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.

CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU

Bacteria protect themselves from infection by bacteriophages (phages) using different defence systems, such as CRISPR-Cas. Although CRISPR-Cas provides phage resistance, fitness costs are incurred, such as through autoimmunity. CRISPR-Cas regulation can optimise defence and minimise these costs. We recently developed a genome-wide functional genomics approach (SorTn-seq) for high-throughput discovery of regulators of bacterial gene expression. Here, we applied SorTn-seq to identify loci influencing expression of the two type III-A Serratia CRISPR arrays. Multiple genes affected CRISPR expression, including those involved in outer membrane and lipopolysaccharide synthesis. By comparing loci affecting type III CRISPR arrays and cas operon expression, we identified PigU (LrhA) as a repressor that co-ordinately controls both arrays and cas genes. By repressing type III-A CRISPR-Cas expression, PigU shuts off CRISPR-Cas interference against plasmids and phages. PigU also represses interference and CRISPR adaptation by the type I-F system, which is also present in Serratia. RNA sequencing demonstrated that PigU is a global regulator that controls secondary metabolite production and motility, in addition to CRISPR-Cas immunity. Increased PigU also resulted in elevated expression of three Serratia prophages, indicating their likely induction upon sensing PigU-induced cellular changes. In summary, PigU is a major regulator of CRISPR-Cas immunity in Serratia.

Potential use of two Serratia strains for cadmium remediation based on microbiologically induced carbonate precipitation and their cadmium resistance

Cadmium (Cd) presence and bioavailability in soils is a serious concern for cocoa producers. Cocoa plants can bioaccumulate Cd that can reach humans through the food chain, thus posing a threat to human health, as Cd is a highly toxic metal. Currently, microbiologically induced carbonate precipitation (MICP) by the ureolytic path has been proposed as an effective technique for Cd remediation. In this work, the Cd remediation potential and Cd resistance of two ureolytic bacteria, Serratia sp. strains 4.1a and 5b, were evaluated. The growth of both Serratia strains was inhibited at 4 mM Cd(II) in the culture medium, which is far higher than the Cd content that can be found in the soils targeted for remediation. Regarding removal efficiency, for an initial concentration of 0.15 mM Cd(II) in liquid medium, the maximum removal percentages for Serratia sp. 4.1.a and 5b were 99.3% and 99.57%, respectively. Their precipitates produced during Cd removal were identified as calcite by X-ray diffraction. Energy dispersive X-ray spectroscopy analysis showed that a portion of Cd was immobilized in this matrix. Finally, the presence of a partial gene from the czc operon, involved in Cd resistance, was observed in Serratia sp. 5b. The expression of this gene was found to be unaffected by the presence of Cd(II), and upregulated in the presence of urea. This work is one of the few to report the use of bacterial strains of the Serratia genus for Cd remediation by MICP, and apparently the first one to report differential expression of a Cd resistance gene due to the presence of urea.

Host-Cell-Dependent Roles of E-Cadherin in Serratia Invasion

Bacteria use cell surface proteins to mediate host-pathogen interactions. Proteins responsible for cell adhesion, including E-cadherin, serve as receptors for entry into the host cell. We have previously shown that an increase in eukaryotic cell sensitivity to Serratia grimesii correlates with an increase in E-cadherin expression. On the other hand, Serratia proteamaculans invasion involves the EGFR, which can interact with E-cadherin on the surface of host cells. Therefore, we investigated the role of E-cadherin in Serratia invasion into M-HeLa and Caco-2 cells. Bacterial infection increased E-cadherin expression in both cell lines. Moreover, E-cadherin was detected in the Caco-2 cells in a full-length form and in the M-HeLa cells in only a truncated form in response to incubation with bacteria. Transfection with siRNA targeting E-cadherin inhibited S. proteamaculans invasion only into the Caco-2 cells. Thus, only full-length E-cadherin is involved in S. proteamaculans invasion. On the other hand, transfection with siRNA targeting E-cadherin inhibited S. grimesii invasion into both cell lines. Thus, not only may full-length E-cadherin but also truncated E-cadherin be involved in S. grimesii invasion. Truncated E-cadherin can be formed as a result of cleavage by bacterial proteases or the Ca2+-activated cellular protease ADAM10. The rate of Ca2+ accumulation in the host cells depends on the number of bacteria per cell upon infection. During incubation, Ca2+ accumulates only when more than 500 S. grimesii bacteria are infected per eukaryotic cell, and only under these conditions does the ADAM10 inhibitor reduce the sensitivity of the cells to bacteria. An EGFR inhibitor has the same quantitative effect on S. grimesii invasion. Apparently, as a result of infection with S. grimesii, Ca2+ accumulates in the host cells and may activate the ADAM10 sheddase, which can promote invasion by cleaving E-cadherin and, as a result, triggering EGFR signaling. Thus, the invasion of S. proteamaculans can only be promoted by full-length E-cadherin, and S. grimesii invasion can be promoted by both full-length and truncated E-cadherin.

In silico exploration of Serratia sp. BRL41 genome for detecting prodigiosin Biosynthetic Gene Cluster (BGC) and in vitro antimicrobial activity assessment of secreted prodigiosin

The raising concern of drug resistance, having substantial impacts on public health, has instigated the search of new natural compounds with substantial medicinal activity. In order to find out a natural solution, the current study has utilized prodigiosin, a linear tripyrrole red pigment, as an active ingredient to control bacterial proliferation and prevent cellular oxidation caused by ROS (Reactive Oxygen Species). A prodigiosin-producing bacterium BRL41 was isolated from the ancient Barhind soil of BCSIR Rajshahi Laboratories, Bangladesh, and its morphological and biochemical characteristics were investigated. Whole genome sequencing data of the isolate revealed its identity as Serratia sp. and conferred the presence of prodigiosin gene cluster in the bacterial genome. "Prodigiosin NRPS", among the 10 analyzed gene clusters, showed 100% similarity with query sequences where pigC, pigH, pigI, and pigJ were identified as fundamental genes for prodigiosin biosynthesis. Some other prominent clusters for synthesis of ririwpeptides, yersinopine, trichrysobactin were also found in the chromosome of BRL41, whilst the rest displayed less similarity with query sequences. Except some first-generation beta-lactam resistance genes, no virulence and resistance genes were found in the genome of BRL41. Structural illumination of the extracted red pigment by spectrophotometric scanning, Thin-Layer Chromatography (TLC), Fourier Transform Infrared Spectroscopy (FTIR), and change of color at different pH solutions verified the identity of the isolated compound as prodigiosin. Serratia sp. BRL41 attained its maximum productivity 564.74 units/cell at temperature 30˚C and pH 7.5 in two-fold diluted nutrient broth medium. The compound exhibited promising antibacterial activity against Gram-positive and Gram-negative bacteria with MIC (Minimum Inhibitory Concentration) and MBC (Minimum Bactericidal Concentration) values ranged from 3.9 to15.62 μg/mL and 7.81 to 31.25 μg/mL respectively. At concentration 500 μg/mL, except in Salmonella enterica ATCC-10708, prodigiosin significantly diminished biofilm formed by Listeria monocytogens ATCC-3193, Pseudomonas aeruginosa ATCC-9027, Escherichia coli (environmental isolate), Staphylococcus aureus (environmental isolate). Cellular glutathione level (GSH) was elevated upon application of 250 and 500 μg/mL pigment where 125 μg/mL failed to show any free radical scavenging activity. Additionally, release of cellular components in growth media of both Gram-positive and Gram-negative bacteria were facilitated by the extract that might be associated with cell membrane destabilization. Therefore, the overall findings of antimicrobial, antibiofilm and antioxidant activities suggest that in time to come prodigiosin might be a potential natural source to treat various diseases and infections.

