In situ biodegradation: microbiological patterns in a contaminated aquifer

The shifting research landscape for PAH bioremediation in water environment: a bibliometric analysis on three decades of development

Polycyclic aromatic hydrocarbons (PAHs) with their carcinogenic, teratogenic, and mutagenic effects can cause great damage to the ecosystem and public health when present in water. With bioremediation, PAH contamination in water environment can be greatly reduced in an eco-friendly manner. It has thus become the research focus for many environmental scientists. In this study, a bibliometric analysis on three-decade (1990-2022) development of PAH bioremediation in water environment was conducted from temporal and spatial dimensions using CiteSpace. A total of 2480 publications, obtained from Web of Science core collection database, were used to explore the basic characteristics, hotspots, and prospects of the research area. The results showed that (1) bioremediation/biodegradation of PAHs in water environment has been getting researchers' attention since 1990, and is gaining even more traction as time goes on. (2) In terms of countries, China and the USA were the major contributors in this research area, while at the institutional level, the Chinese Academy of Sciences has produced the most research results. However, international cooperation across regions was lacking in the field. (3) Environment Science and Technology, Chemosphere, Applied and Environment Microbiology, Journal of Hazardous Materials, and Environment Pollution were the 5 most cited journals in this field. (4) There were three major stages the field has gone through, each with distinct research hotspots, including initial stage (1990-1994), mechanism investigation (1995-2000), and application exploration (2001-2010; 2011-2022). Finally, research perspectives were proposed, covering three directions, namely, bioavailability, immobilization, and viable but nonculturable (VBNC) bacteria.

Remediation of benzo[a]pyrene contaminated soils by moderate chemical oxidation coupled with microbial degradation

Chemical oxidation is a promising technology for the remediation of organics-contaminated soils. However, residual oxidants and transformation products have adverse effects on microbial activities. This work aimed at moderate chemical oxidation coupled with microbial degradation (MOMD) for the removal of benzo[a]pyrene (BaP) by optimizing the type and dosage of oxidants. Potassium permanganate (KMnO₄), Fe²⁺ + sodium persulfate (Fe²⁺ + PS), Fenton's reagent (Fe²⁺ + H₂O₂), and hydrogen peroxide (H₂O₂) were compared for BaP removal from loam clay and sandy soils. Overall, the removal efficiency of BaP by a moderate dose of oxidant coupled indigenous microorganism was slightly lower than that by a high dose of relevant oxidant. The contributions of microbial degradation to the total removal of BaP varied for different oxidants and soils. The removal efficiency of BaP from loam clay sandy soil by a moderate dose of KMnO₄ (25 mmol/L) was 94.3 ± 1.1 % and 92.5 ± 1.8 %, respectively, which were both relatively higher than those under other conditions. The indirect carbon footprint yielded by the moderate dose of oxidants was 39.2-72.8 % less than that by the complete oxidation. A moderate dose of oxidants also reduced disturbances to soil pH and OC. The microbial communities after MOMD treatment were dominated by Burkholderiaceae, Enterobacteriaceae, Alicyclobacillaceae, and Oxalobacteraceae. These dominant microorganisms promoted the removal of BaP through the expression of polycyclic aromatic hydrocarbon-ring hydroxylated dioxygenase gene. Compared with complete chemical oxidation, MOMD is also a promising technique with the utilization of indigenous microorganism for remediating BaP-contaminated soils.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China

The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.

Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater

Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from ¹³ C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.

Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community

Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [¹³C]benzene enabled us to obtain ¹³C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities.

IMPORTANCE

Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.

A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment

A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of ¹³ C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.

Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers

Biodegradation is one of the most favored and sustainable means of removing organic pollutants from contaminated aquifers but the major steering factors are still surprisingly poorly understood. Growing evidence questions some of the established concepts for control of biodegradation. Here, we critically discuss classical concepts such as the thermodynamic redox zonation, or the use of steady state transport scenarios for assessing biodegradation rates. Furthermore, we discuss if the absence of specific degrader populations can explain poor biodegradation. We propose updated perspectives on the controls of biodegradation in contaminant plumes. These include the plume fringe concept, transport limitations, and transient conditions as currently underestimated processes affecting biodegradation.

Evidence of polycyclic aromatic hydrocarbon biodegradation in a contaminated aquifer by combined application of in situ and laboratory microcosms using (13)C-labelled target compounds

The number of approaches to evaluate the biodegradation of polycyclic aromatic hydrocarbons (PAHs) within contaminated aquifers is limited. Here, we demonstrate the applicability of a novel method based on the combination of in situ and laboratory microcosms using (13)C-labelled PAHs as tracer compounds. The biodegradation of four PAHs (naphthalene, fluorene, phenanthrene, and acenaphthene) was investigated in an oxic aquifer at the site of a former gas plant. In situ biodegradation of naphthalene and fluorene was demonstrated using in situ microcosms (BACTRAP(®)s). BACTRAP(®)s amended with either [(13)C6]-naphthalene or [(13)C5/(13)C6]-fluorene (50:50) were incubated for a period of over two months in two groundwater wells located at the contaminant source and plume fringe, respectively. Amino acids extracted from BACTRAP(®)-grown cells showed significant (13)C-enrichments with (13)C-fractions of up to 30.4% for naphthalene and 3.8% for fluorene, thus providing evidence for the in situ biodegradation and assimilation of those PAHs at the field site. To quantify the mineralisation of PAHs, laboratory microcosms were set up with BACTRAP(®)-grown cells and groundwater. Naphthalene, fluorene, phenanthrene, or acenaphthene were added as (13)C-labelled substrates. (13)C-enrichment of the produced CO2 revealed mineralisation of between 5.9% and 19.7% for fluorene, between 11.1% and 35.1% for acenaphthene, between 14.2% and 33.1% for phenanthrene, and up to 37.0% for naphthalene over a period of 62 days. Observed PAH mineralisation rates ranged between 17 μg L(-1) d(-1) and 1639 μg L(-1) d(-1). The novel approach combining in situ and laboratory microcosms allowed a comprehensive evaluation of PAH biodegradation at the investigated field site, revealing the method's potential for the assessment of PAH degradation within contaminated aquifers.

