Shewanella Sp Research Articles

Genome collection of Shewanella spp. isolated from spoiled lamb.

The diversity of the genus Shewanella and their roles across a variety of ecological niches is largely unknown highlighting the phylogenetic diversity of these bacteria. From a food safety perspective, Shewanella species have been recognized as causative spoilage agents of vacuum-packed meat products. However, the genetic basis and metabolic pathways for the spoilage mechanism are yet to be explored due to the unavailability of relevant Shewanella strains and genomic resources. In this study, whole-genome sequencing of 32 Shewanella strains isolated from vacuum-packaged refrigerated spoiled lamb was performed to examine their roles in meat spoilage. Phylogenomic reconstruction revealed their genomic diversity with 28 Shewanella spp. strains belonging to the same putative novel species, two Shewanella glacialipiscicola strains (SM77 and SM91), Shewanella xiamenensis NZRM825, and Shewanella putrefaciens DSM 50426 (ATCC 8072) isolated from butter. Genome-wide clustering of orthologous gene families revealed functional groupings within the major Shewanella cluster but also considerable plasticity across the different species. Pan-genome analysis revealed conserved occurrence of spoilage genes associated with sulfur and putrescine metabolism, while the complete set of trimethylamine metabolism genes was observed in only Shewanella sp. SM74, S. glacialipiscicola SM77 and SM91 strains. Through comparative genomics, some variations were also identified pertaining to genes associated with adaptation to environmental cues such as temperature, osmotic, salt, oxidative, antimicrobial peptide, and drug resistance stresses. Here we provide a reference collection of draft Shewanella genomes for subsequent species descriptions and future investigations into the molecular spoilage mechanisms for further applications in the meat industry.

Characterization of pyomelanin secreted by Shewanella sp. and their application in metal recovery.

Melanin is a biopolymer with versatile structural and functional properties and diverse applications in recovering toxic chemicals from water and wastewater, biomedical imaging, and as theragnostic agent. We report the structural characterization and biosynthetic pathway of an extracellular pyomelanin secreted by a sponge-associated bacterium, Shewanella sp. (Shewanella-melanin), and their potential application in metal recovery from liquid. Pyomelanin particles of > 50µm size were found in the culture medium within 48h of growth, which were formed through the self-polymerization of benzoquinone molecule produced through homogentisic acid pathway. The aspC and hppD genes involved in the biosynthetic pathway of pyomelanin were detected in the whole genome sequence of Shewanella sp. The FT-IR spectra of Shewanella-melanin, at ~ 3300-3420cm-1 corresponding to the stretching vibration of -NH and -OH, was in good agreement with that of Sepia melanin, while its elemental composition (C/N/H/S of 29.2:8.23:6.41:1.58) was unique. Shewanella-melanin showed ~ 300 and ~ 950 times increased chelation of manganese and iron from a liquid medium supplemented with 2mM of MnSO4 and FeSO4, respectively, compared to a control. The FT-IR spectrum showed the binding of metal ions to the carboxylic acid, hydroxyl, and amine groups of Shewanella-melanin. The Shewanella-melanin, with its excellent metal biosorption, could be a potential candidate for removing toxic compounds from water, in turn contributing to the fulfillment of sustainable development goal (SDG) 6.

Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt.

The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.

Interplay between arsenic and selenium biomineralization in Shewanella sp. O23S

Bacteria play crucial roles in the biogeochemical cycle of arsenic (As) and selenium (Se) as these elements are metabolized via detoxification, energy generation (anaerobic respiration) and biosynthesis (e.g. selenocysteine) strategies. To date, arsenic and selenium biomineralization in bacteria were studied separately. In this study, the anaerobic metabolism of As and Se in Shewanella sp. O23S was investigated separately and mixed, with an emphasis put on the biomineralization products of this process. Multiple analytical techniques including ICP-MS, TEM-EDS, XRD, Micro-Raman, spectrophotometry and surface charge (zeta potential) were employed. Shewanella sp. O23S is capable of reducing selenate (SeO42−) and selenite (SeO32−) to red Se(-S)0, and arsenate (AsO43−) to arsenite (AsO33−). The release of H2S from cysteine led to the precipitation of AsS minerals: nanorod AsS and granular As2S3. When As and Se oxyanions were mixed, both As–S and Se(-S)0 biominerals were synthesized. All biominerals were extracellular, amorphous and presented a negative surface charge (−24 to −38 mV). Kinetic analysis indicated the following reduction yields: SeO32− (90%), AsO43− (60%), and SeO42− (<10%). The mix of SeO32− with AsO43− led to a decrease in As removal to 30%, while Se reduction yield was unaffected (88%). Interestingly, SeO42− incubated with AsO43− boosted the Se removal (71%). The exclusive extracellular formation of As and Se biominerals might indicate an extracellular respiratory process characteristic of various Shewanella species and strains. This is the first study documenting a complex interplay between As and Se oxyanions: selenite decreased arsenate reduction, whereas arsenate stimulated selenate reduction. Further investigation needs to clarify whether Shewanella sp. O23S employs multi-substrate respiratory enzymes or separate, high affinity enzymes for As and Se oxyanion respiration.

