Whole genome sequencing data of Acinetobacter venetianus JKSF06 collected from Houston ship channel sediment in La Porte, Texas.

Acinetobacter venetianus is a Gram-negative, mesophilic bacterium that thrives in aquatic environments. Here, we present the whole genome sequence of A. venetianus JKSF06, isolated from sediment that was collected in La Porte, Texas, near the southern terminus of the Houston Ship Channel into the Gulf of Mexico. The JKSF06 strain harbors multiple xenobiotic gene determinants targeting environmental waste that can be found here, including petroleum hydrocarbons and n-alkanes. In addition, JKSF06 can actively degrade organophosphate phophotriesters such ethyl paraoxon. In total, the genome of JKSF06 consists of 3,462,857 bp encoding for 3173 putative proteins. The complete sequence of A. venetianus JKSF06 can be viewed under accession LSVD00000000.1 through the National Center for Biotechnology Information (NCBI).

Whole genome sequencing data of Raoultella ornithinolytica PX02 isolated from San Jacinto river sediment in Baytown, Texas.

Raoultella ornithinolytica PX02 is a Gram-negative, encapsulated bacterium, part of the Enterobacteriaceae family, emerging as a notable human pathogen. Here, we present the whole genome sequence of R. ornithinolytica PX02 isolated from San Jacinto River sediment near a Burnet Shores community in Baytown, Texas. This microorganism harbors a large 200,000 bp incF plasmid and can potentially be a significant antibiotic reservoir. The PX02 genome consists of 5,970,914 base pairs encoding approximately 5,661 functional proteins. Strain PX02 (chromosomal and plasmid) was compiled at the scaffold level and can be accessed through the National Center for Biotechnology Information database under accession NZ_NJBC00000000.1.

Shotgun metagenomics of indigenous bacteria collected from the banks of the San Jacinto River for biodegradation of aromatic waste.

Several Eastern Harris County communities lie near the now enclosed San Jacinto River (SJR) Waste Pit Superfund, a dumping ground for chlorinated dioxins and other paper mill waste products. Currently, no active monitoring of the SJR is conducted for these toxins with the exact concentration and health impact to the area unknown. As such, remediation and monitoring efforts outside of the Superfund itself could be necessary. To better understand the possible environmental fate of these aromatics, here we provide a shotgun metagenomic analysis of the structural and putative functional diversity of the SJR microbiome from two impacted Channelview, Texas communities bordering the Superfund. Results show that the underlying SJR microbiome possesses a core of metabolic enzymes related to the ß-ketoadipate and benzoate degradation pathways. This suggests possible endpoints for many aromatics found deposited in the SJR including dioxin-like compounds. However, degradation biomarkers related to the priming and initial cleavage of chlorinated dioxin-like aromatics while present, are poorly concentrated across sampled sites. This may be due in part to decreased coverage of low abundance bacterial species, but also be a contributing factor leading to increased recalcitrance of these compounds in this environment compared to other aromatics.

Genome data of Stenotrophomonas maltophilia DF07 collected from polluted river sediment reveals an opportunistic pathogen and a potential antibiotic reservoir.

Stenotrophomonas maltophilia DF07 is a gram negative bacterium isolated from polluted San Jacinto River sediment near Moncrief Park in Channelview, Texas. The genome of strain DF07 (chromosome and plasmid) was compiled at the scaffold level and can be accessed through the National Center for Biotechnology Information database under accession NZ_NJGC00000000. The DF07 genome consists of a total of 4,801,842 bp encoding for approximately 4,351 functional proteins. Approximately 86 proteins are associated with broad-spectrum antibiotic resistance, 11 are associated with bacteriocin production, and a total of 17 proteins encode for an assortment of Mycobacterium-like virulence and invasion operons. S. maltophilia DF07 is genetically similar to the nosocomial S. maltophilia strain AU12-09, but also harbors an unusually large plasmid that encodes for over 150 proteins of unknown function. Taken together, this strain is potentially an important antibiotic reservoir and its origin within a recreational park merits further study of the area.

Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity.

