Framework for field-scale application of molecular biological tools to support natural and enhanced bioremediation.

Microorganisms naturally present at environmental contaminated sites are capable of biodegrading, biotransforming, or removing contaminants in soil and groundwater through bioremediation processes. Cleanup strategies and goals for site remediation can be effectively achieved by bioremediation leveraging the capabilities of microorganisms to biotransform contaminants into lesser or non-toxic end products; however, reproducible success can be limited by inadequate design or performance monitoring. A group of biological analyses collectively termed molecular biological tools (MBTs) can be used to assess the contaminant-degrading capabilities and activities of microorganisms present in the environment and appropriately implement bioremediation approaches. While successful bioremediation has been demonstrated through previously described lab-scale studies and field-scale implementation for a variety of environmental contaminants, design and performance monitoring of bioremediation has often been limited to inferring biodegradation potential, occurrence, and pathways based on site geochemistry or lab-scale studies. Potential field-scale application of MBTs presents the opportunity to more precisely design and monitor site-specific bioremediation approaches. To promote standardization and successful implementation of bioremediation, a framework for field-scale application of MBTs within a multiple lines of evidence (MLOE) approach is presented. The framework consists of three stages: (i) "Assessment" to evaluate naturally occurring biogeochemical conditions and screen for potential applicability of bioremediation, (ii) "Design" to define a site-specific bioremediation approach and inform amendment selection, and (iii) "Performance Monitoring" to generate data to measure or infer bioremediation progress following implementation. This framework is introduced to synthesize the complexities of environmental microbiology and guide field-scale application of MBTs to assess bioremediation potential and inform site decision-making.

Increasing in situ bioremediation effectiveness through field-scale application of molecular biological tools.

Leveraging the capabilities of microorganisms to reduce (degrade or transform) concentrations of pollutants in soil and groundwater can be a cost-effective, natural remedial approach to manage contaminated sites. Traditional design and implementation of bioremediation strategies consist of lab-scale biodegradation studies or collection of field-scale geochemical data to infer associated biological processes. While both lab-scale biodegradation studies and field-scale geochemical data are useful for remedial decision-making, additional insights can be gained through the application of Molecular Biological Tools (MBTs) to directly measure contaminant-degrading microorganisms and associated bioremediation processes. Field-scale application of a standardized framework pairing MBTs with traditional contaminant and geochemical analyses was successfully performed at two contaminated sites. At a site with trichloroethene (TCE) impacted groundwater, framework application informed design of an enhanced bioremediation approach. Baseline abundances of 16S rRNA genes for a genus of obligate organohalide-respiring bacteria (i.e., Dehalococcoides) were measured at low abundances (101-102 cells/mL) within the TCE source and plume areas. In combination with geochemical analyses, these data suggested that intrinsic biodegradation (i.e., reductive dechlorination) may be occurring, but activities were limited by electron donor availability. The framework was utilized to support development of a full-scale enhanced bioremediation design (i.e., electron donor addition) and to monitor remedial performance. Additionally, the framework was applied at a second site with residual petroleum hydrocarbon (PHC) impacted soils and groundwater. MBTs, specifically qPCR and 16S gene amplicon rRNA sequencing, were used to characterize intrinsic bioremediation mechanisms. Functional genes associated with anaerobic biodegradation of diesel components (e.g., naphthyl-2-methyl-succinate synthase, naphthalene carboxylase, alkylsuccinate synthase, and benzoyl coenzyme A reductase) were measured to be 2-3 orders of magnitude greater than unimpacted, background samples. Intrinsic bioremediation mechanisms were determined to be sufficient to achieve groundwater remediation objectives. Nonetheless, the framework was further utilized to assess that an enhanced bioremediation could be a successful remedial alternative or complement to source area treatment. While bioremediation of chlorinated solvents, PHCs, and other contaminants has been demonstrated to successfully reduce environmental risk and reach site goals, the application of field-scale MBT data in combination with contaminant and geochemical data analyses to design, implement, and monitor a site-specific bioremediation approach can result in more consistent remedy effectiveness.