Characterization of the differentiated reduction of selenite and tellurite by a halotolerant bacterium: Process and mechanism

Se(IV)- and Te(IV)-containing wastewater usually contains salt, which reduces the activity of conventional microorganisms and may affect their microbial treatment. So far, salt-tolerant Se(IV)- and Te(IV)-reducing bacteria are very limited. Moreover, the detailed molecular response of microbial reduction of Se(IV)/Te(IV) under saline conditions has yet to be reported. In this study, the Se(IV) and Te(IV) reductive processes and mechanisms were investigated with the employment of a marine bacterium Shewanella sp. CNZ-1 (CNZ-1) using process and kinetic analyses, enzymology and RT-qPCR analyses, and differential proteomics approaches. Our results showed that CNZ-1 can effectively reduce Se(IV) and Te(IV) to Se0 and Te0 with the max k (R2) values of 0.0412 h−1 (0.86) and 0.0292 h−1 (0.91) under 2% NaCl conditions, respectively. The mechanism study showed that CNZ-1 mediated Se(IV) reduction was an enzyme-based reductive reaction, whereas CNZ-1 mediated Te(IV) reduction was more like a resistance-related detoxification process (including both bioadsorption and bioreduction). The bioreduction of Se(IV) was mainly depended on functional membrane proteins (>4-fold; e.g., nitrite reductase, polysulfide reductase and fumarate reductase), while proteins related to efflux system and stress resistance system (>2-fold; e.g., Type II secretory pathway and phage shock proteins) were essential for the Te(IV) bioreduction process. Overall, our findings expanded the understanding the fate of Se(IV) and Te(IV) in the saline environment and provided guidance for Se(IV) or Te(IV) pollution control.

Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut.

Simple SummaryThe microbial production of health-beneficial omega-3 fatty acids has gained research attention due to the limitations of availability, sustainability, and contaminants associated with the conventional fish source. Among the marine bacteria, the Shewanella genus is well known for eicosapentaenoic acid (EPA) production along with bioremediation of organic and inorganic pollutants and bioelectricity generation. We report the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gut of a freshwater fish, Tilapia. Analysis of genomic data revealed a variety of antibiotic and stress-responsive genes, metal-reducing genes, and secondary metabolite genes. Overall, the study has provided an understanding of the biosynthetic gene cluster of omega-3 polyunsaturated fatty acids in addition to adaptation strategies of Shewanella sp. N2AIL and could be utilized in developing a strain for the commercial production of EPA.The genus Shewanella is widely distributed in niches ranging from an aquatic environment to spoiled fish and is loaded with various ecologically and commercially important metabolites. Bacterial species under this genus find application in bioelectricity generation and bioremediation due to their capability to use pollutants as the terminal electron acceptor and could produce health-beneficial omega-3 fatty acids, particularly eicosapentaenoic acid (EPA). Here, the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gastrointestinal tract of Tilapia fish, is reported. The genome size of the strain was 4.8 Mb with a GC content of 46.3% containing 4385 protein-coding genes. Taxonogenomic analysis assigned this strain to the genus Shewanella on the basis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), phylogenetically most closely related with S. baltica NCTC 10735T. The comparative genome analysis with the type strain of S. baltica revealed 693 unique genes in the strain N2AIL, highlighting the variation at the strain level. The genes associated with stress adaptation, secondary metabolite production, antibiotic resistance, and metal reduction were identified in the genome suggesting the potential of the bacterium to be explored as an industrially important strain. PUFA synthase gene cluster of size ~20.5 kb comprising all the essential domains for EPA biosynthesis arranged in five ORFs was also identified in the strain N2AIL. The study provides genomic insights into the diverse genes of Shewanella sp. N2AIL, which is particularly involved in adaptation strategies and prospecting secondary metabolite potential, specifically the biosynthesis of omega-3 polyunsaturated fatty acids.