Six organophosphate-degrading bacterial strains collected from farm and ranch soil rhizospheres across the Houston-metropolitan area were identified as strains of Pseudomonas putida (CBF10-2), Pseudomonas stutzeri (ODKF13), Ochrobactrum anthropi (FRAF13), Stenotrophomonas maltophilia (CBF10-1), Achromobacter xylosoxidans (ADAF13), and Rhizobium radiobacter (GHKF11). Whole genome sequencing data was assessed for relevant genes, proteins, and pathways involved in the breakdown of agrochemicals. For comparative purposes, this analysis was expanded to also include data from deposited strains in the National Center for Biotechnology Information's (NCBI) database. This study revealed Zn-dependent metallo-ß-lactamase (MBL)-fold proteins similar to OPHC2 first identified in P. pseudoalcaligenes as the likely agents of organophosphate (OP) hydrolysis in A. xylosoxidans ADAF13, S. maltophilia CBF10-1, O. anthropi FRAF13, and R. radiobacter GHKF11. A search of similar proteins within NCBI identified over 200 hits for bacterial genera and species with a similar OPHC2 domain. Taken together, we conclude from this data that intrinsic low-level OP hydrolytic activity is likely prevalent across the rhizosphere stemming from widespread OPHC2-like metalloenzymes. In addition, P. stutzeri ODKF13, P. putida CBF10-2, O. anthropi FRAF13, and R. radiobacter GHKF11 were found to harbor glycine oxidase (GO) enzymes that putatively possess low-level activity against the herbicide glyphosate. These bacterial GOs are reported to catalyze the degradation of glyphosate to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and suggest a possible link to AMPA that can be found in glyphosate-contaminated agricultural soil. The presence of aromatic degradation proteins were also detected in five of six study strains, but are attributed primarily to components of the widely distributed ß-ketoadipate pathway found in many soil bacteria.

Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements.

Klebsiella aerogenes is a Gram-negative bacterium of the family Enterobacteriaceae which is widely distributed in water, air and soil. It also forms part of the normal microbiota found in human and animal gastrointestinal tracts. Here we report the draft genome sequence (chromosome and 1 plasmid) of K. aerogenes strain PX01 compiled at the scaffold level from 97 contigs totaling 5,262,952 bp. K. aerogenes PX01 was isolated from sediment along the northern face of Burnet Bay west of Baytown, Texas. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession NJBB00000000.

Whole genome sequencing of Microbacterium sp. AISO3 from polluted San Jacinto River sediment reveals high bacterial mobility, metabolic versatility and heavy metal resistance.

The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession NHRF00000000.

Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants.

P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci. In addition, approximately 142 proteins localized on the bacterial chromosome are associated with metabolism of aromatic compounds. A single plasmid approximately 95 kb in size was also detected carrying copies of RNA genes and multiple phage assembly proteins.

Draft Genome Sequence of Pseudomonas putida CBF10-2, a Soil Isolate with Bioremediation Potential in Agricultural and Industrial Environmental Settings.

Pseudomonas putida CBF10-2 is a microorganism isolated from farmland soil in Fairchild, TX, found to degrade high-impact xenobiotics, including organophosphate insecticides, petroleum hydrocarbons, and both monocyclic and polycyclic aromatics. The versatility of CBF10-2 makes it useful for multipurpose bioremediation of contaminated sites in agricultural and industrial environments.

Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13.

ITALIC! Ochrobactrum anthropiFRAF13 was isolated from farmland soil in Jersey Village, Texas. FRAF13 is a bacterial microorganism with broad antibiotic resistance that possesses a number of metal-dependent ß-lactam enzymes with secondary phosphotriesterase activity that can initiate the breakdown of organophosphate compounds.

Draft Genome Sequence of the Broad-Spectrum Xenobiotic Degrader Achromobacter xylosoxidans ADAF13.

Achromobacter xylosoxidansADAF13, isolated from farmland soil, possesses a large number of putative degradation genes and pathways that break down a wide variety of aromatic hydrocarbons, pesticides, endocrine disruptors, and other high-impact xenobiotics. These properties make this strain an excellent candidate for further development as a broad-spectrum bioremediation agent.

Draft Genome Sequence of Alkane-Degrading Acinetobacter venetianus JKSF02, Isolated from Contaminated Sediment of the San Jacinto River in Houston, Texas.

Acinetobacter venetianusJKSF02 was isolated from contaminated sediment in eastern Houston, Texas along the San Jacinto River. This microorganism specializes in n-alkane degradation and is well suited for bioremediation of the petroleum hydrocarbon deposited throughout the region by shipping and industrial activity from the Houston Ship Channel.

