Perchlorate-reducing bacteria from Antarctic marine sediments

Perchlorate is a contaminant that can persist in groundwater and soil, and is frequently detected in different ecosystems at concentrations relevant to human health. This study isolated and characterised halotolerant bacteria that can potentially perform perchlorate reduction. Bacterial microorganisms were isolated from marine sediments on Deception, Horseshoe and Half Moon Islands of Antarctica. The results of the 16S ribosomal RNA (rRNA) gene sequence analysis indicated that the isolates were phylogenetically related to Psychrobacter cryohalolentis, Psychrobacter urativorans, Idiomarina loihiensis, Psychrobacter nivimaris, Sporosarcina aquimarina and Pseudomonas lactis. The isolates grew at a sodium chloride concentration of up to 30% and a perchlorate concentration of up to 10,000 mg/L, which showed their ability to survive in saline conditions and high perchlorate concentrations. Between 21.6 and 40% of perchlorate was degraded by the isolated bacteria. P. cryohalolentis and P. urativorans degraded 30.3% and 32.6% of perchlorate, respectively. I. loihiensis degraded 40% of perchlorate, and P. nivimaris, S. aquimarina and P. lactis degraded 22%, 21.8% and 21.6% of perchlorate, respectively. I. loihiensis had the highest reduction in perchlorate, whereas P. lactis had the lowest reduction. This study is significant as it is the first finding of P. cryohalolentis and. P. lactis on the Antarctic continent. In conclusion, these bacteria isolated from marine sediments on Antarctica offer promising resources for the bioremediation of perchlorate contamination due to their ability to degrade perchlorate, showing their potential use as a biological system to reduce perchlorate in high-salinity ecosystems.

Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts

Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the "flexible ecotype" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the "restricted ecotype" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist. Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.

Bacterial diversity in six species of fresh edible seaweeds submitted to high pressure processing and long-term refrigerated storage

Seaweeds are highly perishable foods due to their richness in nutrients. High pressure processing (HPP) has been applied for extending the shelf life of fresh seaweeds but there is no information on the effect of HPP on the bacterial diversity of seaweeds. The culturable bacteria of six species of fresh edible seaweeds (green seaweeds Codium fragile and Ulva lactuca, brown seaweeds Himanthalia elongata, Laminaria ochroleuca and Undaria pinnatifida, and red seaweed Chondrus crispus) were investigated and compared to those of HPP-treated (400 and 600 MPa for 5 min) seaweeds, at the start and end of their refrigerated storage period. A total of 523 and 506 bacterial isolates were respectively retrieved from untreated and HPP-treated seaweeds. Isolates from untreated seaweeds belonged to 18 orders, 35 families, 71 genera and 135 species whereas isolates from HPP-treated seaweeds belonged to 13 orders, 23 families, 43 genera and 103 species. HPP treatment significantly reduced the number of isolates belonging to 6 families and greatly increased the number of Bacillaceae isolates. At the end of storage, decreases in bacterial diversity at the genus and species level were observed for untreated as well as for HPP-treated seaweeds.

Relationship Between Main Channel Structure of Catalases and the Evolutionary Direction in Cold-Adapted Hydrogen Peroxide-Tolerant Exiguobacteium and Psychrobacter

Catalase has crucial role in adaptive response to H₂O₂. Main channel structure responsible for substrate selectivity was estimated to understand the relationship between the evolutionary direction of catalases from Exiguobacterium oxidotolerans and Psychrobacter piscatorii which survive in cold and high concentration of hydrogen peroxide, and their catalytic property. E. oxidotolerans catalase (EKTA) exhibited a higher ratio of compound I formation rate using peracetic acid (a substrate lager than H₂O₂)/catalase activity using H₂O₂ as the substrate than P. piscatori catalase (PKTA). It was considered that the ratio was attributed to the size of the amino acid residues locating at the bottle neck structure in the main channel. The differences in the ratio of the compound I formation rate with peracetic acid to catalase activity with H₂O₂ between the deeper branches in the phylogenetic tree in both EKTA and PKTA were large. This indicates that catalases from the hydrogen peroxide-tolerant bacteria have evolved in different directions, exhibiting effective catalytic activity and allowing broader substrates size or H₂O₂-specific substrate acceptability in EKTA and PKTA, respectively. It is considered that the main channel structure reflected the difference in the evolutionary direction of clade 1 and clade 3 catalases.

