Microbiological Comparisons within and across Contiguous Lacustrine, Paleosol, and Fluvial Subsurface Sediments

Twenty-six subsurface samples were collected from a borehole at depths of 173.3 to 196.8 m in the saturated zone at the Hanford Site in south-central Washington State. The sampling was performed throughout strata that included fine-grained lacustrine (lake) sediments, a paleosol (buried soil) sequence, and coarse-grained fluvial (river) sediments. A subcoring method and tracers were used to minimize and quantify contamination to obtain samples that were representative of subsurface strata. Sediment samples were tested for total organic carbon, inorganic carbon, total microorganisms by direct microscopic counts, culturable aerobic heterotrophs by plate counts, culturable anaerobes by most-probable-number enumeration, basal respiration rates, and mineralization of (sup14)C-labeled glucose and acetate. Total direct microscopic counts of microorganisms were low, ranging from below detection to 1.9 x 10(sup5) cells g (dry weight)(sup-1). Culturable aerobes and anaerobes were below minimum levels of detection in most samples. Direct microscopic counts, basal respiration rates, and (sup14)C-glucose mineralization were all positively correlated with total organic carbon and were highest in the lacustrine sediments. In contrast to previous subsurface studies, these saturated-zone samples did not have higher microbial abundance and activities than unsaturated sediments sampled from the same borehole, the fine-textured lacustrine sediment had higher microbial numbers and activities than the coarse-textured fluvial sands, and the paleosol samples did not have higher biomass and activities relative to the other sediments. The results of this study expand the subsurface microbiology database to include information from an environment very different from those previously studied.     

Microbial activities in deep subsurface environments

Activities of microorganisms residing in terrestrial deep subsurface sediments were examined in 46 sediment samples from three boreholes. Radiolabeled time course experiments assessing in situ microbial activities were initiated within 30 min of core recovery. [1‐C⁴] Acetate incorporation into lipids, [ methyl‐³H] thymidine incorporation into DNA, [2‐¹⁴C]acetate, and [U‐¹⁴C]glucose mineralization in addition to microbial enrichment and enumeration studies were examined in surface and subsurface sediments. Surface soils contained the greatest biomass and activities, followed by the shallow aquifer zones. Water‐saturated subsurface sands exhibited three to four orders of magnitude greater activity and culturable microorganisms than the dense clay zones, which had low permeability. Regardless of depth, sediments that contained more than 20% clays exhibited the lowest activities and culturable microorganisms.     

Some microbiological aspects of surface and buried soils on Mt. Kenya,East Africa

When numbers of microorganisms in profiles of surface and buried horizons on Mt. Kenya were estimated by dilution plate counting they were found to be consistently lower than those from other soils in different geographical regions as determined from the literature. The lower numbers are probably characteristic of the poorly weathered Inceptisols and Entisols usually found in the alpine zone.The A horizons of the soils studied contain proportionately fewer of the total numbers of organisms in the A, B and C horizons than observed in most soils. Estimates of organic matter were positively correlated with numbers of fungi and bacteria in the A horizons. However, other factors such as severe drought, high light intensity, low temperatures, diurnal frost heaving, low pH and paucity of clay minerals may be significant factors in suppressing the more luxuriant growth of microbial populations.Organic and inorganic horizons of buried soils sometimes exhibit higher counts of microorganisms than adjacent horizons of surface soils. However, the bacteria and fungi even in deeply buried paleosols exhibit characteristics of an unspecialized heterotrophic population. Among fungi the species were obviously the same as those isolated from one or more of the overlying horizons. Taken in conjunction with other evidence from the profiles it is concluded that the microorganisms were introduced and represent a transient or non-active population. Contamination of buried organic horizons may influence the estimated age as assessed by radiocarbon dating.     

Bacterial heterogeneity in deep subsurface tunnels at Rainier Mesa,Nevada test site

