Inquisition of Microcystis aeruginosa and Synechocystis nanowires: characterization and modelling

Identification of extracellular conductive pilus-like structures (PLS) i.e. microbial nanowires has spurred great interest among scientists due to their potential applications in the fields of biogeochemistry, bioelectronics, bioremediation etc. Using conductive atomic force microscopy, we identified microbial nanowires in Microcystis aeruginosa PCC 7806 which is an aerobic, photosynthetic microorganism. We also confirmed the earlier finding that Synechocystis sp. PCC 6803 produces microbial nanowires. In contrast to the use of highly instrumented continuous flow reactors for Synechocystis reported earlier, we identified simple and optimum culture conditions which allow increased production of nanowires in both test cyanobacteria. Production of these nanowires in Synechocystis and Microcystis were found to be sensitive to the availability of carbon source and light intensity. These structures seem to be proteinaceous in nature and their diameter was found to be 4.5-7 and 8.5-11 nm in Synechocystis and M. aeruginosa, respectively. Characterization of Synechocystis nanowires by transmission electron microscopy and biochemical techniques confirmed that they are type IV pili (TFP) while nanowires in M. aeruginosa were found to be similar to an unnamed protein (GenBank : CAO90693.1). Modelling studies of the Synechocystis TFP subunit i.e. PilA1 indicated that strategically placed aromatic amino acids may be involved in electron transfer through these nanowires. This study identifies PLS from Microcystis which can act as nanowires and supports the earlier hypothesis that microbial nanowires are widespread in nature and play diverse roles.

Description of loxocythere (novoloxocythere) pelius subgen. sp. nov. (ostracoda) from the cenozoic of S.E. Australia with comments on species of antarctiloxoconcha hartmann, 1986 and loxoreticulatum benson, 1964 from Australian and Antarctic marine waters

Loxocythere (Novoloxocythere) pelius subgen. et sp. nov. is described from Upper Miocene strata of the Port Phillip and Western Port Basins. Victoria. It has its acme in shallow open marine facies of latest Miocene (Cheltenhamian) age. This species, along with Loxocythere<span style="font-style: italic;"> span>(Novoloxocythere) kerryswansoni Yassini and Jones, 1995, forms a discrete group of rotund Australian Loxocythere species that possess posterior extremities in both valves that are positioned well above mid carapace height (i.e. adjacent to dorsal margin). This feature along with a sub-triangular inner margin outline, defines a carapace shape that is distinct from that of rotund species of Loxocythere (loxocythere) Hornibrook, 1952 and<span style="font-style: italic;"> span>Antarctiloxoconcha Hartmann, 1986. The type species of Antarctiloxoconcha – A.frigida (Neale. 1967), possesses internal carapace features that are very similar to the type species of Loxocythere - L. crassa Hornibrook, 1952. Both have relatively short carapaces and sub-quadrate inner margin outlines with posterior extremities in both valves positioned below mid carapace height. Species of Loxocythere (Novoloxocythere), in particular L. (N.) kerryswansoni, have a carapace shape that is transitional between<span style="font-style: italic;"> span>Loxocythere and Loxoreticulatum Benson, 1964. Species of Loxoreticulatum generally possess a sub-parallelogram shaped carapace/inner margin and arched median hinge element. The latter feature is distinct from the mostly straight median hinge elements of Loxocythere (Loxocythere) and<span style="font-style: italic;"> span>Loxocythere (Novoloxocythere) species. Species of Loxocythere (Novoloxocythere) are also readily distinguishable from relatively elongate species of Loxocythere, such as L. (L.) hornibrooki McKenzie, 1967, as the latter possess long (for genus), sub-rectangular shaped carapaces/inner margin outlines and posterior extremities below mid height.

Degradation of phenanthrene and pyrene in soil slurry reactors with immobilized bacteria Zoogloea sp.

