters of the upper water column

Only very few studies have focussed on the spatial distribution and ecology of calcareous dinoflagellate cysts (dinocysts) in upwelling areas. Here, distributions of individual calcareous dinocyst species in surface sediment samples from the coastal upwelling zone off NW Africa and their relationships with known environmental parameters of the (sub-)surface waters have been analysed in order to enhance our knowledge on their modern distribution patterns and to determine the ecological significance and palaeoenvironmental reconstruction potential of each calcareous dinocyst species within this exemplary high-productivity region. In addition to calculating relative cyst abundances, well-constrained sedimentation rates have allowed the calculation of dinocyst accumulation rates (cysts cm^− 2 ka^− 1) for most of the surface sample positions, thus providing a much more accurate estimation of actual calcareous dinocyst production in the upper water column than could be warranted in similar studies so far. Distinct differences in the geographic distribution patterns of nine species were observed. In general, high accumulation rates of calcareous dinocysts were found around and south of 29°N and offshore the westernmost Canary Island La Palma, with slightly lower accumulation rates in the upwelling-influenced areas off Cape Yubi and in the upwelling filament area off Cape Ghir. Multivariate ordination techniques were applied in order to compare the cyst accumulation rates of individual species with physical parameters (temperature, salinity, density, mixed layer depth) and the trophic state (nitrate, phosphate and chlorophyll concentrations) of the overlying (sub-)surface waters. All species were found to relate significantly to one or more of the environmental parameters, partly confirming previous results on cyst ecology but also providing new information which will be useful for future palaeoenvironmental reconstructions within upwelling areas.     

Levels of Metallic Cations in the Surface Sediments in the Vicinity of the Três Marias Dam Lake (Brazil) Determined by ICP-MS and Microwave Sample Preparation

The presence of toxic elements in sediments is critical in the State of Minas Gerais, which is an important mining area in Brazil. In this work, Ag, As, Ba, Cd, Co, Cr, Cs, Cu, Ga, In, Li, Ni, Pb, Sr, Tl, V and Zn were determined in samples of sediments by ICP-MS after microwave sample preparation. The samples of surface sediments were collected from the vicinity of Três Marias Dam, Brazil. The results using HNO₃+HF+H₃BO₃ and a microwave oven presented adequate precision and accuracy. The accuracy of the method was determined using different certified reference materials. Most of the results agreed within a 95% confidence level. The concentrations of the investigated analytes were below the values of Threshold Effect Level (TEL) and Probable Effect Level (PEL), with the exception of cadmium, chromium, copper, nickel, and zinc. High concentrations of Cr were observed at all the points, Cu and Ni at point SF 011, Cd at point SF 015, and Zn at points SF 011, SF 013, and SF 015. The results demonstrate that the main pollutants were Zn and Cr. Metal mining and processing are potential sources of contamination, since the investigated points are located in areas known for those activities.     

Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.

Strain EB01^T sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes.     

Relationships between DOC bioavailability and nitrate removal in an upland stream: An experimental approach

The Catskill Mountains of southeastern New York State have among thehighest rates of atmospheric nitrogen deposition in the United States. Somestreams draining Catskill catchments have shown dramatic increases in nitrateconcentrations while others have maintained low nitrate concentrations. Streamsin which exchange occurs between surface and subsurface (i.e. hyporheic) watersare thought to be conducive to nitrate removal via microbial assimilationand/ordenitrification. Hyporheic exchange was documented in the Neversink River inthesouthern Catskill Mountains, but dissolved organic carbon (DOC) and nitrate(NO₃ ^–) losses along hyporheic flowpaths werenegligible. In this study, Neversink River water was amended with natural,bioavailable dissolved organic carbon (BDOC) (leaf leachate) in a series ofexperimental mesocosms that simulated hyporheic flowpaths. DOC and N dynamicswere examined before and throughout a three week BDOC amendment. In addition,bacterial production, dissolved oxygen demand, denitrification, and sixextracellular enzyme activities were measured to arrive at a mechanisticunderstanding of potential DOC and NO₃ ^– removalalong hyporheic flowpaths. There were marked declines in DOC and completeremoval of nitrate in the BDOC amended mesocosms. Independent approaches wereused to partition NO₃ ^– loss into two fractions:denitrification and assimilation. Microbial assimilation appears to be thepredominant process explaining N loss. These results suggest that variabilityinBDOC may contribute to temporal differences in NO₃ ^–export from streams in the Catskill Mountains.