To characterize the deep subsurface environment of Rainier Mesa, Nevada Test Site, rock samples were taken from tunnels U 12b, U12g, U12p, and U 12n, which varied in depth from 50 m to 450 m and in gravimetric moisture content from 4% to 27%. Values for total count, viable count, biomass, Simpson diversity, equitability, similarity coefficient, and number of distinct colony types indicated microbiological variability between samples. Viable counts ranged from less than 1 × 10¹ to 2.4 × 10⁵ CFU g dry wt^–1 of rock. Direct counts and enumeration based on phospholipid determination indicated larger numbers of cells g dry wt-1 of rock than viable counts. Simpson diversity indices, equitability, and numbers of distinct colony types varied from 3.00 to 8.05, 0.21 to 0.89, and 7 to 19, respectively, and indicated heterogeneity between samples. Each distinct morphotype was purified and characterized. Gram reaction, morphology, metal and antibiotic resistances, and metabolic activities of each isolate confirmed spatial variability among microbiota isolated from different locations. Most probable numbers of nitrifying, sulfur oxidizing, and sulfur-reducing bacteria were below the limit of detection in all samples, while the numbers of nitrogen fixing bacteria ranged from below the level of detection to 7.8 × 10² cells g dry wt^–1 of rock sample, and the numbers of dentrifying bacteria ranged from below the level of detection to greater than 1.6 × 10³ cells g dry wt^–1 of rock sample. Offprint requests to: P. S. Amy.     

Attached and Unattached Bacterial Communities in a 120-Meter Corehole in an Acidic, Crystalline Rock Aquifer

The bacteria colonizing geologic core sections (attached) were contrasted with those found suspended in the groundwater (unattached) by examining the microbiology of 16 depth-paired core and groundwater samples using a suite of culture-independent and culture-dependent analyses. One hundred twenty-two meters was continuously cored from a buried chalcopyrite ore hosted in a biotite-quartz-monzonite porphyry at the Mineral Park Mine near Kingman, Ariz. Every fourth 1.5-m core was acquired using microbiologically defensible methods, and these core sections were aseptically processed for characterization of the attached bacteria. Groundwater samples containing unattached bacteria were collected from the uncased corehole at depth intervals corresponding to the individual cores using an inflatable straddle packer sampler. The groundwater was acidic (pH 2.8 to 5.0), with low levels of dissolved oxygen and high concentrations of sulfate and metals, including ferrous iron. Total numbers of attached cells were less than 10⁵ cells g of core material⁻¹ while unattached cells numbered about 10⁵ cells ml of groundwater⁻¹. Attached and unattached acidophilic heterotrophs were observed throughout the depth profile. In contrast, acidophilic chemolithotrophs were not found attached to the rock but were commonly observed in the groundwater. Attached communities were composed of low numbers (<40 CFU g⁻¹) of neutrophilic heterotrophs that exhibited a high degree of morphologic diversity, while unattached communities contained higher numbers (ca. 10³ CFU ml⁻¹) of neutrophilic heterotrophs of limited diversity. Sulfate-reducing bacteria were restricted to the deepest samples of both core and groundwater. 16S ribosomal DNA sequence analysis of attached, acidophilic isolates indicated that organisms closely related to heterotrophic, acidophilic mesophiles such as Acidiphilium organovorum and, surprisingly, to the moderately thermophilic Alicyclobacillus acidocaldarius were present. The results indicate that viable (but possibly inactive) microorganisms were present in the buried ore and that there was substantial distinction in biomass and physiological capabilities between attached and unattached populations.     

Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles

We examined sediments collected at Ocean Drilling Program (ODP) Leg 201 Site 1229 on the Peru Margin for microbial populations throughout the sediment column. Heterotrophic cultivation from these sediments yielded numerous colonies from various depths, including 49 bacterial isolates. At ODP Site 1229, there are significant interfaces of sulfate and methane, across which microbial cell numbers increase substantially. At these sulfate/methane transition zones (SMTZs), however, we observed a decrease in the success rate for the cultivation of bacterial colonies. Utilizing both direct plating and enrichment in different media, we cultivated isolates from the upper SMTZ around 30 m below seafloor (mbsf); however, similar attempts yielded no colonies from within the lower zone at 85 mbsf. The phylogenetic relationships of the 16S rRNA gene sequences for the isolates were determined and most were related to other organisms and sequences previously found in the subsurface belonging to the γ‐Proteobacteria, cytophaga–flavobacterium–bacteroides, high G + C Gram‐positives, and Firmicutes groups. The most diverse group of isolates from Site 1229 was found between the SMTZs at 50 mbsf. ODP Leg 201 Site 1228 was examined for comparison and yielded an additional 18 isolates from 16 to 179 mbsf that were similar to those found at Site 1229. Direct plating at Site 1228 also showed decreased colony formation in the area of sulfate/methane transition. Our results suggest that heterotrophic bacterial populations are affected by SMTZs in deeply buried sediment.     