Draft Genome Sequence of Pseudomonas stutzeri ODKF13, Isolated from Farmland Soil in Alvin, Texas.

Pseudomonas stutzeriODKF13 is a bacterial microorganism isolated from farmland soil in Alvin, Texas. This strain is notable for its naphthalene degradation and nitrogen fixation pathways and for its characterization as an organophosphate degrader of phosphotriester and phosphorothioate insecticides.

Draft Genome Sequence of Exiguobacterium sp. KKBO11, Isolated Downstream of a Wastewater Treatment Plant in Houston, Texas.

Exiguobacterium sp. KKBO11, isolated near a wastewater treatment plant in Houston, Texas, USA, possesses a large number of genes involved in stress response and transport critical to survival in adverse environmental conditions. An unusually high copy number of RNA genes also possibly contributes to this microorganism's versatility by promoting nutrient uptake.

Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas.

Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications.

Draft Genome Sequence of Stenotrophomonas maltophilia CBF10-1, an Organophosphate-Degrading Bacterium Isolated from Ranch Soil in Fairchilds, Texas.

Stenotrophomonas maltophilia CBF10-1 was isolated from a ranch in Fairchilds, Texas, USA. Its genome reveals a highly adaptable microorganism with a large complement of antibiotic and heavy metal resistance genes, efflux pumps, multidrug transporters, and xenobiotic degradation pathways.

A review of the Texas, USA San Jacinto Superfund site and the deposition of polychlorinated dibenzo-p-dioxins and dibenzofurans in the San Jacinto River and Houston Ship Channel.

The San Jacinto River (SJR) waste pits that lie just under the 1-10 overpass in eastern Harris County east of Houston, Texas, USA, were created in the 1960s as dumping grounds for paper mill waste. The deposition of this waste led to accumulation of highly toxic polychlorinated dibenzo-p-dioxins and dibenzofurans (PCCDDs/PCDFs) over the course of several decades. After abandonment, the waste material eventually became submerged under the waters of the SJR, resulting in widespread environmental contamination that currently constitutes a significant health concern for eastern Harris County communities. The original waste pits were rediscovered in 2005, and the San Jacinto waste site is now a designated EPA superfund site. The objective of this review then is to discuss the history and current state of containment around the San Jacinto waste pits and analyze spatial and temporal trends in the PCDD/PCDF deposition through the SJR system from the data available. We will discuss the current exposure and health risks represented by the Superfund site and the SJR system itself, as well as the discovery of liver, kidney, brain (glioma), and retinoblastoma cancer clusters in eastern Harris County across multiple census tracts that border the Superfund site. We will also cover the two primary management options, containment versus removal of the waste from the Superfund and provide recommendations for increased monitoring of existing concentrations of polychlorinated waste in the SJR and its nearby associated communities.

Developments in alternative treatments for organophosphate poisoning.

Organophosphosphates (OPs) are highly effective acetylcholinesterase (AChE) inhibitors that are used worldwide as cheap, multi-purpose insecticides. OPs are also used as chemical weapons forming the active core of G-series and V-series chemical agents including tabun, sarin, soman, cyclosarin, VX, and their chemical analogs. Human exposure to any of these compounds leads to neurotoxic accumulation of the neurotransmitter acetylcholine, resulting in abnormal nerve function and multiple secondary health complications. Suicide from deliberate exposure to OPs is particularly prevalent in developing countries across the world and constitutes a major global health crisis. The prevalence and accessible nature of OP compounds within modern agricultural spheres and concern over their potential use in biochemical weapon attacks have incentivized both government agencies and medical researchers to enact stricter regulatory policies over their usage and to begin developing more proactive medical treatments in cases of OP poisoning. This review will discuss the research undertaken in recent years that has investigated new supplementary drug options for OP treatment and support therapy, including progress in the development of enzymatic prophylaxis.

Detection and location of OP-degrading activity: A model to integrate education and research.