The environmental fate of polycyclic aromatic hydrocarbons (PAHs) in soils is motivated by their wide distribution, high persistence, and potentially deleterious effect on human health. Polycyclic aromatic hydrocarbons constitute the largest group of environmental contaminants released in the environment. Therefore, the potential biodegradation of these compounds is of vital importance. A biocarrier suitable for the colonization by micro-organisms for the purpose of purifying soil contaminated by polycyclic aromatic hydrocarbons was developed. The optimized composition of the biocarrier was polyvinyl alcohol (PVA) 10%, sodium alginate (SA) 0.5%, and powdered activated carbon (PAC) 5%. There was no observable cytotoxicity of biocarriers on immobilized cells and a viable cell population of 1.86 × 10¹⁰ g^–1 was maintained for immobilized bacterium. Biocarriers made from chemical methods had a higher biodegradation but lower mechanical strengths. Immobilized bacterium Zoogloea sp. had an ideal capability of biodegradation for phenanthrene and pyrene over a relative wide concentration range. The study results showed that the biodegradation of phenanthrene and pyrene reached 87.0 and 75.4%, respectively, by using the optimal immobilized method of Zoogloea sp. cultivated in a sterilized soil. Immobilized Zoogloea sp. was found to be effective for biodegrading the soil contaminated with phenanthrene and pyrene. Even in "natural" (unsterilized) soil, the biodegradation of phenanthrene and pyrene using immobilized Zoogloea sp. reached 85.0 and 67.1%, respectively, after 168 h of cultivation, more than twice that achieved if the cells were not immobilized on the biocarrier. Therefore, the immobilization technology enhanced the competitive ability of introduced micro-organisms and represents an effective method for the biotreatment of soil contaminated with phenanthrene and pyrene.

Biodegradation of benzo[a]pyrene in soil by Mucor sp. SF06 and Bacillus sp. SB02 co-immobilized on vermiculite

Two indigenous microorganisms, Bacillus sp. SB02 and Mucor sp. SF06, capable of degrading polycyclic aromatic hydrocarbons (PAHs) were co-immobilized on vermiculite by physical adsorption and used to degrade benzo[a] pyrene (BaP). The characteristics of BaP degradation by both free and co-immobilized microorganism were then investigated and compared. The removal rate using the immobilized bacterial-fungal mixed consortium was higher than that of the freely mobile mixed consortium. 95.3% of BaP was degraded using the co-immobilized system within 42 d, which was remarkably higher than the removal rate of that by the free strains. The optimal amount of inoculated co-immobilized system for BaP degradation was 2%. The immobilized bacterial-fungal mixed consortium also showed better water stability than the free strains. Kinetics of BaP biodegradation by co-immobilized SF06 and SB02 were also studied. The results demonstrated that BaP degradation could be well described by a zero-order reaction rate equation when the initial BaP concentration was in the range of 10—200 mg/kg. The scanning electronic microscope (SEM) analysis showed that the co-immobilized microstructure was suitable for the growth of SF06 and SB02. The mass transmission process of co-immobilized system in soil is discussed. The results demonstrate the potential for employing the bacterial-fungal mixed consortium, co-immobilized on vermiculite, for in situ bioremediation of BaP.

Influence of chemical oxidant on degradation of benzo[a]pyrene metabolites by the bacterium-Zoogloea sp.

It is neither comprehensive nor appropriate that the bioremediation of a benzo[a]pyrene (BaP)-contaminated environment be assessed only by its high degradation extent because its metabolites' chemical structures are similar to the parent compound and maybe equally toxic. Therefore, further degradation of BaP metabolites is significant. Three methods, combining the Zoogloea sp. with potassium permanganate, combining the Zoogloea sp. with H₂O₂, Zoogloea sp. alone, were investigated to degrade cis-BP4,5-dihydrodiol and cis-BP7,8-dihydrodiol, which are the metabolites of BaP formed by bacterium-Zoogloea sp. Optimum parameters of degradation in the best method are that: of the three methods, coupling the Zoogloea sp. and KMnO₄ is the best; compared with cis-BP7,8-dihydrodiol, cis-BP4,5-dihydrodiol is the more liable to be accumulated in pure cultures; the degradation effect of the two metabolites is optimal when the initial concentration of KMnO₄ in the cultures is 0.05%; initial concentration of cis-BP4,5-dihydrodiol and cis-BP7,8-dihydrodiol is 4 mg L⁻¹, 8 mg L⁻¹, respectively; cometabolic substance is salicylic acid or sodium succinate. The degradation extent of cis-BP4,5-dihydrodiol and cis-BP7,8-dihydrodiol using combining the Zoogloea sp. and KMnO₄ reach 76.1% and 85.9% after 12 days of cultivation, respectively, which were more than twice compared with conventional method.

Evaluation of fatty acid extraction methods for Thraustochytrium sp. ONC-T18

Various extraction methods were assessed in their capacity to extract fatty acids from a dried biomass of Thraustochytrium sp. ONC-T18. Direct saponification using KOH in ethanol or in hexane:ethanol was one of the most efficient techniques to extract lipids (697 mg g^-1). The highest amount of fatty acids (714 mg g^-1) was extracted using a miniaturized Bligh and Dyer extraction technique. The use of ultrasonics to break down cell walls while extracting with solvents (methanol:chloroform) also offered high extraction yields of fatty acids (609 mg g^-1). Moreover, when the transesterification mixture used for a direct transesterification method was doubled, the extraction of fatty acids increased approximately 77% (from 392 to 696 mg g^-1). This work showed that Thraustochytrium sp. ONC-T18 has the ability to produce over 700 mg g^-1 of lipids, including more than 165 mg g-1 of docosahexaenoic acid, which makes this microorganism a potential candidate for the commercial production of polyunsaturated fatty acids. Finally, other lipids, such as myristic, palmitic, palmitoleic, and oleic acids, were also produced and recovered in significant amounts (54, 196, 123, and 81 mg g^-1), respectively.