Extractable Microbial DNA Pool and Microbial Activity in Paleosols of Southern Urals

An evaluation of microbial DNA pools was performed using direct quantitative isolation of DNA from contemporary soils of Southern Urals and paleosols sealed under burial mounds early in the Bronze Age more than 5000 years B.P. Significant regression dependence was found between the biomass and DNA contents in these soils (R ²= 0.97). Activity and dominant ecological strategies of microbial communities of paleosols and contemporary southern black soil were compared from growth parameters obtained by analysis of respiratory curves. The ratio of maximum specific growth rates of soil microorganisms on glucose and on yeast extract was shown to provide an auxotrophy index for soil microbial communities.     

Effects of buried leaf litter and vertical hydrologic exchange on hyporheic water chemistry and fauna in a gravel-bed river in northern New South Wales, Australia

1. Large amounts of coarse particulate organic matter (CPOM) are buried in the sand and gravel beds of many rivers during spates. The effects of these patchily distributed resources on hyporheic invertebrates and water chemistry are poorly understood. Buried CPOM may provide local ‘hot-spots’ of food for hyporheic detritivores and their predators, alter nutrient supply to nearby sediment biofilms, and generate habitat for some invertebrates. 2. To examine potential short-term effects on hyporheic water chemistry, nutrient concentrations and invertebrate assemblage composition, leaf packs were buried in downwelling (surface water infiltrating the hyporheic zone) and upwelling (hyporheic water emerging to the surface) zones at two sites along a gravel-bed river in northern New South Wales. At one site, pits were excavated to simulate leaf burial (procedural control) and plastic ‘leaves’ were buried to test whether invertebrates might respond to leaves as refuges rather than food. Hyporheic CPOM, sediment size fractions, and interstitial silt content were also quantified at these sites. 3. Dry weights of naturally buried CPOM (leaf litter and wood fragments) varied substantially (0.6–71.7 g L^–1 sediment). Amounts of CPOM did not differ between up- vs. downwelling zones or between sites. Hyporheic dissolved oxygen saturation was generally high (> 75%), and was lower in upwelling zones. The hyporheos was dominated taxonomically by water mites (≈ 20 species), whereas small oligochaetes were most abundant (40% of total abundance). Tiny instars of elmid beetle larvae and leptophlebiid mayfly nymphs were also common. Before experimental manipulation, faunal composition differed between up- and downwelling zones. In upwelling zones, bathynellaceans and blind peracarids were found, whereas small individuals of the surface benthos were common in samples from downwelling zones. This validated stratification of the experiment across zones of hydrologic exchange. 4. Twenty days after leaf burial, there was no effect of the treatments at either site on changes in most variables, including mean numbers of taxa and individuals per sample. Similarly, changes in faunal composition of the hyporheos in the treatments paralleled those in the controls except for a weak response in the buried leaves treatment in the upwelling zone at site 1. Artificially buried leaf litter does not seem to influence hyporheic water chemistry or fauna at these two sites. It is probable that naturally buried leaf litter is swiftly processed soon after entrainment and that repeating this experiment immediately after a flood may yield different results.     

Hydrogeologic parameters affecting vadose‐zone microbial distributions

Abstract

The vadose zone and its contaminant‐attenuating processes are physically interposed between surface contamination and groundwater supplies. Given the potential role of microorganisms in mediating vadose‐zone chemical processes, it is vital to understand vadose microbial distributions and factors controlling those distributions. Vadose and shallow saturated zone sediments obtained from cores drilled to approximately 8 m below the surface at two hydrogeologically contrasting sites, named Dalmeny and Washington State University (WSU), were examined for culturable heterotrophic bacteria, total organic carbon (TOC), and sediment texture. Pore‐water elutions were analyzed for dissolved organic carbon, sulfate, and inorganic nitrogen species. Numbers of cultured bacteria (10³‐10⁷ g^?1) generally decreased with depth at both sites. The TOC decreased uniformly with depth at WSU where soil processes are the sole carbon source; at Dalmeny, where both soil and kerogen carbon are present, TOC was higher and relatively constant with depth. Numbers of distinct colony types at Dalmeny did not decline below the solum. Bacteria at Dalmeny were more numerous, exhibited greater numbers of colony types, and were metabolically more flexible than those at WSU. The smooth decline of numbers with depth at WSU paralleled and may be caused by the TOC decline with distance from a solum source. Sediment permeability and pore‐water flux did not control bulk populations as suggested in previous studies; this may be explained by bacterial residence on fracture surfaces in low‐permeability materials. Psychrotolerant organisms did not appear to be as abundant as mean ambient temperatures might suggest.     

