Physical and chemical factors affecting microbial biomass and activity in contaminated subsurface riverine sediments

Over 80 years of direct discharge of industrial effluents into the Mahoning River, located in northeastern Ohio, USA, has led to the accumulation of a wide variety of pollutants within its sediments. This study examined the physical and chemical parameters, including lipophilic pollutants, affecting microbial activity and biomass in subsurface (10-40 cm horizon) sediments. Microbial biomass was higher in anthropogenically contaminated sediments, and step-wise linear regression showed that approximately 82% of the variation in microbial biomass could be explained by total hexane extractable hydrocarbons, sediment particle size, and water content. There was no correlation between microbial activity and biomass. Independent variables influencing anaerobic activity were temperature and water holding capacity. The results of this study indicate that freshwater, sedimentary anaerobic microbial communities respond to a range of environmental parameters, many of which influence subsurface river sediments, and that lipophilic pollutants, when present, can cause increases in total microbial biomass.     

Microbial biomass and activity in subsurface sediments from Vejen,Denmark

Subsurface sediment samples were collected from 4 to 31 m below landsurface in glacio-fluvial sediments from the Quaternary period. The samples were described in terms of pH, electrical conductivity, chloride concentration, organic matter content, and grain size distribution. Viable counts of bacteria varied from 0.5 to 1,203 x 103 colony forming units/g dry weight (gdw); total numbers of bacteria acridine orange direct counts (AODC) varied from 1.7 to 147 × 10⁷ cells/gdw; growth rates (incorporation of [³H]-thymidine) varied from 1.4 to 60.7 × 10⁴ cells/(gdw · day); and rate constants for mineralization of ¹⁴C-labelled compounds varied from 0.2 to 2.3 × 10^–3 ml/(dpm · day) for acetate, and from 0 to 2.0 × 10^–3 ml/(dpm · day) for phenol. Sediment texture influenced the total number of bacteria and potential for mineralization; with increasing content of clay and silt and decreasing content of sand, AODC increased and the mineralization rate declined. Intrinsic permeability calculated from grain size correlated positively with mineralization rate for acetate. Statistical correlation analysis showed high correlations between some of the abiotic parameters, but it was not possible to point out a single abiotic parameter that could explain the variation of size and activity of the microbial population. The microbial data obtained in these geologically young sediments were compared to literature data from older sediments, and this comparison showed that age and type of geological formation might be important for the size and activity of the microbial populations.Offprint requests to: H.-J. Albrechtsen.     

Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea

The stratified water column of the Black Sea produces a vertical succession of redox zones, stimulating microbial activity at the interfaces. Our study of intact polar membrane lipids (IPLs) in suspended particulate matter and sediments highlights their potential as biomarkers for assessing the taxonomic composition of live microbial biomass. Intact polar membrane lipids in oxic waters above the chemocline represent contributions of bacterial and eukaryotic photosynthetic algae, while anoxygenic phototrophic bacteria and sulfate-reducing bacteria comprise a substantial amount of microbial biomass in deeper suboxic and anoxic layers. Intact polar membrane lipids such as betaine lipids and glycosidic ceramides suggest unspecified anaerobic bacteria in the anoxic zone. Distributions of polar head groups and core lipids show planktonic archaea below the oxic zone; methanotrophic archaea are only a minor fraction of archaeal biomass in the anoxic zone, contrasting previous observations based on the apolar derivatives of archaeal lipids. Sediments contain algal and bacterial IPLs from the water column, but transport to the sediment is selective; bacterial and archaeal IPLs are also produced within the sediments. Intact polar membrane lipid distributions in the Black Sea are stratified in accordance with geochemical profiles and provide information on vertical successions of major microbial groups contributing to suspended biomass. This study vastly extends our knowledge of the distribution of complex microbial lipids in the ocean.     

