The influence of simulated groundwater-movement on the phosphorus release from sediments,as measured in a continuous flow system

An experimental system based on a continuous flow reactor is presented, in which undisturbed sediment cores can be investigated with regard to the release of phosphorus to the overlying water and the characteristics of the interstitial water. In this system the effect of simulated vertical groundwater movement was also studied. The results of three preliminary experiments are shown: 1) undisturbed core, 2) downward migration, 3) upward migration. The latter two experiments showed a rapid loss of phosphorus from the system in contrast to the first experiment. This process was reflected in the phosphorus concentration of the interstitial water.     

A comparison of phosphorus immobilization in sediments of freshwater and coastal marine systems

The extent to which sediments of aquatic systems immobilize or release phosphorus can affect dramatically the P content of overlying waters. Data from 48 different aquatic systems suggests that there may be a major difference between fresh- and salt-water systems in this immobilization. Under oxic conditions (water overlying sediments had dissolved oxygen > 0.5 mg/L) P is strongly immobilized in sediments of most fresh-water systems. In sediments of most salt-water systems P is released from sediments and behaves, essentially, as a conservative tracer of benthic decomposition. This difference in P cycling is large enough to have an influence on the often cited difference in phytoplankton nutrient limitation between fresh- and salt-water systems.     

Arsenic speciation in marine sediments: A comparison between two sequential extraction procedures

ABSTRACT

Arsenic distribution and mobility in marine sediments was investigated by means of total extraction and two sequential extraction procedures i.e. a modified sequential extraction procedure proposed by the European Standard, Measurementand Testing (SM&T) program, formerly the Community Bureau of Reference (BCR) procedure and a five steps sequential extraction based on the Wenzel extraction procedure, called modified Wenzel extraction. Sediments were collected from Cagliari’s harbour and Cagliari’s gulf, in Western Mediterranean Sea, Italy. The modified Wenzel extraction provided a more detailed As binding pattern and turned out to be much more appropriate than the modified SM&T procedure for gaining information regarding the mobilization of As within marine sediments. In the harbour, the largest part of As is contained in the residual fraction. At the contrary, As concentration, which is higher in the Cagliari’s gulf, is primarily associated with amorphous and crystalline hydrous Fe(Mn, Al) oxide. Moreover, this study suggests the possibility to segregate different types of marine sediments depending of human or industrial activities and to trace As contaminated marine sediments to determine the origin of contamination following the percentile of As contained in each extraction steps.     

Lipids as indicators of eutrophication in marine coastal sediments.

Total organic carbon (TOC) and sedimentary lipid contents were investigated in the Bunnefjord, the most inner part of the Oslofjord (Norway). The Bunnefjord is an intermittent anoxic basin and has undergone major eutrophication since the early 1800s. A core from this fjord was collected at 100 m depths under anoxic remnant waters. The first 15 cm corresponding to deposits from 1500 to present were considered for analysis. Lipid classes were quantified by TLC-FID and the molecular composition of selected lipid classes was investigated by GC and GC-MS. Lipids were dominated by two main classes, phospholipids and hydrocarbons. The hydrocarbons represented up to 7.4% of total lipids in the sediment layers covering the period when the most extensive cultural eutrophication took place (1900 to 1970). The higher fluxes of organic carbon produced during this period may have controlled hydrocarbon inputs into the sediments, due to the hydrophobic character of these pollutants. The hydrocarbon concentration reversed toward pre-industrial levels in the more recent layers, which suggests an improvement of the water quality, possibly in response to improved treatment of the sewage in the cities around Bunnefjord.The second most abundant pool of lipids consists in phospholipids, mostly contributed by bacteria. Even though the concentration decreased with depth, their relative proportions to total lipids remained high, mainly in the deepest layers (>80% of total lipids). A rapid decrease of the polyunsaturated fatty acid methyl esters (FAME) from the phospholipid fraction in the upper 4 cm suggests a rapid biodegradation of planktonic inputs and meiofauna. Odd branched fatty acids were more probably contributed by bacteria linked to the high sedimentary hydrocarbon content. The down core distribution of 16:1omega7, 18:1omega7, 18:1omega5 esterified to phospholipids suggests a vertical zonation of the microbial community in relation to redox conditions and available organic matter. In addition to bacterial sulphur biomass, the presence of hopanoic acids in the phospholipids fraction suggests the contribution of bacteria growing on methane. According to the sterol composition, dominated by 4alpha(H)-methylsterols, dinoflagellates represent the major contributors to the organic matter produced in the water column, particularly during the period of extensive eutrophication. Long-chain diols (1,13-C(26), 1,15-C(30) and 1,15-C(32)) and long-chain keto-ols (1,15-C(30) and 1,15-C(32)) are reported for the first time at high latitudes. Their relative distributions (diol and keto-ol indexes of Versteegh et al. [Org. Geochem. 27 (1997)]) have allowed depicting a particular event during the eutrophication period, a freshwater intrusion with inputs of land-derived organic matter. This is in accordance with the downcore distribution of freshwater/terrestrial markers as sitosterol, dehydroabietic acid and iso- and anteiso-pimaric acids. The diol and keto-ol indexes have also underlined the general transition trend from marine to more brackish waters in the Bunnefjord. These last observations provide confidence into the use of these compounds in paleoenvironmental reconstruction.     

DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments

In order to evaluate whether different DNA extraction procedures can affect estimates of benthic bacterial diversity, based on 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique, we compared two in situ lysis procedures (a SDS-based protocol and a commercial kit for DNA recovery) and one cell-extraction protocol on a variety of marine sediments. Despite the two in situ lysis procedures resulted in significantly different DNA yields (highest with the SDS in situ lysis), estimates of bacterial diversity provided a not significantly different ribotype richness, as well as similar values of the Shannon-Wiener (H') and Margalef (d) indices of biodiversity and of evenness (Pielou index, J). Conversely, the cell-extraction procedure for DNA extraction resulted always in a significantly lower ribotype richness and diversity. The analysis of similarities (anosim) among the T-RFLP electropherograms allowed concluding that ribotypes composition did not change significantly using different protocols. However, the analysis of beta-diversity (turnover diversity) revealed that a large number of ribotypes was observed exclusively with one of the three protocols utilized. When unshared ribotypes from in situ lysis and cell extraction were pooled together, total ribotype richness resulted much higher (up to 80%). Our results indicate that estimates of ribotype diversity based on a single protocol of DNA extraction can significantly underestimate the total number of bacterial ribotypes present in the benthic domain. We recommend that future studies will not only integrate different DNA extraction procedures, but also will explore the possibility of integrating two or more different genetic markers in order to increase our ability to detect the actual bacterial diversity in environmental samples.     

An optimized method for the extraction of ancient eukaryote DNA from marine sediments

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo‐communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead‐beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica‐solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size‐selection of low molecular‐weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead‐beating, DNA binding in silica‐solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post‐library LMW size‐selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data‐processing protocol should improve quantitative paleo‐monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.     

Proteinase production by halophilic isolates from marine sediments

Twenty-one strains of spore-forming bacteria were isolated from marine sediments of the Tyrrhenian seaboard (Livorno, Italy) and identified asBacillus licheniformis by their morphological, physiological and biochemical characteristics. All strains were able to grow at 15% NaCl and on media prepared with 100% seawater. In these conditions 75% of the strains were able to produce a bacitracin-like antibiotic and 100% of the strains showed proteolytic activity. Particularly, all strains showed proteinase production with an activity optimum at pH 8.5 and 60°C. Three strains produced high levels of proteolytic activity only when cultured in the presence of seawater.     