Isolation of a novel Orientia species (O. chuto sp. nov.) from a patient infected in Dubai

In July 2006, an Australian tourist returning from Dubai, in the United Arab Emirates (UAE), developed acute scrub typhus. Her signs and symptoms included fever, myalgia, headache, rash, and eschar. Orientia tsutsugamushi serology demonstrated a 4-fold rise in antibody titers in paired serum collections (1:512 to 1:8,192), with the sera reacting strongest against the Gilliam strain antigen. An Orientia species was isolated by the in vitro culture of the patient's acute blood taken prior to antibiotic treatment. The gene sequencing of the 16S rRNA gene (rrs), partial 56-kDa gene, and the full open reading frame 47-kDa gene was performed, and comparisons of this new Orientia sp. isolate to previously characterized strains demonstrated significant sequence diversity. The closest homology to the rrs sequence of the new Orientia sp. isolate was with three strains of O. tsutsugamushi (Ikeda, Kato, and Karp), with a nucleotide sequence similarity of 98.5%. The closest homology to the 47-kDa gene sequence was with O. tsutsugamushi strain Gilliam, with a nucleotide similarity of 82.3%, while the closest homology to the 56-kDa gene sequence was with O. tsutsugamushi strain TA686, with a nucleotide similarity of 53.1%. The molecular divergence and geographically unique origin lead us to believe that this organism should be considered a novel species. Therefore, we have proposed the name “Orientia chuto,” and the prototype strain of this species is strain Dubai, named after the location in which the patient was infected.

Plant extract assisted extracellular tannase production by Aspergillus sp MIK 23

An extracellular tannase (E.C. 3.1.1.20) producing fungal strain was isolated from soil and identified as Aspergillus sp MIK23. Out of various plant extracts, Terminalia chebula powder (TCP) in the optimized medium enhanced enzyme production. Maximum yield of tannase (3 IU ml-1) was obtained with glucose (10 g/L), urea (2 g/L), and yeast extract (2.5 g/L) when inoculated with 10% inoculum in 48 h. An initial medium at pH 6.0 and a cultivation temperature of 37 0C was found to be optimum for enzyme production. Metal ions Mg2+, Zn2+, Ca2+, Cu2+ and Cd2+ did not improve enzyme activity, whereas, Ca2+, Fe2+ and Hg2+ repressed enzyme activity. The enzyme was purified using ammonium sulfate precipitation followed by Q-sepharose ion-exchange chromatography. The enzyme was purified to 42-fold with an overall recovery of 20. The pH and temperature optima of the purified tannase were found to be 7.0 and 37°C, respectively.

Genome sequence of Ensifer sp. TW10, a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert

Ensifer sp. TW10 is novel N2-fixingbacterium isolated from a root nodule of the perennial legume Tephrosia wallichii Graham (known locally as Biyani) found in the Great Indian (or Thar) desert, a large arid regionin the northwestern part of the Indian subcontinent. Strain TW10 is a Gram-negative, rod shaped,aerobic, motile, non-spore forming, species of root nodule bacteria (RNB) that promiscuously nodulates legumes in Thar Desert alkaline soil. It is fast growing, acid-producing, and tolerates up to 2% NaCl and capable of growth at 40C. In this report we describe for the first time the primary features of this Thar Desert soil saprophyte together with genome sequence informationand annotation. The 6,802,256 bp genome has a GC content of 62% and is arranged into 57 scaffolds containing 6,470 protein-coding genes, 73 RNA genes and asingle rRNA operon. This genome is one of 100 RNB genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia

Burkholderiasp. strain WSM2230is an aerobic, motile, Gram-negative,non-spore-forming acid-tolerant rod trapped from acidic soil collected in 2001from Karijini National Park, Western Australia, using Kennedia coccinea (Coral Vine) as a host. WSM2230 was effectivein nitrogen-fixation with K. coccinea, but subsequently lost symbioticcompetence after long-term storage. Here we describe the features of Burkholderia sp. strain WSM2230, togetherwith genome sequence information and its annotation. The 6,309,801 bp high-quality-draftgenome is arranged into 33 scaffolds of 33 contigs containing 5,585 protein-codinggenes and 63 RNA-only encoding genes, and is one of 100 rhizobial genomessequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopediafor Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.