The Environmental Sampling Research Module (ESRM) is an investigative/discovery module that provides undergraduate research experiences for students as part of an interdisciplinary research-based biotechnology curriculum at the University of Houston campus. As part of the ESRM, students collect soil samples from various locations to test for the presence of organophosphorous (OP) degrading bacteria. At the end of this research project students submit a research paper on their field and laboratory activities and discuss their experimental data and observations. Students also record the date, location of collection, and the results of testing the sample for the degradation of two pesticides, methyl parathion or paraoxon, in an electronic laboratory notebook (ELN). Each collection site is recorded on a Google Maps module and the data from student research activities is made available to other undergraduate students. This data is then used to generate a microorganism database of pesticide degrading activity and promote reading, critical thinking, and analytical skills as part of the curriculum. Our sampling of agricultural sites and wastewater within and around the city of Houston has identified seven distinct genera of OP degrading organisms, including Pseudomonas, Stenotrophomonas, Exiguobacterium, Delftia, Agrobacterium, Aeromonas, and Rhizobium. Collected strains exhibit phosphotriesterase-like enzymatic activity with isolates of Pseudomonas putida and Stenotrophomonas maltophilia capable of degrading both the phosphotriester paraoxon and the phosphorothioate methyl parathion. Using this collection of OP-degrading microorganisms, undergraduate students have evaluated their potential for enhancing the removal of harmful organophosphates and their toxic metabolites from contaminated agricultural soil and adjacent bodies of water. This analytical data can potentially be utilized for environmental and industrial applications in bioremediation and ecology providing an innovative method for integrating education and research. In addition, the versatility of the ESRM itself provides for easy and rapid adaptation into varying environmental science courses with significant potential for the discovery and isolation of new and unique organisms to be used as part of ongoing research in the laboratory.

Ribosomal DNA sequence divergence and group I introns within the Leucostoma species L. cinctum, L. persoonii, and L. parapersoonii sp. nov., ascomycetes that cause Cytospora canker of fruit trees.

Leucostoma species that are the causal agents of Cytospora canker of stone and pome fruit trees were studied in detail. DNA sequence of the internal transcribed spacer regions and the 5.8S of the nuclear ribosomal DNA operon (ITS rDNA) supplied sufficient characters to assess the phylogenetic relationships among species of Leucostoma, Valsa, Valsella, and related anamorphs in Cytospora. Parsimony analysis of the aligned sequence divided Cytospora isolates from fruit trees into clades that generally agreed with the morphological species concepts, and with some of the phenetic groupings (PG 1-6) identified previously by isozyme analysis and cultural characteristics. Phylogenetic analysis inferred that isolates of L. persoonii formed two well-resolved clades distinct from isolates of L. cinctum. Phylogenetic analysis of the ITS rDNA, isozyme analysis, and cultural characteristics supported the inference that L. persoonii groups PG 2 and PG 3 were populations of a new species apparently more genetically different from L. persoonii PG 1 than from isolates representative of L. massariana, L. niveum, L. translucens, and Valsella melastoma. The new species, L. parapersoonii, was described. A diverse collection of isolates of L. cinctum, L. persoonii, and L. parapersoonii were examined for genetic variation using restriction fragment length polymorphism (RFLP) analysis of the ITS rDNA and the five prime end of the large subunit of the rDNA (LSU rDNA). HinfI and HpaII endonucleases were each useful in dividing the Leucostoma isolates into RFLP profiles corresponding to the isozyme phenetic groups, PG 1-6. RFLP analysis was more effective than isozyme analysis in uncovering variation among isolates of L. persoonii PG 1, but less effective within L. cinctum populations. Isolates representative of seven of the L. persoonii formae speciales proposed by G. Défago in 1935 were found to be genetically diverse isolates of PG 1. Two large insertions, 415 and 309 nucleotides long, in the small subunit (SSU) of the nuclear rDNA of L. cinctum were identified as Group 1 introns; intron 1 at position 943 and intron 2 at position 1199. The two introns were found to be consistently present in isolates of L. cinctum PG 4 and PG 5 and absent from L. cinctum PG 6 isolates, despite the similarity of the ITS sequence and teleomorph morphology. Intron 1 was of subgroup 1C1 whereas intron 2 was of an unknown subgroup. RFLP patterns and presence/absence of introns were useful characters for expediting the identification of cultures of Leucostoma isolated from stone and pome fruit cankers. RFLP patterns from 13 endonucleases provided an effective method for selecting an array of diverse PG 1 isolates useful in screening plant germplasm for disease-resistance.