Impacts of Nutrients on Alkene Biodegradation Rates and Microbial Community Composition in Enriched Consortia from Natural Inocula

There is a growing need for biological and chemical methods for upcycling plastic waste streams. Pyrolysis processes can accelerate plastic depolymerization by breaking polyethylene into smaller alkene components which may be more biodegradable than the initial polymer. While the biodegradation of alkanes has been extensively studied, the role microorganisms play in alkene breakdown is not well understood. Alkene biodegradation holds the potential to contribute to the coupling of chemical and biological processing of polyethylene plastics. In addition, nutrient levels are known to impact rates of hydrocarbon degradation. Model alkenes were used (C6, C10, C16, and C20) to follow the breakdown capability of microbial communities from three environmental inocula in three nutrient levels over the course of 5 days. Higher-nutrient cultures were anticipated to exhibit enhanced biodegradation capabilities. Alkene mineralization was assessed by measuring CO production in the culture headspace using GC-FID (gas chromatography-flame ionization detection), and alkene breakdown was directly quantified by measuring extracted residual hydrocarbons using gas chromatography-mass spectrometry (GC/MS). Here, the efficacy of enriched consortia derived from the microbial communities of three inoculum sources (farm compost, Caspian Sea sediment, and an iron-rich sediment) at alkene breakdown was investigated over the course of 5 days across three nutrient treatments. No significant differences in CO production across nutrient levels or inoculum types were found. A high extent of biodegradation was observed in all sample types, with most samples achieving 60% to 95% biodegradation of all quantified compounds. Here, our findings indicate that alkene biodegradation is a common metabolic process in diverse environments and that nutrient levels common to culture media can support the growth of alkene-biodegrading consortia, primarily from the families , , and . Excess plastic waste poses a major environmental problem. Microorganisms can metabolize many of the breakdown products (alkenes) of plastics. While microbial degradation of plastics is typically slow, coupling chemical and biological processing of plastics has the potential to lead to novel methods for the upcycling of plastic wastes. Here, we explored how microbial consortia derived from diverse environments metabolize alkenes, which are produced by the pyrolysis of polyolefin plastics such as HDPE, and PP. We found that microbial consortia from diverse environments can rapidly metabolize alkenes of different chain lengths. We also explored how nutrients affect the rates of alkene breakdown and the microbial diversity of the consortia. Here, the findings indicate that alkene biodegradation is a common metabolism in diverse environments (farm compost, Caspian sediment, and iron-rich sediment) and that nutrient levels common to culture medium can support growth of alkene-biodegrading consortia, primarily from the families Xanthamonadaceae, Nocardiaceae, and Beijerinkiaceae

Open source vacuum oven design for low-temperature drying: Performance evaluation for recycled pet and biomass

Vacuum drying can dehydrate materials further than dry heat methods, while protecting sensitive materials from thermal degradation. Many industries have shifted to vacuum drying as cost-or time-saving measures. Small-scale vacuum drying, however, has been limited by the high costs of specialty scientific tools. To make vacuum drying more accessible, this study provides design and performance information for a small-scale open source vacuum oven, which can be fabricated from off-the-shelf and 3-D printed components. The oven is tested for drying speed and effectiveness on both waste plastic polyethylene terephthalate (PET) and a consortium of bacteria developed for bioprocessing of terephthalate wastes to assist in distributed recycling of PET for both additive manufacturing as well as potential food. Both materials can be damaged when exposed to high temperatures, making vacuum drying a desirable solution. The results showed that the open source vacuum oven was effective at drying both plastic and biomaterials, drying at a higher rate than a hot-air dryer for small samples or for low volumes of water. The system can be constructed for less than 20% of commercial vacuum dryer costs for several laboratory-scale applications, including dehydration of bio-organisms, drying plastic for distributed recycling and additive manufacturing, and chemical processing

The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth

Peer reviewedPublisher PD

Clay flocculation effect on microbial community composition in water and sediment

Clay-based flocculation techniques have been developed to mitigate harmful algal blooms; however, the potential ecological impacts on the microbial community are poorly understood. In this study, chemical measurements were combined with 16S rRNA sequencing to characterize the microbial community response to different flocculation techniques, including controls, clay flocculation, clay flocculation with zeolite, and clay flocculation with O2 added zeolite capping. Sediment bacterial biomass measured by PLFA were not significantly altered by the various flocculation techniques used. However, 16S rRNA sequencing revealed differences in water microbial community structure between treatments with and without zeolite capping. The differences were related to significant reductions of total nitrogen (TN), total phosphorus (TP) and ammonia (NH4+) concentration and increase of nitrate (NO3-) concentration in zeolite and O2 loaded zeolite capping. The relative abundance of ammonia oxidizing bacteria increased four-fold in zeolite capping microcosms, suggesting zeolite promoted absorbed ammonia removal in the benthic zone. Zeolite-capping promoted bacteria nitrogen cycling activities at the water-sediment interface. Potential pathogens that are usually adapted to eutrophic water bodies were reduced after clay flocculation. This study demonstrated clay flocculation did not decrease bacterial populations overall and may reduce regulatory indicators and pathogenic contaminants in water. Zeolite capping may also help prevent nutrients from being released back into the water thus preventing additional algal blooms

