Effects of biochar immobilization of Serratia sp. F4 OR414381 on bioremediation of petroleum contamination and bacterial community composition in loess soil.

Petroleum hydrocarbons pose a significant threat to human health and the environment. Biochar has increasingly been utilized for soil remediation. This study investigated the potential of biochar immobilization using Serratia sp. F4 OR414381 for the remediation of petroleum-contaminated soil through a pot experiment conducted over 90 days. The treatments in this study, denoted as IMs (maize straw biochar-immobilized Serratia sp. F4), degraded 82.5% of the total petroleum hydrocarbons (TPH), 59.23% of the aromatic, and 90.1% of the saturated hydrocarbon fractions in the loess soils. During remediation, the soil pH values decreased from 8.76 to 7.33, and the oxidation-reduction potential (ORP) increased from 156 to 229 mV. The treatment-maintained soil nutrients of the IMs were 138.94 mg/kg of NO3- -N and 92.47 mg/kg of available phosphorus (AP), as well as 11.29% of moisture content. The activities of soil dehydrogenase (SDHA) and catalase (CAT) respectively increased by 14% and 15 times compared to the CK treatment. Three key petroleum hydrocarbon degradation genes, including CYP450, AJ025, and xylX were upregulated following IMs treatment. Microbial community analysis revealed that a substantial microbial population of 1.01E+ 09 cells/g soil and oil-degrading bacteria such as Salinimicrobium, Saccharibacteria_genera_incertae_sedis, and Brevundimonas were the dominant genera in IMs treatment. This suggests that the biochar immobilized on Serratia sp. F4 OR414381 improves soil physicochemical properties and enhances interactions among microbial populations, presenting a promising and environmentally friendly approach for the stable and efficient remediation of petroleum-contaminated loess soil.

Characterization of multi-metal-resistant Serratia sp. GP01 for treatment of effluent from fertilizer industries.

The effluent generated from fertilizer plants in Paradeep in the coast of the Bay of Bengal is the major pollutant causing health hazard in the vicinity of the area with respect to plants, animals and microbes. Samples of effluent were found to contain heavy metals (mg L-1): Cr (100), Ni (36.975), Mn (68.673), Pb (20.133), Cu (74.44), Zn (176.716), Hg (5.358) and As (24.287) as analyzed by XRF. Indigenous bacterial strains were screened for chromate and multi-metal resistance to remediate the toxic pollutants. The isolated strain G1 was identified as Serratia sp. through 16S-rDNA sequence homology. The potent strain Serratia sp. GP01 treated with 100 mg L-1 of K2Cr2O7 has shown the efficacy of reducing 69.05 mg L-1 of Cr over 48 h of incubation. Further, presence of chromate reductase gene (ChR) in Serratia sp. confirmed the enzymatic reduction of Cr(VI). SEM-EDX and SEM mapping analysis revealed substantial biosorption of Cr and other heavy metals present in effluent by Serratia sp. GP01. Antioxidant enzymes such as catalase (72.15 U mL-1), SOD (57.14 U mL-1) and peroxidase (62.49 U mL-1) were found to be higher as compared to the control condition. FTIR study also revealed the role of N-H, O-H, C = C, C-H, C-O, C-N, and C = O functional groups of the cell surface of Serratia sp. treated with K2Cr2O7 and effluent from the fertilizer industry. Isolated strain Serratia sp. could be used for the detoxification of Cr(VI) and other heavy metals in fertilizer plant effluent.

Characterisation of hydrocarbon degradation, biosurfactant production, and biofilm formation in Serratia sp. Tan611: a new strain isolated from industrially contaminated environment in Algeria.

A novel bacterial strain was isolated from industrially contaminated waste water. In the presence of crude oil, this strain was shown to reduce the rate of total petroleum hydrocarbons (TPH) up to 97.10% in 24 h. This bacterium was subsequently identified by 16S rRNA gene sequence analysis and affiliated to the Serratia genus by the RDP classifier. Its genome was sequenced and annotated, and genes coding for catechol 1,2 dioxygenase and naphthalene 1,2-dioxygenase system involved in aromatic hydrocarbon catabolism, and LadA-type monooxygenases involved in alkane degradation, were identified. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of crude oil after biological treatment showed that Serratia sp. Tan611 strain was able to degrade n-alkanes (from C13 to C25). This bacterium was also shown to produce a biosurfactant, the emulsification index (E24) reaching 43.47% and 65.22%, against vegetable and crude oil, respectively. Finally, the formation of a biofilm was increased in the presence of crude oil. These observations make Serratia sp. Tan611 a good candidate for hydrocarbon bioremediation.

