Community Metabolism in Microbial Mats: The Occurrence of Biologically-mediated Iron and Manganese Reduction

Community metabolism and nutrient, iron (Fe) and manganese (Mn) cycling were examined in two intertidal, marine, microbial mat communities during short (4–5 days) incubations in closed, flow-through microcosms. Sediment microcosms were incubated under either light (light–dark cycles) or dark (continuous darkness) conditions to assess the effect(s) of photosynthetic oxygen production and microalgal activity on nutrient, Fe and Mn cycling. The effects of chemical redox reactions between reduced sulphur (S), Fe and Mn cycling were examined by blocking sulphate reduction, and reduced S production, with 25 mM molybdate while incubating under dark conditions.In light-incubated microcosms, negligible fluxes of nutrients (nitrogen and phosphorus) and trace metals were observed. A substantial sediment–water flux of reduced Fe (Fe²⁺) and Mn (Mn²⁺) was observed in microcosms incubated under continuous darkness; highest fluxes were observed in molybdate-amended microcosms. At both sites, biologically-mediated redox reactions accounted for a substantial (>50%) portion of the Fe²⁺and Mn²⁺flux. Both microbial mat communities exhibited similar rates of gross photosynthetic oxygen (O₂) production, but dramatically different rates of net benthic O₂flux. Distinct patterns of net O₂production and trace metal cycling arose from differences in either trace metal oxide availability or reactivity (mineralogy), organic carbon mineralization rates, or sediment characteristics (porosity). Variations in the microbial community responsible for trace metal cycling could have also contributed to the pattern. The present data illustrate that chemically-mediated redox reactions between metal oxides and reduced S complicate interpretation of Fe and Mn fluxes, underscoring the need to separate chemical and biological reactions when attempting to determine the role of biological trace metal reduction in organic carbon oxidation.     

Sediment organic matter composition and dynamics in San Francisco Bay, California, USA: Seasonal variation and interactions between water column chlorophyll and the benthos

Sediment and water column data from four sites in North, Central and South San Francisco Bays were collected monthly from November 1999 through November 2001 to investigate the seasonal variation of benthic organic matter and chlorophyll in channel sediments, the composition and quality of sediment organic matter (SOM), and the relationship between seasonal patterns in benthic organic matter and patterns in water column chlorophyll. Water column chlorophyll peaked in the spring of 2000 and 2001, characteristic of other studies of San Francisco Bay phytoplankton dynamics, however an unusual chlorophyll peak occurred in fall 2000. Cross-correlation analysis revealed that water column chlorophyll at these four channel sites lead sediment parameters by an average of 2 to 3 months. Sediment organic matter levels in the San Francisco Bay channel showed seasonal cycles that followed patterns of water column production: peaks in water column chlorophyll were followed by later peaks in sediment chlorophyll and organic matter. Cyclical, seasonal variations also occurred in sediment organic matter parameters with sediment total organic carbon (TOC) and total nitrogen (TN) being highest in spring and lowest in winter, and sediment amino acids being highest in spring and summer and lowest in winter. Sediment chlorophyll, total organic carbon, and nitrogen were generally positively correlated with each other. Sediment organic matter levels were lowest in North Bay, intermediate in Central Bay, and highest in South Bay. C:N ratio and the ratio of enzyme hydrolyzable amino acids to TOC (EHAA:TOC) data suggest that SOM quality is more labile in Central and northern South Bay, and more refractory in North Bay and southern South Bay.     

Oxygenation of intertidal estuarine sediments by benthic microalgal photosynthesis

A mathematical model was used to define the relative importance of microalgal photosynthesis and physical processes in the formation and maintenance of the oxygenated zone on the surface of intertidal estuarine sediments. Manometric measurements of sediment uptake and release showed that gross oxygen production usually exceeded aerobic community respiration. Polarometric microprobes measured vertical oxygen distributions in the sediment. Surface levels of oxygen ranged from 200% saturation in summer to 70% in winter. Profiles and flux measurements allowed calculation of sediment diffusion coefficients. Empirical evaluation of the terms of the model showed that epipelic diatom photosynthesis as a source of oxygen at low tide may exceed atmospheric diffusion by an order of magnitude. On a diurnal and seasonal basis, however, the diatoms may be less important to the oxygenation process than the physical forces of the tide.     

