Lead absorption mechanisms in bacteria as strategies for lead bioremediation

Bacteria exhibit a number of metabolism-dependent and metabolism-independent processes for the uptake and accumulation of toxic metals. The removal of these metals from environmental sources such as soil, sludge, and wastewaters using microbe-based technologies provide an alternative for their recovery and remediation. Lead (Pb) is a pervasive metal in the environment that adversely affects all living organisms. Many aspects of metal-microbe interactions remain unexploited in biotechnology and further development and application is necessary, particularly to the problem of Pb release into the environment. Thus, this review provides a synopsis of the most important bacterial phenotypes and biochemical attributes that are instrumental in lead bioremediation, along with what is known of their genetic background that can be exploited or improved through genetic engineering. This review also highlights the potential of Pb-resistant bacteria in bringing about detoxification of Pb-contaminated terrestrial and aquatic systems in a highly sustainable and environmental friendly manner, and the existing challenges that still lie in the path to in situ and large-scale bioremediation.http://deepblue.lib.umich.edu/bitstream/2027.42/191239/2/AMB Tiquia-Arashiro2018_Article_LeadAbsorptionMechanismsInBact.pdfPublished versio

Sustainable technologies: Bioenergy and biofuel from biowaste and biomass

http://deepblue.lib.umich.edu/bitstream/2027.42/191245/2/Tiquia and Mormile 2013.pdfPublished versio

Butanol tolerance of carboxydotrophic bacteria isolated from manure composts

ABSTRACT: Carboxydotrophic bacteria (carboxydotrophs) have the ability to uptake carbon monoxide (CO) and synthesize butanol. The aims of this study were to determine the butanol tolerance and biological production of butanol carboxydotrophic strains. In this study, 11 carboxydotrophic strains were exposed to increasing n-butanol concentrations (1–3% vol/vol) to determine their effect on growth. Butanol production by the strains was quantified and the identity of the strains was elucidated using 16S rRNA sequencing. The carboxydotrophic strains possessed inherent tolerance to butanol and tolerated up to 3% n-butanol. Among the 11 strains, T1-16, M2-32 and M3-28 were the most tolerant to butanol. The 16S rRNA gene sequence of these strains was similar (99% nucleotide similarity) to the butanol-tolerant strains Bacillus licheniformis YP1A, Pediococcus acidilacti IMUA20068 and Enterococcus faecium IMAU60169, respectively. The carboxydotrophic strains screened in this study have two distinct features: (1) high tolerance to butanol and (2) natural production of low concentration of butanol from CO, which distinguish them from other screened butanol-tolerant strains. The butanol tolerance of these carboxydotrophic strains makes them ideal for genetic studies, particularly the molecular mechanisms that enable them to survive such hostile environmental conditions and the identification of genes that confer tolerance to butanol.http://deepblue.lib.umich.edu/bitstream/2027.42/191243/2/Butanol tolerance of carboxydotrophic bacteria isolated from manure composts (1).pdfPublished versionDescription of Butanol tolerance of carboxydotrophic bacteria isolated from manure composts (1).pdf : Accepted versio

Screening for novel bacteria from the bioenergy feedstock switchgrass (Panicum virgatum L.)

Switchgrass is considered as a good candidate for biofuel, especially ethanol production due to its huge biomass output and high cellulose content. In a search for novel microorganisms capable of using and degrading switchgrass to produce sugars and ethanol, enrichment experiments were established to screen for microorganisms from soil samples obtained at the University of Tennessee Agricultural Research Station, Jackson, Tennessee. Three enrichments were prepared and incubated at different pH and temperatures: (1) 30°C, pH 5, (2) 30°C, pH 8 and (3) 60°C, pH5. Bulk community DNA was directly extracted from the enrichments. Microbial community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichment cultures containing switchgrass as the carbon source. The mesophilic enrichments were dominated by Sarcina, Anaerobacter, and Clostrium, which were not found in the thermophilic enrichment. The thermophilic enrichment selected for two types of bacteria belonging to the class Bacilli (Geobacillus and Saccharococcus). The thermophilic enrichments were dominated by the Geobacillus spp. (Firmicutes, class Bacilli), and Saccharococcus (Firmicutes, class Bacilli); both containing thermophilic microorganisms with some cellulolytic members. Enzymatic assays detected the presence of enzymes involved in cellulose (β-glucosidase and cellobiohydrolase) and hemicellulose degradations (β-xylosidase); and the activity tends to be higher in the enrichments incubated at 30°C. © 2013 Taylor and Francis.http://deepblue.lib.umich.edu/bitstream/2027.42/191246/2/Plecha et al., 2013.pdfPublished versio

Applicability of API ZYM to capture seasonal and spatial variabilities in lake and river sediments

