Simple Genomic Traits Predict Rates of Polysaccharide Biodegradation.

Natural and chemically modified polysaccharides are extensively employed across a wide array of industries, leading to their prevalence in the waste streams of industrialized societies. With projected increasing demand, a pressing challenge is to swiftly assess and predict their biodegradability to inform the development of new sustainable materials. In this study, we developed a scalable method to evaluate polysaccharide breakdown by measuring microbial growth and analyzing microbial genomes. Our approach, applied to polysaccharides with various structures, correlates strongly with well-established regulatory methods based on oxygen demand. We show that modifications to the polysaccharide structure decreased degradability and favored the growth of microbes adapted to break down chemically modified sugars. More broadly, we discovered two main types of microbial communities associated with different polysaccharide structures─one dominated by fast-growing microbes and another by specialized degraders. Surprisingly, we were able to predict biodegradation rates based only on two genomic features that define these communities: the abundance of genes related to rRNA (indicating fast growth) and the abundance of glycoside hydrolases (enzymes that break down polysaccharides), which together predict nearly 70% of the variation in polysaccharide breakdown. This suggests a trade-off, whereby microbes are either adapted for fast growth or for degrading complex polysaccharide chains, but not both. Finally, we observe that viral elements (prophages) encoded in the genomes of degrading microbes are induced in easily degradable polysaccharides, leading to complex dynamics in biomass accumulation during degradation. In summary, our work provides a practical approach for efficiently assessing polymer degradability and offers genomic insights into how microbes break down polysaccharides.

Exploring structure-activity relationships for polymer biodegradability by microorganisms.

Research on the environmental biodegradation or microbial biodegradation of polymers has substantially increased recently due to growing demand for biodegradable polymers for certain applications. Environmental biodegradation of a polymer depends on the intrinsic biodegradability of the polymer and the characteristics of the receiving environment. The intrinsic biodegradability of a polymer is determined by the chemical structure and resulting physical properties (e.g., glass transition temperature, melting temperature, modulus of elasticity, crystallinity, and crystal structure) of the polymer. Quantitative structure-activity relationships (QSARs) on biodegradability have been well-established for discrete (non-polymeric) organic chemicals, but not for polymers due to the absence of adequate biodegradability data based on consistent and standardized biodegradation tests with appropriate characterization and reporting of the polymers tested. This review summarizes empirical structure-activity relationships (SARs) for biodegradability of polymers in laboratory studies involving various environmental matrices. In general, polyolefins with carbon-carbon chain are not biodegradable, while polymers containing labile bonds such as ester, ether, amide, or glycosidic bonds in their polymer chain may be favorable for biodegradation. Under a univariate scenario, polymers with higher molecular weight, higher crosslinking, lower water solubility, higher degree of substitution (i.e., higher average number of substituted functional groups per monomer unit), and higher crystallinity may result in reduced biodegradability. This review paper also highlights some of the challenges that hamper QSAR development for polymer biodegradability, stresses the need for better characterization of polymer structures used in biodegradation studies, and emphasizes the necessity for consistent testing conditions for the ease of cross-comparison and quantitative modeling analysis during future QSAR development.

Synthesis and Biodegradation Studies of Low-Dispersity Poly(acrylic acid).

Poly(acrylic acid) (PAA) is produced on an industrial scale and widely-used in applications such as personal care products and cleaning formulations that end up "down-the-drain." Relatively high molecular weight PAA is considered poorly biodegradable, but little is known about the biodegradability of low molecular weight PAA at the wastewater treatment plant according to current regulatory and industrial Organization for Economic Co-operation and Development (OECD) standards. The synthesis, separation, and characterization of a series of ultralow dispersity PAA oligomers (i.e., D < 1.10) in the molecular weight range Mn ≈ 350-1200 Da and the results of biodegradability testing are reported. Miniaturized, high-throughput screening studies in a parallel respirometer reveals a strong trend toward lower biodegradation at higher molecular weight; these results are confirmed and expanded using standardized method OECD 301F. Biodegradability reaches ≈40% at Mn = 380 Da, ≈26% at Mn = 770 Da, and ≈17% at Mn = 1190 Da for discrete polyacid oligomers. These data not only shed light on potential biodegradation mechanisms for linear PAA, but also may inspire the future design of biodegradable PAA-containing macromolecules.