Complete Genome Resource of Serratia plymuthica C-1 that Causes Root Rot Disease in Korean Ginseng.

Serratia plymuthica C-1, a biocontrol agent, was isolated from soil collected from a mountain forest in Korea. Previous studies have shown that certain strains of S. plymuthica cause root rot disease in ginseng. To the best of our knowledge, this is the first report of the sequence of the circular chromosome of S. plymuthica C-1, which plays a dual role by causing root rot in ginseng and exhibiting biocontrol activity. The findings of this study will assist in analyzing the genes associated with the pathogenicity and biocontrol properties of S. plymuthica.

Growth stimulatory effect of AHL producing Serratia spp. from potato on homologous and non-homologous host plants.

Plant growth promoting rhizobacteria are known to improve plant performance by developing healthy and productive interactions with the host plants. These associations may be symbiotic or asymbiotic depending upon the genetic potential of the resident microbe and promiscuity of the host. Present study describes the potential of two Serratia spp. strains for promotion of plant growth in homologous as well as non-homologous hosts. The strains KPS-10 and KPS-14; native to potato rhizosphere belong to genus Serratia based on 16S rRNA gene sequences (accession no. LN831934 and LN831937 respectively) and contain multiple plant growth promoting properties along-with the production of quorum sensing acyl homoserine lactone (AHL) molecules. Both Serratia spp. strains showed solubilization of inorganic tri-calcium phosphate while KPS-14 also exhibited phytase activity (1.98 10-10 kcat). KPS-10 showed higher P-solubilization activity (128.5 µg/mL), IAA production (8.84 µg/mL), antifungal activity and also showed the production of two organic acids i.e., gluconic acid and lactic acid. Both strains produced three common AHLs: C6-HSL, 3oxo-C10-HSL, 3oxo-C12-HSL while some strain-specific AHLs (3OH-C5-HSL, 3OH-C6-HSL, C10-HSL specific to KPS-10 and 3OH-C6-HSL, C8-HSL, 3oxo-C9-HSL, 3OH-C9-HSL specific to KPS-14). Strains showed roots and rhizosphere colonization of potato and other non-homologous hosts up to one month. In planta AHLs-detection confirmed a likely role of AHLs during seedling growth and development where both extracted AHLs or bacteria inoculated roots showed extensive root hair. A significant increase in root/shoot lengths, root/ shoot fresh weights, root/shoot dry weights was observed by inoculation in different hosts. PGP-characteristics along with the AHLs-production signify the potential of both strains as candidate for the development of bio-inoculum for potato crop in specific and other crops in general. This inoculum will not only reduce the input of chemical fertilizer to the environment but also improve soil quality and plant growth.

The nematicide Serratia plymuthica M24T3 colonizes Arabidopsis thaliana, stimulates plant growth, and presents plant beneficial potential.

Nine bacterial strains were previously isolated in association with pinewood nematode (PWN) from wilted pine trees. They proved to be nematicidal in vitro, and one of the highest activities, with potential to control PWN, was showed by Serratia sp. M24T3. Its ecology in association with plants remains unclear. This study aimed to evaluate the ability of strain M24T3 to colonize the internal tissues of the model plant Arabidopsis thaliana using confocal microscopy. Plant growth-promoting bacteria (PGPB) functional traits were tested and retrieved in the genome of strain M24T3. In greenhouse conditions, the bacterial effects of all nematicidal strains were also evaluated, co-inoculated or not with Bradyrhizobium sp. 3267, on Vigna unguiculata fitness. Inoculation of strain M24T3 increased the number of A. thaliana lateral roots and the confocal analysis confirmed effective bacterial colonization in the plant. Strain M24T3 showed cellulolytic activity, siderophores production, phosphate and zinc solubilization ability, and indole acetic acid production independent of supplementation with L-tryptophan. In the genome of strain M24T3, genes involved in the interaction with the plants such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinolytic activity, and quorum sensing were also detected. The genomic organization showed ACC deaminase and its leucine-responsive transcriptional regulator, and the activity of ACC deaminase was 594.6 nmol α-ketobutyrate µg protein-1 µl-1. Strain M24T3 in co-inoculation with Bradyrhizobium sp. 3267 promoted the growth of V. unguiculata. In conclusion, this study demonstrated the ability of strain M24T3 to colonize other plants besides pine trees as an endophyte and displays PGPB traits that probably increased plant tolerance to stresses.