Abundant porewater Mn(III) is a major component of the sedimentary redox system.

Soluble manganese(III) [Mn(III)] can potentially serve as both oxidant and reductant in one-electron-transfer reactions with other redox species. In near-surface sediment porewater, it is often overlooked as a major component of Mn cycling. Applying a spectrophotometric kinetic method to hemipelagic sediments from the Laurentian Trough (Quebec, Canada), we found that soluble Mn(III), likely stabilized by organic or inorganic ligands, accounts for up to 90% of the total dissolved Mn pool. Vertical profiles of dissolved oxygen and dissolved and solid Mn suggest that soluble Mn(III) is primarily produced via oxidation of Mn(II) diffusing upwards from anoxic sediments with lesser contributions from biotic and abiotic reductive dissolution of MnO2. The conceptual model of the sedimentary redox cycle should therefore explicitly include dissolved Mn(III).

The molecular biogeochemistry of manganese(II) oxidation.

Micro-organisms capable of oxidizing the redox-active transition metal manganese play an important role in the biogeochemical cycle of manganese. In the present mini-review, we focus specifically on Mn(II)-oxidizing bacteria. The mechanisms by which bacteria oxidize Mn(II) include a two-electron oxidation reaction catalysed by a novel multicopper oxidase that produces Mn(IV) oxides as the primary product. Bacteria also produce organic ligands, such as siderophores, that bind to and stabilize Mn(III). The realization that this stabilized Mn(III) is present in many environments and can affect the redox cycles of other elements such as sulfur has made it clear that manganese and the bacteria that oxidize it profoundly affect the Earth's biogeochemistry.

Simultaneous determination of soluble manganese(III), manganese(II) and total manganese in natural (pore)waters.

A new spectrophotometric protocol was developed for the simultaneous determination of soluble Mn(III), Mn(II) and total Mn [sum of soluble Mn(III) and Mn(II)] in sediment porewaters using a water soluble meso-substituted porphyrin [α,ß,γ,δ-tetrakis(4-carboxyphenyl)porphine (T(4-CP)P)]. A simple kinetic rate model is used to quantify soluble Mn(II), Mn(III) and total Mn concentrations during a metal substitution reaction. Under optimized conditions, the method accurately determines soluble Mn(II) and Mn(III) within a concentration range of 100 nM-10 µM. The detection limit of total soluble Mn is 50 nM. Using this method, soluble Mn(II) and Mn(III) concentrations were determined in standard solutions within 0.4-2% of the known values and agreed closely with results of inductively coupled plasma mass spectrometric and voltammetric analyses. The procedure was successfully applied to determine soluble Mn(II), Mn(III) and total Mn in sediment porewaters of the Lower St. Lawrence Estuary. Mn(III) represented up to 85% of the total soluble Mn pool in surface sediments.

Marine chemical technology and sensors for marine waters: potentials and limits.

A significant need exists for in situ sensors that can measure chemical species involved in the major processes of primary production (photosynthesis and chemosynthesis) and respiration. Some key chemical species are O2, nutrients (N and P), micronutrients (metals), pCO2, dissolved inorganic carbon (DIC), pH, and sulfide. Sensors need to have excellent detection limits, precision, selectivity, response time, a large dynamic concentration range, low power consumption, robustness, and less variation of instrument response with temperature and pressure, as well as be free from fouling problems (biological, physical, and chemical). Here we review the principles of operation of most sensors used in marine waters. We also show that some sensors can be used in several different oceanic environments to detect the target chemical species, whereas others are useful in only one environment because of various limitations. Several sensors can be used truly in situ, whereas many others involve water brought into a flow cell via tubing to the analyzer in the environment or aboard ship. Multi-element sensors that measure many chemical species in the same water mass should be targeted for further development.