Knowledge Gaps in Polymer Biodegradation Research.

The environmental fate of polymers has attracted growing attention in the academic, industrial, and regulatory communities as well as in the general public as global production and use of polymers continue to increase. Biodegradable polymers especially have drawn significant interest. Polymer biodegradation literature published over the past decade was reviewed to compare test methods commonly used for evaluating polymer biodegradation, and to identify key areas for improvement. This paper examines key aspects of study design for polymer biodegradation such as physical form of the test material, use of appropriate reference materials, selection of test systems, and advantages and limitations of various analytical methods for determining biodegradation. Those aspects of study design are critical for determining the outcome of polymer biodegradation studies. This paper identifies several knowledge gaps for assessing polymer biodegradation and provides four key recommendations. (1) develop standardized guidelines for each specific environmental matrix (compost, activated sludge, marine environments, etc.) that can used for all polymer types, (2) develop accelerated biodegradation test methods and predictive methods for polymers, (3) develop an integrated analytical approach using multiple simple, and effective analytical methods, and (4) develop new frameworks for assessing the overall persistence of polymers and are accepted by the greater scientific community.

Multi-laboratory Validation of a New Marine Biodegradation Screening Test for Chemical Persistence Assessment.

Current biodegradation screening tests are not specifically designed for persistence assessment of chemicals, often show high inter- and intra-test variability, and often give false negative biodegradation results. Based on previous studies and recommendations, an international ring test involving 13 laboratories validated a new test method for marine biodegradation with a focus on improving the reliability of screening to determine the environmental degradation potential of chemicals. The new method incorporated increased bacterial cell concentrations to better represent the microbial diversity; a chemical is likely to be exposed in the sampled environments and ran beyond 60 days, which is the half-life threshold for chemical persistence in the marine environment. The new test provided a more reliable and less variable characterization of the biodegradation behavior of five reference chemicals (sodium benzoate, triethanolamine, 4-nitrophenol, anionic polyacrylamide, and pentachlorophenol), with respect to REACH and OSPAR persistence thresholds, than the current OECD 306 test. The proposed new method provides a cost-effective screening test for non-persistence that could streamline chemical regulation and reduce the cost and animal welfare implications of further higher tier testing.

Dissipation of double-stranded RNA in aquatic microcosms.

Silencing genes of a pest with double-stranded RNA (dsRNA) is a promising new pest management technology. As part of the environmental risk assessment for dsRNA-based products, the environmental fate and the potential for adverse effects to on-target organisms should be characterized. In the present study, a nonbioactive dsRNA was spiked into the water column of a water and sediment microcosm to mimic drift from a spray application run off of unbound dsRNA or transport of plant tissues. Dissipation of dsRNA in the water column and partitioning into sediment was determined. The dsRNA rapidly dissipated in the water column and was below the limit of detection after 96 h. The levels detected in the sediment were not significant and may indicate rapid degradation in the water column prior to partitioning to sediment. Environ Toxicol Chem 2017;36:1249-1253. © 2016 SETAC.

Enzyme-linked immunosorbent assay detection and bioactivity of Cry1Ab protein fragments.

The continuing use of transgenic crops has led to an increased interest in the fate of insecticidal crystalline (Cry) proteins in the environment. Enzyme-linked immunosorbent assays (ELISAs) have emerged as the preferred detection method for Cry proteins in environmental matrices. Concerns exist that ELISAs are capable of detecting fragments of Cry proteins, which may lead to an overestimation of the concentration of these proteins in the environment. Five model systems were used to generate fragments of the Cry1Ab protein, which were then analyzed by ELISAs and bioassays. Fragments from 4 of the model systems were not detectable by ELISA and did not retain bioactivity. Fragments from the proteinase K model system were detectable by ELISA and retained bioactivity. In most cases, ELISAs appear to provide an accurate estimation of the amount of Cry proteins in the environment, as detectable fragments retained bioactivity and nondetectable fragments did not retain bioactivity. Environ Toxicol Chem 2016;35:3101-3112. © 2016 SETAC.