Trace elements and polycyclic aromatic hydrocarbons (PAHs) concentrations in deep Gulf of Mexico sediments

The concentrations of polycyclic aromatic hydrocarbons (PAHs) and trace elements were determined for surface (top 2 cm) sediment samples collected during the deep Gulf of Mexico benthos (DGoMB) study .These elements and compounds are known to be toxic to organisms at high concentrations and may affect biological communities. There is no indication of major anthropogenic input of the elements Be, Co, Cr, Fe, Si, Tl, V, K, Mg, Ca, Sr and Zn, based on normalization to Al. The concentrations of these metals in the sediment are a function of the relative amounts of trace-metal-rich Mississippi River-derived silicate material and trace-metal-poor plankton-derived carbonate. This is not true for the elements Ba, Ni, Pb, Cd, As, Cu and Mn, whose concentrations show considerable scatter when normalized to Al and a general enrichment. On a normalized basis, Mn is enriched 5–10 fold, Cu and Ni 2–3 fold and Pb 2 fold over Mississippi River-derived material. These enrichments are likely the result of remobilization of metals from depths in the sediment column where reducing conditions exist. The Ba concentrations at selected sites are higher than those of average clay-rich sediments, but are typical of sediments from near oil well platforms in the northern Gulf of Mexico. In the case of Ba, it seems likely that the enrichments, as high as a factor of 10, are due to disposal of oil well drilling mud. The Ba-enriched samples are from the three shallowest water sites in the Mississippi Trough (sites MT1, 2 and 3) and from site C1 and WC5. All are in an area of intense petroleum exploration and development. PAH concentrations are also elevated at MT1, MT3 and C1. The total PAH concentration ranged from not detected (ND) to 1033 ng/g with a mean of 140 ng/g. Even at the sites most enriched in PAHs and trace elements, the concentrations are not at the levels expected to adversely affect the biota. However, these predicted non-effects are based on research using mostly near-shore estuarine species, not on the indigenous species at the sampling sites.     

Meiofauna and chlorophyll associated with Beggiatoa mats of a natural submarine petroleum seep

Previous studies at the Isla Vista oil seep have suggested that meiofauna, particularly nematodes, might be an important factor in explaining macrofaunal enrichment by making bacterial biomass available to the benthic food web. To explore this possibility, we analyzed meiofaunal abundance and microalgal pigments inside and just outside of bacterial mats at this natural oil seep.The bacterial mats occur where crude oil and natural gas are actively seeping out of the sediment; cores from within the mats contained a great deal of crude oil (up to 50 %). Meiofaunal abundances were the same in and out of the bacterial mats (averaging 1·-9 × 10⁶ individuals m^-2). However, dramatic changes in community structure were noticed. Harpacticoids made up 19 % of the fauna outside the mats but only 1 % inside. Pigment concentrations were also the same in both sites with phaeophytin dominating chlorophyll (120 compared to 29.8 mg m^-2). The variance of both microalgal pigments and meiofauna was much greater inside than outside, suggesting that the bacterial mats are a more heterogeneous environment.Although the effect of crude oil toxicity is not clear, the high abundances of microbial and meiofaunal biomass support the hypothesis of benthic enrichment via microbes and meiofauna.     

Microbial colonisation of artificial and deep‐sea sediments in the Arctic Ocean

Although environmental factors such as grain size and organic carbon content may influence the distribution of microbes in marine sediments, there has been little experimental study of the topic to date. To investigate how those sediment variables affect microbial colonisation under in situ conditions, deep‐sea sediments and artificial sediments (glass beads, sands) were incubated in the Arctic deep sea at 2500 m water depth with or without chitin, one of the most important carbon polymers in marine environments. Microbial abundance, biomass, chitobiase activity and changes in community structure were monitored after 7 days and 1 year. In control sediments without chitin addition, no significant changes in microbial abundance, biomass and activity were observed after 1 year. In the presence of chitin, however, considerable increases in these parameters were recorded in all three sediment types tested. Regardless of chitin addition, natural deep‐sea sediments were always associated with higher values of microbial abundance, biomass and activity compared with artificial sediments. Sediment type was always found to be the most significant factor explaining variation in enzymatic activity and bacterial community structure as compared to the effects of chitin amount, incubation time, and changes in cell number or biomass. Overall, this is the first in situ study that has addressed the effects of multiple factors and their interactions on abundance, biomass, activity and community structure of microbial communities in the deep Arctic Ocean.     

