Shigella Strains Are Not Clones of Escherichia coli but Sister Species in the Genus Escherichia

Shigella species and Escherichia coli are closely related organisms. Early phenotyping experiments and several recent molecular studies put Shigella within the species E. coli. However, the whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species, Shigella boydii, Shigella sonnei, Shigella felxneri and Shigella dysenteriae, are distinct from E. coli strains, and form sister species to E. coli within the genus Escherichia. In view of the overall success and high resolution power of the CVTree approach, this result should be taken seriously. We hope that the present report may promote further in-depth study of the Shigella-E. coli relationship.     

NGS-based characterization of microbial diversity and functional profiling of solid tannery waste metagenomes

Tanneries pose a serious threat to the environment by generating large amount of solid tannery waste (STW). Two metagenomes representing tannery waste dumpsites Jajmau (JJK) and Unnao (UNK) were sequenced using Illumina HiSeq platform. Microbial diversity analysis revealed domination of Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Planctomycetes in both metagenomes. Presence of pollutant degrading microbes such as Bacillus, Clostridium, Halanaerobium and Pseudomonas strongly indicated their bioremediation ability. KEGG and SEED annotated main functional categories included carbohydrate metabolism, amino acids metabolism, and protein metabolism. KEGG displayed 5848 and 9633 proteases encoding ORFs compared to 5159 and 8044 ORFs displayed by SEED classification in JJK and UNK metagenomes, respectively. Abundantly present serine- and metallo-proteases belonging to Bacillaceae, Clostridiaceae, Xanthomonadaceae, Flavobacteriaceae and Chitinophagaceae families exhibited proteinaceous waste degrading ability of these metagenomes. Further structural and functional analysis of metagenome encoded enzymes may facilitate the discovery of novel proteases useful in bioremediation of STW.     

Molecular approach for the rapid detection of Bacillus and Pseudomonas genera—dominant antagonistic groups—from diverse ecological niches using colony multiplex PCR

Bacillus and Pseudomonas are the dominant groups of bacteria known for their antagonistic potential against many plant and animal pathogens. Presently, exploration of these genera with antagonistic property for disease management of aquaculture system is gaining more importance to overcome the use of antibiotics and related resistance issues. Rapid screening and identification of these genera from diverse bacterial populations by conventional methods is laborious, cost-intensive, and time-consuming. To overcome these limiting factors, in the present study, a colony multiplex PCR (cmPCR) method was developed and evaluated for the rapid detection of Bacillus and Pseudomonas. The technique amplifies the partial 16S rRNA gene of Bacillus and Pseudomonas with a product size of ~1,100 and ~375 bp, respectively, using single forward (BSF2) and two reverse primers (PAGSR and BK1R). Reliability of the cmPCR method was confirmed by screening 472 isolates obtained from ten different eco-stations, of which 133 isolates belonged to Bacillus and 32 to Pseudomonas. The cmPCR method also helped to identify six different Pseudomonas spp. and 14 different Bacillus spp. from environmental samples. Of the total 472 isolates studied, 46 showed antagonistic activity, among which 63 % were Bacillus and 17.4 % were Pseudomonas. Thus, the newly developed molecular approach provides a quick, sensitive, and potential screening tool to detect novel, antagonistically important Bacillus and Pseudomonas genera for their use in aquaculture. Further, it can also act as a taxonomic tool to understand the distribution of these genera from wide ecological niches and their exploitation for diverse biotechnological applications.     

16S rRNA PCR followed by restriction endonuclease digestion: A rapid approach for genus level identification of important enteric bacterial pathogens

The study describes a rapid approach for detection of common enteric bacterial pathogens, which involves partial amplification of the 16S rRNA gene by PCR using a colony from selective medium followed by restriction enzyme (RE) digestion using the EcoRI, HindIII and SalI enzymes. On the basis of RE digestion analysis different genera namely, Escherichia, Salmonella, Shigella, Vibrio, Campylobacter, Arcobacter, Yesinia and Listeria were differentiated.     