Heterotrophic microbial activity in shallow aquifer sediments of Long Island,New York

Bacterial numbers and activities (as estimated by glucose uptake and total thymidine incorporation) were investigated at two sites in Long Island, New York aquifer sediments. In general, bacterial activities were higher in shallow (1.5–4.5 m below the water table or BWT), oxic sediments than in deep (10–18 m BWT), anoxic sediments. The average total glucose uptake rates were 0.18 ± 0.10 ng gdw^–1 h^–1 in shallow sediments and 0.09 ± 0.11 ng gdw^–1 h^–1 in deep sediments; total thymidine incorporation rates were 0.10 ± 0.13 pmol gdw^–1 h^–1 and 0.03 ± 0.03 pmol gdw^–1 h^–1 in shallow and deep sediments, respectively. Incorporation of glucose was highly efficient, as only about 10% of added label was recovered as CO₂. Bacterial abundance (estimated from acridine orange direct counts) was 2.5 ± 2.0 × 10⁷ cells gdw^–1 and 2.0 ± 1.3 × 10⁷ cells gdw^–1 in shallow and deep sediments, respectively. These bacterial activity and abundance estimates are similar to values found in other aquifer environments, but are 10- to 1000-fold lower than values in soil or surface sediment of marine and estuarine systems. In general, cell specific microbial activities were lower in sites from Connetquot Park, a relatively pristine site, when compared to activities found in sites from Jamesport, which has had a history of aldicarb (a pesticide) contamination. To our knowledge, this is the first report of bacterial activity measurements in the shallow, sandy aquifers of Long Island, New York.Correspondence to: D.G. Capone     

Innate immune recognition of microbial cell wall components and microbial strategies to evade such recognitions

The innate immune system constitutes the first line of defence against invading microbes. The basis of this defence resides in the recognition of defined structural motifs of the microbes called “Microbial associated molecular patterns” that are absent in the host. Cell wall, the outer layer of both bacterial and fungal cells, a unique structure that is absent in the host and is recognized by the germ line encoded host receptors. Nucleotide oligomerization domain proteins, peptidoglycan recognition proteins and C-type lectins are host receptors that are involved in the recognition of bacterial cell wall (usually called peptidoglycan), whereas fungal cell wall components (N- and O-linked mannans, β-glucans etc.) are recognized by host receptors like C-type lectins (Dectin-1, Dectin-2, mannose receptor, DC-SIGN), Toll like receptors-2 and -4 (TLR-2 and TLR-4). These recognitions lead to activation of a variety of host signaling cascades and ultimate production of anti-microbial compounds including phospholipase A2, antimicrobial peptides, lysozyme, reactive oxygen and nitrogen species. These molecules act in cohort against the invading microbes to eradicate infections. Additionally pathogen recognition leads to the production of cytokines, which further activate the adaptive immune system. Both pathogenic and commensal bacteria and fungus use numerous strategies to subvert the host defence. These strategies include bacterial peptidoglycan glycan backbone modifications by O-acetylation, N-deacetylation, N-glycolylation and stem peptide modifications by amidation of meso-Diaminopimelic acid; fungal cell wall modifications by shielding the β-glucan layer with mannoproteins and α-1,3 glucan. This review focuses on the recent advances in understanding the role of bacterial and fungal cell wall in their innate immune recognition and evasion strategies.     

Kinetic and microbial community analysis of methyl ethyl ketone biodegradation in aquifer sediments

Methyl ethyl ketone (MEK) is a common groundwater contaminant often present with more toxic compounds of primary interest. Because of this, few studies have been performed to determine the effect of microbial community structure on MEK biodegradation rates in aquifer sediments. Here, microcosms were prepared with aquifer sediments containing MEK following a massive spill event and compared to laboratory-spiked sediments, with MEK biodegradation rates quantified under mixed aerobic/anaerobic conditions. Biodegradation was achieved in MEK-contaminated site sediment microcosms at about half of the solubility (356 mg/L) with largely Firmicutes population under iron-reducing conditions. MEK was biodegraded at a higher rate [4.0 ± 0.74 mg/(L days)] in previously exposed site samples compared to previously uncontaminated sediments [0.51 ± 0.14 mg/(L days)]. Amplicon sequencing and denaturing gradient gel electrophoresis of 16S rRNA genes were combined to understand the relationship between contamination levels, biodegradation, and community structure across the plume. More heavily contaminated sediments collected from an MEK-contaminated field site had the most similar communities than less contaminated sediments from the same site despite differences in sediment texture. The more diverse microbial community observed in the laboratory-spiked sediments reduced MEK concentration 47 % over 92 days. Results of this study suggest lower rates of MEK biodegradation in iron-reducing aquifer sediments than previously reported for methanogenic conditions and biodegradation rates comparable to previously reported nitrate- and sulfate-reducing conditions.     

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.     