Anaerobic metabolic processes in the deep terrestrial subsurface

Anaerobic microorganisms were enumerated and metabolic activities measured in deep Coastal Plain sediments sampled from three water‐bearing formations at depths down to 300 m. Aseptically obtained sediment cores harbored the potential for anaerobic biodegradation of various substrates in almost all samples. Although the sediments were not predominantly anaerobic, viable methanogens and sulfate‐reducing bacteria (SRB) were present almost throughout the depth profile. Coliform organisms were also found at various locations, but were not recoverable from drilling muds or water used to slurry the muds. The anaerobic metabolism of lactate and formate was easily detected in most samples. However, acetate and benzoate were degraded only in portions of the subsurface that harbored methanogens. The water‐saturated transmissive zones harbored the highest numbers of SRB and the potential for the widest variety of anaerobic metabolic activities. Small or negligible anaerobic microbial activity was associated with thick clay layers. The accumulation of acetate and the production of methane in samples not amended with exogenous organic matter demonstrated that some strata contained reserves of fermentable carbon and suggested that environmental factors or nutrients other than carbon were potentially limiting in situ microbial activity.     

Factors influencing the abundance and metabolic capacities of microorganisms in Eastern Coastal Plain sediments

The abundance and metabolic capacities of microorganisms residing in 49 sediment samples from 4 boreholes in Atlantic Coastal Plain sediments were examined. Radiolabeled time-course experiments assessing in situ mirobial capacities were initiated within 30 min of core recovery. Acetate (1-¹⁴C- and³H-) incorporation into lipids, microbial colony forming units, and nutrient limitations were examined in aliquots of subsurface sediments. Water-saturated sands exhibited activity and numbers of viable microorganisms that were orders of magnitude greater than those of the low permeability dense clays. Increased radioisotope utilization rates were observed after 6–24-h incubation times when sediments were amended with additional water and/or nutrients. Supplements of water, phosphate, nitrate, sulfate, glucose, or minerals resulted in the stimulation of microbial activities, as evidenced by the rate of acetate incorporation into microbial lipids. Additions of water or phosphate resulted in the greatest stimulation of microbial activities. Regardless of depth, sediments that contained >20% clay particles exhibited lower activities and biomass densities, and greater stimulation with abundant water supplementation than did sediments containing >66% sands and hydraulic conductivities > 200 μm sec.^?1.     

Dysfunctional Activation of Neurotensin/IL-8 Pathway in Hepatocellular Carcinoma Is Associated with Increased Inflammatory Response in Microenvironment,More Epithelial Mesenchymal Transition in Cancer and Worse Prognosis in Patients

Aim

To investigate the role of neurotensin (NTS) in hepatocellular carcinoma (HCC) sub- grouping and the clinical and pathological significance of activation of NTS/IL-8 pathway in HCC.

Methods

The genome-wide gene expression profiling were conducted in 10 pairs of cancer tissues and corresponding normal adjacent tissues samples using Affymetrix GeneChip® Human Genome U133 Plus 2.0 microarray to screen differentially expressing genes and enrich dysfunctional activated pathways among different HCC subgroups. The levels of NTS protein and multiple inflammation and epithelial mesenchymal transition (EMT) related proteins, including IL-8, VEGF, MMP9, CD68, E-Cadherin, β-Catenin and Vimentin were examined in 64 cases of paraffin-embedded HCC samples using immunohistochemistry (IHC) staining method. The clinical outcome and overall survival (OS) were compared.

Results

A subgroup of HCC characterized by up-regulated NTS expression was accompanied by up-regulated inflammatory responses and EMT. The direct interaction between NTS and IL-8 was identified by pathway enrichment analysis. Significantly increased IL-8 protein was confirmed in 90.91% of NTS⁺ HCC samples and significantly positively correlated to the levels of NTS protein in cancer tissues (P = 0.036), which implied activation of NTS/IL-8 pathway in HCC. The levels of VEGF and MMP9 correlated with co-expression of NTS and IL-8. Increased infiltration of CD68⁺ macrophages and more cancer cells displaying EMT features were found in NTS⁺IL-8⁺ samples. The co-expression of NTS and IL-8 in cancer significantly correlated with the clinical outcomes, as the mortality rate of NTS⁺IL-8⁺ HCC patients is 2.5-fold higher than the others after the surgery (P = 0.022). Accordingly, the OS of NTS⁺IL-8⁺ HCC patients significantly decreased who are under a higher hazard of death at an expected hazard ratio (HR) of 3.457.