Biofilm formation in an ice cream plant

The sites of biofilm formation in an ice cream plant were investigated by sampling both the production line and the environment. Experiments were carried out twice within a 20-day period. First, stainless steel coupons were fixed to surfaces adjacent to food contact surfaces, the floor drains and the doormat. They were taken for the analysis of biofilm at three different production stages. Then, biofilm forming bacteria were␣enumerated and also presence of Listeria monocytogenes was monitored. Biofilm forming isolates were selected on the basis of colony morphology and Gram’s reaction; Gram negative cocci and rod, Gram positive cocci and spore forming isolates were identified. Most of the biofilm formations were seen on the conveyor belt of a packaging machine 8 h after the beginning of the production, 6.5 × 10³ cfu cm⁻². Most of the Gram negative bacteria identified belong to Enterobacteriaceae family such as Proteus, Enterobacter, Citrobacter, Shigella, Escherichia, Edwardsiella. The other Gram negative microflora included Aeromonas, Plesiomonas, Moraxella, Pseudomonas or Alcaligenes spp. were also isolated. Gram positive microflora of the ice cream plant included Staphyloccus, Bacillus, Listeria and lactic acid bacteria such as Streptococcus, Leuconostoc or Pediococcus spp. The results from this study highlighted the problems of spread of pathogens like Listeria and Shigella and spoilage bacteria. In the development of cleaning and disinfection procedures in ice cream plants, an awareness of these biofilm-forming bacteria is essential for the ice cream plants.     

Mechanism of hexavalent chromium detoxification by microorganisms and bioremediation application potential: A review

Chromium has been widely used in various industries. Hexavalent chromium (Cr⁶⁺) is a priority toxic, mutagenic and carcinogenic chemical, whereas its reduced trivalent form (Cr³⁺) is much less toxic and insoluble. Hence, the basic process for chromium detoxification is the transformation of Cr⁶⁺ to Cr³⁺. A number of aerobic and anaerobic microorganisms are capable of reducing Cr⁶⁺. In the presence of oxygen, microbial reduction of Cr⁶⁺ is commonly catalyzed by soluble enzymes, except in Pseudomonas maltophilia O-2 and Bacillus megaterium TKW3, which utilize membrane-associated reductases. Recently, two soluble Cr⁶⁺ reductases, ChrR and YieF, have been purified from Pseudomonas putida MK1 and Escherichia coli, respectively. ChrR catalyzes an initially one-electron shuttle followed by a two-electron transfer to Cr⁶⁺, with the formation of intermediate(s) Cr⁵⁺ and/or Cr⁴⁺ before further reduction to Cr³⁺. YieF displays a four-electron transfer that reduces Cr⁶⁺ directly to Cr³⁺. The membrane-associated Cr⁶⁺ reductase of B. megaterium TKW3 was isolated, but its reduction kinetics is as yet uncharacterized. Under anaerobic conditions, both soluble and membrane-associated enzymes of the electron transfer system were reported to mediate Cr⁶⁺ reduction as a fortuitous process coupled to the oxidation of an electron donor substrate. In this process, Cr⁶⁺ serves as the terminal electron acceptor of an electron transfer chain that frequently involves cytochromes (e.g., b and c). An expanding array of Cr⁶⁺ reductases allows the selection of enzymes with higher reductive activity, which genetic and/or protein engineering may further enhance their efficiencies. With the advancement in technology for enzyme immobilization, it is speculated that the direct application of Cr⁶⁺ reductases may be a promising approach for bioremediation of Cr⁶⁺ in a wide range of environments.     