Sterols as markers of sewage contamination in a tropical urban estuary (Guanabara Bay, Brazil): space–time variations

Guanabara Bay, located adjacent to Rio de Janeiro in Brazil, is highly contaminated by substances derived from domestic and industrial effluents as well as from agricultural runoff. In the present work, sedimentary coprostanol and other faecal sterols were used to investigate historical trends in sewage contamination. Sediment cores were collected from eight different (and characterized) locations in the bay and were sectioned into dated segments. Organic carbon was determined by dry combustion and sterols were separated and quantified by GC/MS. The space-distribution of organic carbon and faecal sterol concentrations generally coincided with the presence of known pollution sources. Concentrations of coprostanol as high as 40 μg g⁻¹ were found, indicating areas of severe sewage contamination. Faecal sterol ratios, commonly used as tools to investigate contamination in temperate environments, however, were found to have limited applicability to this tropical estuarine system, probably due to the influence of intensive primary production and microbial processes.     

Seasonal and spatial variation in the denitrifying activity in estuarine and lagoonal sediments

We have elucidated the seasonal and spatial variation in the potential denitrifying activity in estuarine and coastal lagoonal sediments in Lakes Shinji and Nakaumi, Japan. The denitrifying activity increased from summer through autumn and was positively correlated with the temperature of the overlying water at all sites except one, where the bottom was always more reductive than at the other sites and there was no NO₃ ⁻ as a substrate for denitrification from spring to autumn. Moreover, the relationship between the denitrifying activity and the distance from the sea showed different trends in estuarine and lagoonal sediments. These spatial differences indicate that different factors regulate the denitrification in estuarine and lagoonal sediments. Denitrifying activity in estuarine sediment was regulated by the discharge of freshwater containing NO₃ ⁻ or organic matter, while in the lagoonal sediments the occurrence of nitrification via the intrusion of oxic seawater into the reductive sediment appears to be a key requirement for the process of denitrification. Therefore, the denitrifying activity in the lagoonal sediment appears to be greater near the sea. Water intrusion is one of the key factors controlling denitrification in coastal marine ecosystems by affecting the supply of substrate available for denitrification.     

Cellular responses of oysters, Crassostrea virginica, to metal-contaminated sediments

Elevation of metal concentrations in coastal environments associated with anthropogenic enrichment pose a significant threat to estuarine organisms. The purpose of this study was to evaluate the relationships between cellular responses that may be potentially valuable as indicators of chronic stress and metal-contaminated sediments. For these studies, hatchery-reared juvenile oysters were deployed in situ at 15 sites for approximately 1 month around Charleston Harbor, SC. The effects on lysosomal destabilization and glutathione concentrations were determined; and the relationships between the cellular responses and sediment metal concentrations were described. Both single metal and multiple metal parameters (based on total metal concentrations, aluminum normalizations, and summed sediment quality guidelines) were considered. Generally, significant correlations were observed for individual metal analytes and multiple metal parameters. Since many of the individual metal analytes covary, the responses may reflect overall contaminant loading rather than responses to individual metals. Methods for estimating overall contaminant loading based on multiple analytes provide a more realistic estimate of potential adverse effects.     

Sediment grain size measurements are affected by site-specific sediment characteristics and analysis methods: implications for environmental monitoring

Sediment grain size, and specifically changes in the percent mud content (i.e. the fraction <63?µm) over time is often used as an indicator of estuarine environmental health. Using sediment samples from three distinct estuarine systems, we determined that different analytical methods (laser diffraction and wet sieving) gave significantly different results in terms of percent mud content. These differences are also ecologically meaningful when considering the influence of mud on estuarine macrofauna. We propose an approach to measuring sediment grain size termed Environmentally Available Sediment (EAS), which advocates for the measurement of the sediment that biota are directly exposed to. For the purposes of environmental monitoring, it is also essential to monitor sediment grain size in a repeatable way which is likely to be achieved using consistent (or no) pre-treatment and the use of a measurement technique that is unlikely to change over time, e.g. wet sieving.     