Excellent N-fixing and P-solubilizing traits in earthworm gut-isolated bacteria: A vermicompost based assessment with vegetable market waste and rice straw feed mixtures.

Vermicomposting is a dependable waste recycling technology which greatly augments N and P levels mainly through microbial action. This paper aims to identify efficient N-fixing (NFB) and P-solubilizing (PSB) bacteria from earthworm intestines. Various combinations of vegetable market waste, rice straw, and cowdung were fed to two earthworm species (Eisenia fetida and Perionyx excavatus). Total organic C decreased, pH shifted towards neutrality, and NPK availability, and microbial (NFB, PSB, and total bacteria) population increased remarkably during vermicomposting with E. fetida. Therefore, 45 NFB and 34 PSB strains isolated from Eisenia gut were initially screened, their inter-dominance assessed, and 8 prolific strains were identified through 16SrRNA sequencing. Interestingly, two novel N-fixing strains of Kluyvera ascorbata emerged as an efficient biofertilizer candidate. Moreover, both N-fixing and P-solubilizing strains of Serratia and Bacillus were isolated from earthworm gut. All the isolated strains significantly improved soil health and facilitated crop growth as compared to commercial biofertilizers.

Role of 1-acyl-sn-glycerol-3-phosphate acyltransferase in psychrotrophy and stress tolerance of Serratia plymuthica RVH1.

A mutant with a transposon insertion just upstream of the lysophosphatidic acid acyltansferase gene plsC was isolated in a screen for mutants affected in growth at low temperature of the psychrotroph Serratia plymuthica RVH1. This mutant had lost its ability to grow at 4 °C and was severely affected in growth at 10 °C, but showed only slightly reduced growth at 30 °C. Fatty acid analysis of membrane extracts showed that the ratio of C16:1/C18:1 fatty acids was six-to sevenfold reduced in the mutant, although the ratio of unsaturated to saturated fatty acids was unaffected. The homeoviscous adaptation ability of the mutant was also unaffected. Growth and fatty acid composition were mostly restored by overexpressing plsC on a plasmid. Supplementation of C16:1 (palmitoleic acid) into the growth medium partially rescued low temperature growth, indicating that a balanced ratio of the two main unsaturated fatty acids is required for psychrotrophy. The mutant was significantly more strongly inactivated by high pressure treatment at 250 MPa, but not at higher pressures. It also showed reduced growth at low pH, but not at increased NaCl concentrations. This work provides novel information on the role of membrane fatty acid composition in stress tolerance.

Draft genome sequence of the biocontrol strain Serratia plymuthica A30, isolated from rotting potato tuber tissue.

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 ("Dickeya solani"). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissue.

Quantitative and specific detection of the biocontrol agent, Serratia plymuthica, in plant extracts using a real-time TaqMan® assay.

A Serratia plymuthica-specific TaqMan® assay was designed based on the consensus nucleotide sequence from the 3'- end of the luxS gene present in all S. plymuthica strains tested. The specificity of the assay was demonstrated by testing 21 Serratia spp. strains and 30 isolates belonging to various species that can potentially coexist with S. plymuthica in the same environment. Positive reactions in the TaqMan® assay were observed only for S. plymuthica isolates and not for other bacteria. The TaqMan® assay could detect down to 1.95 ng of S. plymuthica DNA, down to 5 bacterial cells per reaction (100 cfu ml(-1)) in vitro, down to 50 bacterial cells per reaction (1,000 cfu ml(-1)) in spiked potato root extracts and down to 5 bacterial cells per reaction (100 cfu ml(-1)) in spiked potato haulm extracts. We used this assay to quantify S. plymuthica A30 cells in potato and tomato haulms and roots grown from S. plymuthica A30-inoculated potato seed tubers and tomato seeds. The results were comparable with the spread-plating of plant extracts on a newly developed S. plymuthica A30 selective medium (CVTR2Arif). The TaqMan® assay can be used to quantify S. plymuthica isolates in different ecosystems and in complex substrates.