The identification of sulfide oxidation as a potential metabolism driving primary production on late Noachian Mars

The transition of the martian climate from the wet Noachian era to the dry Hesperian (4.1-3.0 Gya) likely resulted in saline surface waters that were rich in sulfur species. Terrestrial analogue environments that possess a similar chemistry to these proposed waters can be used to develop an understanding of the diversity of microorganisms that could have persisted on Mars under such conditions. Here, we report on the chemistry and microbial community of the highly reducing sediment of Colour Peak springs, a sulfidic and saline spring system located within the Canadian High Arctic. DNA and cDNA 16S rRNA gene profiling demonstrated that the microbial community was dominated by sulfur oxidising bacteria, suggesting that primary production in the sediment was driven by chemolithoautotrophic sulfur oxidation. It is possible that the sulfur oxidising bacteria also supported the persistence of the additional taxa. Gibbs energy values calculated for the brines, based on the chemistry of Gale crater, suggested that the oxidation of reduced sulfur species was an energetically viable metabolism for life on early Mars.

American Lobsters (Homarus Americanus) not Surviving During Air Transport: Evaluation of Microbial Spoilage

Eighteen American lobsters (Homarus americanus), dead during air transport, were analysed in order to evaluate the microbial population of meat, gills and gut: no specific studies have ever been conducted so far on the microbiological quality of American lobsters’ meats in terms of spoilage microbiota. The meat samples showed very limited total viable counts, in almost all the cases below the level of 6 Log CFU/g, while higher loads were found, as expected, in gut and gills, the most probable source of contamination. These data could justify the possibility to commercialise these not-surviving subjects, without quality concerns for the consumers. Most of the isolates resulted to be clustered with type strains of Pseudoalteromonas spp. (43.1%) and Photobacterium spp. (24.1%), and in particular to species related to the natural marine environment. The distribution of the genera showed a marked inhomogeneity among the samples. The majority of the isolates identified resulted to possess proteolytic (69.3%) and lipolytic ability (75.5%), suggesting their potential spoilage ability. The maintanance of good hygienical practices, especially during the production of ready-to-eat lobsters-based products, and a proper storage could limit the possible replication of these microorganisms.

Draft Genome Sequence of Psychrobacter piscatorii Strain LQ58, a Psychrotolerant Bacterium Isolated from a Deep-Sea Hydrothermal Vent

Here, we report the 3.1-Mb draft genome sequence of Psychrobacter piscatorii strain LQ58, isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The sequence will provide further insight into the environmental adaptation of psychrotolerant bacteria and the development of novel cold-active enzymes for industrial application.

Tailoring nutritional and process variables for hyperproduction of catalase from a novel isolated bacterium Geobacillus sp. BSS-7

Background

Catalase (EC 1.11.1.6) is one of the important industrial enzyme employed in diagnostic and analytical methods in the form of biomarkers and biosensors in addition to their enormous applications in textile, paper, food and pharmaceutical sectors. The present study demonstrates the utility of a newly isolated and adapted strain of genus Geobacillus possessing unique combination of several industrially important extremophilic properties for the hyper production of catalase. The bacterium can grow over a wide range of pH (3–12) and temperature (10–90 °C) with extraordinary capability to produce catalase.

Results

A novel extremophilic strain belonging to genus Geobacillus was exploited for the production of catalase by tailoring its nutritional requirements and process variables. One variable at a time traditional approach followed by computational designing was applied to customize the fermentation process. A simple fermentation media containing only three components namely sucrose (0.55 %, w/v), yeast extract (1.0 %, w/v) and BaCl₂ (0.08 %, w/v) was designed for the hyperproduction of catalase. A controlled and optimum air supply caused a tremendous increase in the enzyme production on moving the bioprocess from the flask to bioreactor level. The present paper reports high quantum of catalase production (105,000 IU/mg of cells) in a short fermentation time of 12 h. To the best of our knowledge, there is no report in the literature that matches the performance of the developed protocol for the catalase production. This is the first serious study covering intracellular catalase production from thermophilic genus Geobacillus.