Metabolomic Insights of the Effects of Bacterial Algicide IRI-160AA on Dinoflagellate Karlodinium veneficum.

Shewanella sp. IRI-160 is an algicidal bacterium that secretes an algicide, IRI-160AA. This algicide specifically targets dinoflagellates, while having no adverse effects on other algal species tested. Dinoflagellates exposed to IRI-160AA exhibited increased production of reactive oxygen species (ROS), DNA damage, and cell cycle arrest, implying a programmed pathway leading to cell death (PCD). Here, a metabolomic analysis was conducted on dinoflagellate Karlodinium veneficum and a control cryptophyte species Rhodomonas exposed to IRI-160AA to investigate the cellular mechanisms behind the physiological effects and the specificity of this algicide. Results of this research supported previous observations about physiological responses to the algicide. A suite of metabolites was identified that increased in the cell pellets of K. veneficum but not in Rhodomonas, including oxidative stress biomarkers, antioxidants, and compounds involved in DNA damage and PCD. Overall, the results of this study illustrated the metabolomic mechanisms underlying the algicidal effects of IRI-160AA on dinoflagellates. This research also provided insights and future directions for studies on the cellular response of dinoflagellates exposed to antagonistic bacteria in the environment.

Assessment of Spoilage Microbiota of Rainbow Trout (Oncorhynchus mykiss) during Storage by 16S rDNA Sequencing

Due to the high contents of protein and fat in rainbow trout, it is highly susceptible to spoilage, which limits the storage and transportation processes. Exploring the spoilage microbial community during rainbow trout storage is essential to develop an effective preservation method. Here, the changes in the total bacterial colony and total volatile base nitrogen (TVB-N) during the storage of rainbow trout were investigated. Storage at 0 °C can effectively slow down the spoilage process with bacterial counts and TVB-N contents decreased from 8.7 log CFU/g and 18.7 mg/100 g obtained at 4 °C to 5.6 log CFU/g and 14.5 mg/100 g, respectively. 16S rDNA high-throughput sequencing results showed that the diversity of microbial genera decreased during storage. Acinetobacter, Pseudomonas, and Shewanells gradually became the dominant spoilage genera with contents of 59.9%, 18.6%, and 1.7%, respectively, in the late stage of storage. The spoilage abilities of bacteria belonging to the Pseudomonas and Shewanells genera were analyzed. Shewanella sp. S5-52 showed the highest level of TVB-N content (100.6 mg/100 g) in sterile fish juice, indicating that it had a strong spoilage ability. This study confirmed the dominant spoilage bacterial genera and evaluated the spoilage abilities of isolated strains during the storage of rainbow trout, which laid the foundation for further investigation of the spoilage mechanism of rainbow trout and other aquatic products.

Mutual interaction between the secreted flavins and immobilized quinone in anaerobic removal of high-polarity aromatic compounds containing nitrogen by Shewanella sp. RQs-106

The immobilized anthraquinone-2-sulfonate (iAQS) could significantly promote anaerobic biotransformation of the contaminants. During this process, the role of flavins secreted by bacteria remains unclear. In the present study, mutual interaction between extracellular flavins and AQS-modified polyurethane foam (AQS-PUF) during the reduction of azo dye Acid Red 18 and 3-nitrobenzenesulfonate (3-NBS) was investigated. Results showed that the amount of extracellular flavins secreted by Shewanella sp. RQs-106 was positively correlated with the concentration of iAQS ranging from 10 to 100 μM. The presence of iAQS resulted in the increased concentration of extracellular and intracellular flavins, implying that iAQS could induce the synthesis and secretion of flavins. The deletion of gene bfe encoding the flavin adenine dinucleotide exporter resulted in approximately 63.8% decrease in the amount of extracellular flavins. Further analysis showed that the decreased amount of extracellular flavins could contribute to around 50.8% reduction of iAQS. Moreover, around 23.2% and 34.0% decreases were observed in AQS-PUF-mediated removal rates of AR 18 and 3-NBS by mutant lacking bfe gene, respectively, compared with that by wild type strain RQs-106. These results indicated that the secreted flavins played an important role in the bio-reduction of AQS-PUF, resulting in their contribution to AQS-PUF-mediated removals of high-polarity aromatic compounds containing nitrogen.

