Genetic Characterization of Periphyton Communities Associated with Selenium Bioconcentration and Trophic Transfer in a Simple Food Chain.

A major source of uncertainty in predicting selenium (Se) distribution in aquatic food webs lies in the enrichment factor (EF), the ratio of Se bioconcentration in primary producers and microorganisms relative to the concentration of Se in the surrounding water. It has been well demonstrated that EFs can vary dramatically among individual algal taxa, but data are lacking regarding the influence of periphyton community composition on EFs for a given geochemical form of Se. Therefore, the goals of this study were first to assess whether different periphyton communities could be established in aquaria with the same starting inoculum using different light and nutrient regimes, and second, to determine if the periphyton assemblage composition influences the uptake of waterborne Se (as selenite) and subsequent Se transfer to a model macroinvertebrate primary consumer. Periphyton biofilms were grown in aquaria containing filtered pond water (from Saskatoon, SK) spiked with approximately 20 µg Se/L (mean measured concentration 21.0 ± 1.2 µg Se/L), added as selenite. Five different light and nutrient regimes were applied to the aquaria (three replicates per treatment) to influence biofilm community development. After 6 weeks of biofilm maturation, 40 to 80 immature cultured snails (Stagnicola elodes) were added to each aquarium. The bacterial and algal members of the periphyton community were characterized by targeted metagenomic analyses before and after addition of snails to ensure the snails themselves did not significantly alter the biofilm community. Samples were collected for Se analysis of water, periphyton, and whole-body snail. The nutrient and light treatments resulted in substantially different compositions of the periphytic biofilms, with each being relatively consistent across replicates and throughout the study. Although the aqueous concentration of dissolved Se administered to treatments was constant, uptake by the different periphytic biofilms differed significantly. Both the low-light (61.8 ± 12.1 µg Se/g d.w.) and high-light (30.5 ± 4.7 µg Se/g d.w.) biofilms, which were found to have high proportions of cyanobacteria, contained statistically higher concentrations of Se relative to the other treatments. Furthermore, the concentration of Se in bulk periphyton was predictive of Se bioaccumulation in grazing snails but as an inverse relationship, opposite to expectations. The trophic transfer factor was inversely correlated with periphyton enrichment factor (r = -0.841). A number of different bacterial and algal taxa were correlated (either positively or negatively) with Se accumulation in periphyton biofilm and snails. Recent advancements in genetic methods make it possible to conduct detailed characterization of periphyton assemblages and begin to understand the influence that periphyton composition has on Se biodynamics in aquatic systems.

Influence of commercial (Fluka) naphthenic acids on acid volatile sulfide (AVS) production and divalent metal precipitation.

Energy-derived waters containing naphthenic acids (NAs) are complex mixtures often comprising a suite of potentially problematic constituents (e.g. organics, metals, and metalloids) that need treatment prior to beneficial use, including release to receiving aquatic systems. It has previously been suggested that NAs can have biostatic or biocidal properties that could inhibit microbially driven processes (e.g. dissimilatory sulfate reduction) used to transfer or transform metals in passive treatment systems (i.e. constructed wetlands). The overall objective of this study was to measure the effects of a commercially available (Fluka) NA on sulfate-reducing bacteria (SRB), production of sulfides (as acid-volatile sulfides [AVS]), and precipitation of divalent metals (i.e. Cu, Ni, Zn). These endpoints were assessed following 21-d aqueous exposures of NAs using bench-scale reactors. After 21-days, AVS molar concentrations were not statistically different (p<0.0001; α=0.05) among NA treatments (10, 20, 40, 60, and 80mg NA/L) and an untreated control (no NAs). Extent of AVS production was sufficient in all NA treatments to achieve ∑SEM:AVS <1, indicating that conditions were conducive for treatment of metals, with sulfide ligands in excess of SEM (Cu, Ni, and Zn). In addition, no adverse effects to SRB (in terms of density, relative abundance, and diversity) were measured following exposures of a commercial NA. In this bench-scale study, dissimilatory sulfate reduction and subsequent metal precipitation were not vulnerable to NAs, indicating passive treatment systems utilizing sulfide production (AVS) could be used to treat metals occurring in NAs affected waters.

Equivalent input produces different output in the UniFrac significance test.

BACKGROUND: UniFrac is a well-known tool for comparing microbial communities and assessing statistically significant differences between communities. In this paper we identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance. RESULTS: The phylogenetic trees that are input into UniFrac may or may not contain abundance counts. An isomorphic transform can be defined that will convert trees between these two formats without altering the semantic meaning of the trees. UniFrac produces different outputs for these equivalent forms of the same input tree. This is illustrated using metagenomics data from a lake sediment study. CONCLUSIONS: Results from the UniFrac tool can vary greatly for the same input depending on the arbitrary choice of input format. Practitioners should be aware of this issue and use the tool with caution to ensure consistency and validity in their analyses. We provide a script to transform inputs between equivalent formats to help researchers achieve this consistency.

