Going from Microbial Ecology to Genome Data and Back: Studies on a Haloalkaliphilic Bacterium Isolated from Soap Lake, Washington State

Soap Lake is a meromictic, alkaline (∼pH 9.8) and saline (∼14-140 g liter-1) lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years) and the extremely high sulfide level (∼140 mM) in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment

Relative significance of environmental factors affecting hydrogen production from landfilled refuse samples

The relative significance of 11 environmental factors on the apparent steady-state concentration of hydrogen (ASSCH2) achieved during anaerobic degradation of refuse collected from landfills was evaluated by using multiple regression analysis. Simple correlation analysis revealed a significant negative association of ASSCH2 with newsprint moisture content (NMO) and pH of the sample. Application of five different variable selection procedures, which are commonly used in multiple regression analyses, showed that NMO, amylase (AMY), esterase (EST), cellulose to lignin ratio (CLR), volatile solids (VS), and nitrogen content (NIT) were significantly associated with ASSCH2 simultaneously. The other five factors did not show any significant effect on ASSCH 2 in the presence of the six significant factors. Further analysis showed that the influence of AMY and EST on ASSCH2 was weak, hence they were not included in the regression model. CLR was also deleted from the final model because of the multicollinearity resulting from its high correlation with VS. The final model incorporated NMO, NMO2, VS2 and NIT2; it explained 95% of the total variability and predicted 98% of the observed ASSCH2. An assessment of the relative significance of the independent variables indicated that NMO contributed the most, followed by NMO2 and VS2, in that order, and the least by NIT2 towards ASSCH2. The NMO and NIT 2 showed an inhibitory effect on ASSCH2. The results indicated that maintaining optimum moisture, along with optimum organic loading, and nitrogen content in landfills is necessary to achieve and maintain a low ASSCH2 and maximize refuse methanogenesis.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans

Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction

The Use of a Fractional Factorial Design to Determine the Factors That Impact 1,3-Propanediol Production from Glycerol by Halanaerobium Hydrogeniformans

In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this former commodity a waste product. However, Halanaerobium hydrogeniformans, a haloalkaliphilic bacterium, possesses the metabolic capability to convert glycerol into 1,3-propanediol, a valuable commodity compound, without the need for salt dilution or adjusting pH when grown on this waste. Experiments were performed with different combinations of 24 medium components to determine their impact on the production of 1,3-propanediol by using a fractional factorial design. Tested medium components were selected based on data from the organism\u27s genome. Analysis of HPLC data revealed enhanced production of 1,3-propanediol with additional glycerol, pH, vitamin B12, ammonium ions, sodium sulfide, cysteine, iron, and cobalt. However, other selected components; nitrate ions, phosphate ions, sulfate ions, sodium:potassium ratio, chloride, calcium, magnesium, silicon, manganese, zinc, borate, nickel, molybdenum, tungstate, copper and aluminum, did not enhance 1,3-propanediol production. The use of a fractional factorial design enabled the quick and efficient assessment of the impact of 24 different medium components on 1,3-propanediol production from glycerol from a haloalkaliphilic bacterium

Conversion of Glycerol to 1,3-propanediol under Haloalkaline Conditions

A method of producing 1,3-propanediol. The method comprises fermenting a haloalkaliphilic species of Halanaerobium with a source of glycerol into 1,3-propanediol, at a pH of greater than about 10 and at a salt concentration of greater than about 5% w/v. Furthermore, with supplementation of vitamin B12, the yield of 1,3-propanediol to glycerol can be increased

Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia

Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Australia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. The complete genome sequence is presented in this report