The stationary phase sigma factor, RpoS, regulates the production of a carbapenem antibiotic, a bioactive prodigiosin and virulence in the enterobacterial pathogen Serratia sp. ATCC 39006.

Serratia sp. ATCC 39006 (S39006) is a Gram-negative bacterium that is virulent in plant (potato) and invertebrate animal (Caenorhabditis elegans) models. It produces two secondary metabolite antibiotics, a prodigiosin and a carbapenem, and the exoenzymes pectate lyase and cellulase. We showed previously that deletion of the RNA chaperone Hfq abolished antibiotic production and attenuated virulence in both animal and plant hosts. Hfq and dependent small RNAs (sRNAs) are known to regulate the post-transcriptional expression of rpoS, which encodes σ(S), the stationary phase sigma factor subunit of RNA polymerase. An S39006 hfq deletion mutant showed decreased transcript levels of rpoS. Therefore, in this study we investigated whether the phenotypes regulated by Hfq were mediated through its control of rpoS. Whereas loss of Hfq abolished prodigiosin and carbapenem production and attenuated virulence in both C. elegans and potato, characterization of an S39006 rpoS mutant showed unexpectedly elevated prodigiosin and carbapenem production. Furthermore, the rpoS mutant exhibited attenuated animal pathogenesis, but not plant pathogenesis. Additionally, a homologue of the Hfq-dependent sRNA, RprA, was identified and shown to regulate prodigiosin production in a manner consistent with its role in positively regulating translation of rpoS mRNA. Combined, these results demonstrate that Hfq regulation of secondary metabolism and plant pathogenesis is independent of RpoS and establishes RpoS and RprA as regulators of antibiotic production.

The RNA chaperone, Hfq, controls two luxR-type regulators and plays a key role in pathogenesis and production of antibiotics in Serratia sp. ATCC 39006.

Serratia sp. ATCC 39006 (S39006) is a Gram-negative bacterium that is virulent in plant (potato) and animal (Caenorhabditis elegans) models. It produces two secondary metabolite antibiotics, a prodigiosin and a carbapenem, and the exoenzymes, pectate lyase and cellulase. A complex regulatory network that includes quorum sensing (QS) controls production of prodigiosin. While many aspects of the regulation of the metabolites and exoenzymes are well understood, the potential role in this network of the RNA chaperone Hfq and dependent small regulatory RNAs has not been characterized. Hfq is an RNA chaperone involved in post-transcriptional regulation that plays a key role in stress response and virulence in diverse bacterial species. To explore whether Hfq-dependent processes might contribute to the regulation of antibiotic production we constructed an S39006 Δhfq mutant. Production of prodigiosin and carbapenem was abolished in this mutant strain, while production of the QS signalling molecule, butanoyl homoserine lactone (BHL), was unaffected. Using transcriptional fusions, we found that Hfq regulates the QS response regulators, SmaR and CarR. Additionally, exoenzyme production and swimming motility were decreased in a Δhfq mutant, and virulence was attenuated in potato and C. elegans models. These results suggest that an Hfq-dependent pathway is involved in the regulation of virulence and secondary metabolite production in S39006.

Two types of phytases (histidine acid phytase and ß-propeller phytase) in Serratia sp. TN49 from the gut of Batocera horsfieldi (coleoptera) larvae.

Microbial phytases play a major role in the mineralization of organic phosphorous, especially in symbiotic plants and animals. In this study, we identified two types of phytases in Serratia sp. TN49 that was harbored in the gut of Batocera horsfieldi (Coleoptera) larvae. The two phytases, an acidic histidine acid phosphatase (PhyH49) and an alkaline ß-propeller phytase (PhyB49), shared low identities with known phytases (61% at most). PhyH49 and PhyB49 produced in Escherichia coli exhibited maximal activities at pH 5.0 (60°C) and pH 7.5-8.0 (45°C), respectively, and are complementary in phytate degradation over the pH range 2.0-9.0. Serratia sp. TN49 harboring both PhyH49 and PhyB49 might make it more adaptive to environment change, corresponding to the evolution trend of microorganism.