Integration of proteome and metabolome profiling to reveal heat stress response and tolerance mechanisms of Serratia sp. AXJ-M for the bioremediation of papermaking black liquor

The use of thermophilic bacteria for treating paper black liquor seems to be an efficient bioremediation strategy. In our previous work, the lignin-degrading bacterium Serratia sp. AXJ-M exhibited excellent heat tolerance ability. However, the molecular mechanism of its response to heat stress is unknown. Therefore, the heat stress response of AXJ-M was investigated using morphological and analytical methods. A comparative genomics analysis revealed interesting insights into the adaptability of the genetic basis of AXJ-M to harsh environments. Moreover, TMT quantitative proteomic analysis and parallel reaction monitoring (PRM) assays revealed that proteins related to both component systems, ABC transporters, carbohydrate, and amino metabolism, energy metabolism, etc., were differentially expressed. The non-targeted metabolome analysis revealed that the metabolic pathways associated with the fatty acid and amino acid biosynthesis and metabolism, together with the TCA cycle were most significantly enriched. Furthermore, integrated omics suggested that AXJ-M made metabolic adaptations to compensate for the increased energy demand caused by adverse environmental stimuli. The dominant heat regulator HspQ mediated heat adaptation of AXJ-M at high temperatures and modulated DyP expression. To summarize, the present study sheds light on the effect of high temperature on the lignin-degrading bacterium and its tolerance and underlying regulatory mechanisms.

Growth Phase Influence the Gene Expression and Metabolite Production Related to Indole-3-Acetic Acid (IAA) Biosynthesis by Serratia plymuthica UBCF_13

<b>Background and Objective:</b> The optimization of the indole-3-acetic acid (IAA) producing capability of <i>Serratia plymuthica</i> UBCF_13 has been intensively studied. This work tried to reveal the effect of growth phases on IAA production, gene expression and metabolite synthesis related to the IAA biosynthesis pathway. <b>Materials and Methods:</b> The growth curve and IAA production were measured every 3 hrs. The putative IAA biosynthesis pathway was investigated based on the UBCF_13 genome. To identify the possible pathway of IAA biosynthesis in UBCF_13, we applied the Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) and High-Performance Liquid Chromatography (HPLC) analysis to measure the transcript levels of each gene and indole metabolite production based on tryptophan treatment at different times of incubation. <b>Results:</b> The optimal IAA production on colorimetric assay was at 9 hrs of incubation (initial stationary phase). The level expression of <i>puuC</i>, <i>DDC</i>, <i>oxdA</i>, <i>amiE</i>, <i>nthA</i> and <i>nthB</i> have been upregulated maximum in 3 hrs of culture time (lag phase), except <i>tyrB</i> and <i>ipdC</i>. The highest transcript level of the genes was found in nitrile hydratase genes (<i>nthA</i> and <i>nthB</i>) and indole-3- acetamide (IAM) has been detected as the only intermediate in the crude extract of UBCF_13 thus the IAM pathway may be used to produce IAA. The maximum IAA production on HPLC analysis was found at 21 hrs of incubation (late stationary phase). <b>Conclusion:</b> This study gives a new insight that the best time to measure gene expression and intermediates related to the IAA biosynthetic pathway in bacteria was found at a specific growth phase.

Serratia spp. Are Responsible for Nitrogen Fixation Fueled by As(III) Oxidation, a Novel Biogeochemical Process Identified in Mine Tailings

Biological nitrogen fixation (BNF) has important environmental implications in tailings by providing bioavailable nitrogen to these habitats and sustaining ecosystem functions. Previously, chemolithotrophic diazotrophs that dominate in mine tailings were shown to use reduced sulfur (S) as the electron donor. Tailings often contain high concentrations of As(III) that might function as an alternative electron donor to fuel BNF. Here, we tested this hypothesis and report on BNF fueled by As(III) oxidation as a novel biogeochemical process in addition to BNF fueled by S. Arsenic (As)-dependent BNF was detected in cultures inoculated from As-rich tailing samples derived from the Xikuangshan mining area in China, as suggested by nitrogenase activity assays, quantitative polymerase chain reaction, and ¹⁵N₂ enrichment incubations. As-dependent BNF was also active in eight other As-contaminated tailings and soils, suggesting that the potential for As-dependent BNF may be widespread in As-rich habitats. DNA-stable isotope probing identified Serratia spp. as the bacteria responsible for As-dependent BNF. Metagenomic binning indicated that the essential genes for As-dependent BNF [i.e., nitrogen fixation, As(III) oxidation, and carbon fixation] were present in Serratia-associated metagenome-assembled genomes. Over 20 Serratia genomes obtained from NCBI also contained essential genes for both As(III) oxidation and BNF (i.e., aioA and nifH), suggesting that As-dependent BNF may be a widespread metabolic trait in Serratia spp.

Host plant adaptability and proteomic differences of diverse Rhopalosiphum maidis (Fitch) lineages

Corn leaf aphid Rhopalosiphum maidis (Fitch) can feed on various cereal crops and transmit viruses that may cause serious economic losses. To test the impact of both host plant species and age on R. maidis, as well as the proteomic difference of diverse populations, we first investigated the survival and reproduction of six R. maidis populations (i.e., LF, HF, GZ, DY, BJ, and MS) via a direct observation method in the laboratory on 10 and 50 cm high maize seedlings, and 10 cm high barley seedlings. Then a proteomic approach was implemented to identify the differentially expressed proteins from both aphids and endosymbionts of BJ and MS populations. Results indicated that the BJ population performed significantly better than the others on both barley and 50 cm high maize seedlings, while no population could survive on 10 cm high maize seedlings. The proteomic results demonstrated that the expression levels of myosin heavy chain (muscle isoform X12) (spot 781) and peroxidase (spot 1383) were upregulated, while ATP-dependent protease Hsp 100 (spot 2137) from Hamiltonella defensa and protein SYMBAF (spot 2703) from Serratia symbiotica were downregulated in the BJ population when compared to expression levels of the MS population. We hypothesize that the fatalness observed on 10 cm high maize seedlings may be caused by secondary metabolites that are synthesized by the seedlings and the MS population of R. maidis should be more stress-resistant than the BJ population. Our results also provide insights for understanding the interaction between host plants and aphids.

Natural combinatorial genetics and prolific polyamine production enable siderophore diversification in Serratia plymuthica

BACKGROUND

Iron is essential for bacterial survival. Bacterial siderophores are small molecules with unmatched capacity to scavenge iron from proteins and the extracellular milieu, where it mostly occurs as insoluble Fe3+. Siderophores chelate Fe3+ for uptake into the cell, where it is reduced to soluble Fe2+. Siderophores are key molecules in low soluble iron conditions. The ability of bacteria to synthesize proprietary siderophores may have increased bacterial evolutionary fitness; one way that bacteria diversify siderophore structure is by incorporating different polyamine backbones while maintaining the catechol moieties.

RESULTS

We report that Serratia plymuthica V4 produces a variety of siderophores, which we term the siderome, and which are assembled by the concerted action of enzymes encoded in two independent gene clusters. Besides assembling serratiochelin A and B with diaminopropane, S. plymuthica utilizes putrescine and the same set of enzymes to assemble photobactin, a siderophore found in the bacterium Photorhabdus luminescens. The enzymes encoded by one of the gene clusters can independently assemble enterobactin. A third, independent operon is responsible for biosynthesis of the hydroxamate siderophore aerobactin, initially described in Enterobacter aerogenes. Mutant strains not synthesizing polyamine-siderophores significantly increased enterobactin production levels, though lack of enterobactin did not impact the production of serratiochelins. Knocking out SchF0, an enzyme involved in the assembly of enterobactin alone, significantly reduced bacterial fitness.

CONCLUSIONS

This study shows the natural occurrence of serratiochelins, photobactin, enterobactin, and aerobactin in a single bacterial species and illuminates the interplay between siderophore biosynthetic pathways and polyamine production, indicating routes of molecular diversification. Given its natural yields of diaminopropane (97.75 μmol/g DW) and putrescine (30.83 μmol/g DW), S. plymuthica can be exploited for the industrial production of these compounds.