Analysis of sediment stability on the Peru‐Chile continental slope

Abstract

Potential sediment mass movement was analyzed at ten locations on the continental slope off Peru and northern Chile, using samples obtained from up to 3 m below the seafloor. Shear strength parameters were obtained from consolidated‐undrained triaxial compression tests. Sediment behavior in these tests reflects the influence of organic matter, which is concentrated in the slope deposits by coastal upwelling. High water content of the organic‐rich sediments and the high de‐formability of organic matter contribute to the prevalent ductile behavior. Aggregation of clays by organic matter is apparently responsible for the high friction angles, up to 44°, displayed by the slope deposits. Sediment stability was assessed using infinite slope analyses. These analyses indicate that gravitational forces alone are not sufficient to cause sediment failure at any of the slope locations. Sediment accumulation on the slope is not rapid enough to generate excess pore pressure and reduce the resistance to gravitational sliding. Effects of earthquakes on slope stability were evaluated by modeling earthquake‐induced inertia forces as static forces and estimating pore pressures developed during cyclic loading. This analysis shows that sediments of the lower slope off Peru possess the highest susceptibility to failure during earthquakes. Earthquake accelerations on the order of 0.2 gravity are sufficient to trigger slumping at all ten slope locations. Indirect evidence suggests that creep and mass flows initiated at shallower water depths are factors that might contribute to sediment failure on the slope.     

Benthic microalgal biomass in sediments of Onslow Bay, North Carolina

Sediment samples were collected at stations along cross-shelf transects in Onslow Bay, North Carolina, during two cruises in 1984 and 1985. Station depths ranged from 11 to 285 m. Sediment chlorophyll a concentrations ranged from 0·06 to 1·87 μg g⁻¹ sediment (mean, 0·55), or 2·6–62·0 mg m². Areal sediment chlorophyll a exceeded water column chlorophyll a a at 16 of 17 stations, especially at inshore and mid-shelf stations. Sediment ATP concentrations ranged from 0 to 0·67 μg g⁻¹ sediment (mean, 0·28). Values for both biomass indicators were lowest in the depth range including the shelf break (50–99 m). Organic carbon contents of the sediments were uniformly low across the shelf, averaging 0·159% by weight. Photography of the sediments revealed extensive patches of microalgae on the sediment surface.Our data suggest that viable benthic microalgae occur across the North Carolina continental shelf. The distribution of benthic macroflora on the North Carolina shelf indicates that sufficient light and nutrients are available to support primary production out to the shelf break. Frequent storm-induced perturbations do not favour settling of phytoplankton, an alternative explanation for the presence of microalgal pigments in the sediments. Therefore, we propose that a distinct, productive benthic microflora exists across the North Carolina continental shelf.     

Synthetic shorelines in New Zealand? Quantification and characterisation of microplastic pollution on Canterbury's coastlines

Microplastics are persistent environmental contaminants found in marine environments worldwide. Microplastic particles isolated from coastlines in the Canterbury region of New Zealand were quantified and characterised. Sediment samples were collected from 10 locations representing exposed-beach, estuarine and harbour environments in both urban and non-urban settings. Particles were isolated from sediments using an NaCl density-separation procedure and quantified and characterised with a combination of optical/fluorescence imaging and micro-Raman spectroscopy. Microplastics were detected at eight out of 10 locations, at concentrations ranging from 0–45.4 particles kg^?1 of dry sediment. The majority of microplastics were identified as polystyrene (55%), polyethylene (21%) and polypropylene (11%). Microplastic concentrations in exposed-beach environments were significantly greater than in harbour and estuarine environments.     

Postulated responses of phytoplankton and bacteria to predicted increases of inorganic suspended sediments in oligotrophic lakes