Arsenic biotransformation in industrial wastewater treatment residue: Effect of co-existing Shewanella sp. ANA-3 and MR-1

Shewanella sp. ANA-3 with the respiratory arsenate reductase (ArrAB) and MR-1 with ferric reduction ability always coexist in the presence of high arsenic (As)-containing waste residue. However, their synergistic impacts on As transformation and mobility remain unclear. To identify which bacterium, ANA-3 or MR-1, dominates As mobility in the coexisting environment, we explored the As biotransformation in the industrial waste residue in the presence of Shewanella sp. ANA-3 and MR-1. The incubation results show that As(III) was the main soluble species, and strain ANA-3 dominated As mobilization. The impact of ANA-3 was weakened by MR-1, probably due to the survival competition between these two bacteria. The results of micro X-ray fluorescence and X-ray photoelectron spectroscopy analyses further reveal the pathway for ANA-3 to enhance As mobility. Strain ANA-3 almost reduced 100% surface-bound Fe(III), and consequently led to As(V) release. The dissolved As(V) was then reduced to As(III) by ANA-3. The results of this study help to understand the fate of arsenic in the subsurface and highlight the importance of the safe disposal of high As-containing industrial waste.

Antibacterial effect of copper nanoparticles produced in a Shewanella-supported non-external circuit bioelectrical system on bacterial plant pathogens.

The use of copper nanoparticles for the inhibition of plant pathogens Ralstonia solanacearum, which causes wilt disease, and Xanthomonas axonopodis, which causes citrus canker, was investigated in this study. To avoid the inhibiting effect of Cu2+ ions on the bacterial cells, the copper nanoparticles were synthesized in the cathode chamber of a non-external circuit bioelectrochemical system (nec_BES) inoculated with Shewanella sp. HN-41 at the anode. The electrons produced by the oxidation of lactate by Shewanella sp. HN-41 were directly transferred to the anolyte in the cathode via a graphite electrode connecting the anode and cathode chambers. SEM images of the produced particles revealed that the copper nanoparticles were aggregated into spherical shapes with an average size of 2.9 μm from smaller particles with a size range from 30 nm to approximately 190 nm. X-ray diffraction demonstrated that the copper nanoparticles were mainly in the form of a single-phase crystal mixture of atacamite (Cu2Cl(OH)3) and paracatamite (Cu2Cl(OH)3). Finally, for the application of synthesized nanoparticles, an agar diffusion test was applied to assess the antibacterial activity of the formed copper nanoparticles in propylene glycol solvent against R. solanacearum and X. axonopodis. The results showed that the nanoparticles damaged the cells of R. solanacearum, with a half maximum inhibition (IC50) value of 42 ppm, but did not damage X. axonopodis cells.

Identification of changes in the microflora composition of Japanese horse mackerel (Trachurus japonicus) during storage to identify specific spoilageorganisms

Japanese horse mackerel (Trachurus japonicus) is an important marine resource, and its loss and waste should be reduced. This study aimed to identify the changes in the microflora composition during storage and specific spoilage organisms (SSOs) in Japanese horse mackerel, for spoilage prevention. They were stored at either 20 °C or 4 °C aerobically, and the bacterial viable counts, concentration of total volatile basic nitrogen (TVB-N), and microflora composition for each group were analyzed. Samples stored at 20 °C for 48 h showed similar viable counts to those stored at 4 °C for 168 h; however, the TVB-N concentrations increased at 20 °C, but not at 4 °C. 16S rRNA metagenome analysis showed that Shewanella became dominant genus in the microflora regardless of the storage temperature. However, dominant amplicon sequence variants (ASVs), which are a more detailed classification level than the genus, differed depending on the storage temperatures; therefore, dominant ASVs at 20 °C were assumed to be potential SSOs. Shewanella sp. Strain NFH-SH190041, which was genetically closely related to the dominant ASVs at 20 °C, was isolated, and its spoilage ability was verified. The strain NFH-SH190041 may be considered a novel SSO of Japanese horse mackerel because its 16S rRNA sequence is clearly different from those of known species.