Diversity and enzymatic potentialities of <Emphasis Type="Italic">Bacillus</Emphasis> sp. strains isolated from a polluted freshwater ecosystem in Cuba

Genotypic and phenotypic characterization of Bacillus spp. from polluted freshwater has been poorly addressed. The objective of this research was to determine the diversity and enzymatic potentialities of Bacillus spp. strains isolated from the Almendares River. Bacilli strains from a polluted river were characterized by considering the production of extracellular enzymes using API ZYM. 14 strains were selected and identified using 16S rRNA, gyrB and aroE genes. Genotypic diversity of the Bacillus spp. strains was evaluated using pulsed field gel electrophoresis. Furthermore, the presence of genetic determinants of potential virulence toxins of the Bacillus cereus group and proteinaceous crystal inclusions of Bacillus thuringiensis was determined. 10 strains were identified as B. thuringiensis, two as Bacillus megaterium, one as Bacillus pumilus and one as Bacillus subtilis. Most strains produced proteases, amylases, phosphatases, esterases, aminopeptidases and glucanases, which reflect the abundance of biopolymeric matter in Almendares River. Comparison of the typing results revealed a spatio-temporal distribution among B. thuringiensis strains along the river. The results of the present study highlight the genotypic and phenotypic diversity of Bacillus spp. strains from a polluted river, which contributes to the knowledge of genetic diversity of Bacilli from tropical polluted freshwater ecosystems.     

Horizontal arsC gene transfer among microorganisms isolated from arsenic polluted soil

The study of recent evolution of the arsC genes amplified from microorganisms inhabiting a Colombian oil-polluted soil with high concentrations of arsenic was performed through the isolation of 26 bacterial morphotypes resistant to 10 mM of arsenate. A 353 bp fragment of the gene coding for arsenate-reductase enzyme (i.e. arsC), and a 500 bp 16S rDNA partial sequence were sequenced for 16 morphotypes of the 26 previously isolated. arsC sequences clustered on the same clade with previously reported arsC chromosomal genes of Escherichia coli and Shigella sp.; while 16S rDNA sequences grouped within the genus Pseudomonas and Bacillus. The GC content and the Codon Adaptation Index (CAI) were calculated and statistically compared, both supported the previous results. The Isolation-Migration model (IM model) was applied to calculate the genetic flux between each clade defined by the phylogenetic analysis. In general, the existence of recent horizontal gene transfer (HGT) events was confirmed, and the presence of the arsC gene in Bacillus sphaericus is reported for the first time.     

Isolation of Shigella dysenteriae Type 1 and S. flexneri Strains from Surface Waters in Bangladesh: Comparative Molecular Analysis of Environmental Shigella Isolates versus Clinical Strains

Bacillary dysentery caused by Shigella species is a public health problem in developing countries including Bangladesh. Although, shigellae-contaminated food and drinks are often the source of the epidemic's spread, the possible presence of the pathogen and transmission of it through environmental waters have not been adequately examined. We analyzed surface waters collected in Dhaka, Bangladesh, for the presence of shigellae by a combination of PCR assays followed by concentration and culturing of PCR-positive samples. Analysis of 128 water samples by PCR assays for Shigella-specific virulence genes including ipaBCD, ipaH, and stx1 identified 14 (10.9%) samples which were positive for one or more of these virulence genes. Concentration of the PCR-positive samples by filtration followed by culturing identified live Shigella species in 11 of the 14 PCR-positive samples. Analysis of rRNA gene restriction patterns (ribotype) showed that the environmental isolates shared ribotypes with a collection of clinical isolates, but in contrast to the clinical isolates, 10 of the 11 environmental isolates were either negative or carried deletions in the plasmid-encoded invasion-associated genes ipaB, ipaC, and ipaD. However, all environmental Shigella isolates were positive for the chromosomal multicopy invasion-associated gene ipaH and all Shigella dysenteriae type 1 isolates were positive for the stx1 gene in addition to ipaH. This study demonstrated the presence of Shigella in the aquatic environment and dispersion of different virulence genes among these isolates which appear to constitute an environmental reservoir of Shigella-specific virulence genes. Since critical virulence genes in Shigella are carried by plasmids or mobile genetic elements, the environmental gene pool may contribute to an optimum combination of genes, causing the emergence of virulent Shigella strains which is facilitated in particular by close contact of the population with surface waters in Bangladesh.     