[Pleiotropic effects of chitinase gene from Serratia plymuthica in transgenic potato].

We estimate the influence of transgenic bacterial chitinase from soilborne Serratia plymuthica onto agronomical important traits of potato, such as productivity and non-specific resistance. Transgene has been delivered into potato variety Delfin via Agrobacterial transformation with pGreen0229 and pBI121-based vectors. Growth inhibition of chitin-containing pathogenic fungi was shown. However, over 40% oftransgenic lines demonstrated decreased non-specific resistance to late blight (down to 62% compared to control genotype), as well as 40-60% productivity drop.

Microbial studies of a selenium-contaminated mine site and potential for on-site remediation.

Surface water Selenium (Se) concentrations are above regulatory standards at several active and inactive phosphate mine sites in the US Western Phosphate Resource Area. The focus of the present study was to examine the impacts of the microbial communities on the oxidation state of Se in overburden waste from the Smoky Canyon phosphate mine in Idaho, USA. Microbial populations were found that reduce soluble selenate (SeO (4) (2-) ) to insoluble elemental Se. Microcosm experiments were conducted for molecular genetic analysis of this microbial community by rRNA gene profiling. An acetone pretreatment step was developed to remove interfering pre-petroleum hydrocarbons from the samples prior to extraction. PCR was used to amplify 16S and 18S rRNA genes present in the microbial community DNA. The amplified products were subjected to denaturing gradient gel electrophoresis (DGGE). Isolates and excised DGGE bands were amplified and sequenced for identification to determine the relative importance of culturable isolates to the total microbial population. Analysis of samples from different sites at the mine showed how Se contamination and previous remediation treatments changed the microbial populations across the site. Members of the family Enterobacteriaceae were dominant among the selenate reducing isolates from the site containing high Se levels. In particular, Serratia fonticola was isolated repeatedly from contaminated Smoky Canyon Mine site samples. Packed column studies were performed with seleniferous waste rock fractions from Smoky Canyon Mine. Column amendments consisted of combinations of iron, compost, and whey. Eh, pH, and extractable Se measurements were taken. Tests with infiltrated water showed columns containing an organic amendment combined with iron metal were the most resistant to Se leaching. Iron-based compounds from the corroding metal are thought to strongly bind the Se reduced by microbial activity, thereby stabilizing the Se in an insoluble form. We conclude that long-term stabilization of selenium at contaminated mine sites may require reductive microbial processes combined with abiotic immobilization by iron, either natural or engineered, to stabilize the Se and retard re-oxidation and release. Iron-selenide or iron-selenite compounds are more stable and resistant to leaching, especially when removed from active weathering.

Strategy to select and assess antagonistic bacteria for biological control of Rhizoctonia solani Kühn.

A screening strategy was developed to assess the potential of plant-associated bacteria to control diseases caused by Rhizoctonia solani Kühn. About 434 already characterized antagonistic bacterial strains isolated from diverse plant species and microenvironments were evaluated for biocontrol and plant growth promotion by a hierarchical combination of assays. Analyzing in vitro antagonism towards different Rhizoctonia isolates resulted in a selection of 20 potential biocontrol agents. The strains were characterized by their antagonistic mechanisms in vitro as well as their production of the plant growth hormone indole-3-acetic acid. The plant growth promoting effect by antagonistic bacteria was determined using a microtiter plate assay on the basis of lettuce seedlings. Lettuce and sugar beet as host plant were included in the biocontrol experiments in which the antagonistic effect of 17 bacterial isolates could be confirmed in vivo. Sequencing of the 16S rDNA gene and (or) fatty acid methyl ester gas chromatography was used to identify the antagonistic isolates. Molecular fingerprints of isolates obtained by BOX-polymerase chain reaction were compared to avoid further investigation with genetically very similar strains and to obtain unique molecular fingerprints for quality control and patent licensing. According to our strategy, an assessment scheme was developed and four interesting biological control agents, Pseudomonas reactans B3, Pseudomonas fluorescens B1, Serratia plymuthica B4, and Serratia odorifera B6, were found. While S. plymuthica B4 was the best candidate to biologically control Rhizoctonia in lettuce, P. reactans B3 was the best candidate to suppress the pathogen in sugar beet.