Microbial community dynamics during lake ice freezing

Many freshwater environments experience dramatic seasonal changes with some systems remaining ice-covered for most of the winter. Freshwater systems are also highly sensitive to environmental change. However, little is known about changes in microbial abundance and community composition during lake ice formation and times of persistent ice cover. The goal of this study is to characterize temporal dynamics of microbial communities during ice formation and persistent ice cover. Samples were collected in triplicate, five days per week from surface water in the Keweenaw Waterway between November and April. Environmental conditions along with microbial abundance and microbial community composition was determined. Distinct community composition was found between ice-free and ice-covered time periods with significantly different community composition between months. The microbial community underwent dramatic shifts in microbial abundance and diversity during the transitions into and out of ice cover. The richness of the microbial community increased during times of ice cover. Relatives of microbes involved in nitrogen cycling bloomed during times of ice cover as sequences related to known nitrifying taxa were significantly enriched during ice cover. These results help to elucidate how microbial abundance and diversity change over drastic seasonal transitions and how ice cover may affect microbial abundance and diversity

Evidence for Horizontal Gene Transfer of Anaerobic Carbon Monoxide Dehydrogenases

Carbon monoxide (CO) is commonly known as a toxic gas, yet both cultivation studies and emerging genome sequences of bacteria and archaea establish that CO is a widely utilized microbial growth substrate. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases ([Ni,Fe]-CODHs) in currently available genomic sequence databases. Currently, 185 out of 2887, or 6% of sequenced bacterial and archaeal genomes possess at least one gene encoding [Ni,Fe]-CODH, the key enzyme for anaerobic CO utilization. Many genomes encode multiple copies of [Ni,Fe]-CODH genes whose functions and regulation are correlated with their associated gene clusters. The phylogenetic analysis of this extended protein family revealed six distinct clades; many clades consisted of [Ni,Fe]-CODHs that were encoded by microbes from disparate phylogenetic lineages, based on 16S rRNA sequences, and widely ranging physiology. To more clearly define if the branching patterns observed in the [Ni,Fe]-CODH trees are due to functional conservation vs. evolutionary lineage, the genomic context of the [Ni,Fe]-CODH gene clusters was examined, and superimposed on the phylogenetic trees. On the whole, there was a correlation between genomic contexts and the tree topology, but several functionally similar [Ni,Fe]-CODHs were found in different clades. In addition, some distantly related organisms have similar [Ni,Fe]-CODH genes. Thermosinus carboxydivorans was used to observe horizontal gene transfer (HGT) of [Ni,Fe]-CODH gene clusters by applying Kullback–Leibler divergence analysis methods. Divergent tetranucleotide frequency and codon usage showed that the gene cluster of T. carboxydivorans that encodes a [Ni,Fe]-CODH and an energy-converting hydrogenase is dissimilar to its whole genome but is similar to the genome of the phylogenetically distant Firmicute, Carboxydothermus hydrogenoformans. These results imply that T carboxydivorans acquired this gene cluster via HGT from a relative of C. hydrogenoformans

COREXIT 9500 enhances oil biodegradation and changes microbial community structure of oil-enriched microcosms

To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio, Idiomarina, Marinobacter, Alcanivorax, and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium, Alcanivorax, and Oleispira. Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira, Marinobacter, and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C

Colwellia psychrerythraea Strains from Distant Deep Sea Basins Show Adaptation to Local Conditions

Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraeawas investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from the Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. There appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates

Surface Water Microbial Community Response to the Biocide 2,2-Dibromo-3-Nitrilopropionamide, Used in Unconventional Oil and Gas Extraction.

Production of unconventional oil and gas continues to rise, but the effects of high-density hydraulic fracturing (HF) activity near aquatic ecosystems are not fully understood. A commonly used biocide in HF, 2,2-dibromo-3-nitrilopropionamide (DBNPA), was studied in microcosms of HF-impacted (HF+) versus HF-unimpacted (HF-) surface water streams to (i) compare the microbial community response, (ii) investigate DBNPA degradation products based on past HF exposure, and (iii) compare the microbial community response differences and similarities between the HF biocides DBNPA and glutaraldehyde. The microbial community responded to DBNPA differently in HF-impacted versus HF-unimpacted microcosms in terms of the number of 16S rRNA gene copies quantified, alpha and beta diversity, and differential abundance analyses of microbial community composition through time. The differences in microbial community changes affected degradation dynamics. HF-impacted microbial communities were more sensitive to DBNPA, causing the biocide and by-products of the degradation to persist for longer than in HF-unimpacted microcosms. A total of 17 DBNPA by-products were detected, many of them not widely known as DBNPA by-products. Many of the brominated by-products detected that are believed to be uncharacterized may pose environmental and health impacts. Similar taxa were able to tolerate glutaraldehyde and DBNPA; however, DBNPA was not as effective for microbial control, as indicated by a smaller overall decrease of 16S rRNA gene copies/ml after exposure to the biocide, and a more diverse set of taxa was able to tolerate it. These findings suggest that past HF activity in streams can affect the microbial community response to environmental perturbation such as that caused by the biocide DBNPA.IMPORTANCE Unconventional oil and gas activity can affect pH, total organic carbon, and microbial communities in surface water, altering their ability to respond to new environmental and/or anthropogenic perturbations. These findings demonstrate that 2,2-dibromo-3-nitrilopropionamide (DBNPA), a common hydraulic fracturing (HF) biocide, affects microbial communities differently as a consequence of past HF exposure, persisting longer in HF-impacted (HF+) waters. These findings also demonstrate that DBNPA has low efficacy in environmental microbial communities regardless of HF impact. These findings are of interest, as understanding microbial responses is key for formulating remediation strategies in unconventional oil and gas (UOG)-impacted environments. Moreover, some DBNPA degradation by-products are even more toxic and recalcitrant than DBNPA itself, and this work identifies novel brominated degradation by-products formed