We establish the relationships between concentrations of inorganic suspended sediments (ISS) on light, nutrients, phytoplankton, and bacteria in three oligotrophic lakes (four sites) and we use these relationships to predict the impacts of increasing concentrations of ISS on the biomass and productivity of phytoplankton and bacteria in the lakes. Increased concentrations of ISS contributed little available nutrient to the lakes. The relationships between ISS and underwater light attenuation differed among lakes because of variation in sediment size‐structure, and composition. Only at the site with the highest ISS concentrations and a relatively deep mixing depth, were phytoplankton apparently light‐limited and, thus, predicted to decline with increased ISS concentrations. In contrast to previously published studies, bacterial abundance and production were not highly correlated to suspended sediment concentrations in these lakes. However, bacterial biomass, productivity, and specific productivity were more strongly correlated to phytoplankton production. As a result of light limitation and stimulation of bacterial production, increases in ISS concentrations are not predicted to significantly shift the metabolic balance in the planktonic ecosystem of three of the sites towards greater heterotrophy. Where light limits phytoplankton production, increases in ISS are predicted to reduce the productivity of both phytoplankton and bacteria by direct inhibition of phytoplankton production, again without a large shift towards greater importance of the microbial loop. By reducing phytoplankton production and inhibiting larger cladoceran grazers, we predict that high concentrations of ISS will reduce available energy and its flow up the food chain.     

Variations in the composition of particulate organic matter in a time-series sediment trap

A time-series sediment trap was used to collect material for organic geochemical analyses as part of the Sediment Trap Intercomparison Experiment. The flux of particulate matter was more likely related to a change in current direction during the course of the experiment than to small-scale changes in surface productivity. Of the compounds measured, the n-alkanes reflected this change most dramatically, decreasing with the change in current direction.Amino acid and lipid components were measured in the samples. Amino acids made up 15–35% of the total organic carbon flux and 35–75% of the total organic nitrogen flux collected in the traps. Specific amino acids indicative of bacterial biomass or activity suggested that microbial growth occurred in the traps, probably as a result of incomplete poisoning by NaN₃. However, the effect of this growth on the bulk composition of particulate matter appeared to be minimal.The amino acid distribution of particulate organic material collected by large volume filtration (LVF) was not significantly different from the sediment trap material, except that the LVF material did not appear to be affected by bacterial growth.     

Linking pollution induced community tolerance (PICT) and microbial community structure in chronically metal polluted estuarine sediments

We tested the ability of pollution induced community tolerance (PICT) to detect the effects of chronic metal pollution on estuarine sediment microbial communities, along a gradient spanning two orders of magnitude in metal concentrations. In tandem, we investigated the associated microbial community structure using terminal restriction fragment length polymorphism (T-RFLP). Tolerance of microbes to Cu, measured as IC50 (inhibitory concentration 50%), was strongly correlated with pore water Cu concentration (r(2)=0.842). No strong correlation existed for other metals tested, highlighting the ability of PICT to identify the pollutant causing a toxic effect. There was no correlation between microbial community structure and community tolerance to metals tested, but analysis of community structure did provide some information on reasons for observed PICT response. PICT methodology used here provided a greater strength and consistency of association with pollutant concentration compared to microbial community structure and can be recommended as a sensitive indicator of metal pollution on estuarine sediment microbial communities.     

ENSO as a natural experiment to understand environmental control of meiofaunal community structure

The sediments of the Bay of Concepción and the adjacent shelf underlie one of the most productive upwelling areas in the SE Pacific margin. Reports on factors controlling meiofaunal community structure in these kinds of organic‐rich and oxygen‐deficient habitats are scarce in the literature. In this study, five sites along a transect from the mid‐Bay of Concepción (27 m) to the outer shelf (120 m) were studied on fives dates (May, August, November 1997, and March and May 1998) in order to assess the dynamic relationships between sedimentary organic matter and metazoan meiofauna. The sampling period coincided with the 1997–1998 El Niño event. Sediment parameters investigated were the redox potential discontinuity depth, photosynthetic pigment concentrations (chlorophyll a and phaeopigments), organic carbon, nitrogen, total lipids, carbohydrates, and proteins. In general, lowest values of meiofauna abundance and biomass were found within the naturally eutrophic Bay of Concepción and towards the shelf break, while maximum values occurred at intermediate depths. During the whole period, the meiofaunal abundance was negatively correlated with the concentration of most of the biochemical components of organic matter, as well as with the sediment phaeopigment content. However, positive correlations were found with chlorophyll a derived indices and with bottom‐water oxygen content. Most of the sediment parameters displayed a seasonal cycle, but towards the beginning of 1998, an effect of the 1997–1998 El Niño was evident. Typical austral‐summer (i.e. oxygen‐deficient) conditions did not develop, and sedimentary parameters reflected a decreased input of phytodetritus. Along the transect, the magnitude of this effect on meiofauna varied among sites. An overall positive response, in terms of meiofaunal abundance was observed, probably due to the amelioration of low oxygen conditions in the sediment.     