Conclusion

Dysfunctional activation of the NTS/IL-8 pathway was detected in HCC which is associated with increased inflammatory response in microenvironment, enhanced EMT in cancer, and worse prognosis in HCC patients.     

Effects of culture conditions on production of antibiotically active metabolites by the marine alga Spyridia filamentosa (Ceramiaceae, Rhodophyta). I. Light

The effect of irradiance over the range 5 to 70 μmol photon m⁻² s⁻¹ on production of antibiotically active metabolites was assessed for male and female gametophytes and tetrasporophytes of the red alga Sphyridia filamentosa (Wulfen) Harvey in Hooker in culture. Whole-algal extracts and ten recognizable TLC-separable zones were assayed against five human microorganisms pathogenic to humans. For all experimental irradiance conditions, the ten TLC zones displayed activity against four of the microorganisms. The maximum number of TLC zones with activity under any of the culture conditions was six each for male and female Spyridia at 70 μmol photon m⁻² s⁻¹. Small changes in irradiance resulted both in different activities against specific microorganisms and degree of activity. The fact that every TLC zone showed differing activities at different light conditions or when extracted from different life history stages strongly suggests the presence of multiple antibiotic principals in individual TLC zones. This revised version was published online in July 2006 with corrections to the Cover Date.     

Microbiology of vadose zone paleosols in south-central Washington State

Three unsaturated subsurface paleosols influenced by moisture recharge, including a highly developed calcic paleosol, were studied to investigate the microbiology of paleosols. Two near-surface paleosols, one impacted by moisture recharge and the other beyond the influence of recharge, were also sampled to directly assess the effect of moisture recharge on the activity and composition of the microbial community associated with paleosols. The highly developed paleosol had a higher population of culturable heterotrophs, a greater glucose mineralization potential, a higher microbial diversity based on colony morphology, and a more than 20-fold higher concentration of ATP than the two weakly developed paleosols. The recharged near-surface paleosol, as compared to the near-surface paleosol unaffected by recharge, had a lower population of culturable heterotrophs, smaller mineralization rate constant, and lower richness based on colony morphology. The recharged paleosols contained predominantly gram-negative isolates, whereas the paleosol unaffected by recharge contained predominantly gram-positive isolates. Storage at 4°C of subsurface and near-surface paleosol samples containing high water potential increased the population of culturable aerobic heterotrophs, decreased diversity in colony morphology, and increased first-order rate constants and decreased lag times for glucose mineralization. These results indicate that aerobic heterotrophs are present in deep vadose zone paleosols and that there is potential for stimulation of their in situ growth and activity.Offprint requests to: F. J. Brockman.     

Geomicrobiology of High-Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), ¹³⁷Cs, and ⁹⁹Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ~10⁴ CFU g⁻¹, but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 μCi of ¹³⁷Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 μCi of ¹³⁷Cs g⁻¹) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste.     

Seawater recirculation through subducting sediments sustains a deeply buried population of sulfate‐reducing bacteria

Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment–basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero‐tolerant sulfate‐reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen‐tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51–1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate‐reducing bacteria living at ~480 m below subducting seafloor.     

Comparative analysis of the functional activity and composition of hydrolytic microbial complexes from the lower Volga barrow and modern chestnut soils

The structure and specific characteristics of the hydrolytic microbial complexes from chestnut paleosols buried under the barrows of different ages (～4500 and ～3500 years) was compared with their modern analogue in microcosm experiments. Potential activity of the hydrolytic complex of the microbial community of the barrow paleosols was found to be higher than in the modern soil complex. The share of metabolically active cells revealed by FISH after the introduction of a growth-stimulating polysaccharide into the paleosol microcosm was 50% of the whole prokaryotic cell number. The paleosol community exhibited a more pronounced response to addition of the substrate than the modern soil community. The differences in the phylogenetic taxonomic structure of the prokaryotic metabolically active hydrolytic complex in the buried and modern soils were revealed. The hydrolytic complex of modern soil was more diverse, while the dominant hydrolytic organisms revealed in paleosols were unicellular and mycelial Actinobacteria, as well as Proteobacteria.     