Responses of soil microbial and nematode communities to aluminum toxicity in vegetated oil-shale-waste lands

Both soil nematodes and microorganisms have been shown to be sensitive bioindicators of soil recovery in metal-contaminated habitats; however, the underlying processes are poorly understood. We investigated the relationship among soil microbial community composition, nematode community structure and soil aluminum (Al) content in different vegetated aluminum-rich ecosystems. Our results demonstrated that there were greater soil bacterial, fungal and arbuscular mycorrhizal fungal biomass in Syzygium cumini plantation, greater abundance of soil nematodes in Acacia auriculiformis plantation, and greater abundance of soil predatory and herbivorous nematodes in Schima wallichii plantation. The concentration of water-soluble Al was normally greater in vegetated than non-vegetated soil. The residual Al and total Al concentrations showed a significant decrease after planting S. cumini plantation onto the shale dump. Acid extractable, reducible and oxidisable Al concentrations were greater in S. wallichii plantation. Stepwise linear regression analysis suggests the concentrations of water-soluble Al and total Al content explain the most variance associated with nematode assembly; whereas, the abundance of early-successional nematode taxa was explained mostly by soil moisture, soil organic C and total N rather than the concentrations of different forms of Al. In contrast, no significant main effects of either Al or soil physico-chemical characteristics on soil microbial biomass were observed. Our study suggests that vegetation was the primary driver on soil nematodes and microorganisms and it also could regulate the sensitivity of bio-indicator role mainly through the alteration of soil Al and physico-chemical characteristics, and S. cumini is effective for amending the Al contaminated soils.

Natural attenuation of contaminated marine sediments from an old floating dock Part II: changes of sediment microbial community structure and its relationship with environmental variables

Changes of microbial community structure and its relationship with various environmental variables in surface marine sediments were examined for a one-year period after the removal of an old floating dock in Hong Kong SAR, South China. Temporal variations in the microbial community structure were clearly revealed by principal component analysis (PCA) of the microbial ester-linked fatty acid methyl ester (EL-FAME) profiles. The most obvious shift in microbial community structure was detected 6 months after the removal of the dock, although no significant decline in the levels of pollutants could be detected. As determined by EL-FAME profiles, the microbial diversity recovered and the predominance of gram-negative bacteria was gradually replaced by gram-positive bacteria and fungi in the impacted stations. With redundancy analysis (RDA), the concentration of total polycyclic aromatic hydrocarbons (PAHs) was found to be the second important determinant of microbial community structure, next to Time. The relative abundance of 18:1ω9c and hydroxyl fatty acids enriched in the PAH hot spots, whereas 16:1ω9 and 18:1ω9t were negatively correlated to total PAH concentration. The significant relationships observed between microbial EL-FAME profiles and pollutants, exampled by PAHs in the present study, suggested the potential of microbial community analysis in the assessment of the natural attenuation process in contaminated environments.

Role of nitrogen fixation in the autecology of Polaromonas naphthalenivorans in contaminated sediments

Polaromonas naphthalenivorans strain CJ2 is a Gram-negative betaproteobacterium that was identified, using stable isotope probing in 2003, as a dominant in situ degrader of naphthalene in coal tar-contaminated sediments. The sequenced genome of strain CJ2 revealed several genes conferring nitrogen fixation within a 65.6 kb region of strain CJ2's chromosome that is absent in the genome of its closest sequenced relative Polaromonas sp. strain JS666. Laboratory growth and nitrogenase assays verified that these genes are functional, providing an alternative source of nitrogen in N-free media when using naphthalene or pyruvate as carbon sources. Knowing this, we investigated if nitrogen-fixation activity could be detected in microcosms containing sediments from the field site where strain CJ2 was isolated. Inducing nitrogen limitation with the addition of glucose or naphthalene stimulated nitrogenase activity in amended sediments, as detected using the acetylene reduction assay. With the use of fluorescence microscopy, we screened the microcosm sediments for the presence of active strain CJ2 cells using a dual-labelling approach. When we examined the carbon-amended microcosm sediments stained with both a strain CJ2-specific fluorescent in situ hybridization probe and a polyclonal fluorescently tagged antibody, we were able to detect dual-labelled active cells. In contrast, in sediments that received no carbon addition (showing no nitrogenase activity), no dual-labelled cells were detected. Furthermore, the naphthalene amendment enhanced the proportion of active strain CJ2 cells in the sediment relative to a glucose amendment. Field experiments performed in sediments where strain CJ2 was isolated showed nitrogenase activity in response to dosing with naphthalene. Dual-label fluorescence staining of these sediments showed a fivefold increase in active strain CJ2 in the sediments dosed with naphthalene over those dosed with deionized water. These experiments show that nitrogen fixation may play an important role in naphthalene biodegradation by strain CJ2 and contribute to its ecological success.

Natural attenuation of contaminated marine sediments from an old floating dock - Part I: Spatial and temporal changes of organic and inorganic pollutants

Temporal and spatial changes of mixed pollutants, including eight heavy metals, 16 US EPA priority polycyclic aromatic hydrocarbons (PAHs) and tributyltin (TBT) in surface marine sediments were examined for a one-year period after the removal of an old floating dock in Hong Kong SAR, South China. The sediments from the impacted stations close to the dock were highly polluted with zinc (Zn) and copper (Cu), and were moderately polluted with TBT and total PAHs, based on their effects range-low (ERL) guideline values, while those collected in the reference stations away from the dock were lower than the ERL. Strong, positive correlations were found between the organic pollutants and heavy metals only in the impacted stations, suggesting that the old floating dock was a significant source of mixed pollutants. There was no significant decline in the levels of total PAHs, TBT and heavy metals and "hot spots" of contamination were still detected a year after the removal of the dock. However, the profiles of 16 PAHs in the impacted stations changed 6 months after the removal of the dock, with decreases of certain low-molecular-weight PAHs, especially fluorene, as a sign of biodegradation in situ. Further, principal component analysis (PCA) based on an integrated dataset of the pollutants together with general sediment properties showed that the temporal changes of the biodegradable low-molecular-weight PAHs were highly associated with the pH value and total Kjeldahl nitrogen, while heavy metals were independent of time and other sediment properties during natural attenuation in the dock area.