Serratia sp. CP-13 alleviates Cd toxicity by morpho-physio-biochemical improvements, antioxidative potential and diminished Cd uptake in Zea mays L. cultivars differing in Cd tolerance

Cadmium (Cd) is highly toxic for plant metabolic processes even in low concentration due to higher retention rates, longer half-life and non-biodegradable nature. The current study was designed to assess the bioremediation potential of Cd tolerant PGPR, Serratia sp. CP-13 together with two differentially Cd tolerant maize cultivars (MMRI-Yellow, Sahiwal-2002) selected amongst ten cultivars after screening. The maize cultivars were grown under different Cd treatments (0, 6, 12, 18, 24, 30 µM) in Petri plates both with and without Serratia sp. CP-13 inoculation. Treated plants were analyzed for their biomass accumulation, chlorophylls, carotenoids, proline, anthocyanin, protein, malondialdehyde (MDA), H₂O₂ as well as for antioxidants (POD, SOD, CAT) and mineral elements (Ca, Mg, Zn, K, Fe, Na, Cd). The maize cultivar MMRI-Yellow (tolerant) and Sahiwal-2002 (sensitive) exhibited significant reduction in leaf area, nutrient contents, plant biomass, activity of antioxidants, total proteins, photosynthetic pigments as well as flavonoids with increased production of H₂O₂, proline, MDA and relative membrane permeability (RMP) under Cd stress. However, this reduction was cultivar specific and recorded higher in cv. Sahiwal-2002 as compared to MMRI-Yellow. Application of Serratia sp. CP-13 significantly augmented plant biomass, photosynthetic pigments, antioxidative machinery, as well as flavonoids and proline while diminishing H₂O_2, RMP MDA production even under Cd stress in studied cultivars. Furthermore, CP-13 inoculation assisted the Cd stressed plants to sustain an optimal level of essential nutrients (Ca, Mg, Zn, K, Fe) except for Na and Cd which responded antagonistically. It was inferred that both inoculated maize cultivars exhibited better health and metabolism but substantial Cd tolerance was acquired by the sensitive cv. Sahiwal-2002 than the tolerant cv. MMRI-Yellow under applied Cd regimes. Furthermore, studied maize cultivars depicted maximum Cd tolerance in order of 30 < 24 < 18 < 12 < 6 < 0 µM Cd treatments under Serratia sp. CP-13 inoculation. Findings of current work highlighted the importance of Serratia sp. CP-13 and its inoculation impact on morpho-physio-biochemical attributes of maize growth under Cd dominant environment, which is likely an addition towards efficient approaches for bacterially-assisted Cd bioremediation and minimal Cd retention in edible plant parts.

Chromium metabolism characteristics of coexpression of ChrA and ChrT gene

OBJECTIVE

Serratia sp. S2 is a wild strain with chromium resistance and reduction ability. Chromium(VI) metabolic-protein-coding gene ChrA and ChrT were cloned from Serratia sp. S2, and ligated with prokaryotic expression vectors pET-28a (+) and transformed into E. coli BL21 to construct ChrA, ChrT and ChrAT engineered bacteria. By studying the characteristics of Cr(VI) metabolism in engineered bacteria, the function and mechanism of the sole expression and coexpression of ChrA and ChrT genes were studied.

METHODS

Using Serratia sp. S2 genome as template, ChrA and ChrT genes were amplified by PCR, and prokaryotic expression vectors was ligated to form the recombinant plasmid pET-28a (+)-ChrA, pET-28a (+)-ChrT and pET-28a (+)-ChrAT, and transformed into E. coli BL21 to construct ChrA, ChrT, ChrAT engineered bacteria. The growth curve, tolerance, and reduction of Cr(VI), the distribution of intracellular and extracellular Cr, activity of chromium reductase and intracellular oxidative stress in engineered bacteria were measured to explore the metabolic characteristics of Cr(VI) in ChrA, ChrT, ChrAT engineered bacteria.

RESULTS

ChrA, ChrT and ChrAT engineered bacteria were successfully constructed by gene recombination technology. The tolerance to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrA > ChrT > Control (P < 0.05), and the reduction ability to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrT > ChrA (P < 0.05). The chromium distribution experiments confirmed that Cr(VI) and Cr(III) were the main valence states. Effect of electron donors on chromium reductase activity was NADPH > NADH > non-NAD(P)H (P < 0.05). The activity of chromium reductase increased significantly with NAD(P)H (P < 0.05). The Glutathione and NPSH (Non-protein Sulfhydryl) levels of ChrA, ChrAT engineered bacteria increased significantly (P < 0.05) under the condition of Cr(VI), but there was no significant difference in the indexes of ChrT engineered bacteria (P > 0.05).

CONCLUSION

ChrAT engineered bacteria possesses resistance and reduction abilities of Cr(VI). ChrA protein endows the strain with the ability to resist Cr(VI). ChrT protein reduces Cr(VI) to Cr(III) by using NAD(P)H as electronic donor. The reduction process promotes the production of GSH, GSSG and NPSH to maintain the intracellular reduction state, which further improves the Cr(VI) tolerance and reduction ability of ChrAT engineered bacteria.

Contamination or serendipity - doing the wrong thing by chance

The Editors consider contaminant proteins.

Self-limiting paratransgenesis

Presently, the principal tools to combat malaria are restricted to killing the parasite in infected people and killing the mosquito vector to thwart transmission. While successful, these approaches are losing effectiveness in view of parasite resistance to drugs and mosquito resistance to insecticides. Clearly, new approaches to fight this deadly disease need to be developed. Recently, one such approach–engineering mosquito resident bacteria to secrete anti-parasite compounds–has proven in the laboratory to be highly effective. However, implementation of this strategy requires approval from regulators as it involves introduction of recombinant bacteria into the field. A frequent argument by regulators is that if something unexpectedly goes wrong after release, there must be a recall mechanism. This report addresses this concern. Previously we have shown that a Serratia bacterium isolated from a mosquito ovary is able to spread through mosquito populations and is amenable to be engineered to secrete anti-plasmodial compounds. We have introduced a plasmid into this bacterium that carries a fluorescent protein gene and show that when cultured in the laboratory, the plasmid is completely lost in about 130 bacterial generations. Importantly, when these bacteria were introduced into mosquitoes, the bacteria were transmitted from one generation to the next, but the plasmid was lost after three mosquito generations, rendering the bacteria non-recombinant (wild type). Furthermore, no evidence was obtained for horizontal transfer of the plasmid to other bacteria either in culture or in the mosquito. Prior to release, it is imperative to demonstrate that the genes that thwart parasite development in the mosquito are safe to the environment. This report describes a methodology to safely achieve this goal, utilizing transient expression from a plasmid that is gradually lost, returning the bacterium to wild type status.

The intolerable burden of malaria demands the development of novel approaches to fight this deadly disease. Previously, the engineered symbiotic bacterium Serratia AS1 was shown in the laboratory to be able to spread through mosquito populations and render mosquitoes resistant to the parasite. However, a major concern of regulators for the release of such engineered bacteria into the field is that there is no option for “recall” in case something goes wrong. Here we show that Serratia AS1 loses plasmids as it replicates in mosquitoes and in culture, reverting to wild type. We also show that horizontal transfer of the plasmid from Serratia AS1 to other bacteria is extremely rare, as this was undetectable in the mosquito and in culture. Our results suggest that initial field trials can make use of this reversible system whereby released recombinant bacteria expressing anti-plasmodial compounds from a plasmid revert to wild type at a predictable rate.

Bacterial Actin-Specific Endoproteases Grimelysin and Protealysin as Virulence Factors Contributing to the Invasive Activities of Serratia

The article reviews the discovery, properties and functional activities of new bacterial enzymes, proteases grimelysin (ECP 32) of Serratia grimesii and protealysin of Serratia proteamaculans, characterized by both a highly specific "actinase" activity and their ability to stimulate bacterial invasion. Grimelysin cleaves the only polypeptide bond Gly42-Val43 in actin. This bond is not cleaved by any other proteases and leads to a reversible loss of actin polymerization. Similar properties were characteristic for another bacterial protease, protealysin. These properties made grimelysin and protealysin a unique tool to study the functional properties of actin. Furthermore, bacteria Serratia grimesii and Serratia proteamaculans, producing grimelysin and protealysin, invade eukaryotic cells, and the recombinant Escherichia coli expressing the grimelysin or protealysins gene become invasive. Participation of the cellular c-Src and RhoA/ROCK signaling pathways in the invasion of eukaryotic cells by S. grimesii was shown, and involvement of E-cadherin in the invasion has been suggested. Moreover, membrane vesicles produced by S. grimesii were found to contain grimelysin, penetrate into eukaryotic cells and increase the invasion of bacteria into eukaryotic cells. These data indicate that the protease is a virulence factor, and actin can be a target for the protease upon its translocation into the host cell.