Changes in the lipid and protein components of thymus cell membrane during lipid peroxidation]

Nonenzymatic lipid peroxidation in thymus cell plasma membranes was studied. The composition of lipid and protein components, intensity of fluorescence of the membrane probes (1-anilinonaphthalene-8-sulfonate, 4-dimethylaminochalcon, eosin, pyronin and rhodamine), fluorescence polarization of tryptophan residues of membrane proteins and quenching by acrylamide of intrinsic fluorescence of proteins were determined. Induction of lipid peroxidation by the Fe(2+)-ascorbate system caused changes in the composition and structure of lipids. This was paralleled with changes in the structural-dynamic organization of membrane proteins, transition of some peripheral proteins to the water phase and increased solubilization of integral proteins by Triton X-100.     

Effects of integrin-mediated cell adhesion on plasma membrane lipid raft components and signaling

Anchorage dependence of cell growth, which is mediated by multiple integrin-regulated signaling pathways, is a key defense against cancer metastasis. Detachment of cells from the extracellular matrix triggers caveolin-1-dependent internalization of lipid raft components, which mediates suppression of Rho GTPases, Erk, and phosphatidylinositol 3-kinase in suspended cells. Elevation of cyclic adenosine monophosphate (cAMP) following cell detachment is also implicated in termination of growth signaling in suspended cells. Studies of integrins and lipid rafts, however, examined mainly ganglioside GM1 and glycosylphosphatidylinositol-linked proteins as lipid raft markers. In this study, we examine a wider range of lipid raft components. Whereas many raft components internalized with GM1 following cell detachment, flotillin2, connexin43, and Gα(s) remained in the plasma membrane. Loss of cell adhesion caused movement of many components from the lipid raft to the nonraft fractions on sucrose gradients, although flotillin2, connexin43, and H-Ras were resistant. Gα(s) lost its raft association, concomitant with cAMP production. Modification of the lipid tail of Gα(s) to increase its association with ordered domains blocked the detachment-induced increase in cAMP. These data define the effects of that integrin-mediated adhesion on the localization and behavior of a variety of lipid raft components and reveal the mechanism of the previously described elevation of cAMP after cell detachment.     

The effects of heavy metals on microbial biomass in sediments of Palestine Lake

Effects of metal contamination on microbial biomass in sediment samples from three areas in Palestine Lake (one area highly polluted with chromium, cadmium and zinc) were determined. Adenosine triphosphate (ATP) concentrations, determined by the luciferin-luciferase bioluminescent technique, and microbial colony numbers on pour plates were used as biomass indicators. Plate counts showed a significant (P < 0.01) site effect with the highly contaminated area having an order of magnitude lower microbial population than the control area. ATP concentrations also indicated lower microbial biomass in contaminated sediments. The metal concentrations of the most contaminated area averaged 17,840 µg Zn/g, 4380 µg Cr/g and 585 µg Cd/g based on dry weight of sediments. A suppression of organic decomposition was evident in the impacted area; high metal levels and resultant low microbial biomass may have been causative.     

Plant cell wall secretion and lipid traffic at membrane contact sites of the cell cortex

Plant cell wall secretion is the result of dynamic vesicle fusion events at the plasma membrane. The importance of the lipid bilayer environment of the plasma membrane and its interactions with the endomembrane system through vesicle traffic are well recognized. Recent advances in yeast molecular biology and biochemistry lead us to re-examine the hypothesis that non-vesicular traffic of lipids through close contact sites of the plasma membrane and endoplasmic reticulum could also be important in plant cell wall biosynthesis. Non-vesicular traffic is the extraction and transfer of individual lipid molecules from a donor bilayer to a target bilayer, usually with the assistance of lipid transfer proteins.     

Plant cell wall secretion and lipid traffic at membrane contact sites of the cell cortex

Plant cell wall secretion is the result of dynamic vesicle fusion events at the plasma membrane. The importance of the lipid bilayer environment of the plasma membrane and its interactions with the endomembrane system through vesicle traffic are well recognized. Recent advances in yeast molecular biology and biochemistry lead us to re-examine the hypothesis that non-vesicular traffic of lipids through close contact sites of the plasma membrane and endoplasmic reticulum could also be important in plant cell wall biosynthesis. Non-vesicular traffic is the extraction and transfer of individual lipid molecules from a donor bilayer to a target bilayer, usually with the assistance of lipid transfer proteins.     