Dissolution and transport of coal tar compounds in fractured clay-rich residuum

We investigated the dissolution and transport of organic contaminants from a crude coal tar mixture in a monolith of fractured clay-rich residuum. An electrolyte solution was eluted through the residuum monolith containing a small emplaced source of coal tar under biologically inhibited and mildly acidic conditions. Concentrations of 10 coal tar compounds, representing mono-, poly-, and heterocyclic aromatic hydrocarbons that constitute crude coal tar were monitored in the effluent over a period of 377 days. Most compounds appeared in the effluent within the first 0.1 pore volume eluted indicating the importance of rapid dissolution and transport through the fracture networks. The concentrations continued to rise but did not reach the corresponding effective solubility limit in most cases. Compounds that were less soluble and those that were more susceptible to sorption or matrix diffusion eluted at a much slower rate. Analysis of contaminant concentrations in microcore residuum samples indicated that all 10 compounds had spread throughout the entire monolith and had diffused into the fine-grained matrix between fractures. These data suggest that the predominantly fine pore structure did not appear to inhibit coal tar dissolution and subsequent transport, even though only a small portion of tar was in direct contact with fractures and macropores that control most flow.

Structured multiple endosymbiosis of bacteria and archaea in a ciliate from marine sulfidic sediments: a survival mechanism in low oxygen, sulfidic sediments?

Marine micro-oxic to sulfidic environments are sites of intensive biogeochemical cycling and elemental sequestration, where prokaryotes are major driving forces mediating carbon, nitrogen, sulfur, phosphorus, and metal cycles, important from both biogeochemical and evolutionary perspectives. Associations between single-celled eukaryotes and bacteria and/or archaea are common in such habitats. Here we describe a ciliate common in the micro-oxic to anoxic, typically sulfidic, sediments of Santa Barbara Basin (CA, USA). The ciliate is 95% similar to Parduzcia orbis (18S rRNA). Transmission electron micrographs reveal clusters of at least three different endobiont types organized within membrane-bound sub-cellular regions. Catalyzed reporter deposition-fluorescent in situ hybridization and 16S rRNA clone libraries confirm the symbionts include up to two sulfate reducers (Desulfobulbaceae, Desulfobacteraceae), a methanogen (Methanobacteriales), and possibly a Bacteroidete (Cytophaga) and a Type I methanotroph, suggesting synergistic metabolisms in this environment. This case study is discussed in terms of implications to biogeochemistry, and benthic ecology.

Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization

This is the second paper in a series of three that investigates eukaryotic microbial diversity and taxon distribution in the Cariaco Basin, Venezuela, the ocean's largest anoxic marine basin. Here, we use phylogenetic information, multivariate community analyses and statistical richness predictions to test whether protists exhibit habitat specialization within defined geochemical layers of the water column. We also analyze spatio-temporal distributions of protists across two seasons and two geographic sites within the basin. Non-metric multidimensional scaling indicates that these two basin sites are inhabited by distinct protistan assemblages, an observation that is supported by the minimal overlap in observed and predicted richness of sampled sites. A comparison of parametric richness estimations indicates that protistan communities in closely spaced-but geochemically different-habitats are very dissimilar, and may share as few as 5% of total operational taxonomic units (OTUs). This is supported by a canonical correspondence analysis, indicating that the empirically observed OTUs are organized along opposing gradients in oxidants and reductants. Our phylogenetic analyses identify many new clades at species to class levels, some of which appear restricted to specific layers of the water column and have a significantly nonrandom distribution. These findings suggest many pelagic protists are restricted to specific habitats, and likely diversify, at least in part due to separation by geochemical barriers.

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

Microbial diversity and distribution are topics of intensive research. In two companion papers in this issue, we describe the results of the Cariaco Microbial Observatory (Caribbean Sea, Venezuela). The Basin contains the largest body of marine anoxic water, and presents an opportunity to study protistan communities across biogeochemical gradients. In the first paper, we survey 18S ribosomal RNA (rRNA) gene sequence diversity using both Sanger- and pyrosequencing-based approaches, employing multiple PCR primers, and state-of-the-art statistical analyses to estimate microbial richness missed by the survey. Sampling the Basin at three stations, in two seasons, and at four depths with distinct biogeochemical regimes, we obtained the largest, and arguably the least biased collection of over 6000 nearly full-length protistan rRNA gene sequences from a given oceanographic regime to date, and over 80,000 pyrosequencing tags. These represent all major and many minor protistan taxa, at frequencies globally similar between the two sequence collections. This large data set provided, via the recently developed parametric modeling, the first statistically sound prediction of the total size of protistan richness in a large and varied environment, such as the Cariaco Basin: over 36,000 species, defined as almost full-length 18S rRNA gene sequence clusters sharing over 99% sequence homology. This richness is a small fraction of the grand total of known protists (over 100,000-500,000 species), suggesting a degree of protistan endemism.

Biomagnification of cadmium selenide quantum dots in a simple experimental microbial food chain

Previous studies have shown that engineered nanomaterials can be transferred from prey to predator, but the ecological impacts of this are mostly unknown. In particular, it is not known if these materials can be biomagnified-a process in which higher concentrations of materials accumulate in organisms higher up in the food chain. Here, we show that bare CdSe quantum dots that have accumulated in Pseudomonas aeruginosa bacteria can be transferred to and biomagnified in the Tetrahymena thermophila protozoa that prey on the bacteria. Cadmium concentrations in the protozoa predator were approximately five times higher than their bacterial prey. Quantum-dot-treated bacteria were differentially toxic to the protozoa, in that they inhibited their own digestion in the protozoan food vacuoles. Because the protozoa did not lyse, largely intact quantum dots remain available to higher trophic levels. The observed biomagnification from bacterial prey is significant because bacteria are at the base of environmental food webs. Our findings illustrate the potential for biomagnification as an ecological impact of nanomaterials.