Characterization of plant growth-promoting bacteria associated with avocado trees (Persea americana Miller) and their potential use in the biocontrol of Scirtothrips perseae (avocado thrips)

Plants interact with a great variety of microorganisms that inhabit the rhizosphere or the epiphytic and endophytic phyllosphere and that play critical roles in plant growth as well as the biocontrol of phytopathogens and insect pests. Avocado fruit damage caused by the thrips species Scirtothrips perseae leads to economic losses of 12–51% in many countries. In this study, a screening of bacteria associated with the rhizosphere or endophytic phyllosphere of avocado roots was performed to identify bacterial isolates with plant growth-promoting activity in vitro assays with Arabidopsis seedlings and to assess the biocontrol activity of the isolates against Scirtothrips perseae. The isolates with beneficial, pathogenic and/or neutral effects on Arabidopsis seedlings were identified. The plant growth-promoting bacteria were clustered in two different groups (G1 and G3B) based on their effects on root architecture and auxin responses, particularly bacteria of the Pseudomonas genus (MRf4-2, MRf4-4 and TRf2-7) and one Serratia sp. (TS3-6). Twenty strains were selected based on their plant growth promotion characteristics to evaluate their potential as thrips biocontrol agents. Analyzing the biocontrol activity of S. perseae, it was identified that Chryseobacterium sp. shows an entomopathogenic effect on avocado thrips survival. Through the metabolic profiling of compounds produced by bacteria with plant growth promotion activity, bioactive cyclodipeptides (CDPs) that could be responsible for the plant growth-promoting activity in Arabidopsis were identified in Pseudomonas, Serratia and Stenotrophomonas. This study unravels the diversity of bacteria from the avocado rhizosphere and highlights the potential of a unique isolate to achieve the biocontrol of S. perseae.

Effect of Serratia sp. K3 combined with organic materials on cadmium migration in soil-vetiveria zizanioides L. system and bacterial community in contaminated soil

Phytoremediation is an economical strategy to harvest cadmium (Cd) from contaminated soil, but the efficiency of phytoremediation was affected by many factors. This study investigated the potential of Serratia sp. K3 (K3) assisted with straw biogas residue (SBR) or leavening fertilizer (LF) on improving the Cd migration efficiency and micro-environment in soil-vetiveria zizanioides L. system. The results showed that the acid soluble Cd in soil was increased by 2.83-29.79% in treatments compared with control (CK). In addition, Cd accumulation in the roots and shoots of vetiveria zizanioides were significantly enhanced by the combination of K3 and SBR/LF. Especially, the translocation factor of Cd increased by 21.53-62.37% in groups with K3 compared with the groups without K3, correspondingly. Furthermore, SBR/LF effectively changed bacterial community structure, and improved bacterial abundance. Relative abundance of functional genes related with carbohydrate/energy/amino acid metabolism were increased in groups of SBRB/LFB rhizosphere compared with CK. These results provide insight into the change of phytoremediation efficiency and soil bacterial communities in the vetiveria zizanioides rhizosphere after inoculation. This study may provide a promising method for improving phytoremediation in Cd contaminated soil.

Cyclic Dipeptides Mediating Quorum Sensing and Their Biological Effects in Hypsizygus Marmoreus

A novel quorum sensing (QS) system was discovered in Serratia odorifera, the symbiotic bacterium of Hypsizygus marmoreus. This system uses cyclo(Pro-Phe), cyclo(Pro-Tyr), cyclo(Pro-Val), cyclo(Pro-Leu), cyclo(Tyr-Leu), and cyclo(Tyr-Ile) as autoinducers. This discovery is the first attempt to characterize cyclic dipeptides as QS signaling molecules in S. odorifera and improves the classical QS theory. Significantly, except for cyclo(Tyr-Leu), these QS autoinducers can increase the transcription level of lignin-degrading enzyme genes of H. marmoreus. The cyclo(Pro-Phe) can increase the activity of extracellular laccase (1.32-fold) and manganese peroxidase (20%), which may explain why QS potentially regulates the hyphal growth, primordium formation, and fruit body development of H. marmoreus. Furthermore, it was demonstrated that the cyclo(Tyr-Ile) biosynthesis in S. odorifera was catalyzed by the nonribosomal peptide synthetase (NRPS). This study supports exploring the growth and development of H. marmoreus promoted by its symbiotic bacteria at QS signal transduction level.

Current Approaches to and Future Perspectives on Methomyl Degradation in Contaminated Soil/Water Environments

Methomyl is a broad-spectrum oxime carbamate commonly used to control arthropods, nematodes, flies, and crop pests. However, extensive use of this pesticide in agricultural practices has led to environmental toxicity and human health issues. Oxidation, incineration, adsorption, and microbial degradation methods have been developed to remove insecticidal residues from soil/water environments. Compared with physicochemical methods, biodegradation is considered to be a cost-effective and ecofriendly approach to the removal of pesticide residues. Therefore, micro-organisms have become a key component of the degradation and detoxification of methomyl through catabolic pathways and genetic determinants. Several species of methomyl-degrading bacteria have been isolated and characterized, including Paracoccus, Pseudomonas, Aminobacter, Flavobacterium, Alcaligenes, Bacillus, Serratia, Novosphingobium, and Trametes. The degradation pathways of methomyl and the fate of several metabolites have been investigated. Further in-depth studies based on molecular biology and genetics are needed to elaborate their role in the evolution of novel catabolic pathways and the microbial degradation of methomyl. In this review, we highlight the mechanism of microbial degradation of methomyl along with metabolic pathways and genes/enzymes of different genera.

Increased biological removal of 1-chloronaphthalene as a result of exposure: A study of bacterial adaptation strategies

Effective biodegradation of hydrophobic pollutants, such as 1-chloronaphthalene, is strictly associated with the adaptation of environmental bacteria to their assimilation. This study explores the relation between the modifications of cell properties of bacteria belonging to Pseudomonas and Serratia genera resulting from a 12-month exposure to 1-chloronaphthalene, and their biodegradation efficiency. In the presented study, both bacterial strains exhibited higher (70%) degradation of this compound after exposure compared to unexposed (55%) systems. This adaptation can be associated with increased ratio of polysaccharides in the outer layers of bacterial cells, which was confirmed using infrared spectroscopy analysis. Additionally, the analysis of Raman spectra indicated conformational changes of extracellular carbohydrates from α- to β-anomeric structure. Moreover, the changes in the cell surface hydrophobicity and cell membrane permeability differed between the strains and the Pseudomonas strain exhibited more significant modifications of these parameters. The results suggest that adaptation strategies of both tested strains are different and involve diverse reconstructions of the cell wall and membranes. The results provide a novel and deep insight into the interactions between environmental bacterial strains and chloroaromatic compounds, which opens new perspectives for applying spectrometric methods in investigation of cell adaptation strategies as a result of long-term contact with toxic pollutants.

Metabolic response of bacteria to elevated concentrations of glyphosate-based herbicide

Glyphosate-based herbicides (GBHs) are the most widespread commonly used broad-spectrum herbicides that contaminate soils and waters, are toxic to bacteria, plants and animals, and have been classified as 'probably carcinogenic to humans' by the International Agency for Research on Cancer in 2015. Particular soil bacteria and fungi can degrade GBHs, hence, search for new GBH-degrading strains or microbial consortia, effective under specific growth conditions and local environment, seems to be a promising solution for bio-remediation of glyphosate-contaminated environment. Consequently, there is a need for rapid and informative methods to evaluate the GBH-induced changes of the metabolic pathways in cells, that may serve as indicators of GBH-degrading potential. Three new GBH-degrading bacterial strains, Pseudomonas sp., Actinobacteria and Serratia sp. were isolated from sludge of municipal waste water treatment plant (Daugavgriva, Riga, Latvia), agricultural soil and plant tissue, respectively. This study examined the response of these isolates to elevated concentrations of glyphosate (GLP) (100 and 500 mg/L) in GBH Klinik® 360 SL. The GBH-induced shift of metabolic activity in cells of Pseudomonas sp. was shown by tests on EcoPlates™. Fourier transform infrared (FTIR) spectroscopy analyses were used to evaluate the metabolomic response of bacteria to elevated concentrations of GBH in the growth environment. The spectra of Pseudomonas sp. and Serratia sp., incubated with and without GBH, were similar, thus indicating their GBH-resistance. The absorption at 1736 cm-1, assigned to ester carbonyl stretch vibrations, was detected in spectra of all three bacteria. The highest ester content was detected in Actinobacteria grown in medium with 1.0% molasses and 100 or 500 mg/L GLP in GBH Klinik®. An increase of cellular amounts of esters, either those of phospholipids or poly-β-hydroxybutyrates, indicates degradation of GLP. Therefore, monitoring the ester carbonyl stretch vibration band in FTIR spectra of bacterial biomass may speed up the search GBH-degrading strains. Microbiological tests and cell metabolic response studies by FTIR spectroscopy showed that the three new isolates of Pseudomonas sp., Actinobacteria and Serratia sp. were resistant to elevated concentrations of GBH Klinik® in growth environment and exhibited the potential for GBH degradation.

Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins

ADP-ribosylation of proteins can profoundly impact their function and serves as an effective mechanism by which bacterial toxins impair eukaryotic cell processes. Here, we report the discovery that bacteria also employ ADP-ribosylating toxins against each other during interspecies competition. We demonstrate that one such toxin from Serratia proteamaculans interrupts the division of competing cells by modifying the essential bacterial tubulin-like protein, FtsZ, adjacent to its protomer interface, blocking its capacity to polymerize. The structure of the toxin in complex with its immunity determinant revealed two distinct modes of inhibition: active site occlusion and enzymatic removal of ADP-ribose modifications. We show that each is sufficient to support toxin immunity; however, the latter additionally provides unprecedented broad protection against non-cognate ADP-ribosylating effectors. Our findings reveal how an interbacterial arms race has produced a unique solution for safeguarding the integrity of bacterial cell division machinery against inactivating post-translational modifications.

A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones

Enzymatic core components from trans-acyltransferase polyketide synthases (trans-AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans-AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N-acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)-tethered intermediates, we show that the enzyme inserts oxygen into β-ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non-hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.

Diesel oil removal by Serratia sp. W4-01 immobilized in chitosan-activated carbon beads

Serratia sp. W4-01 was immobilized in chitosan-activated carbon beads and used for diesel oil removal. The type and concentration of chitosan, activated carbon content, and bead diameter were investigated as factors affecting diesel oil removal. The results showed that 2% (w/v) squid pen chitosan beads modified with 1% activated carbon (w/v) and with a 3-mm diameter had a good spherical shape and strength as well as diesel oil removal capability. The immobilized W4-01 cells removed more than 40% of diesel oil after 7 days when the initial diesel oil concentration was 100 to 400 mg L^-1, whereas 29-36% of diesel oil was removed after 14 days when the initial concentration was 800 to 1000 mg L^-1. Additionally, the immobilized cells maintained the ability to remove diesel oil over a pH range of 5-11. The addition of a biosurfactant increased the diesel oil removal from 62 to 75%. The reusability tests revealed that the ability of immobilized cells to remove diesel oil was enhanced after reuse, and 50-90% of diesel oil was removed during 2 to 12 reuse cycles. The stability and survival of W4-01 cells was confirmed by scanning electron microscopy and confocal laser scanning microscopy. The results of this study showed the potential use of W4-01 cells immobilized in chitosan-activated carbon beads for future applications in remediating diesel contamination.

Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens

Symbiotic bacteria can produce secondary metabolites and volatile compounds that contribute to amphibian skin defense. Some of these symbionts have been used as probiotics to treat or prevent the emerging disease chytridiomycosis. We examined 20 amphibian cutaneous bacteria for the production of prodigiosin or violacein, brightly colored defense compounds that pigment the bacteria and have characteristic spectroscopic properties making them readily detectable, and evaluated the antifungal activity of these compounds. We detected violacein from all six isolates of Janthinobacterium lividum on frogs from the USA, Switzerland, and on captive frogs originally from Panama. We detected prodigiosin from five isolates of Serratia plymuthica or S. marcescens, but not from four isolates of S. fonticola or S. liquefaciens. All J. lividum isolates produced violacein when visibly purple, while prodigiosin was only detected on visibly red Serratia isolates. When applied to cultures of chytrid fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), prodigiosin caused significant growth inhibition, with minimal inhibitory concentrations (MIC) of 10 and 50 μM, respectively. Violacein showed a MIC of 15 μM against both fungi and was slightly more active against Bsal than Bd at lower concentrations. Although neither violacein nor prodigiosin showed aerosol activity and is not considered a volatile organic compound (VOC), J. lividum and several Serratia isolates did produce antifungal VOCs. White Serratia isolates with undetectable prodigiosin levels could still inhibit Bd growth indicating additional antifungal compounds in their chemical arsenals. Similarly, J. lividum can produce antifungal compounds such as indole-3-carboxaldehyde in addition to violacein, and isolates are not always purple, or turn purple under certain growth conditions. When Serratia isolates were grown in the presence of cell-free supernatant (CFS) from the fungi, CFS from Bd inhibited growth of the prodigiosin-producing isolates, perhaps indicative of an evolutionary arms race; Bsal CFS did not inhibit bacterial growth. In contrast, growth of one J. lividum isolate was facilitated by CFS from both fungi. Isolates that grow and continue to produce antifungal compounds in the presence of pathogens may represent promising probiotics for amphibians infected or at risk of chytridiomycosis. In a global analysis, 89% of tested Serratia isolates and 82% of J. lividum isolates were capable of inhibiting Bd and these have been reported from anurans and caudates from five continents, indicating their widespread distribution and potential for host benefit.

Cultivar and Metal-Specific Effects of Endophytic Bacteria in Helianthus tuberosus Exposed to Cd and Zn

Plant growth promoting endophytic bacteria (PGPB) isolated from Brassica napus were inoculated in two cultivars of Helianthus tuberosus (VR and D19) growing on sand supplemented with 0.1 mM Cd or 1 mM Zn. Plant growth, concentrations of metals and thiobarbituric acid (TBA) reactive compounds were determined. Colonization of roots of H. tuberosus D19 by Pseudomonas sp. 262 was evaluated using confocal laser scanning microscopy. Pseudomonas sp. 228, Serratia sp. 246 and Pseudomonas sp. 262 significantly enhanced growth of H. tuberosus D19 exposed to Cd or Zn. Pseudomonas sp. 228 significantly increased Cd concentrations in roots. Serratia sp. 246, and Pseudomonas sp. 256 and 228 resulted in significantly decreased contents of TBA reactive compounds in roots of Zn exposed D19 plants. Growth improvement and decrease of metal-induced stress were more pronounced in D19 than in VR. Pseudomonas sp. 262-green fluorescent protein (GFP) colonized the root epidermis/exodermis and also inside root hairs, indicating that an endophytic interaction was established. H. tuberosus D19 inoculated with Pseudomonas sp. 228, Serratia sp. 246 and Pseudomonas sp. 262 holds promise for sustainable biomass production in combination with phytoremediation on Cd and Zn contaminated soils.

Bioelectrochemical treatment of acid mine drainage (AMD) from an abandoned coal mine under aerobic condition

In this study, a bioelectrochemical system (BES) was used to treat acid mine drainage (AMD) from an abandoned coal mine in the cathode chamber under aerobic condition. Activated sludge from a local wastewater treatment plant was used in the anode chamber of the BES to supply electrons to the treatment. After 7days, the pH of the cathode solution enhanced from 2.5 to 7.3. More than 99% of Al, Fe and Pb were removed, and removal rates of 93%, 91%, 89% and 69% were achieved for Cd, Zn, Mn and Co respectively with biocathode. Energy-dispersive X-ray spectroscopy (EDS) study revealed the deposition of the various types of metals on the cathode surface, and some metals were detected in the precipitates of the cathode chamber. The bacteria for AMD treatment was identified to be Serratia spp. using 16s rRNA gene amplification and sequencing. Scanning electron microscopy showed attached growth of the bacteria on the cathode. The bioelectrochemical treatment of the AMD was also compared with the biological treatment in a continuously stirred batch reactor (CSBR).

The endophytic bacterium Serratia sp. PW7 degrades pyrene in wheat

This research was conducted to isolate polycyclic aromatic hydrocarbon-degrading (PAH-degrading) endophytic bacteria and investigate their potential in protecting plants against PAH contamination. Pyrene-degrading endophytic bacteria were isolated from plants grown in PAH-contaminated soil. Among these endophytic bacteria, strain PW7 (Serratia sp.) isolated from Plantago asiatica was selected to investigate the suppression of pyrene accumulation in Triticum aestivum L. In the in vitro tests, strain PW7 degraded 51.2% of the pyrene in the media within 14 days. The optimal biodegradation conditions were pH 7.0, 30 °C, and MS medium supplemented with additional glucose, maltose, sucrose, and peptones. In the in vivo tests, strain PW7 successfully colonized the roots and shoots of inoculated (E⁺) wheat plants, and its colonization decreased pyrene accumulation and pyrene transportation from roots to shoots. Remarkably, the concentration of pyrene in shoots decreased much more than that in roots, suggesting that strain PW7 has the potential for protecting wheat against pyrene contamination and mitigating the threat of pyrene to human health via food consumption.