Bioremediation of naphthalene in water by Sphingomonas paucimobilis using new biodegradable surfactants based on poly (ɛ-caprolactone)

New amphiphilic block surfactants ABA based on a central segment of polycaprolactone with different molecular composition were evaluated in the bioremediation of naphthalene in water by Sphingomonas paucimobilis and compared with sodium dodecyl sulphate as reference surfactant (SDS). Also the biodegradation of the new surfactants by bacteria, S. paucimobilis and a mixture of bacteria (Pseudomonas aureginosa, Bacillus subtilis, Bacillus amyloliquefaciens and Bacillus megaterium) was studied by indirect impedance technique and carbon dioxide determination. All the bacteria biodegraded in solution and micellar phase the central segment of PCL with mineralization rates in the range of 0.024–0.036 mg of CO₂ per day.S. paucimobilis biodegraded naphthalene in the presence of the new surfactants and GC analysis demonstrated that conversion to products started immediately after inoculum. In all the experiments, except for SDS, at 140 h of incubation time, the remaining naphthalene concentration was about 10% of the initial concentration. In contrast, the production of CO₂ was delayed 4–7 days and values around 75% of naphthalene mineralization degree were achieved in three weeks. The addition of PCL-surfactants, in solution and in micellar phase, not interfered in the naphthalene mineralization. These results have shown promising potential of these biodegradable PCL-surfactants in surfactant-enhanced remediation (SER) technology for removing residual organics from contaminated groundwater and soils.     

Oily sludge degradation by bacteria from Ankleshwar, India

Three bacterial strains, Bacillus sp. SV9, Acinetobacter sp. SV4 and Pseudomonas sp., SV17 from contaminated soil in Ankleshwar, India were tested for their ability to degrade the complex mixture of petroleum hydrocarbons (such as alkanes, aromatics, resins and asphaltenes), sediments, heavy metals and water known as oily sludge. Gravimetric analysis showed that Bacillus sp. SV9 degraded approx. 59% of the oily sludge in 5 days at 30 °C whereas Acinetobacter sp. SV4 and Pseudomonas sp. SV17 degraded 37% and 35%. Capillary gas chromatographic analysis revealed that after 5 days the Bacillus strain was able to degrade oily sludge components of chain length C₁₂–C₃₀ and aromatics more effectively than the other two strains. Maximum drop in surface tension (from 70 to 28.4 mN/m) was accompanied by maximum biosurfactant production (6.7 g l⁻¹) in Bacillus sp. SV9 after 72 h, these results collectively indicating that this bacterial strain has considerable potential for bioremediation of oily sludge.     

Identification and characterization of PAH-degrading endophytes isolated from plants growing around a sludge dam

Abstract

This study involved the isolation of bacteria endophytes with PAH-degrading ability from plants growing around a sludge dam. A total of 19 distinct isolates that were morphologically identified were isolated from 4 species of plant with a follow-up confirmatory identification using the molecular technique. Polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (16S-27F PCR and 16S-1491R PCR) was carried out. The sequence of the PCR products was carried out, compared with similar nucleotides available in GenBank. Results of the phylogenetic analysis of the isolates indicated their belonging to 4 different clades including Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. These were related to the genera Bacillus, Pseudomonas, Terribacillus, Virgibacillus, Stenotrophomonas, Paenibacillus, Brevibacterium, Geobacillus, Acinetobacter. From the result, Pseudomonas demonstrated a high incidence in the plants sampled. The in-vitro degradation study and the presence of dioxygenase genes indicated that these lists of endophytes are able to use the list of PAHs tested as their source of food and energy leading to their breakdown. This means that the bacterial endophytes contributed to the remediation of petroleum hydrocarbons in planta, a situation that may have been phytotoxic to plant alone. Therefore, these bacteria endophytes could be potential organisms for enhanced phytoremediation of PAHs.     