Disinfection of Swine Wastewater Using Chlorine, Ultraviolet Light and Ozone

Veterinary antibiotics are widely used at concentrated animal feeding operations (CAFOs) to prevent disease and promote growth of livestock. However, the majority of antibiotics are excreted from animals in urine, feces, and manure. Consequently, the lagoons used to store these wastes can act as reservoirs of antibiotics and antibiotic-resistant bacteria. There is currently no regulation or control of these systems to prevent the spread of these bacteria and their genes for antibiotic resistance into other environments. This study was conducted to determine the disinfection potential of chlorine, ultraviolet light and ozone against swine lagoon bacteria. Results indicate that a chlorine dose of 30 mg/L could achieve a 2.2-3.4 log bacteria reduction in lagoon samples. However, increasing the dose of chlorine did not significantly enhance the disinfection activity due to the presence of chlorine-resistant bacteria. The chlorine resistant bacteria were identified to be closely related to Bacillus subtilis and Bacillus licheniformis. A significant percentage of lagoon bacteria were not susceptible to the four selected antibiotics: chlortetracycline, lincomycin, sulfamethazine and tetracycline (TET). However, the presence of both chlorine and TET could inactivate all bacteria in one lagoon sample. The disinfection potential of UV irradiation and ozone was also examined. Ultraviolet light was an effective bacterial disinfectant, but was unlikely to be economically viable due to its high energy requirements. At an ozone dose of 100 mg/L, the bacteria inactivation efficiency could reach 3.3−3.9 log

Early Acidification of Mars and the Potential Implications for Biology

A leading paleoclimate theory for Mars, based on the identification of phyllosilicate minerals in ancient terrains, posits that the first several million years of the planet’s history were dominated by neutral to alkaline pH. However, evidence is mounting for the consideration of an alternate hypothesis: that some smectites on Mars formed under acidic conditions, and that the early surface of Mars may not have been subject to circum-neutral pH conditions, at least not uniformly. Work on shergottitic liquids suggests that up to 2400 ppm of sulfur could have degassed from martian magma, supplying more than enough sulfur for the planet’s sulfate-rich sediments and sedimentary rocks, and isotopic evidence of mass independent fractionation reveals that sulfur in martian meteorites underwent atmospheric reactions. Radiative modeling of sulfur volatiles in the martian atmosphere indicates that SO2 and H2S would have acted as powerful greenhouse gases trapping heat in different wavelength-dependent atmospheric windows than CO2 and H2O, supplying the necessary heat for surface temperatures to rise above freezing. Photochemistry suggests that sulfur would have been removed from the atmosphere through the deposition of sulfur dioxide, oxidized to sulfate at the surfaceatmosphere interface. This, in turn, could have led to the early acidification of the surface, thereby explaining the paucity of carbonates on Mars. This idea is supported by 1) the recent laboratory synthesis of Fe/Mg smectite from an Adirondack basalt simulant in an acidic hydrothermal system, and 2) studies of the mineral composition of terrestrial analogs, particularly at acid salt lakes

A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium

Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium hydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5- and 6-carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen, acetate, and formate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources

Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, \u3ci\u3eBacillus\u3c/i\u3e sp. isolated from salt flat sediments of Soap Lake

A halotolerant, alkaliphilic dissimilatory Fe(III)-reducing bacterium, strain SFB, was isolated from salt flat sediments collected from Soap Lake, WA. 16S ribosomal ribonucleic acid gene sequence analysis identified strain SFB as a novel Bacillus sp. most similar to Bacillus agaradhaerens (96.7% similarity). Strain SFB, a fermentative, facultative anaerobe, fermented various hexoses including glucose and fructose. The fructose fermentation products were lactate, acetate, and formate. Under fructose-fermenting conditions in a medium amended with Fe(III), Fe(II) accumulated concomitant with a stoichiometric decrease in lactate and an increase in acetate and CO2. Strain SFB was also capable of respiratory Fe(III) reduction with some unidentified component(s) of Luria broth as an electron donor. In addition to Fe(III), strain SFB could also utilize nitrate, fumarate, or O2 as alternative electron acceptors. Optimum growth was observed at 30°C and pH 9. Although the optimal salinity for growth was 0%, strain SFB could grow in a medium with up to 15% NaCl by mass. These studies describe a novel alkaliphilic, halotolerant organism capable of dissimilatory Fe(III) reduction under extreme conditions and demonstrate that Bacillus species can contribute to the microbial reduction of Fe(III) in environments at elevated pH and salinity, such as soda lakes