Bioremediation of synthetic fatliquors under microaerobic condition

Synthetic fatliquors are useful as a fatliquoring agent, flotation agent and emulsifying agent in a wide range of industrial applications such as leather, pharmacy and farm chemicals. These fatliquors remain recalcitrant to natural biota in existing treatment plants. In the present study, the isolated microaerophilic Serratia sp. HA1 strain CSMB3 is capable of utilizing structurally different fatliquors as the sole substrate for their growth under microaerobic conditions. Degradation of vegetable fatliquors was observed from 95 to 97% in terms of lipids, with the production of lipase at 72 h. Degradation of synthetic fatliquors was observed in terms of chemical oxygen demand from 85% to a minimum of 25%. It is in the order of sulfited/sulfated fatliquors > sulfochlorinated fatliquors > chlorinated fatliquors. A thin layer chromatography chromatogram confirmed the degradation of non polar fatliquor to polar compounds. Production of the red pigment prodigiosin in synthetic fatliquors enhanced the growth of the isolate. Fourier transform infrared spectroscopy (FTIR) confirmed the bioremediation of sulfochlorinated fatliquor into lipids and fatty acids and gas chromatography-mass spectrometry (GC-MS) results confirmed that alcohols and esters are the final end products. Thus the isolated strain CSMB3 may be used in the treatment of wastewaters containing vegetable and synthetic fatliquors.

Construction and evaluation of a modular biofilm-forming chamber for microbial recovery of neodymium and semi-continuous biofilm preparation. Tolerance of Serratia sp.N14 on acidic conditions and neutralized aqua regia

Recovery of neodymium from liquid metallic wastes and scrap leachates is a crucial step for its recycling, which can take place through the immobilized biofilms of Serratia sp. N14. These biofilms are produced in a fermentor vessel with a turnaround time of 10-14 days, which is unacceptable from an economic point of view for an industrial process. This study proposes the construction and evaluation of a modular system, whereby a biofilm-forming chamber is inserted into the continuous biomass outflow of the main chemostat vessel, for an alternative semi-continuous and economic production of biofilm. The activity of the biofilm from the outflow chamber was found to be the same as the one from the main chamber, which was stored in a cold room (4°C), for 9-12 months, depending on a 24 h nucleation step.Moreover, the ability of the biofilm to function in the presence of a leaching agent (aqua regia) or in acidic conditions was also evaluated. The biofilm of the main chamber can remain active even at 50% neutralized aqua regia (pH 3.0), while at acidic conditions, phosphate release of the cells is reduced to 50%. This strain proves to be very tolerant in low pH or high salt concentration solutions. The biofilm produced from the outflow of the main fermentor vessel is of acceptable activity, rather than being disposed.

Growth promotion of Lactuca sativa in response to volatile organic compounds emitted from diverse bacterial species

Agrochemicals are currently used in horticulture to increase crop production. Nevertheless, their indiscriminate use is a relevant issue for environmental and legal aspects. Alternative tools for reducing fertilizers and synthetic phytohormones are being investigated, such as the use of volatile organic compounds (VOCs) as growth inducers. Some soil bacteria, such as Pseudomonas and Bacillus, stimulate Arabidopsis and tobacco growth by releasing VOCs, but their effects on vegetables have not been investigated. Lactuca sativa was used as model vegetable to investigate bacterial VOCs as growth inducers. We selected 10 bacteria strains, belonging to Bacillus, Staphylococcus and Serratia genera that are able to produce 3-hydroxy-2-butanone (acetoin), a compound with proven growth promoting activity. Two-day old-seedlings of L. sativa were exposed to VOCs emitted by the selected bacteria grown in different media cultures for 7 days. The results showed that the VOCs released from the bacteria elicited an increase in the number of lateral roots, dry weight, root growth and shoot length, depending on the media used. Three Bacillus strains, BCT53, BCT9 and BCT4, were selected according to its their growth inducing capacity. The BCT9 strain elicited the greatest increases in dry weight and primary root length when L. sativa seedlings were subjected to a 10-day experiment. Finally, because acetoin only stimulated root growth, we suggest that other volatiles could be responsible for the growth promotion of L. sativa. In conclusion, our results strongly suggest that bacteria volatiles can be used as growth-inducers as alternative or complementary strategies for application in horticulture species.

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.

Carbon dioxide sequestration by chemolithotrophic oleaginous bacteria for production and optimization of polyhydroxyalkanoate

The present work involved screening of a previously reported carbon concentrating oleaginous bacterial strain Serratia sp. ISTD04 for production of PHA and optimization of process parameters for enhanced PHA and biomass generation. The selected bacterial strain was screened for PHA production based on Nile red staining followed by visualization under fluorescence microscope. Spectrofluorometric measurement of Nile red fluorescence of the bacterial culture was also done. Confirmatory analysis of PHA accumulation by GC-MS revealed the presence of 3-hydroxyvalerate. Detection of characteristic peaks in the FT-IR spectrum further confirmed the production of PHA by the bacterium. Response Surface Methodology was used for optimization of pH and carbon sources' concentrations for higher PHA production. There was almost a 2 fold increase in the production of PHA following optimization as compared to un-optimized condition. The study thus establishes the production of PHA by Serratia sp. ISTD04.

Crystal Structure and Function of PqqF Protein in the Pyrroloquinoline Quinone Biosynthetic Pathway

Pyrroloquinoline quinone (PQQ) has received considerable attention due to its numerous important physiological functions. PqqA is a precursor peptide of PQQ with two conserved residues: glutamate and tyrosine. After linkage of the Cγ of glutamate and Cϵ of tyrosine by PqqE, these two residues are hypothesized to be cleaved from PqqA by PqqF. The linked glutamate and tyrosine residues are then used to synthesize PQQ. Here, we demonstrated that the pqqF gene is essential for PQQ biosynthesis as deletion of it eliminated the inhibition of prodigiosin production by glucose. We further determined the crystal structure of PqqF, which has a closed clamshell-like shape. The PqqF consists of two halves composed of an N- and a C-terminal lobe. The PqqF-N and PqqF-C lobes form a chamber with the volume of the cavity of ∼9400 Å(3) The PqqF structure conforms to the general structure of inverzincins. Compared with the most thoroughly characterized inverzincin insulin-degrading enzyme, the size of PqqF chamber is markedly smaller, which may define the specificity for its substrate PqqA. Furthermore, the 14-amino acid-residue-long tag formed by the N-terminal tag from expression vector precisely protrudes into the counterpart active site; this N-terminal tag occupies the active site and stabilizes the closed, inactive conformation. His-48, His-52, Glu-129 and His-14 from the N-terminal tag coordinate with the zinc ion. Glu-51 acts as a base catalyst. The observed histidine residue-mediated inhibition may be applicable for the design of a peptide for the inhibition of M16 metalloproteases.

Bioaugmentation for treatment of full-scale diethylene glycol monobutyl ether (DGBE) wastewater by Serratia sp. BDG-2

A novel bacterial strain BDG-2 was isolated and used to augment the treatment of silicon plate manufacturing wastewater that primarily contains diethylene glycol monobutyl ether (DGBE). BDG-2 was identified as a Serratia sp. Under the optimal conditions of 30 °C, pH 9 and DGBE concentration of 2000 mg L(-1), the bioaugmented system achieved 96.92% COD removal after 39.9h. Laboratory-scale technological matching results indicated that, in a biofilm process with the addition of 100 mg L(-1) ammonia and 5 mg L(-1) total phosphorus (TP), 70.61% COD removal efficiency could be obtained in 46 h. Addition of polyaluminium chloride (PAC) to the reactors during the suspension process enhanced the settleability of the BDG-2 culture. Subsequently, successful start-up and stable operation of a full-scale bioaugmented treatment facilities were accomplished, and the volumetric organic load in the plug-flow aeration tank was 2.17 ± 0.81 kg m(-3) d(-1). The effluent COD of the facilities was stable and always below 100 mg L(-1).