Towards large-scale FAME-based bacterial species identification using machine learning techniques

In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species identification strategy.     

Class-specific restrictions define primase interactions with DNA template and replicative helicase

Bacterial primase is stimulated by replicative helicase to produce RNA primers that are essential for DNA replication. To identify mechanisms regulating primase activity, we characterized primase initiation specificity and interactions with the replicative helicase for gram-positive Firmicutes (Staphylococcus, Bacillus and Geobacillus) and gram-negative Proteobacteria (Escherichia, Yersinia and Pseudomonas). Contributions of the primase zinc-binding domain, RNA polymerase domain and helicase-binding domain on de novo primer synthesis were determined using mutated, truncated, chimeric and wild-type primases. Key residues in the β4 strand of the primase zinc-binding domain defined class-associated trinucleotide recognition and substitution of these amino acids transferred specificity across classes. A change in template recognition provided functional evidence for interaction in trans between the zinc-binding domain and RNA polymerase domain of two separate primases. Helicase binding to the primase C-terminal helicase-binding domain modulated RNA primer length in a species-specific manner and productive interactions paralleled genetic relatedness. Results demonstrated that primase template specificity is conserved within a bacterial class, whereas the primase–helicase interaction has co-evolved within each species.     

Biosurfactants,bioemulsifiers and exopolysaccharides from marine microorganisms

Marine biosphere offers wealthy flora and fauna, which represents a vast natural resource of imperative functional commercial grade products. Among the various bioactive compounds, biosurfactant (BS)/bioemulsifiers (BE) are attracting major interest and attention due to their structural and functional diversity. The versatile properties of surface active molecules find numerous applications in various industries. Marine microorganisms such as Acinetobacter, Arthrobacter, Pseudomonas, Halomonas, Myroides, Corynebacteria, Bacillus, Alteromonas sp. have been studied for production of BS/BE and exopolysaccharides (EPS). Due to the enormity of marine biosphere, most of the marine microbial world remains unexplored. The discovery of potent BS/BE producing marine microorganism would enhance the use of environmental biodegradable surface active molecule and hopefully reduce total dependence or number of new application oriented towards the chemical synthetic surfactant industry. Our present review gives comprehensive information on BS/BE which has been reported to be produced by marine microorganisms and their possible potential future applications.     

Assessment of atrazine decontamination by epiphytic root bacteria isolated from emergent hydrophytes

Aim of the study was to identify atrazine remediating bacteria that can potentially succeed in situ where they encounter varied environmental conditions. Three epiphytic root bacteria, genus Pseudomonas and Arthrobacter, were isolated from rhizoplanes of hydrophytes Acorus calamus, Typha latifolia, and Phragmites karka. Potential of these strains to decontaminate environmentally relevant concentrations of atrazine was determined in liquid atrazine medium (LAM) and Luria-Bertani (LB) medium at varying pH and temperature. There was an increase in decontamination by the strains with time upon exposure to 2.5 to 10 mg l^?1 atrazine over a period of 15 days, notably, in both minimal and nutrient-rich media. Growth in terms of O.D.₆₀₀ and biomass determined during the same period also showed a corresponding surge. Pseudomonas sp. strain AACB mitigated atrazine in a wide range of pH (5 to 8). Pseudomonas sp. strains AACB and TTLB decontaminated >?62% atrazine at 10 °C. All the strains exhibited plant growth–promoting traits in vitro, reported for the first time in the presence of atrazine. Strain AACB exhibits the novel trait of atrazine decontamination under harsh environmental conditions mimicked in lab. Strains isolated in the present study promise success in in situ remediation. Bioreactors and water treatment plants can be designed comprising the hydrophytes and the strains inoculated into their rhizospheres to improve efficacy of the treatment. They can be used to study plant-bacterium mutualistic symbiosis or other interactions occurring during atrazine mitigation.     