Isolation and characterization of novel 1,3-propanediol-producing Lactobacillus panis PM1 from bioethanol thin stillage.

Conversion of glycerol to 1,3-propanediol (1,3-PDO) is an attractive option to increase the economic efficiency of the biofuel industry. A bacterial strain that produced 1,3-PDO in the presence of glycerol was isolated from thin stillage, the fermentation residue of bioethanol production. This 1,3-PDO-producing organism was identified as Lactobacillus panis through biochemical characteristics and by 16S rRNA sequencing. Characterization of the L. panis strain hereafter designated as PM1 revealed it was an aerotolerant acidophilic anaerobe able to grow over a wide range of temperatures; tolerant to high concentrations of sodium chloride, ethanol, acetic acid, and lactic acid; and resistant to many common antibiotics. L. panis PM1 could utilize glucose, lactose, galactose, maltose, xylose, and arabinose, but could not grow on sucrose or fructose. Production of 1,3-PDO by L. panis PM1 occurred only when glucose was available as the carbon source in the absence of oxygen. These metabolic characteristics strongly suggested NADH recycling for glucose metabolism is achieved through 1,3-PDO production by this strain. These characteristics classified L. panis PM1 within the group III heterofermentative lactic acid bacteria, which includes the well-characterized 1,3-PDO-producing strain, Lactobacillus reuteri. Metabolite production profiles showed that L. panis PM1 produced considerable amounts of succinic acid (~11-12 mM) from normal MRS medium, which distinguishes this strain from L. reuteri strains.

Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T.

Pediococcus claussenii is a common brewery contaminant. We have sequenced the chromosome and plasmids of the type strain P. claussenii ATCC BAA-344. A ropy variant was chosen for sequencing to obtain genetic information related to growth in beer, as well as exopolysaccharide and possibly biofilm formation by this organism.

Reclassification of Paralactobacillus selangorensis Leisner et al. 2000 as Lactobacillus selangorensis comb. nov.

The taxonomic status of Paralactobacillus selangorensis is described and, based on evidence presented, transfer of the species to the genus Lactobacillus with the name Lactobacillus selangorensis comb. nov. is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and portions of the cpn60, pheS and rpoA genes. Mode of cell division and existing phenotypic information also show that P. selangorensis cannot be differentiated from the genus Lactobacillus. The type strain of Lactobacillus selangorensis comb. nov. is ATCC BAA-66(T) (=LMG 17710(T) =CIP 106482(T)).

Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera.

BACKGROUND: The increasing availability of whole genome sequences allows the gene or protein content of different organisms to be compared, leading to burgeoning interest in the relatively new subfield of pan-genomics. However, while several studies have analyzed protein content relationships in specific groups of bacteria, there has yet to be a study that provides a general characterization of protein content relationships in a broad range of bacteria. RESULTS: A variation on reciprocal BLAST hits was used to infer relationships among proteins in several groups of bacteria, and data regarding protein conservation and uniqueness in different bacterial genera are reported in terms of "core proteomes", "unique proteomes", and "singlets". We also analyzed the relationship between protein content similarity and the percent identity of the 16S rRNA gene in pairs of bacterial isolates from the same genus, and found that the strength of this relationship varied substantially depending on the genus, perhaps reflecting different rates of genome evolution and/or horizontal gene transfer. Finally, core proteomes and unique proteomes were used to study the proteomic cohesiveness of several bacterial species, revealing that some bacterial species had little cohesiveness in their protein content, with some having fewer proteins unique to that species than randomly-chosen sets of isolates from the same genus. CONCLUSIONS: The results described in this study aid our understanding of protein content relationships in different bacterial groups, allowing us to make further inferences regarding genome-environment relationships, genome evolution, and the soundness of existing taxonomic classifications.

Susceptibility of Pediococcus isolates to antimicrobial compounds in relation to hop-resistance and beer-spoilage.