Waters draining into a lake carry with them much of the suspended sediment that is transported by rivers and streams from the local drainage basin. The organic matter processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and evaluate some of these variabilities in the sediments, we sampled six sites: three from the St. Clair River and three from Lake St. Clair in spring, summer, fall, and winter of 2016. At all sites and dates, we investigated the spatial and temporal variations in 19 extracellular enzyme activities using API ZYM. Our results indicated that a broad range of enzymes were found to be active in the sediments. Phosphatases, lipases, and esterases were synthesized most intensively by the sediment microbial communities. No consistent difference was found between the lake and sediment samples. Differences were more obvious between sites and seasons. Sites with the highest metabolic (enzyme) diversity reflected the capacity of the sediment microbial communities to breakdown a broader range of substrates and may be linked to differences in river and lake water quality. The seasonal variability of the enzymes activities was governed by the variations of environmental factors caused by anthropogenic and terrestrial inputs, and provides information for a better understanding of the dynamics of sediment organic matter of the river and lake ecosystems. The experimental results suggest that API ZYM is a simple and rapid enzyme assay procedure to evaluate natural processes in ecosystems and their changes.http://deepblue.lib.umich.edu/bitstream/2027.42/191235/2/2019 API ZYM paper.pdfPublished versionDescription of 2019 API ZYM paper.pdf : Published versio

Lead-resistant bacteria from Saint Clair River sediments and Pb removal in aqueous solutions

Lead is an extensive contaminant. Pb-resistant bacterial strains were isolated from Saint Clair River sediments on two enrichment media with increasing concentrations of Pb (NO3)2. Bacterial strains that grew at 1.25 or 1.5 g L−1 of Pb (NO3)2 L−1) were purified and selected for further study. Ninety-seven Pb-resistant strains were screened for the ability to produce bioflocculants. The majority of the Pb-resistant strains demonstrated moderate to high flocculation activity. Metal removal assays demonstrated that the higher is the flocculation activity, the higher is the efficiency of metal removal. In the multi-metal solutions, the bacterial strain with the highest flocculation activity (R19) had the highest metal removing capability (six out of eight metals) and the highest metal removal efficiency. The highly selective affinity towards Pb2+ observed for strain R19 suggests its use for the recovery of Pb2+ from multiple metal solutions. Because they are well adapted to unfavorable conditions due to their resistance to metals (e.g., Pb) and antibiotics, these characteristics may help in developing an effective process for wastewater treatment using these strains.http://deepblue.lib.umich.edu/bitstream/2027.42/191240/2/Applied Microbiology and Biotechnology_2018.pdfPublished versionDescription of Applied Microbiology and Biotechnology_2018.pdf : Accepted versio

Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability.http://deepblue.lib.umich.edu/bitstream/2027.42/191244/2/Flood et al. 2015.pdfPublished versio

Isolation and screening of carboxydotrophs isolated from composts and their potential for butanol synthesis

Carboxydotrophs are known for their ability to convert carbon monoxide (CO) to butanol through fermentation. Such a platform offers a promising alternative approach to biofuel production from synthesis gas feedstocks. In this study, carboxydotrophs were isolated from various manure compost. Out of 500 isolates, only 11 carboxydotrophs (7 mesophiles and 4 thermophiles) were found to utilize CO as the sole source of carbon and energy. To assess the biochemical basis for their ability to produce biofuel (butanol), the level of activities of CO dehydrogenase (CODH), hydrogenase and butanol dehydrogenase (BDH) enzymes for these isolates against the known carboxydotroph, Butyribacterium methylotrophicum was assessed. All isolates showed evidence of enzyme activities (0.16-2.20 μmol min-1), with the majority exhibiting higher activities compared with the known carboxydotroph, B. methylotrophicum (0.33-0.71 μmol min-1). The level of activities for CODH and BDH ranged from 0.163-3.59 μmol min-1 and 0.19-2.2 μmol min -1, respectively. Three isolates (M7-1, T2-22, and T3-14) demonstrated enzymatic activity three to seven times higher than B. methylotrophicum. Of these, T2-22 exhibited the highest BDH activity and shows great promise in the conversion of toxic CO into butanol more so than other carboxytotrophs known thus far. This study revealed some biochemical basis for butanol production from CO by carboxydotrophs. However, more research is needed to discover a direct biological route for butanol production from CO to strengthen their potential for synthesis gas bioprocessing. Follow-up work will focus on whole-genome sequencing of the promising isolate T2-22 to provide system-level insights into how carboxydotrophs utilize and regulate their molecular machineries for butanol production. © 2013 Taylor and Francis.http://deepblue.lib.umich.edu/bitstream/2027.42/191247/2/Nguyen et al., 2013.pdfPublished versio

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations

High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ∼74% detected in the proteome, ∼6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu stress was downregulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.http://deepblue.lib.umich.edu/bitstream/2027.42/191241/2/ISME Journal_2018.pdfPublished versionDescription of ISME Journal_2018.pdf : Accepted versio