Dissolved Vanillin as Tracer for Estuarine Lignin Conversion

Lignin is produced only by vascular plants and therefore can be used as a tracer for terrestrial organic carbon input to the estuarine and marine environments. Lignin measurements have been done by analyses of the oxidation products such as vanillin or 4-hydroxybenzaldehyde.In the Elbe Estuary, free dissolved vanillin was analysed in order to test whether such measurements yield information on terrestrial carbon inputs into the Estuary and on the vanillin derived from lignin oxidation. In the period 1990–1992, concentrations of dissolved vanillin in the Elbe ranged from 0 to 60 μg l⁻¹(mean: 8 μg l⁻¹). Higher values were found in areas of increased microbial activity such as the turbidity zone and the river mouth where the water chemistry is influenced by large tidal flats. No correlation was found between dissolved vanillin and suspended matter concentrations, although lignin is normally associated with suspended particulate matter, nor was a covariance seen between dissolved vanillin and the terrestrial carbon inputs into the Estuary. Apparently, biological conversion of lignin was faster than the transport processes, and local sources were more dominant for the vanillin concentration than riverine sources. The dissolved vanillin turnover was fast and, consequently, a significant amount of lignin may be converted within an estuary. In sediments from the Estuary, the concentrations of dissolved vanillin were similar to those found in the water phase and showed no clear vertical profile. The sediment is unlikely to be the source for vanillin.     

Sulphide mineralisation in the deep sea hydrothermal vent polychaete, Alvinella pompejana: implications for fossil preservation

Hydrothermal vent fauna, particularly vestimentiferan and polychaete worm tubes, are occasionally preserved in the geological record. The early stages of mineralisation are particularly important in defining whether or not preservation will occur, and they are poorly understood. Tube samples of the polychaete worm Alvinella pompejana collected from 13°N on the East Pacific Rise have been studied to identify the processes occurring during early pyrite/marcasite mineralisation. Iron sulphide mineralisation is present within the walls of the organic dwelling tube, and is induced by microbial fauna preserved within the tube micro-layers. Various microorganisms were observed coating the inner tube surfaces, together with 10-100 μm-sized Fe- and Zn-sulphide particles precipitated from vent fluids. The microbes and particulate sulphides become entombed within the tube wall as further layers of organic material are secreted by the worm, during tube-building episodes. This results in a laminated tube structure being formed, composed of alternating layers of tube material and microbial/sulphide-rich interlayers. The microbial/sulphide layers provide a template for further mineralisation and replacement of the microbes with pyrite while degradation of the organic components occurs. The iron monosulphides mackinawite and greigite have been identified as intermediatory phases that occur as precursor minerals during the formation of pyrite. Later marcasite mineralisation is observed to form over some of the pyritised organic layers. Once mineralisation has replaced most of the organic tube material, the structure will then be preserved along with the host sulphide body. These observations enhance our understanding of the mechanisms of fossil pyritisation in fine-scaled organic structures throughout the geological record.     

Sediment dynamic processes of the Yuehu inlet system, Shandong Peninsula, China

In order to investigate the sediment dynamic behavior of the Yuehu, a small inlet system characterized by abundant sediment supply and rapid sediment infilling, measurements and sampling were undertaken to obtain data sets of tidal water levels, current velocities, suspended sediment concentrations, grain size parameters, deposition rates and organic carbon contents. Sediment budget and the time–velocity asymmetry patterns of the inlet system were analyzed. The results show that the deposition rates are relatively high within the tidal basin. The total sediment flux cannot be balanced by the input from the open sea, the aerosol and biological production; rather, the material from land (which has been intensified by agricultural activities over the past several decades) represents a major component for the balance. Thus, the denudation rate must be reduced to protect the Yuehu as a natural reserve. Furthermore, it is found from the present study that the Yuehu inlet system exhibits all of the four time–velocity asymmetry patterns with varied frequencies of occurrence, compared with the two asymmetry patterns identified for larger inlet systems; such phenomena are partly due to the adjustment of entrance channel geometry. This behavior may be representative of the small tidal inlets at their late stage of morphological evolution and, therefore, may be utilized to prolong the lifespan of small inlet systems.