Distribution of microbial biomass and potential for anaerobic respiration in Hanford Site 300 Area subsurface sediment

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The nosZ gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most nosZ sequences were affiliated with Ochrobactrum anthropi (97 sequence similarity) or had a nearest neighbor of Achromobacter xylosoxidans (90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the dsrA gene and Geobacteraceae had the highest relative abundance. The majority of dsrA genes detected near the interface were related to Desulfotomaculum spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.     

Induction of heat sensitivity of wheat roots and its effects on mitochondria, adenosine triphosphate, triglyceride, and total lipid content

Wheat seedlings were subjected to heat shock for 2 min at 45 °C. After heat treatment, the wheat seedlings were incubated at 25 or 35 °C. At 25 °C, but not at 35 °C, the root tips survived the heat shock. Immediately after the heat treatment the free triglyceride content in the treated root tips was higher than in the untreated roots, but the total lipid content was not changed. The ATP content immediately after the heat treatment was variable, but after about 1 h it stabilized at the same level as in the control or at a higher level. After 45 min at 25 °C after heat shock, the endoplasmic reticulum cisternae had expanded, giving rise to small irregular vacuoles. Golgi vesicles were also irregular. Four hours after heat treatment the endoplasmic reticulum and Golgi vesicles again were normal, but mitochondria were irregular with fewer tubules and with adhering membrane curls containing lipids. These membrane curls were not observed 24 h after heat treatment. When incubated at 35 °C after heat shock wheat root meristems died. Some cells in the meristem were still alive 4 h after treatment. They had large vacuoles with membrane whorls and plasmalemmasomes, and in some cases the cells were partly lysed.     

Changes in mitochondrial mass,membrane potential,and cellular adenosine triphosphate content during the cell cycle of human leukemic (HL-60) cells

Oxidative phosphorylation within the inner mitochondrial membrane generates the majority of cellular adenosine triphosphate (ATP) required for normal physiological functions (including regulation of cell volume and solute concentration, maintenance of cellular architecture, and synthesis of essential macromolecules). Its efficient functioning depends on the maintenance of an electrochemical gradient and is tightly coupled to the energetic demands of the cell and/or tissue. Commitment to and completion of the cell division cycle are sensitive to changes in the availability of mitochondrially derived ATP, although the relationship between cell cycle and mitochondrial physiology is poorly understood. Using vital, mitochondrial-specific fluorochromes to differentiate between mitochondrial mass (10-N-nonyl acridine orange) and mitochondrial membrane potential (Rhodamine123), together with a quantification of total cellular ATP levels, it was possible to generate profiles of these mitochondrial characteristics in HL-60 cells at different stages of their cell cycle. The data suggest that the availability of ATP changes in a cell cycle-specific manner and cannot be predicted by changes in mitochondrial mass or membrane potential. Furthermore, transition points in the cell cycle where ATP availability is low with respect to the amount of functional inner mitochondrial membrane have been observed. We suggest that these cell cycle phase transitions are sensitive to inhibition of mitochondrial activity because the basal levels of available ATP at these points are nearer to a theoretical “minimal threshold” below which cell cycle progression is inhibited. J. Cell. Physiol. 180:91–96, 1999. © 1999 Wiley-Liss, Inc.     

Mineralogical composition and biomass studies of the microbial mats sediments from the Ebro Delta, Spain.

The mineral composition of the microbial mats at La Banya spit was studied. The spit is formed by a narrow sand bar and a peninsula and is located south of the main body of the Ebro Delta (Tarragona, Spain). Although quartz was the predominant mineral component in all sampling sites, clay, feldspars, calcite, aragonite, halite, dolomite and gypsum were also found. An increase in both the fine material (clay) and the halite content was observed in the sites influenced by nearby salterns. The amount of each mineral did not differ significantly along a 55 cm deep profile, except for halite and aragonite, which reached a maximum in the surface and decreased with depth. Dolomite, which ranged from 0.5 to 5% (w/w), is a possible indicator of sulfate-reducing bacteria activity in the past. Organic carbon and total nitrogen were quantified for biomass assessment. Total nitrogen ranged from 0.1 to 0.56% in the uppermost layer, where the microbial mat is active, but was undetectable at deeper layers. Organic carbon ranged from 1 to 5.5% in the active microbial mat layers and decreased to 0.3% at deeper layers. During the summer, both organic carbon and total nitrogen contents (biomass) of the microbial mat samples from some sites increase, whereas other sites show constant concentrations throughout the year, and others have a fluctuant biomass content.