Conclusions

An increase in intracellular catalase production by 214.72 % was achieved in the optimized medium when transferred from the shake flask to the fermenter level. The extraordinary high production of catalase from Geobacillus sp. BSS-7 makes the isolated strain a prospective candidate for bulk catalase production on an industrial scale.

Psychrobacter fjordensis sp. nov., a psychrotolerant bacterium isolated from an Arctic fjord in Svalbard

A Gram-negative, non-motile, non-spore-forming, psychrotolerant and halotolerant bacterium designated BSw21516B(T), was obtained from seawater in Kongsfjorden, a glacial fjord in the Arctic Svalbard and subjected to taxonomic analysis using a polyphasic approach. This bacterium was observed to optimally grow at 25-29 °C; between at 4 and 34 °C, but not at >35 °C; and in the presence of 0-8 % (w/v) NaCl at an optimum concentration of 2-5 % (w/v) NaCl. Strain BSw21516B(T) was found to contain Ubiquinone-8 (Q-8) as a predominant respiratory lipoquinone and C18:1 ω9c and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as predominant cellular fatty acids. Phylogenetic analysis of 16S rRNA and gyrB gene sequences showed that this isolate belongs to the genus Psychrobacter and is closely related to Psychrobacter fozii LMG 21280(T), which was isolated from a sediment sample in Antarctica. DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 58.6 %) between strain BSw21516B(T) and its closest relatives. Based on these results a new species Psychrobacter fjordensis sp. nov. is proposed (type strain BSw21516B(T) = KCTC 42279(T) = CCTCC AB 2014020(T)).

Psychrobacter oceani sp. nov., isolated from marine sediment

A novel marine bacterium, designated strain 4k5T, was isolated from a sediment sample of the Pacific Ocean. The strain was Gram-stain-negative, strictly aerobic, non-motile, oxidase-positive and catalase-positive and required Na+ for growth. Its major isoprenoid quinone was ubiquinone 8 (Q-8), and its cellular fatty acid profile consisted mainly of C18 : 1v9c (71.4 %), C16 : 1v7c (9.1 %) and C18 : 0. The DNA G+C content was 45.3 mol%. 16S rRNA gene sequence analysis suggested that strain 4k5T is a member of the genus Psychrobacter . Strain 4k5T exhibited the closely phylogenetic affinity to Psychrobacter pacificensis IFO 16270T (99.4 % 16S rRNA gene sequence similarity), P. piscatorii T-3-2T (97.7 %), P. nivimaris 88/2-7T (97.7 %), P. celer SW-238T (97.7 %), P. aestuarii SC35T (97.6 %) and P. vallis CMS39T (97.6 %). DNA–DNA hybridization between strain 4k5T and P. pacificensis NBRC 103191T, P. piscatorii JCM 15603T. P. nivimaris DSM 16093T, P. celer JCM 12601T, P. aestuarii JCM 16343T and P. vallis DSM 15337T was 42.5, 47.0, 38.1, 23.7, 9.0 and 27.4 %, respectively. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, phylogenetic analysis based on the 16S rRNA gene sequence and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter oceani sp. nov. is proposed. The type strain is 4k5T ( = JCM 30235T = NCIMB 14948T).

Growth-dependent catalase localization in Exiguobacterium oxidotolerans T-2-2T reflected by catalase activity of cells

A psychrotolerant and H₂O₂-resistant bacterium, Exiguobacterium oxidotolerans T-2-2^T, exhibits extraordinary H₂O₂ resistance and produces catalase not only intracellularly but also extracellularly. The intracellular and extracellular catalases exhibited the same enzymatic characteristics, that is, they exhibited the temperature-dependent activity characteristic of a cold-adapted enzyme, their heat stabilities were similar to those of mesophilic enzymes and very high catalytic intensity. In addition, catalase gene analysis indicated that the bacterium possessed the sole clade 1 catalase gene corresponding to intracellular catalase. Hence, intracellular catalase is secreted into the extracellular space. In addition to intracellular and extracellular catalases, the inner circumference of the cells showed the localization of catalase in the mid-stationary growth phase, which was observed by immunoelectron microscopy using an antibody against the intracellular catalase of the strain. The cells demonstrated higher catalase activity in the mid-stationary growth phase than in the exponential growth phase. The catalase localized in the inner circumference can be dissociated by treatment with Tween 60. Thus, the localized catalase is not tightly bound to the inner circumference of the cells and may play a role in the oxidative defense of the cells under low metabolic state.