Association of plant growth-promoting Serratia spp. with the root nodules of chickpea

Serratia species-affiliated DNA sequences have recently been discovered in the root nodules of two chickpea cultivars; however, little is known about their potential influence on chickpea plant growth. All Serratia-affiliated sequences (1136) could be grouped into two clusters at 98% DNA similarity. The major cluster, represented by 96% of sequences, was closely associated with Serratia marcescens sequences from GenBank. In the current study, we isolated two Serratia strains, 5D and RTL100, from root nodules of a field-grown Desi cultivar from Faisalabad and Thal areas, respectively. In vitro, strain 5D showed significantly higher phosphate (P) solubilization and lactic acid production than RTL100, whereas a comparable concentration of phytohormone was produced by both isolates. The application of Serratia strain 5D as an inoculum resulted in 25.55% and 30.85% increases in the grain yield of crops grown on fertile soil in irrigated areas and nutrient-deficient soil in rainfed areas, respectively, compared to the non-inoculated control. Results of plant inoculations indicated that Serratia sp. 5D and RTL100 can serve as effective microbial inoculants, particularly in nutrient-deficient soils in rainfed areas, where chickpea is the only major crop grown during the entire year.

Enhancement of a Novel Isolate of Serratia plymuthica as Potential Candidate for an Antianthracnose

BACKGROUND AND OBJECTIVE

A new rhizobacteria isolate of Serratia plymuthica (strain UBCR_12) exhibited a promising potential as a biocontrol agent for anthracnose causing agent Colletotrichum gloeosporioides. The aim of this study was to characterize its antagonistic activity and explore the factors contributing to a higher inhibition activity.

MATERIALS AND METHODS

The antifungal effect of UBCR_12 against C. gloeosporioides was assayed under various pH values and nutritional sources. Culture supernatant obtained from UBCR_12 and C. gloeosporioides co-culture was also tested for its inhibitory activity. In addition, the antagonistic range of this isolate was examined against Sclerotium rolfsii and Fusarium oxysporum. Statistical analysis was done using one way analysis of variance and further processed using Fisher's Least Significant Difference (LSD) test with a p<0.05.

RESULTS

The UBCR_12 induced inhibition was shown to be stable over time at pH 7, while peptone addition led to a faster induction (2 days after treatment) and glucose treatment to a higher activity. Of all these modifications, preliminary co-culture experiments with fungal cells resulted in the best antagonistic activity of UBCR_12 culture supernatant of about 30.66%. This isolate also showed a wide range of antagonistic activity due to its high suppression against S. rolfsii and F. oxysporum from soybean.

CONCLUSION

Both environmental and biotic manipulations contributed an elevated inhibition rate of UBCR_12 against C. gloeosporioides. A proportional combination of the factors stimulating antagonistic activity of this strain is recommended to be utilized for the development of this strain as an antianthracnose. The enhanced antifungal effects of UBCR_12 resulted under each type of modification were varied indicating the difference of cell responses. It suggests that certain antifungal mechanism could be generated by modifying the environmental factor required for its induction. In addition, the application of cell-free culture supernatant provides an alternative solution in the utilization of biocontrol agents. For large scale application, it could minimize the risk of population outbreaks and harmful effects due to the living cells application.

Biodecolorization of Reactive Yellow-2 by Serratia sp. RN34 Isolated from Textile Wastewater

Remediation of colored textile wastewaters is a matter of interest. In this study, 49 bacteria were isolated from the textile wastewater and tested for their ability to decolorize reactive yellow-2 (RY2) dye. The most efficient isolate, RN34, was identified through amplification, sequencing, and phylogenetic analysis of its 16S rDNA and was designated as Serratia sp. RN34. This bacterium was also found capable of decolorizing other related reactive azo-dyes, including reactive black-5, reactive red-120, and reactive orange-16 but at varying rates. The optimum pH for decolorization of RY2 by the strain RN34 was 7.5 using yeast extract as cosubstrate under static incubation at 30 °C. The strain RN34 also showed potential to decolorize RY2 in the presence of considerable amounts of hexavalent chromium and sodium chloride. A phytotoxicity study demonstrated relatively reduced toxicity of RY2 decolorized products on Vigna radiata plant as compared to the uninoculated RY2 solution.

Improvement in phytoremediation potential of Solanum nigrum under cadmium contamination through endophytic-assisted Serratia sp. RSC-14 inoculation

The growth of hyperaccumulator plants is often compromised by increased toxicity of metals like cadmium (Cd). However, extraction of such metals from the soil can be enhanced by endophytic microbial association. Present study was aimed to elucidate the potential of microbe-assisted Cd phytoextraction in hyperaccumulator Solanum nigrum plants and their interactions under varied Cd concentrations. An endophytic bacteria Serratia sp. RSC-14 was isolated from the roots of S. nigrum. In addition to Cd tolerance up to 4 mM, the RSC-14 exhibited phosphate solubilization and secreted plant growth-promoting phytohormones such as indole-3-acetic acid (54 μg/mL). S. nigrum plants were inoculated with RSC-14 and were grown in different concentrations of Cd (0, 10, and 30 mg Cd kg(-1) sand). Results revealed that Cd treatment caused significant cessation in plant growth, biomass, and chlorophyll content, whereas significantly higher malondialdehyde (MDA) and electrolyte production in leaves were observed in a dose-dependent manner. Conversely, RSC-14 inoculation relived the toxic effects of Cd-induced stress by significantly increasing root/shoot growth, biomass production, and chlorophyll content and decreasing MDA and electrolytes contents. Ameliorative effects on host growth were also observed by the regulation of metal-induced oxidative stress enzymes such as catalase, peroxidase, and polyphenol peroxidase. Activities of these enzymes were significantly reduced in RSC-14 inoculated plants as compared to control plants under Cd treatments. The lower activities of stress responsive enzymes suggest modulation of Cd stress by RSC-14. The current findings support the beneficial uses of Serratia sp. RSC-14 in improving the phytoextraction abilities of S. nigrum plants in Cd contamination.

[Immobilization of Estrogen-degrading Bacteria to Remove the 17β-estradiol and Diethylstilbestrol from Polluted Water and Cow Dung]

Estradiol (E2) and diethylstilbestrol (DES) can be enriched in sewage and cow dung, posing serious threats to human and ecological health. Strain Rhodococcus sp. JX-2 and strain Serratia sp. S, which could degrade 17β-estradiol and diethylstilbestrol, respectively, were immobilized by alginate and then added into sewage and cow dung to remove E2 and DES. The immobilization was determined by orthogonal experiment, and the removal of E2 and DES from sewage and cow dung was compared between treatments of immobilized bacteria, free bacteria and control without bacteria. The influencing factors including inoculation amount, pH value, moisture content, turning time on the removal of E2 and DES were investigated. The optimal conditions of JX-2 and S immobilization were as follows: Strain JX-2: strain S (V/V) 1: 1, alginate concentration 5%, calcium chloride concentration 4%, bacteria-cement ratio 1 : 2. The immobilized strains removed 99. 42% and 84. 59% of the 2 mg.L-1 E2 and DES under laboratory conditions, respectively. The optimal conditions for E2 and DES removal from water by the immobilized strains were as follows: 300 g.L-1 inoculation volume of immobilized strains and pH 5. 0-6. 0. Immobilized bacteria could completely remove DES and remove 95. 85% of E2 from water. The optimal conditions for E2 and DES removal from cow dung by the immobilized strains were: inoculation volume 600 g.kg-1, moisture content 70% and pile turning time 12 h. The immobilized bacteria could completely remove E2 and remove 97. 41% of DES from cow dung.

Uranium Biominerals Precipitated by an Environmental Isolate of Serratia under Anaerobic Conditions

Stimulating the microbially-mediated precipitation of uranium biominerals may be used to treat groundwater contamination at nuclear sites. The majority of studies to date have focussed on the reductive precipitation of uranium as U(IV) by U(VI)- and Fe(III)-reducing bacteria such as Geobacter and Shewanella species, although other mechanisms of uranium removal from solution can occur, including the precipitation of uranyl phosphates via bacterial phosphatase activity. Here we present the results of uranium biomineralisation experiments using an isolate of Serratia obtained from a sediment sample representative of the Sellafield nuclear site, UK. When supplied with glycerol phosphate, this Serratia strain was able to precipitate 1 mM of soluble U(VI) as uranyl phosphate minerals from the autunite group, under anaerobic and fermentative conditions. Under phosphate-limited anaerobic conditions and with glycerol as the electron donor, non-growing Serratia cells could precipitate 0.5 mM of uranium supplied as soluble U(VI), via reduction to nano-crystalline U(IV) uraninite. Some evidence for the reduction of solid phase uranyl(VI) phosphate was also observed. This study highlights the potential for Serratia and related species to play a role in the bioremediation of uranium contamination, via a range of different metabolic pathways, dependent on culturing or in situ conditions.