U (VI) tolerance affects Shewanella sp. RCRI7 biological responses: growth, morphology and bioreduction ability

Native Shewanella sp. RCRI7 is recently counted as an operative bacterium in the uranium bio-reduction. The aim of this study was to investigate the effects of uranium tolerance on the morphology and population of RCRI7, following its potential removal capacity in different time intervals. In this research, the bacterial growth and uranium removal kinetic were evaluated in aerobic TSB medium, uranium-reducing condition (URC), aerobic uranium-containing (AUC) and anaerobic uranium-free (AUF) solution, following evaluations of omcAB gene expressions. In addition, spectrophotometry analyses were performed in URC confirming the bio-reduction mechanism. It was found that the bacteria can grow efficiently in the presence of 0.5mM uranium anaerobically, unlike AUC and AUF solutions. Since the bacterium's adsorption capacity is quickly saturated, it can be deduced that uranium reduction should be dominant as incubation times proceed up to 84h in URC. In 92h incubation, the adsorbed uranium containing unreduced and reduced (U (IV) monomeric), was released to the solution due to either increased pH or bacterial death. In AUC and AUF, improper conditions lead to the reduced bacterial size (coccus-shape formation) and increased bacterial aggregations; however, membrane vesicles produced by the bacteria avoid the uranium incrustation in AUC. In overall, this study implies that Shewanella sp. RCRI7 are well tolerated by uranium under anaerobic conditions and the amount of regenerated uranium increases over time in the reduced form.

Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome.

Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.

Biogenic synthesis of selenium nanoparticles by Shewanella sp. HN-41 using a modified bioelectrochemical system

Synthesis of selenium nanoparticles from selenite by Shewanella sp. HN-41 demonstrated that particle size depended on the reaction time and biomass of cells. The slow reaction and low biomass tended to form small particles. In this study, Shewanella sp. HN-41 was introduced into the anode of a nonexternal circuit bioelectrochemical system (nec_BES) to convert chemical energy from lactate to low electron current to the cathode, where selenite was reduced. Our experiment with two systems, one bioelectrochemical system with a cathode flushed with nitrogen and the other with a no-nitrogen-flushing cathode, showed that the former could not produce Se nanoparticles after 21 d, but the latter formed them with an average size of 37.7 nm. The SEM and TEM images demonstrated that the particle size of 10 nm occupied over 10% and most of the particles were in the range of 30–60 nm. The XRD result and SAED image demonstrated no clear peaks of crystal and proved that the Se nanoparticles are amorphous. The clean Se nanoparticles were synthesized and completely separated from bacterial cells in the bioelectrochemical system. This study opened a new approach for the biological synthesis of metal nanoparticles. Finally, the Se products in the range of 30–60 nm can be tested for antimicrobial activities in medical applications. How to cite: Ho CT, Nguyen T-H, Lam T-T, et al. Biogenic synthesis of selenium nanoparticles by Shewanella sp. HN-41 using a modified bioelectrochemical system. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.07.004

Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome.

Shewanella is a ubiquitous bacterial genus of aquatic ecosystems, and its bacteriophages are also isolated from aquatic environments (oceans, lakes, ice, and wastewater). In this study, the isolation and characterization of a novel virulent Shewanella phage vB_SspS_KASIA and the identification of three prophages of its host, Shewanella sp. M16, including a mitomycin-inducible Mu-like siphovirus, vB_SspS_MuM16-1, became the starting point for comparative analyses of phages infecting Shewanella spp. and the determination of their position among the known bacterial viruses. A similarity networking analysis revealed the high diversity of Shewanella phages in general, with vB_SspS_KASIA clustering exclusively with Colwellia phage 9A, with which it forms a single viral cluster composed of two separate viral subclusters. Furthermore, vB_SspS_MuM16-1 presented itself as being significantly different from the phages deposited in public databases, expanding the diversity of the known Mu-like phages and giving potential molecular markers for the identification of Mu-like prophages in bacterial genomes. Moreover, the functional analysis performed for vB_SspS_KASIA suggested that, despite the KASIA host, the M16 strain grows better in a rich medium and at 30 °C the phage replication cycle seems to be optimal in restrictive culture conditions mimicking their natural environment, the Zloty Stok gold and arsenic mine.