Molecular analysis of the diversity of genus Psychrobacter present within a temperate estuary

Many members of the genus Psychrobacter are endemic in extremely cold and saline environments and the genus has been described as only marginally successful in warmer habitats. In a previous study the Psychrobacter genus was, unexpectedly, the most frequently isolated bacterial genus from the sea-surface microlayer (SML) and the underlying water (UW) of a temperate estuary (Ria de Aveiro, Portugal). Here we analysed the diversity in Psychrobacter populations inhabiting this estuary. Samples were collected at three dates and three locations from sea-SML and UW. Isolated Psychrobacter strains were well-adapted to temperatures and salt concentrations above the ones described as optimal for most members of this genus. Hydrocarbon-degrading potential was not confirmed for these strains. We developed and optimized a reliable and specific denaturing gradient gel electrophoresis (DGGE)-based method for the analysis of Psychrobacter populations in aquatic systems. DGGE profiles inferred that Psychrobacter populations were very stable in the estuary, a strong indication for the presence of well-adapted phylotypes. The analysis of genus-specific clone libraries revealed a surprisingly high diversity among Psychrobacter in Ria de Aveiro. Results indicated that novel species were probably cultivated. Significant differences between sea-SML and UW Psychrobacter communities were revealed. Observed diversity trends may be related to environmental factors such as salinity and/or anthropogenic pressures such as contamination with hydrocarbons.

Characterization of catalase from psychrotolerant Psychrobacter piscatorii T-3 exhibiting high catalase activity

A psychrotolerant bacterium, strain T-3 (identified as Psychrobacter piscatorii), that exhibited an extraordinarily high catalase activity was isolated from the drain pool of a plant that uses H₂O₂ as a bleaching agent. Its cell extract exhibited a catalase activity (19,700 U·mg protein⁻¹) that was higher than that of Micrococcus luteus used for industrial catalase production. Catalase was approximately 10% of the total proteins in the cell extract of the strain. The catalase (PktA) was purified homogeneously by only two purification steps, anion exchange and hydrophobic chromatographies. The purified catalase exhibited higher catalytic efficiency and higher sensitivity of activity at high temperatures than M. luteus catalase. The deduced amino acid sequence showed the highest homology with catalase of Psycrobacter cryohalolentis, a psychrotolelant bacterium obtained from Siberian permafrost. These findings suggest that the characteristics of the PktA molecule reflected the taxonomic relationship of the isolate as well as the environmental conditions (low temperatures and high concentrations of H₂O₂) under which the bacterium survives. Strain T-3 efficiently produces a catalase (PktA) at a higher rate than Exiguobacterium oxidotolerans, which produces a very strong activity of catalase (EktA) at a moderate rate, in order to adapt to high concentration of H₂O₂.

Psychrobacter aestuarii sp. nov., isolated from a tidal flat sediment

A Gram-negative-staining, non-motile, non-spore-forming and strictly aerobic bacterial strain, SC35T, was isolated from tidal flat sediment collected from the South Sea, Korea, and subjected to a taxonomic study using a polyphasic approach. The organism grew optimally at 20–30 °C and with 1–2 % (w/v) NaCl. Strain SC35T contained ubiquinone-8 as the predominant respiratory lipoquinone and C18 : 1 ω9c as the major fatty acid. The DNA G+C content was 48.5 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SC35T formed a lineage within the genus Psychrobacter (94.3–96.5 % sequence similarity), forming a distinct branch in a clade also containing Psychrobacter pacificensis NIBH P2K6T and Psychrobacter celer SW-238T. On the basis of phenotypic and phylogenetic data, strain SC35T (=KCTC 22503T=JCM 16343T) was placed in the genus Psychrobacter as the type strain of a novel species, for which the name Psychrobacter aestuarii sp. nov. is proposed.