Tape underlayment rotary-node (TURN) valves for simple on-chip microfluidic flow control

We describe a simple and reliable fabrication method for producing multiple, manually activated microfluidic control valves in polydimethylsiloxane (PDMS) devices. These screwdriver-actuated valves reside directly on the microfluidic chip and can provide both simple on/off operation as well as graded control of fluid flow. The fabrication procedure can be easily implemented in any soft lithography lab and requires only two specialized tools-a hot-glue gun and a machined brass mold. To facilitate use in multi-valve fluidic systems, the mold is designed to produce a linear tape that contains a series of plastic rotary nodes with small stainless steel machine screws that form individual valves which can be easily separated for applications when only single valves are required. The tape and its valves are placed on the surface of a partially cured thin PDMS microchannel device while the PDMS is still on the soft-lithographic master, with the master providing alignment marks for the tape. The tape is permanently affixed to the microchannel device by pouring an over-layer of PDMS, to form a full-thickness device with the tape as an enclosed underlayment. The advantages of these Tape Underlayment Rotary-Node (TURN) valves include parallel fabrication of multiple valves, low risk of damaging a microfluidic device during valve installation, high torque, elimination of stripped threads, the capabilities of TURN hydraulic actuators, and facile customization of TURN molds. We have utilized these valves to control microfluidic flow, to control the onset of molecular diffusion, and to manipulate channel connectivity. Practical applications of TURN valves include control of loading and chemokine release in chemotaxis assay devices, flow in microfluidic bioreactors, and channel connectivity in microfluidic devices intended to study competition and predator/prey relationships among microbes.

Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community

The propensity for groundwater ecosystems to recover from contamination by organic chemicals (in this case, coal-tar waste) is of vital concern for scientists and engineers who manage polluted sites. The microbially mediated cleanup processes are also of interest to ecologists because they are an important mechanism for the resilience of ecosystems. In this study we establish the long-term dynamic nature of a coal-tar waste-contaminated site and its microbial community. We present 16 years of chemical monitoring data, tracking responses of a groundwater ecosystem to organic contamination (naphthalene, xylenes, toluene, 2-methyl naphthalene and acenaphthylene) associated with coal-tar waste. In addition, we analyzed small-subunit (SSU) ribosomal RNA (rRNA) genes from two contaminated wells at multiple time points over a 2-year period. Principle component analysis of community rRNA fingerprints (terminal-restriction fragment length polymorphism (T-RFLP)) showed that the composition of native microbial communities varied temporally, yet remained distinctive from well to well. After screening and analysis of 1178 cloned SSU rRNA genes from Bacteria, Archaea and Eukarya, we discovered that the site supports a robust variety of eukaryotes (for example, alveolates (especially anaerobic and predatory ciliates), stramenopiles, fungi, even the small metazoan flatworm, Suomina) that are absent from an uncontaminated control well. This study links the dynamic microbial composition of a contaminated site with the long-term attenuation of its subsurface contaminants.

Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ní Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72:4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low ( approximately 10(2) ppb; approximately 1 muM) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.

Assessment of the stability of human viruses and coliphage in groundwater by PCR and infectivity methods

AIM

To investigate the potential health hazard from infectious viruses where coliphages, or viruses by polymerase chain reaction (PCR), have been detected in groundwater. Two aspects were investigated: the relationship between infectivity and detection by PCR and the stability of coliphage compared to human viruses.

METHODS AND RESULTS

Virus decay (1 year) and detection (2 years) studies were undertaken on groundwater at 12 degrees C. The order of virus stability from most to least stable in groundwater, based on first-order inactivation, was: coliphage PhiX174 (0.5 d(-1)) > adenovirus 2 > coliphage PRD1 > poliovirus 3 > coxsackie virus B1 (0.13 d(-1)). The order for PCR results was: norovirus genotype II > adenovirus > norovirus genotype I > enterovirus.

CONCLUSIONS

Enterovirus and adenovirus detection by PCR and the duration of infectivity in groundwater followed similar trends over the time period studied. Adenovirus might be a better method for assessing groundwater contamination than using enterovirus; norovirus detection would provide information on a significant human health hazard. Bacteriophage is a good alternative indicator.

SIGNIFICANCE AND IMPACT OF THE STUDY

PCR is a useful tool for identifying the health hazard from faecal contamination in groundwater where conditions are conducive to the survival of viruses and their nucleic acid.

Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate

Eukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sediment-associated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of the Basidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellate Heteromita globosa (Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 10(2) to 10(3) cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.

Enumeration of aromatic oxygenase genes to evaluate monitored natural attenuation at gasoline-contaminated sites

Monitoring groundwater benzene, toluene, ethylbenzene, and xylene (BTEX) concentrations is the typical method to assess monitored natural attenuation (MNA) and bioremediation as corrective actions at gasoline-contaminated sites. Conclusive demonstration of bioremediation, however, relies on converging lines of chemical and biological evidence to support a decision. In this study, real-time PCR quantification of aromatic oxygenase genes was used to evaluate the feasibility of MNA at two gasoline-impacted sites. Phenol hydroxylase (PHE), ring-hydroxylating toluene monooxygenase (RMO), naphthalene dioxygenase (NAH), toluene monooxygenase (TOL), toluene dioxygenase (TOD), and biphenyl dioxygenase (BPH4) genes were routinely detected in BTEX-impacted wells. Aromatic oxygenase genes were not detected in sentinel wells outside the plume indicating that elevated levels of oxygenase genes corresponded to petroleum hydrocarbon contamination. Total aromatic oxygenase gene copy numbers detected in impacted wells were on the order of 10(6)-10(9)copies L(-1). PHE, RMO, NAH, TOD, and BPH4 gene copies positively correlated to total BTEX concentration. Mann-Kendall analysis of benzene concentrations was used to evaluate the status of the dissolved BTEX plume. The combination of trend analysis of contaminant concentrations with quantification of aromatic oxygenase genes was used to assess the feasibility of MNA as corrective measures at both sites.

Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11

Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 microM, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations.