[ENTRY OF FACULTATIVE PATHOGEN SERRATIA GRIMESII INTO HELA CELLS. ELECTRON MICROSCOPIC ANALYSIS]

Facultative pathogens Serratia grimesii are able to invade eukaryotic cells where they have been found in vacuoles and free in the cytoplasm (Efremova et al., 2001; Bozhokina et al., 2011). However, efficiency of this invasion is low, and the mechanisms of the invasion related to the initial steps of the process are not known. In the present study, we have increased the invasion efficiency by incubation of HeLa cells with N-acetylcysteine (NAC) preceding the infection. In the NAC-pretreated cells, two modes of S. grimesii to enter HeLa cells were observed. In the most cases, the penetration of S. grimesii into the cell was consistent with the "zipper mechanism", involving specific interaction of bacterial invasin with a host cell surface receptor. However, in some cases, bacteria were trapped by membrane ruffling probably produced by injected bacterial proteins that trigger the bacterial uptake process, as described in the "trigger mechanism". Further elucidation of bacterial and cellular factors involved in the bacteria-host cell interaction should clarify whether two different mechanisms or a predominant one operate during S. grimesii invasion.

Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate

Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO3 respectively. These six isolates were tested for sequestration of carbon dioxide by (14)C metabolic labeling of NaH(14)CO3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH(14)CO3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm(-1). Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.

Chromium (VI) remediation by a native strain: effect of environmental conditions and removal mechanisms involved

A native bacterial strain with high capability for Cr (VI) removal was isolated from tannery sediments located in Elena (Córdoba Province, Argentina). The strain was characterized by amplification of 16S rRNA gene and identified as Serratia sp. C8. It was able to efficiently remove different Cr (VI) concentrations in a wide range of pHs and temperatures. The addition of different carbon sources as well as initial inoculum concentration were analyzed, demonstrating that Serratia sp. C8 could reduce 80 % of 20 mg/L Cr (VI) in a medium containing glucose 1 g/L, at pH 6-7 and 28 °C as optimal conditions, using 5 % inoculum concentration. The mechanisms involved in Cr (VI) removal were also evaluated. The strain was capable of biosorpting around 7.5-8.5 % of 20 mg/L Cr on its cell surface and to reduce Cr (VI). In addition, approximately a 54 and 46 % of total Cr was detected in the biomass and in the culture medium, respectively, and in the culture medium, Cr (III) was the predominant species. In conclusion, Serratia sp. C8 removed Cr (VI) and the mechanisms involved in decreasing order of contribution were as follows: reduction catalyzed by intracellular enzymes, accumulation into the cells, and biosorption to the microbial biomass. This strain could be a suitable microorganism for Cr (VI) bioremediation of tannery sediments and effluents or even for other environments contaminated with Cr.

Production and characterization of rhamnolipids produced by Serratia rubidaea SNAU02 under solid-state fermentation and its application as biocontrol agent

The present study aimed at exploring mahua (Madhuca indica) oil cake as a novel substrate for the production of biosurfactant by Serratia rubidaea SNAU02 under solid-state fermentation (SSF). Response surface methodology showed followings as the optimal conditions for the production of biosurfactant: mahua oil cake 7.48 g, 2.5 ml inoculum size (1×10(8) cells/ml), and pH 7.22 and 31 °C temperature. The characterization of the biosurfactant by TLC, FT-IR and GC-MS revealed the presence of rhamnolipid. The presence of rhamnosyl transferase gene responsible for biosynthesis of rhamnolipid was identified. The strain SNAU02 exhibited antifungal activity and demonstrated no toxicity against the seeds of Brassica oleracea and Artemia salina employed as a bio-indicator. The present findings indicated the potential of mahua oil cake as suitable substrate for the production of rhamnolipids in SSF by S. rubidaea SNAU02 and application potential of the biosurfactant produced as biocontrol agent against plant pathogens.

Extracellular polymeric substances production kinetics of 13 sludge isolates using wastewater sludge as raw material and its flocculation potential

The kinetics of batch fermentation of 13 extracellular polymeric substances (EPS) producing bacterial strains (9 Bacillus, 2 Serratia and 2 Yersinia) were carried out using sterilized sludge as a raw material. The most of Bacillus (µ(max): 0.11-0.27 h⁻¹), Serratia (µ(max): 0.23-0.27 h⁻¹) and Yersinia (µ(max): 0.18-0.19 h⁻¹) strains had capability to grow and produce EPS (1.36-2.12 g/L) in the sterilized sludge. In general, EPS production was mixed growth associated for all the bacterial strains cultivated independently. Bacillus sp. 7, Serratia sp. 2 and Yersinia sp. 2 produced higher concentration (1.95-2.12 g/L) of EPS than the other remaining bacterial strains. Protein and carbohydrate contents of EPS remained constant during fermentation. Broth EPS (B-EPS) exhibited high kaolin flocculation activity (≥ 75%) in most of the cases except Bacillus sp. 1, Bacillus sp. 5 and Bacillus sp. 9, respectively. In general, high flocculation activities (FAs) (≥ 75%), were attained using 1.31-1.70 mg B-EPS/g kaolin, 0.45-0.97 mg protein/g kaolin and 0.11-0.21 mg carbohydrates/g kaolin. The study suggests that further systematic exploration is required for optimizing the process of EPS production. EPS produced in the sludge can potentially be used for different water and wastewater treatments.

Extraction of extracellular lipids from chemoautotrophic bacteria Serratia sp. ISTD04 for production of biodiesel

A CO2 sequestering bacterial strain, Serratia sp. ISTD04, that produces a significant amount of extracellular lipids was isolated from marble mine rocks. (14)C labeling analysis revealed that the rate of assimilation of CO2 by the strain is 0.756×10(-9)μmolCO2fixedcell(-1)h(-1). It was found to produce 466mg/l of extracellular lipid which was characterized using (1)H NMR. After transesterification of lipids, the total saturated and unsaturated FAME was found to be 51% and 49% respectively. The major FAME contained in the biodiesel were palmitic acid methyl ester (C16:0), oleic acid methyl ester (C18:1) and 10-nonadecenoic acid methyl ester (C19:1). Biodiesel produced by Serratia sp. ISTD04 is balanced in terms of FAME composition of good quality. It also contained higher proportion of oleic acid (35%) which makes it suitable for utilization in existing engines. Thus, the strain can be harnessed commercially to sequester CO2 into biodiesel.

[Isolation, identification and characterization of a diethylstilbestrol-degrading bacterial strain Serratia sp]

Utilizing the diethylstilbestrol (DES)-degrading bacteria to biodegrade DES is a most reliable technique for cleanup of DES pollutants from the environment. However, little information is available heretofore on the isolation of DES-degrading bacteria and their DES removal performance in the environment. A novel bacterium capable of degrading DES was isolated from the activated sludge of a wastewater treatment plant. According to its morphology, physiochemical characteristics, and 16S rDNA sequence analysis, this strain was identified as Serratia sp.. The strain was an aerobic bacterium, and it could degrade 68.3% of DES (50 mg x L(-1)) after culturing for 7 days at 30 degrees C, 150 r x min(-1) in shaking flasks. The optimal conditions for DES biodegradation by the obtained strain were 30 degrees C, 40-60 mg x L(-1) DES, pH 7.0, 5% of inoculation volume, 0 g x L(-1) of added NaCl, and 10 mL of liquid medium volume in 100 mL flask.

Dynamic trapping and two-dimensional transport of swimming microorganisms using a rotating magnetic microrobot

Manipulation of microorganisms with intrinsic motility is a challenging yet important task for many biological and biomedical applications. Currently, such a task has only been accomplished using optical tweezers, while at the risk of averse heating and photodamage of the biological samples. Here, we proposed a new micro-robotic approach for fluidic trapping and two-dimensional transportation of motile microorganisms near a solid surface in fluids. We demonstrated selective trapping and transportation of individual freely swimming multi-flagellated bacteria over a distance of 30 μm (7.5 body length of the carrier) on a surface, using the rotational flows locally induced by a rotating magnetic microparticle. Only a weak uniform magnetic field (<3 mT) was applied to actuate the microparticle. The microparticle can translate on a glass substrate by rotating at a speed of up to 100 μm s(-1), while providing a fluidic force of a few to tens of pico-Newtons.