BACKGROUND: Though important in the context of food microbiology and as potential pathogens in immuno-compromised humans, bacterial isolates belonging to the genus Pediococcus are best known for their association with contamination of ethanol fermentation processes (beer, wine, or fuel ethanol). Use of antimicrobial compounds (e.g., hop-compounds, Penicillin) by some industries to combat Pediococcus contaminants is long-standing, yet knowledge about the resistance of pediococci to antimicrobial agents is minimal. Here we examined Pediococcus isolates to determine whether antibiotic resistance is associated with resistance to hops, presence of genes known to correlate with beer spoilage, or with ability to grow in beer. RESULTS: Lactic acid bacteria susceptibility test broth medium (LSM) used in combination with commercially available GPN3F antimicrobial susceptibility plates was an effective method for assessing antimicrobial susceptibility of Pediococcus isolates. We report the finding of Vancomycin-susceptible Pediococcus isolates from four species. Interestingly, we found that hop-resistant, beer-spoilage, and beer-spoilage gene-harbouring isolates had a tendency to be more susceptible, rather than more resistant, to antimicrobial compounds. CONCLUSION: Our findings indicate that the mechanisms involved in conferring hop-resistance or ability to spoil beer by Pediococcus isolates are not associated with resistance to antibiotics commonly used for treatment of human infections. Also, Vancomycin-resistance was found to be isolate-specific and not intrinsic to the genus as previously believed.

Influence of CuSO4 and chelated copper algaecide exposures on biodegradation of microcystin-LR.

Copper exposures from algaecide applications in aquatic systems are hypothesized to impede bacterial degradation of microcystin (MC), a cyanobacterial produced hepatotoxin. Despite regulatory implications of this hypothesis, limited data exist on influences of copper-exposures on MC-degrading bacteria and consequent MC-degradation. In this study, influences of copper-algaecide concentrations and formulations on bacterial composition and microcystin-LR (MCLR) degradation were investigated. Microcystis aeruginosa was exposed to four concentrations (0-5.0 mg Cu L-1) of three copper-algaecide formulations, and rates and extents of MCLR degradation were measured. In untreated controls and following exposures of 0.1, 0.5, and 1.0 mg Cu L-1, MCLR concentrations decreased at a rate of ∼41-53 µg MCLR/L d-1. Following exposure to 5.0 mg Cu L-1 MCLR degradation rates decreased an order of magnitude to ∼3-7 µg MCLR/L d-1. Bacterial diversity decreased following copper-exposures greater than 0.1 mg Cu L-1 for all formulations. Relative abundance of certain groups of MC-degrading bacteria identified in treatments increased with increasing copper concentration, suggesting they may be less sensitive to copper exposures than other, MCLR and non MC-degrading heterotrophic bacteria present in the assemblage. Results from this study revealed that copper concentration can influence degradation rates of MCLR, however this influence was not significant within copper concentrations currently registered for use (≤1.0 mg Cu L-1) of the tested algaecides. Copper formulation did not significantly alter degradation rates or bacterial composition. These data augment our understanding of the influences of copper algaecide-exposures on MCLR degradation, and can be used to inform more accurate risk evaluations and use of copper-algaecides for management of MCLR-producing cyanobacteria.

A risk-based approach for identifying constituents of concern in oil sands process-affected water from the Athabasca Oil Sands region.

Mining leases in the Athabasca Oil Sands (AOS) region produce large volumes of oil sands process-affected water (OSPW) containing constituents that limit beneficial uses and discharge into receiving systems. The aim of this research is to identify constituents of concern (COCs) in OSPW sourced from an active settling basin with the goal of providing a sound rational for developing mitigation strategies for using constructed treatment wetlands for COCs contained in OSPW. COCs were identified through several lines of evidence: 1) chemical and physical characterization of OSPW and comparisons with numeric water quality guidelines and toxicity endpoints, 2) measuring toxicity of OSPW using a taxonomic range of sentinel organisms (i.e. fish, aquatic invertebrates, and a macrophyte), 3) conducting process-based manipulations (PBMs) of OSPW to alter toxicity and inform treatment processes, and 4) discerning potential treatment pathways to mitigate ecological risks of OSPW based on identification of COCs, toxicological analyses, and PBM results. COCs identified in OSPW included organics (naphthenic acids [NAs], oil and grease [O/G]), metals/metalloids, and suspended solids. In terms of species sensitivities to undiluted OSPW, fish ≥ aquatic invertebrates > macrophytes. Bench-scale manipulations of the organic fractions of OSPW via PBMs (i.e. H2O2+UV254 and granular activated charcoal treatments) eliminated toxicity to Ceriodaphnia dubia (7-8 d), in terms of mortality and reproduction. Results from this study provide critical information to inform mitigation strategies using passive or semi-passive treatment processes (e.g., constructed treatment wetlands) to mitigate ecological risks of OSPW to aquatic organisms.

Effects of environmental conditions on aerobic degradation of a commercial naphthenic acid.