Protozoan grazing increases mineralization of naphthalene in marine sediment

Bacterial decomposition of organic matter is frequently enhanced when protozoa are present. Various mechanisms have been proposed to account for this phenomenon, including effects associated with grazing by protozoa (such as increased recycling of limiting nutrients, removal of senescent cells, or reduction of competition among bacteria) and indirect effects of grazers (such as excretion of bacterial growth factors). Few studies have examined the role of protozoa in bacterial degradation of xenobiotic compounds in sediment containing a natural community of microbes. The effect of protozoa on mineralization of naphthalene was investigated in this study. Laboratory experiments were conducted using field-contaminated estuarine sediment, with the indigenous microbial populations. Mineralization of naphthalene was up to four times greater in treatments with actively grazing protozoa than in treatments containing the grazing inhibitor cytochalasin B. Control experiments confirmed that the grazing inhibitor was not toxic to ciliates but did prevent them from grazing. The grazing inhibitor did not affect growth rates of a mixed culture of sediment bacteria or a pure polycyclic-aromatic-hydrocarbon-degrading strain. Once grazing had been inhibited, supplementing treatments with inorganic N and P, glucose, or additional protozoa failed to stimulate naphthalene mineralization. Naphthalene-degrading bacteria were four to nine times less abundant when protozoan grazing was suppressed. We suggest that protozoa enhance naphthalene mineralization by selectively grazing on those sediment bacteria that ordinarily would outcompete naphthalene-degrading bacteria.

Mobility of protozoa through narrow channels

Microbes in the environment are profoundly affected by chemical and physical heterogeneities occurring on a spatial scale of millimeters to micrometers. Physical refuges are critical for maintaining stable bacterial populations in the presence of high predation pressure by protozoa. The effects of microscale heterogeneity, however, are difficult to replicate and observe using conventional experimental techniques. The objective of this research was to investigate the effect of spatial constraints on the mobility of six species of marine protozoa. Microfluidic devices were created with small channels similar in size to pore spaces in soil or sediment systems. Individuals from each species of protozoa tested were able to rapidly discover and move within these channels. The time required for locating the channel entrance from the source well increased with protozoan size and decreased with channel height. Protozoa of every species were able to pass constrictions with dimensions equal to or smaller than the individual's unconstrained cross-sectional area. Channel geometry was also an important factor affecting protozoan mobility. Linear rates of motion for various species of protozoa varied by channel size. In relatively wide channels, typical rates of motion were 300 to 500 microm s(-1) (or about 1 m per hour). As the channel dimensions decreased, however, motilities slowed more than an order of magnitude to 20 microm s(-1). Protozoa were consistently observed to exhibit several strategies for successfully traversing channel reductions. The empirical results and qualitative observations resulting from this research help define the physical limitations on protozoan grazing, a critical process affecting microbes in the environment.

The soil flagellate Heteromita globosa accelerates bacterial degradation of alkylbenzenes through grazing and acetate excretion in batch culture

The impact of grazing by soil flagellates Heteromita globosa on aerobic biodegradation of benzene by Pseudomonas strain PS+ was examined in batch culture. Growth of H. globosa on these bacteria obeyed Monod kinetics (mu(max), 0.17 +/- 0.03 h(-1); K(s), 1.1 +/- 0.2 x 10(7) bacteria mL(-1)) and was optimal at a bacteria/ flagellate ratio of 2000. Carbon mass balance showed that 5.2% of total [ring-U-(14)C]benzene fed to bacteria was subsequently incorporated into flagellate biomass. Growth-inhibiting concentrations (IC50) of alkylbenzenes (benzene, toluene, ethylbenzene) were inversely related with their octanol/ water partitioning coefficients, and benzene was least toxic for bacteria and flagellates with IC50 values of 4392 (+/- 167) microM and 2770 (+/- 653) microM, respectively. The first-order rate constant for benzene degradation (k1, 0.48 +/- 0.12 day(-1)) was unaffected by the presence or absence of flagellates in cultures. However, the rate of benzene degradation by individual bacteria averaged three times higher in the presence of flagellates (0.73 +/- 0.13 fmol cell(-1) h(-1)) than in their absence (0.26 +/- 0.03 fmol cell(-1) h(-1)). Benzene degradation also coincided with higher levels of dissolved oxygen and a higher rate of nitrate reduction in the presence of flagellates (p < 0.02). Grazing by flagellates may have increased the availability of dissolved oxygen to a smaller surviving population of bacteria engaged in the aerobic reactions initiating benzene degradation. In addition, flagellates may also have increased the rate of nitrate reduction through the excretion of acetate as an additional electron donor for these bacteria. Indeed, acetate was shown to progressively accumulate in cultures where flagellates grazed on heat-killed bacteria. This study provided evidence that grazing flagellates stimulate bacterial degradation of alkylbenzenes and provide a link for carbon cycling to consumers at higher trophic levels. This may have important implications for bioremediation processes.

Characterization in Pseudomonas putida Cg1 of nahR and its role in bacterial survival in soil

Sequencing, RFLP analyses and experiments utilizing a lacZ transcriptional reporter fused to the promoter regions of nahR and nahG in Pseudomonas putida Cg1 confirmed that regulation of naphthalene degradation in both P. putida Cg1 and the type strain, P. putida NCIB 9816-4, is consistent with that of NAH7 from P. putida G7. Two nahR knockout strains (RK1 and Cg1-NAHR from P. putida NCIB 9816-4 and Cg1, respectively) showed a growth defect in the presence of naphthalene as sole carbon and energy source. We hypothesized that nahR influences ecological fitness of bacteria in naphthalene-contaminated soil and tested this hypothesis using both parent and nahR-knockout strains introduced to soil microcosms with and without added naphthalene. After 21 days, loss of cell viability was pronounced in the presence of added naphthalene crystals for nahR mutants of both test bacteria, relative to the wild types. Diminished viable counts were attributed to toxicity. Thus, our data indicated that NahR in P. putida Cg1 is virtually identical to its homologues in other pseudomonads and that nahR is required for resistance to naphthalene toxicity, hence the persistence of bacterial cells in soil with high concentrations of naphthalene.

Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment

Strain CJ2T, capable of growth on naphthalene as a sole carbon and energy source, was isolated from coal-tar-contaminated freshwater sediment. The Gram reaction of strain CJ2Twas negative. The cells were non-spore-forming, non-motile cocci (without flagella). The isolate was found to be an aerobic heterotroph capable of utilizing glucose and other simple sugars. Growth was observed between 4 and 25 °C (optimum, 20 °C) and between pH 6·0 and 9·0 (optimum, pH 7·0–7·5). The G+C content of the genomic DNA was 61·5 mol% and the major quinone was ubiquinone-8. The peptidoglycan of strain CJ2Twas determined as belonging to type A1-γ,meso-diaminopimelic acid. The major fatty acids of strain CJ2Twere 16 : 1ω7c(67·0 %), 16 : 0 (19·6 %), 18 : 1ω7c(∼7·9 %) and 10 : 0 3-OH (∼2·5 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Mycolic acid and glycolipids could not be detected. Comparative 16S rDNA analysis indicated that strain CJ2Tis related to the familyComamonadaceaeand that the nearest phylogenetic relative wasPolaromonas vacuolata34-PT(97·1 % similarity). On the basis of the physiological and molecular properties, the naphthalene-degrading isolate was designatedPolaromonas naphthalenivoranssp. nov. The type strain is CJ2T(=ATCC BAA-779T=DSM 15660T).

Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment

Microorganisms maintain the biosphere by catalyzing biogeochemical processes, including biodegradation of organic chemical pollutants. Yet seldom have the responsible agents and their respective genes been identified. Here we used field-based stable isotopic probing (SIP) to discover a group of bacteria responsible for in situ metabolism of an environmental pollutant, naphthalene. We released 13C-labeled naphthalene in a contaminated study site to trace the flow of pollutant carbon into the naturally occurring microbial community. Using GC/MS, molecular biology, and classical microbiological techniques we documented 13CO2 evolution (2.3% of the dose in 8 h), created a library of 16S rRNA gene clones from 13C labeled sediment DNA, identified a taxonomic cluster (92 of 95 clones) from the microbial community involved in metabolism of the added naphthalene, and isolated a previously undescribed bacterium (strain CJ2) from site sediment whose 16S rRNA gene matched that of the dominant member (48%) of the clone library. Strain CJ2 is a beta proteobacterium closely related to Polaromonas vacuolata. Moreover, strain CJ2 hosts the sequence of a naphthalene dioxygenase gene, prevalent in site sediment, detected before only in environmental DNA. This investigative strategy may have general application for elucidating the bases of many biogeochemical processes, hence for advancing knowledge and management of ecological and industrial systems that rely on microorganisms.

Identification and characterization of the conjugal transfer region of the pCg1 plasmid from naphthalene-degrading Pseudomonas putida Cg1

Hybridization and restriction fragment length polymorphism data (K. G. Stuart-Keil, A. M. Hohnstock, K. P. Drees, J. B. Herrick, and E. L. Madsen, Appl. Environ. Microbiol. 64:3633-3640, 1998) have shown that pCg1, a naphthalene catabolic plasmid carried by Pseudomonas putida Cg1, is homologous to the archetypal naphthalene catabolic plasmid, pDTG1, in P. putida NCIB 9816-4. Sequencing of the latter plasmid allowed PCR primers to be designed for amplifying and sequencing the conjugal transfer region in pCg1. The mating pair formation (mpf) gene, mpfA encoding the putative precursor of the conjugative pilin subunit from pCg1, was identified along with other trb-like mpf genes. Sequence comparison revealed that the 10 mpf genes in pCg1 and pDTG1 are closely related (61 to 84% identity) in sequence and operon structure to the putative mpf genes of catabolic plasmid pWW0 (TOL plasmid of P. putida) and pM3 (antibiotic resistance plasmid of Pseudomonas. spp). A polar mutation caused by insertional inactivation in mpfA of pCg1 and reverse transcriptase PCR analysis of mRNA showed that this mpf region was involved in conjugation and was transcribed from a promoter located upstream of an open reading frame adjacent to mpfA. lacZ transcriptional fusions revealed that mpf genes of pCg1 were expressed constitutively both in liquid and on solid media. This expression did not respond to host exposure to naphthalene. Conjugation frequency on semisolid media was consistently 10- to 100-fold higher than that in liquid media. Thus, conjugation of pCg1 in P. putida Cg1 was enhanced by expression of genes in the mpf region and by surfaces where conditions fostering stable, high-density cell-to-cell contact are manifest.

Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments

Several distinct naphthalene dioxygenases have been characterized to date, which provides the opportunity to investigate the ecological significance, relative distribution, and transmission modes of the different analogs. In this study, we showed that a group of naphthalene-degrading isolates from a polycyclic aromatic hydrocarbon (PAH)-contaminated hillside soil were phenotypically and genotypically distinct from naphthalene-degrading organisms isolated from adjacent, more highly contaminated seep sediments. Mineralization of (14)C-labeled naphthalene by soil slurries suggested that the in situ seep community was more acclimated to PAHs than was the in situ hillside community. phnAc-like genes were present in diverse naphthalene-degrading isolates cultured from the hillside soil, while nahAc-like genes were found only among isolates cultured from the seep sediments. The presence of a highly conserved nahAc allele among gram-negative isolates from the coal tar-contaminated seep area provided evidence for in situ horizontal gene transfer and was reported previously (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). Natural horizontal transfer of the phnAc sequence was also suggested by a comparison of the phnAc and 16S ribosomal DNA sequences of the hillside isolates. Analysis of metabolites produced by cell suspensions and patterns of amplicons produced by PCR analysis suggested both genetic and metabolic diversity among the naphthalene-degrading isolates of the contaminated hillside. These results provide new insights into the distribution, diversity, and transfer of phnAc alleles and increase our understanding of the acclimation of microbial communities to pollutants.

Coupled oxidation of aromatic hydrocarbons by horseradish peroxidase and hydrogen peroxide

The oxidation capability of horseradish peroxidase (HRP) and hydrogen peroxide (H2O2) coupled oxidation of aromatic hydrocarbons (o-xylene-d10 and naphthalene-d8) was investigated. Batch experiments were conducted using horseradish peroxidase prepared in potassium phosphate buffer in the presence of H2O2. The oxidation of aromatic hydrocarbon was tested as a function of HRP at a fixed concentration of H2O2, and as a function of the concentration of H2O2 at a constant HRP activity (4000 units/ml). The mass removal of o-xylene-d10 and naphthalene-ds increased with increasing HRP enzymatic activity, and up to 54% and 51% of mass removal were observed for o-xylene-d10 and naphthalene-d8, respectively. Increasing the concentration of H2O2 resulted in increased mass removal of aromatic hydrocarbons.