Fungi populate deep-sea coral gardens as well as marine sediments in the Irish Atlantic Ocean

Fungi populate deep Oceans in extreme habitats characterized by high hydrostatic pressure, low temperature and absence of sunlight. Marine fungi are potential major contributors to biogeochemical events, critical for marine communities and food web equilibrium under climate change conditions and a valuable source of novel extremozymes and small molecules. Despite their ecophysiological and biotechnological relevance, fungal deep-sea biodiversity has not yet been thoroughly characterized. In this study, we describe the culturable mycobiota associated with the deepest margin of the European Western Continental Shelf: sediments sampled at the Porcupine Bank and deep-water corals and sponges sampled in the Whittard Canyon. Eighty-seven strains were isolated, belonging to 43 taxa and mainly Ascomycota. Ten species and four genera were detected for the first time in the marine environment and a possible new species of Arachnomyces was isolated from sediments. The genera Cladosporium and Penicillium were the most frequent and detected on both substrates, followed by Candida and Emericellopsis. Our results showed two different fungal communities: sediment-associated taxa which were predominantly saprotrophic and animal-associated taxa which were predominantly symbiotic. This survey supports selective fungal biodiversity in the deep North Atlantic, encouraging further mycological studies on cold water coral gardens, often overexploited marine habitats.     

Determination of total phosphorus in lake sediments

Several methods are in use to measure total phosphorus in lake sediments making cross-study comparisons tenuous, and may lead to potential errors in calculating other phosphorus fractions. Four methods in common use in the limnological literature were compared using sediments spanning a range of organic content from 2 to 35% C. No significant differences were found in within-lake comparisons, although a method using persulfate oxidation was highly variable, and this variability was correlated with organic content suggesting inconsistent oxidation. The other methods (combustion, acid digestion with HClO₄, H₂SO₄ + H₂O₂) gave uniformly small variances.     

Nitrogen-fixation associated with the marine blue-green alga,Trichodesmium, as measured by the acetylene-reduction technique

Summary The marine blue-green alga, Trichodesmium, was collected from the Gulf Stream, near Miami, and occurred in two distinct colonial forms both of which reduced acetylene to ethylene. Trichodesmium was more abundant during the summer but its acetylene-reducing potential showed no obvious seasonal variation. Illuminated Trichodesmium reduced acetylene to ethylene equally well either anaerobically or aerobically (20% oxygen). Acetylene-reduction in the dark, however, was oxygen-dependent and was usually 25% or less of the activity recorded in the light. 0.3–1.0 nmoles of ethylene were produced per minute per mg of protein, by illuminated cultures, and these values compare favorably with those recorded for other nitrogen-fixing blue-green algae. However, the possibility that bacteria contributed to the acetylene-reducing activity associated with Trichodesmium was not completely eliminated.Contribution No. 1578 from the University of Miami, Rosenstiel School of Marine and Atmospheric Science, 10 Rickenbacker Causeway, Miami, Florida 33149, U.S.A.     

Available phosphorus in lake sediments in The Netherlands

The amount of phosphorus available to algae in the sediments of four lakes in the western part of the Netherlands has been assessed by means of chemical extraction and bioassay techniques. In addition to direct chemical sediment analyses, extractions were carried out with an NTA column method and a stepwise NH₄ Cl-NaOH-HCI shaking method, the latter supposedly separating the weakly bound, the Fe- and Al-bound and the Ca-bound phosphates in the sediments. Bioassays, with sediment as the sole source of P, were made withScenedesmus quadricauda in modified Skulberg's 28 medium to determine the amount of phosphates available to algae.The average total P concentration of the sediments varied from 0.8 to 3.6 mg P g^–1 dry wt and correlated well with the net external P loading of the lakes. Uptake of P by algae in the bioassays varied from 0.4 to 36% — while NTA extracted 36–69% of the total P. The ratio NH₄Cl extracted/ NaOH extracted/ HCI extracted phosphates is different from lake to lake, although in all lakes the highest extractions (27–62% of total P) are found in the NaOH fraction. However, in the peaty sediments of these lakes, the NaOH step extracted not only the Fe- and Al-bound phosphates but, also, large amounts of humus compounds. Hence, this fraction also contains non-available organic P.The results are related to soil type and chemical characteristics of the sediments, and compared with data from other authors. A positive correlation was found between phosphate available to algae and NTA- and NaOH-extractable P, but the correlation with total phosphorus was higher. Moreover, algal-extractable P proved to be positively correlated with total iron and clay content and negatively with the amount of organic matter.It is concluded that the sediments in the investigated lakes show great variability and that the chemical extraction techniques cannot replace the bioassays to assess the amount of phosphorus available to algae.     