Soils,time, and primate paleoenvironments

Soils are the skin of the earth. From both poles to the equator, wherever rocks or sediment are exposed at the surface, soils are forming through the physical and chemical action of climate and living organisms. The physical attributes (color, texture, thickness) and chemical makeup of soils vary considerably, depending on the composition of the parent material and other variables: temperature, rainfall and soil moisture, vegetation, soil fauna, and the length of time that soil–forming processes have been at work. United States soil scientists¹ have classified modern soils into ten major groups and numerous subgroups, each reflecting the composition and architecture of the soils and, to some extent, the processes that led to their formation. The physical and chemical processes of soil formation have been active throughout geologic time; the organic processes have been active at least since the Ordovician.² Consequently, nearly all sedimentary rocks that were deposited in nonmarine settings and exposed to the elements contain a record of ancient, buried soils or paleosols. A sequence of these rocks, such as most ancient fluvial (stream) deposits, provides a record of soil paleoenvironments through time. Paleosols are also repositories of the fossils of organisms (body fossils) and the traces of those organisms burrowing, food–seeking, and dwelling activities (ichnofossils). Indeed, most fossil primates are found in paleosols. Careful study of ancient soils gives new, valuable insights into the correct temporal reconstruction of the primate fossil record and the nature of primate paleoenvironments.     

Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and an urban coal-tar disposal site

The abundance and distribution of microorganisms and their potential for mineralizing polycyclic aromatic hydrocarbons (PAHs) were measured in subsurface sediment samples at two geographically separate buried coal-tar sites. At a relatively undisturbed forested site in the northeastern United States, metabolic adaptation to the PAHs was evident: Radiolabeled naphthalene and phenanthrene were converted to ¹⁴CO₂ in core material from inside but not outside a plume of groundwater contamination. However, at the urban site in the midwestern United States these PAHs were mineralized in sediments from both contaminated and uncontaminated boreholes. Thus, clear qualitative evidence showing an adaptational response by the subsurface microbial community was not obtained at the urban site. Instead, subtler clues suggesting metabolic adaptation by subsurface microorganisms from the urban site were discerned by comparing lag periods and extents of ¹⁴CO₂ production from radiolabeled PAHs added to samples from contaminated and uncontaminated boreholes. Despite slightly higher PAH mineralization activity in contaminated borehole samples, p-hydroxybenzoate was mineralized equally in all samples from the urban site regardless of location. No striking trends in the abundances of actinomycetes, fungi, and either viable or total bacteria were encountered. However, colonies of the soil bacterium, Bacillus mycoides, were detected on enumeration plates of several samples from unsaturated and saturated zones in both urban boreholes. Furthermore, other common soil bacteria, Myxococcus xanthus and Chromobacterium violaceum, were identified in samples from the uncontaminated urban borehole. The occurrence of bacteria usually restricted to surface soil, combined with the observation of fragments of building materials in many of the core samples, suggested that past excavation and backfilling operations may have caused mixing of surface soil with subsurface materials at the urban site. We speculate that this mixing, as well as non-coal-tar-derived sources of PAHs, contributed to the PAH-mineralizing activity present in the sediment samples from the uncontaminated urban borehole.     

Distribution of live benthic Foraminifera at three oceanographically dissimilar sites in the northeast Atlantic: preliminary results

Live (i.e. rose Bengal stained) benthic foraminiferal assemblages in the 0–1 cm layer of multiple core samples were examined at three contrasting sites in the northeast Atlantic as part of the Natural Environment Research Council Deep Ocean Benthic Boundary Layer (BENBO) Thematic Programme. Sites A (3600 m water depth) and C (1900 m) were located in the Rockall Trough while Site B (1100 m) was in the Hatton–Rockall Basin. Wet-sorting sediment residues (>125 m fraction) revealed more abundant (98–190 individuals/10 cm²) and diverse (71–99 species /27 cm²) assemblages than found previously in studies employing dry-sorting techniques. At all three sites, the assemblages were numerically dominated by delicate soft-bodied and agglutinated species, most of which are undescribed. Calcareous taxa formed a relatively small proportion of the assemblages (23% of individuals at Site B, 13% at Site C and 7% at Site A). Conversely, the agglutinated hormosinaceans (mainly Reophax species) became more prominent with increasing depth and accounted for 8% of the assemblage at Site B, 33% at Site C and 51% at Site A. Foraminifera represented 67–81% of the fauna in the samples and greatly outnumbered the metazoans. The assemblage at Site A has similarities with abyssal assemblages, while those at Sites B and C contain characteristic bathyal species. At Site B, Uvigerina peregrina and Melonis barleeanum are abundant, suggesting that there are high organic carbon inputs at this site. Reduced species diversity was observed at Site A following the spring phytodetritus bloom due to the presence of large numbers of juvenile Hoeglundina elegans, although it is not clear whether this species is responding to phytodetritus inputs.