A Review of Cry Protein Detection with Enzyme-Linked Immunosorbent Assays.

The widespread use of Cry proteins in insecticide formulations and transgenic crops for insect control has led to an increased interest in the environmental fate of these proteins. Although several detection methods are available to monitor the fate of Cry proteins in the environment, enzyme-linked immunosorbent assays (ELISAs) have emerged as the preferred detection method, due to their cost-effectiveness, ease of use, and rapid results. Validation of ELISAs is necessary to ensure accurate measurements of Cry protein concentrations in the environment. Validation methodology has been extensively researched and published for the areas of sensitivity, specificity, accuracy, and precision; however, cross validation of ELISA results has been studied to a lesser extent. This review discusses the use of ELISAs for detection of Cry proteins in environmental samples and validation of ELISAs and introduces cross validation. The state of Cry protein environmental fate research is considered through a critical review of published literature to identify areas where the use of validation protocols can be improved.

Disposition of atrazine metabolites following uptake and degradation of atrazine in switchgrass.

Extensive use of the agricultural herbicide atrazine has led to contamination of numerous ground and surface water bodies. Research has shown that it can have a variety of negative impacts on numerous non-target organisms in the environment. Phytoremediation is one strategy that has been studied to remove atrazine contamination. This paper investigates the hypothesis that switchgrass (Panicum virgatum) can exude metabolites of atrazine after uptake and degradation, which has been suggested by prior research. Pots planted with switchgrass were treated with a 4 ppm solution of atrazine spiked with [14C]atrazine. After 4 days, switchgrass plants were transplanted to new pots with fresh sand. Four days later, the pots were sacrificed, and sand and plant samples were extracted. Plant and sand samples were analyzed for the presence of atrazine and its major metabolites. The percentage of radiotracer remaining as the parent atrazine was observed to decrease over the course of the study while the percentages of the metabolites were observed to increase. The presence of the metabolite cyanuric acid in a switchgrass phytoremediation system is reported for the first time.

Fate of atrazine in switchgrass-soil column system.

Atrazine, a broad-leaf herbicide, has been used widely to control weeds in corn and other crops for several decades and its extensive used has led to widespread contamination of soils and water bodies. Phytoremediation with switchgrass and other native prairie grasses is one strategy that has been suggested to lessen the impact of atrazine in the environment. The goal of this study is to characterize: (1) the uptake of atrazine into above-ground switchgrass biomass; and (2) the degradation and transformation of atrazine over time. A fate study was performed using mature switchgrass columns treated with an artificially-created agricultural runoff containing 16 ppm atrazine. Soil samples and above-ground biomass samples were taken from each column and analyzed for the presence of atrazine and its chlorinated metabolites. Levels of atrazine in both soil and plant material were detectable through the first 2 weeks of the experiment but were below the limit of detection by Day 21. Levels of deethylatrazine (DEA) and didealkylatrazine (DDA) were detected in soil and plant tissue intermittently over the course of the study, deisopropylatrazine (DIA) was not detected at any time point. A radiolabel study using [(14)C]atrazine was undertaken to observe uptake and degradation of atrazine with more sensitivity. Switchgrass columns were treated with a 4 ppm atrazine solution, and above-ground biomass samples were collected and analyzed using HPLC and liquid scintillation counting. Atrazine, DEA, and DIA were detected as soon as 1d following treatment. Two other metabolites, DDA and cyanuric acid, were detected at later time points, while hydroxyatrazine was not detected at all. The percentage of atrazine was observed to decrease over the course of the study while the percentages of the metabolites increased. Switchgrass plants appeared to exhibit a threshold in regard to the amount of atrazine taken up by the plants; levels of atrazine in leaf material peaked between Days 3 and 4 in both studies.