Isolation and characterization of aerobic,culturable, arsenic-tolerant bacteria from lead–zinc mine tailing in southern China

Bioremediation of arsenic (As) pollution is an important environmental issue. The present investigation was carried out to isolate As-resistant novel bacteria and characterize their As transformation and tolerance ability. A total of 170 As-resistant bacteria were isolated from As-contaminated soils at the Kangjiawan lead–zinc tailing mine, located in Hunan Province, southern China. Thirteen As-resistant isolates were screened by exposure to 260 mM Na₂HAsO₄·7H₂O, most of which showed a very high level of resistance to As⁵⁺ (MIC?≥?600 mM) and As³⁺ (MIC?≥?10 mM). Sequence analysis of 16S rRNA genes indicated that the 13 isolates tested belong to the phyla Firmicutes, Proteobacteria and Actinobacteria, and these isolates were assigned to eight genera, Bacillus, Williamsia, Citricoccus, Rhodococcus, Arthrobacter, Ochrobactrum, Pseudomonas and Sphingomonas. Genes involved in As resistance were present in 11 of the isolates. All 13 strains transformed As (1 mM); the oxidation and reduction rates were 5–30% and 10–51.2% within 72 h, respectively. The rates of oxidation by Bacillus sp. Tw1 and Pseudomonas spp. Tw224 peaked at 42.48 and 34.94% at 120 h, respectively. For Pseudomonas spp. Tw224 and Bacillus sp. Tw133, the highest reduction rates were 52.01% at 48 h and 48.66% at 144 h, respectively. Our findings will facilitate further research into As metabolism and bioremediation of As pollution by genome sequencing and genes modification.     

Assessing the diversity of bacterial communities from marine sponges and their bioactive compounds

Symbiotic bacteria play vital roles in the survival and health of marine sponges. Sponges harbor rich, diverse and species-specific microbial communities. Symbiotic marine bacteria have increasingly been reported as promising source of bioactive compounds. A culturomics-based study was undertaken to study the diversity of bacteria from marine sponges and their antimicrobial potential. We have collected three sponge samples i.e. Acanthaster carteri, Rhytisma fulvum (soft coral) and Haliclona caerulea from north region (Obhur) of Red Sea, Jeddah Saudi Arabia. Total of 144 bacterial strains were isolated from three marine sponges using culture dependent method. Screening of isolated strains showed only 37 (26%) isolates as antagonists against oomycetes pathogens (P. ultimum and P. capsici). Among 37 antagonistic bacteria, only 19 bacterial strains exhibited antibacterial activity against human pathogens (Methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300, Pseudomonas aeruginosa ATCC 27853, Escherichia coli ATCC 8739, Enterococcus faecalis ATCC 29212). Four major classes of bacteria i.e γ-Proteobacteria, α-Proteobacteria, Firmicutes and Actinobacteria were recorded from three marine sponges where γ-Proteobacteria was dominant class. One potential bacterial strain Halomonas sp. EA423 was selected for identification of bioactive metabolites using GC and LC-MS analyses. Bioactive compounds Sulfamerazine, Metronidazole-OH and Ibuprofen are detected from culture extract of strain Halomonas sp. EA423. Overall, this study gives insight into composition and diversity of antagonistic bacterial community of marine sponges and coral from Red Sea and presence of active metabolites from potential strain. Our results showed that these diverse and potential bacterial communities further need to be studied to exploit their biotechnological significance.     

Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions

Bacillus and Pseudomonas ubiquitously occur in natural environments and are two of the most intensively studied bacterial genera in the soil. They are often coisolated from environmental samples, and as a result, several studies have experimentally cocultured bacilli and pseudomonads to obtain emergent properties. Even so, the general interaction between members of these genera is virtually unknown. In the past decade, data on interspecies interactions between natural isolates of Bacillus and Pseudomonas has become more detailed, and now, molecular studies permit mapping of the mechanisms behind their pairwise ecology. This review addresses the current knowledge about microbe–microbe interactions between strains of Bacillus and Pseudomonas and discusses how we can attempt to generalize the interaction on a taxonomic and molecular level.