Field evidence for a protistan role in an organically-contaminated aquifer

The association between protists, bacteria, and dissolved organic carbon (DOC) in an oxygen-depleted, 6 km-long wastewater contaminant plume within a sandy aquifer (Cape Cod, MA) was investigated by comparing abundance patterns along longitudinal and vertical transects and at a control site. Strong linear correlations were observed between unattached bacterial abundance and DOC for much of the upgradient-half of the plume (0.1-2.5 km downgradient from the source) that is characterized by quasi-steady state chemistry. However, a logarithmic decrease was observed between the number of protists supported per mg of DOC and the estimated age of the DOC within the plume. The relatively labile dissolved organic contaminants that characterize the groundwater sampled from the plume < or = 0.1 km downgradient from the contaminant source appeared to indirectly support 3-4 times as many protists (per mg of DOC) as the older, more recalcitrant DOC in the alkylbenzene sulfonate (ABS)-contaminated zone at 3 km downgradient (approximately 30 years travel time). Substantive numbers of protists (>10(4)/cm3) were recovered from suboxic zones of the plume. The higher than expected ratios of protists to unattached bacteria (10 to 100:1) observed in much of the plume suggest that protists may be grazing upon both surface-associated and unattached bacterial communities to meet their nutritional requirements. In closed bottle incubation experiments, the presence of protists caused an increase in bacterial growth rate, which became more apparent at higher amendments of labile DOC (3-20 mgC/L). The presence of protists resulted in an increase in the apparent substrate saturation level for the unattached bacterial community, suggesting an important role for protists in the fate of more-labile aquifer organic contaminants.

The bacterivorous soil flagellate Heteromita globosa reduces bacterial clogging under denitrifying conditions in sand-filled aquifer columns

An exopolymer (slime)-producing soil bacterium Pseudomonas sp. (strain PS+) rapidly clogged sand-filled columns supplied with air-saturated artificial groundwater containing glucose (500 mg liter(-1)) as a sole carbon source and nitrate (300 mg liter(-1)) as an alternative electron acceptor. After 80 days of operation under denitrifying conditions, the effective porosity and saturated hydraulic conductivity (permeability) of sand in these columns had fallen by 2.5- and 26-fold, respectively. Bacterial biofilms appeared to induce clogging by occluding pore spaces with secreted exopolymer, although there may also have been a contribution from biogas generated during denitrification. The bacterivorous soil flagellate Heteromita globosa minimized reductions in effective porosity (1.6-fold) and permeability (13-fold), presumably due to grazing control of biofilms. Grazing may have limited growth of bacterial biomass and hence the rate of exopolymer and biogas secretion into pore spaces. Evidence for reduction in biogas production is suggested by increased nitrite efflux from columns containing flagellates, without a concomitant increase in nitrate consumption. There was no evidence that flagellates could improve flow conditions if added once clogging had occurred (60 days). Presumably, bacterial biofilms and their secretions were well established at that time. Nevertheless, this study provides evidence that bacterivorous flagellates may play a positive role in maintaining permeability in aquifers undergoing remediation treatments.

nahR, encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA

In Pseudomonas putida strain G7, a LysR-type positive transcriptional activator protein encoded by nahR is necessary for activation of two operons involved in naphthalene catabolism [Schell, M. A. & Poser, E. F. (1989). J Bacteriol 171, 837-846]. The role of an nahR homologue, NCIB-nahR, in another naphthalene-metabolizing bacterium, P. putida NCIB 9816-4 was verified. Targeted disruption of NCIB-nahR by homologous recombination resulted in a growth defect in the presence of naphthalene or salicylate as sole carbon and energy source. The nahR homologues and intergenic regions between nahR-like and nahG-like genes from P. putida NCIB 9816-4 and seven bacteria native to a naphthalene-rich coal tar contaminated site were amplified by PCR using degenerate primers. The amplified nahR homologues and the intergenic regions were cloned and sequenced. Alignment of the deduced amino acid sequences from NahR homologues revealed that NahR-like proteins showed only minor variations in all investigated naphthalene-degrading isolates. The intergenic regions, together with known NahR-binding sites showed the consensus NahR-protein-binding sites (5'-ATTCACGCTN(2)TGAT-3'). Surprisingly, amplified intergenic regions from naphthalene-degrading micro-organisms native to this study site were 100% identical to that of the pDTG1 plasmid (an archetypal naphthalene-catabolic plasmid from Pseudomonas putida NCIB 9816-4), but the nahR coding regions were not. DNA representing the uncultured microbial community was extracted from six sediment samples with varying coal tar exposure histories. PCR amplification of nahR from sediment DNA was observed in contaminated samples, but in uncontaminated samples only following laboratory incubation with naphthalene. The sediment-derived PCR products were sequenced and also found to be almost identical to known nahR genes. Thus, the structure and function of nahR-nahG regulatory genes appear to be highly conserved.

Effect of growth conditions and staining procedure upon the subsurface transport and attachment behaviors of a groundwater protist

The transport and attachment behaviors of Spumella guttula (Kent), a nanoflagellate (protist) found in contaminated and uncontaminated aquifer sediments in Cape Cod, Mass., were assessed in flowthrough and static columns and in a field injection-and-recovery transport experiment involving an array of multilevel samplers. Transport of S. guttula harvested from low-nutrient (10 mg of dissolved organic carbon per liter), slightly acidic, granular (porous) growth media was compared to earlier observations involving nanoflagellates grown in a traditional high-nutrient liquid broth. In contrast to the highly retarded (retardation factor of approximately 3) subsurface transport previously reported for S. guttula, the peak concentration of porous-medium-grown S. guttula traveled concomitantly with that of a conservative (bromide) tracer. About one-third of the porous-medium-grown nanoflagellates added to the aquifer were transported at least 2.8 m downgradient, compared to only approximately 2% of the broth-grown nanoflagellates. Flowthrough column studies revealed that a vital (hydroethidine [HE]) staining procedure resulted in considerably less attachment (more transport) of S. guttula in aquifer sediments than did a staining-and-fixation procedure involving 4',6'-diamidino-2-phenylindole (DAPI) and glutaraldehyde. The calculated collision efficiency (approximately 10(-2) for porous-medium-grown, DAPI-stained nanoflagellates) was comparable to that observed earlier for the indigenous community of unattached groundwater bacteria that serve as prey. The attachment of HE-labeled S. guttula onto aquifer sediment grains was independent of pH (over the range from pH 3 to 9) suggesting a primary attachment mechanism that may be fundamentally different from that of their prey bacteria, which exhibit sharp decreases in fractional attachment with increasing pH. The high degree of mobility of S. guttula in the aquifer sediments has important ecological implications for the protistan community within the temporally changing plume of organic contaminants in the Cape Cod aquifer.