Naphthenic acids (NAs) are problematic constituents in energy-derived waters, and aerobic degradation may provide a strategy for mitigating risks to aquatic organisms. The overall objective of this study was to determine the influence of concentrations of N (as ammonia) and P (as phosphate), and DO, as well as pH and temperatures on degradation of a commercial NA in bench-scale reactors. Commercial NAs provided replicable compounds necessary to compare influences of environmental conditions on degradation. NAs were quantified using high performance liquid chromatography. Microbial diversity and relative abundance were measured in treatments as explanatory parameters for potential effects of environmental conditions on microbial populations to support analytically measured NA degradation. Environmental conditions that positively influenced degradation rates of Fluka NAs included nutrients (C:N 10:1-500:1, C:P 100:1-5000:1), DO (4.76-8.43 mg L(-1)), pH (6-8), and temperature (5-25 °C). Approximately 50% removal of 61 ± 8 mg L(-1) was achieved in less than 2 d after NA introduction, achieving the method detection limit (5 mg L(-1)) by day 6 of the experiment in treatments with a C:N:P ratio of 100:10:1, DO > 8 mg L(-1), pH ∼8-9, and temperatures >23 °C. Microbial diversity was lowest in lower temperature treatments (6-16 °C), which may have resulted in observed slower NA degradation. Based on results from this study, when macro- and micronutrients were available, DO, pH, and temperature (within environmentally relevant ranges) influenced rates of aerobic degradation of Fluka NAs. This study could serve as a model for systematically evaluating environmental factors that influence NA degradation in field scenarios.

The characterization of Helicobacter pylori DNA associated with ancient human remains recovered from a Canadian glacier.

Helicobacter pylori is a gram-negative bacterium that colonizes the stomach of nearly half of the world's population. Genotypic characterization of H. pylori strains involves the analysis of virulence-associated genes, such as vacA, which has multiple alleles. Previous phylogenetic analyses have revealed a connection between modern H. pylori strains and the movement of ancient human populations. In this study, H. pylori DNA was amplified from the stomach tissue of the Kwäday Dän Ts'ìnchi individual. This ancient individual was recovered from the Samuel Glacier in Tatshenshini-Alsek Park, British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations and radiocarbon dated to a timeframe of approximately AD 1670 to 1850. This is the first ancient H. pylori strain to be characterized with vacA sequence data. The Tatshenshini H. pylori strain has a potential hybrid vacA m2a/m1d middle (m) region allele and a vacA s2 signal (s) region allele. A vacA s2 allele is more commonly identified with Western strains, and this suggests that European strains were present in northwestern Canada during the ancient individual's time. Phylogenetic analysis indicated that the vacA m1d region of the ancient strain clusters with previously published novel Native American strains that are closely related to Asian strains. This indicates a past connection between the Kwäday Dän Ts'ìnchi individual and the ancestors who arrived in the New World thousands of years ago.

Reclassification of Pediococcus dextrinicus (Coster and White 1964) back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. nov., and emended description of the genus Lactobacillus.

The taxonomic status of Pediococcus dextrinicus is described and transfer of the species to the genus Lactobacillus, with the name Lactobacillus dextrinicus comb. nov., is proposed. This reclassification is supported by multilocus sequence analysis of the 16S rRNA gene and Cpn60, PheS, RecA and RpoA proteins. The mode of cell division and existing phenotypic information also show that P. dextrinicus does not belong to the genus Pediococcus, but rather to the genus Lactobacillus. As such, we propose that Pediococcus dextrinicus is reclassified as Lactobacillus dextrinicus comb. nov. (type strain ATCC 33087(T)=DSM 20335(T)=JCM 5887(T)=LMG 11485(T)=NCDO 1561(T)).

Identification of novel horA-harbouring bacteria capable of spoiling beer.

An ATP-binding cassette (ABC) multi-drug resistance (MDR) gene was found in 4 Gram-positive bacterial isolates of environmental origin and found capable of spoiling beer. The bacteria isolated were Bacillus cereus, Bacillus licheniformis, Paenibacillus humicus, and Staphylococcus epidermidis; all of which were previously unappreciated as beer-spoilage bacteria. The MDR gene found in these bacteria has less than 37% similarity to known ABC MDR proteins described for Bacillus and Staphylococcus, and this is the first finding of an ABC MDR gene in the genus Paenibacillus. The sequenced region of the gene was translated and compared phylogenetically with the closest GenBank matches of the respective species and the closest GenBank matches overall. The ABC MDR proteins from these isolates were found to cluster among known sequences of HorA, sharing 99.5% identity within the sequenced region. In the beer-spoilage-associated genera Lactobacillus and Pediococcus, the presence of the MDR gene horA correlates with the ability to grow in beer. As the unique horA-harbouring isolates described here are capable of growing in beer, it is likely that the presence of the horA gene likewise confers hop resistance to these organisms.