Identification dehydratase domains from Schizochytrium sp. and Shewanella sp. and distinct functions in biosynthesis of fatty acids.

Polyunsaturated fatty acid (PUFA) synthase is a special and effective enzyme for PUFA synthesis, and dehydratase (DH) domain played a crucial role in it. In this work, we compared four different DH domains from different strains (Schizochytrium sp. HX-308 and Shewanella sp. BR-2) and different gene clusters. First bioinformatics analysis showed that DH1, 2 and DH3 were similar to FabA and PKS-DH, respectively, and all of them got a hot-dog structure. Second, four DH domains were expressed in Escherichia coli that increased biomass. Especially, Schi-DH1,2 presented the highest dry cell weight of 2.3g/L which was 1.62 times of that of control. Fatty acids profile analysis showed that DH1,2 could enhance the percentage of unsaturated fatty acids, especially DH1,2 from Schizochytrium sp., while DH3 benefited for the saturated fatty acid biosynthesis. Furthermore, five kinds of fatty acids were added to the medium to study the substrate preferences. Results revealed that DH1,2 domain preferred to acting on C16:0, while DH3 domain trended acting on C14:0 and C15:0, which illustrated DH from different clusters do have specific substrate preference. Besides, DH expression could save the cell growth inhibition by mid-chain fatty acids. This study provided more information about the catalysis mechanism of polyunsaturated fatty acid synthase and might promote the modification study based on this enzyme.

Draft Genome Sequences of Three Shewanella sp. Strains Isolated from Urban Freshwaters in the Ohio River Valley, USA.

ABSTRACTDraft genome sequences of three Shewanella sp. strains are reported. The strains NKUCC01_JLK, NKUCC05_KAH, and NKUCC06_TVS were isolated from freshwater sources in the Ohio River Valley, USA. These genome sequences provide insights into Shewanella adaptation to urban freshwaters and may help to elucidate their roles in biogeochemical cycling.

Expression and Characterization of a Novel Cold-Adapted and Stable β-Agarase Gene agaW1540 from the Deep-Sea Bacterium Shewanella sp. WPAGA9.

The neoagaro-oligosaccharides, degraded from agarose by agarases, are important natural substances with many bioactivities. In this study, a novel agarase gene, agaW1540, from the genome of a deep-sea bacterium Shewanella sp. WPAGA9, was expressed, and the recombinant AgaW1540 (rAgaW1540) displayed the maximum activity under the optimal pH and temperature of 7.0 and 35 °C, respectively. rAgaW1540 retained 85.4% of its maximum activity at 0 °C and retained more than 92% of its maximum activity at the temperature range of 20–40 °C and the pH range of 4.0–9.0, respectively, indicating its extensive working temperature and pH values. The activity of rAgaW1540 was dramatically suppressed by Cu2+ and Zn2+, whereas Fe2+ displayed an intensification of enzymatic activity. The Km and Vmax of rAgaW1540 for agarose degradation were 15.7 mg/mL and 23.4 U/mg, respectively. rAgaW1540 retained 94.7%, 97.9%, and 42.4% of its maximum activity after incubation at 20 °C, 25 °C, and 30 °C for 60 min, respectively. Thin-layer chromatography and ion chromatography analyses verified that rAgaW1540 is an endo-acting β-agarase that degrades agarose into neoagarotetraose and neoagarohexaose as the main products. The wide variety of working conditions and stable activity at room temperatures make rAgaW1540an appropriate bio-tool for further industrial production of neoagaro-oligosaccharides.

Complete Genome Sequence of Shewanella sp. Strain Lzh-2, an Algicidal Bacterial Strain Isolated from Lake Taihu, People's Republic of China.

Shewanella sp. strain Lzh-2 is an algicidal bacterium isolated from surface water samples collected from Meiliang Bay of Lake Taihu in China. Here, we present the complete genome sequence of Shewanella sp. Lzh-2. Some functional genes and secondary metabolite gene clusters were predicted.