Cryoprotection in hearts as measured by CPK

Rat hearts were treated with a cryoprotectant solution composed of glycerol and DMSO in concentrations ranging from 10–25% $\text{v}\text{v}$, and then frozen in liquid nitrogen. Creatine phosphokinase activity was then measured spectrophotometrically and activities were compared with activities of frozen-untreated hearts, unfrozen-treated hearts, and unfrozen-untreated hearts. Independently freezing or treating increased enzyme activity, but when hearts were treated and then frozen, activity diminished below that of the unfrozen-untreated group. Evidence suggests (1) DMSO-glycerol solution either has a toxic effect that increases with concentration and freezing additionally aggravates this effect, or the concentrations of cryoprotectants used do not adequately protect the tissue during freezing which causes damage to the contractile mechanism; and (2) the anoxic state of the tissue causes depletion of ATP and creatine phosphate such that creatine phosphokinase is inactive or not able to function.     

Bacterial diversity in marine hydrocarbon seep sediments

Marine seeps introduce significant amounts of hydrocarbons into oceans and create unusual habitats for microfauna and -flora. In the vicinity of chronic seeps, microbes likely exert control on carbon quality entering the marine food chain and, in turn, hydrocarbons could influence microbial community composition and diversity. To determine the effects of seep oil on marine sediment bacterial communities, we collected sediment piston cores within an active marine hydrocarbon seep zone in the Coal Oil Point Seep Field, at a depth of 22 m in the Santa Barbara Channel, California. Cores were taken adjacent to an active seep vent in a hydrocarbon volcano, on the edge of the volcano, and at the periphery of the area of active seepage. Bacterial community profiles were determined by terminal restriction fragment length polymorphisms (TRFLPs) of 16S ribosomal genes that were polymerase chain reaction (PCR)-amplified with eubacterial primers. Sediment carbon content and C/N ratio increased with oil content. Terminal restriction fragment length polymorphisms suggested that bacterial communities varied both with depth into sediments and with oil concentration. Whereas the apparent abundance of several peaks correlated positively with hydrocarbon content, overall bacterial diversity and richness decreased with increasing sediment hydrocarbon content. Sequence analysis of a clone library generated from sediments collected at the periphery of the seep suggested that oil-sensitive species belong to the gamma Proteobacteria and Holophaga groups. These sequences were closely related to sequences previously recovered from uncontaminated marine sediments. Our results suggest that seep hydrocarbons exert a strong selective pressure on bacterial communities in marine sediments. This selective pressure could, in turn, control the effects of oil on other biota in the vicinity of marine hydrocarbon seeps.     

Prokaryotic diversity in Zostera noltii-colonized marine sediments

The diversity of microorganisms present in a sediment colonized by the phanerogam Zostera noltii has been analyzed. Microbial DNA was extracted and used for constructing two 16S rDNA clone libraries for Bacteria and Archaea. Bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. Eight major lineages of the Domain Bacteria were represented in the library. The most frequently retrieved bacterial group (36% of the clones) was delta-Proteobacteria related to sulfate-reducing bacteria. The second most abundant group (27%) was gamma-Proteobacteria, including five clones closely related to S-oxidizing endosymbionts. The archaeal clone library included members of Crenarchaeota and Euryarchaeota, with nine different sequences among the 15 analyzed clones, indicating less diversity when compared to the Bacteria organisms. None of these sequences was closely related to cultured Archaea organisms.     

Determination of virus abundance in marine sediments

In this study, we optimized procedures to enumerate viruses from marine sediments by epifluorescence microscopy using SYBR Green I as a stain. The highest virus yields from the bulk of the sediments were obtained by utilizing pyrophosphate and 3 min of sonication. The efficiency of extraction benthic viruses by pyrophosphate-ultrasound treatment was about 60% of the extractable virus particles. Samples treated with nucleases had increased virus counts, suggesting a masking effect of extracellular DNA. No significant differences were observed between virus counts obtained by epifluorescence microscopy and transmission electron microscopy. Both formaldehyde and glutaraldehyde gave significant reductions of virus counts after only 24 h of sediment storage, but no further loss occurred after 7 days.     

Anaerobic microbial methanol conversion in marine sediments

Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.