Humic acid enhanced remediation of an emplaced diesel source in groundwater. 1. Laboratory-based pilot scale test

The enhanced solubility of petroleum-derived compounds in humic acid solutions is the basis for a new groundwater remediation technology. In this unique pilot-scale test, a stationary contaminant source consisting of diesel fuel was placed below the water table in a model sand aquifer (1.2 x 5.5 x 1.8-m deep) and flushed with water at a flow rate of 2 cm/h over 5 years. At 51 days, laboratory grade humic acid was added to the water and maintained at a level of approximately 0.8 g/l. The addition of humic acid had only a small impact on the aqueous transport of the BTEX components, which were rapidly dissolved from the diesel, but had a large effect on the flushing of PAHs, including methylated naphthalenes (MNs). Binding to aqueous humic acid enhanced the solubilization of MNs two- to tenfold. During aqueous transport, biodegradation of the BTEX and PAHs occurred, limiting the lateral and longitudinal extent of the diesel contaminant plume in the model aquifer. It appears that through enhanced solubilization, the overall biodegradation rate of the MNs was increased. As the various MNs were depleted from the diesel source, the MN plume shrank and then disappeared.

Marine protozoa produce organic matter with a high affinity for PCBs during grazing

Processes influencing organic carbon distribution and composition can control the speciation of organic contaminants such as polychlorinated biphenyls (PCBs) and ultimately determine their residence time in aquatic environments. Protozoan grazers are active in the remineralization and recycling of organic material both in the water column and at the sediment-water interface. Thus, they influence the quality and quantity of potential PCB binding substrates in the suspended and dissolved phases of aqueous systems. In this study, common headspace systems were used to compare the chlorobiphenyl-binding affinity of dissolved organic carbon (DOC) in protozoan and bacterial culture filtrates (<0.2 microm) relative to DOC in a seawater control. Culture filtrates from three marine protozoan species were compared-Uronema sp., Cafeteria sp., and Paraphysomonas imperforata. Each protozoan species was fed the same bacterial prey, Halomonas halodurans, which was also used as a bacterial control. Affinities of culture DOC for [14C]3,3',4,4'-tetrachlorobiphenyl (IUPAC 77) were normalized to DOC and surfactant concentrations. Values of DOC equilibrium partition coefficients (K(DOC)) ranged from 10(4.6) in seawater (Vineyard Sound, MA) to 10(5.4) and 10(5.5) in protist cultures, indicating that grazer-modified DOC was a better sorbent for PCBs than DOC in bacterial or seawater controls.

An assessment of natural biotransformation of petroleum hydrocarbons and chlorinated solvents at an aquifer plume transect

Field biogeochemical characterization and laboratory microcosm studies were performed to assess the potential for future biotransformation of trichloroethylene (TCE) and toluene in a plume containing petroleum hydrocarbons and chlorinated solvents at the former Wurtsmith Air Force Base in Oscoda, MI. In situ terminal electron accepting processes (TEAPs), contaminant composition and microbial phylogeny were studied at a plume transect 100 m downgradient of the source. The presence of reduced electron acceptors, relevant microbial communities, and elevated dissolved methane and carbon dioxide concentrations at the transect, as well as downgradient accumulation of BTEX metabolites and dechlorination products, indicated that past or current reductive dechlorination at the transect was likely driven by BTEX biodegradation in the methanogenic zone. However, TCE and toluene mineralization in sediment-groundwater microcosms without added electron acceptors did not exceed 5% during 300 days of incubation and was nearly invariant with original sediment TEAP, even following amendments of nitrogen and phosphorus. Mineralization rates were on the order of 0.0015-0.03 mumol/g day. After 8 months, microcosms showed evidence of methanogenesis, but CH4 and CO2 production arose from the degradation of contaminants other than toluene. Cis-dichloroethylene was observed in only one methanogenic microcosm after more than 500 days. It appears likely that spatially and temporally dynamic redox zonation at the plume transect will prevent future sustained reductive dehalogenation of highly chlorinated solvents, for during the course of a year, the predominant TEAP at the highly contaminated water table shifted from methanogenesis to iron- and sulfate-reduction. It is recommended that biotransformation studies combine considerations of long-term, spatially relevant changes in redox zonation with laboratory-scale studies of electron donor utilization and cometabolic substrate transformation to yield a more accurate assessment of natural bioattenuation of specific pollutants in aquifers contaminated by undefined organic waste mixtures.

The predatory soil flagellate Heteromita globosa stimulates toluene biodegradation by a Pseudomonas sp

A model food chain was established to investigate the influence of grazing by flagellates on bacteria degrading toluene in batch culture. The rate of toluene consumed by a Pseudomonas sp. strain PS+ (max. 0.37 fmol cell(-1) h(-1)) was significantly higher in the presence of the bacterivorous flagellate Heteromita globosa (max. 1.38 fmol cell(-1) h(-1)). A maximum increase of up to 7.5 times was observed in the rate of toluene consumed by these bacteria during exponential growth of this flagellate. Carbon conversion efficiency (CCE) of bacteria to flagellate biomass was estimated to be 33.4% based on measured biovolumes and published values for carbon contents. However, the CCE for toluene-derived carbon was lower (max. 4.9%) when calculations were based on incorporation of [ring-U-(14)C]toluene into biomass of flagellates grazing on labelled bacteria. The findings suggest a potential role for flagellates in bioremediation processes.