Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest

Plant growth-promoting rhizobacterial secondary metabolites in augmenting heavy metal(loid) phytoremediation: An integrated green in situ ecorestorative technology

In recent times, increased geogenic and human-centric activities have caused significant heavy metal(loid) (HM) contamination of soil, adversely impacting environmental, plant, and human health. Phytoremediation is an evolving, cost-effective, environment-friendly, in situ technology that employs indigenous/exotic plant species as natural purifiers to remove toxic HM(s) from deteriorated ambient soil. Interestingly, the plant's rhizomicrobiome is pivotal in promoting overall plant nutrition, health, and phytoremediation. Certain secondary metabolites produced by plant growth-promoting rhizobacteria (PGPR) directly participate in HM bioremediation through chelation/mobilization/sequestration/bioadsorption/bioaccumulation, thus altering metal(loid) bioavailability for their uptake, accumulation, and translocation by plants. Moreover, the metallotolerance of the PGPR and the host plant is another critical factor for the successful phytoremediation of metal(loid)-polluted soil. Among the phytotechniques available for HM remediation, phytoextraction/phytoaccumulation (HM mobilization, uptake, and accumulation within the different plant tissues) and phytosequestration/phytostabilization (HM immobilization within the soil) have gained momentum in recent years. Natural metal(loid)-hyperaccumulating plants have the potential to assimilate increased levels of metal(loid)s, and several such species have already been identified as potential candidates for HM phytoremediation. Furthermore, the development of transgenic rhizobacterial and/or plant strains with enhanced environmental adaptability and metal(loid) uptake ability using genetic engineering might open new avenues in PGPR-assisted phytoremediation technologies. With the use of the Geographic Information System (GIS) for identifying metal(loid)-impacted lands and an appropriate combination of normal/transgenic (hyper)accumulator plant(s) and rhizobacterial inoculant(s), it is possible to develop efficient integrated phytobial remediation strategies in boosting the clean-up process over vast regions of HM-contaminated sites and eventually restore ecosystem health.

Combinatorial Therapy: Targeting CD133+ Glioma Stem-like Cells with a Polysaccharide-Prodrug Complex Functionalised Gold Nanocages

Cancer treatments are advancing to harness the body's immune system against tumours, aiming for lasting effects. This progress involves combining potent chemotherapy drugs with immunogens to kill cancer cells and trigger lasting immunity. Developing new prodrugs that integrate both chemotherapy and immune-boosting elements could significantly improve anticancer outcomes by activating multiple mechanisms to kill cancer cells. While bacterial polysaccharides are typically not used in therapy due to their immune-stimulating properties, we propose a safe application of an extremophilic bacterial polysaccharide, Mauran (MR), modified with the anticancer drug 5-fluorouracil (5FU) to create a novel prodrug. This obtained prodrug, chloracetyl-MR-5FU, is specifically targeted using gold nanocages to CD133+ glioma cells. Test results have shown a high encapsulation efficiency of the drug during the polysaccharide modification process; its anticancer activity was demonstrated in vitro and the release of the prodrug was demonstrated in ex vivo studies.

Traversing the diverse avenues of exopolysaccharides-based nanocarriers in the management of cancer

Exopolysaccharides are unique polymers generated by living organisms such as algae, fungi and bacteria to protect them from environmental factors. After a fermentative process, these polymers are extracted from the medium culture. Exopolysaccharides have been explored for their anti-viral, anti-bacterial, anti-tumor, and immunomodulatory effects. Specifically, they have acquired massive attention in novel drug delivery strategies owing to their indispensable properties like biocompatibility, biodegradability, and lack of irritation. Exopolysaccharides such as dextran, alginate, hyaluronic acid, pullulan, xanthan gum, gellan gum, levan, curdlan, cellulose, chitosan, mauran, and schizophyllan exhibited excellent drug carrier properties. Specific exopolysaccharides, such as levan, chitosan, and curdlan, have demonstrated significant antitumor activity. Moreover, chitosan, hyaluronic acid and pullulan can be employed as targeting ligands decorated on nanoplatforms for effective active tumor targeting. This review shields light on the classification, unique characteristics, antitumor activities and nanocarrier properties of exopolysaccharides. In addition, in vitro human cell line experiments and preclinical studies associated with exopolysaccharide-based nanocarriers have also been highlighted.

Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities

The degradation and bioaccumulation of selected antibiotics such as the sulfonamide sulfamethoxazole (SMX) and the fluoroquinolones enrofloxacin (ENR) and ciprofloxacin (CIP) were investigated in soil microcosm experiments where Lactuca sativa was grown with manure or digestate (1%) and spiked with a mixture of the three antibiotics (7.5 mg/kg each). The soil, rhizosphere and leaf phyllosphere were sampled (at 0 and 46 days) from each microcosm to analyze the antibiotic concentrations, main resistance genes (sul1, sul2, qnrS, aac-(6')-Ib-crand qepA), the intI1and tnpA mobile genetic elements and the microbial community structure.Overall results showed that SMX and CIP decreased (70-85% and 55-79%, respectively), and ENR was quite persistent during the 46-day experiment. In plant presence, CIP and ENR were partially up-taken from soil to plant. In fact the bioaccumulation factors were > 1, with higher values in manure than digestate amended soils. The most abundant gene in soil was sul2 in digestate- and aac-(6')-Ib-cr in the manure-amended microcosms. In soil, neither sulfamethoxazole-resistance (sul1 and sul2), nor fluoroquinolone-resistance (aac-(6')-Ib-cr, qepA and qnrS) gene abundances were correlated with any antibiotic concentration. On the contrary, in lettuce leaves, the aac-(6')-Ib-cr gene was the most abundant, in accordance with the fluoroquinolone bioaccumulation. Finally, digestate stimulated a higher soil microbial biodiversity, introducing and promoting more bacterial genera associated with antibiotic degradation and involved in soil fertility and decreased fluoroquinolone bioaccumulation.

Diversity of Culturable Alkaliphilic Nitrogen-Fixing Bacteria from a Soda Lake in the East African Rift Valley

Lake Chitu is a highly productive soda lake found in the East African Rift Valley, where Arthrospira fusiformis (Spirulina platensis) is the main primary producer. High biomass accumulation requires an adequate supply of nitrogen. However, Lake Chitu is a closed system without any external nutrient input. A recent study has also demonstrated the presence of a diverse group of denitrifying bacteria, indicating a possible loss of nitrate released from the oxidation of organic matter. The aim of this study was to isolate culturable nitrogen-fixing alkaliphiles and evaluate their potential contribution in the nitrogen economy of the soda lake. A total of 118 alkaliphiles belonging to nine different operational taxonomic units (OTUs) were isolated using a nitrogen-free medium. Nineteen isolates were tested for the presence of the nifH gene, and 11 were positive. The ability to fix nitrogen was tested by co-culturing with a non-nitrogen-fixing alkaliphile, Alkalibacterium sp. 3.5*R1. When inoculated alone, Alkalibacterium sp. 3.5*R1 failed to grow on a nitrogen-free medium, but grew very well when co-cultured with the nitrogen-fixing alkaliphile NF10m6 isolated in this study, indicating the availability of nitrogen. These results show that nitrogen fixation by alkaliphiles may have an important contribution as a source of nitrogen in soda lakes.

Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil

Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total of 414 strains isolated from root tissues (RT), root-adhering soil (RAS), non-adhering rhizospheric soil (NARS) and bulk soil (BS) using different NaCl concentrations. Our data showed that halophilic and halotolerant bacterial isolates in BS and the rhizosphere belonged to 32 genera distributed in Proteobacteria (49%), Firmicutes (36%), Actinobacteria (14%) and Bacteroidetes (1%). Bacterial population size and species diversity were greatly increased in the rhizosphere (factor 100). The reservoir of diversity in BS was dominated by the genera Bacillus and Halomonas. Bacillus/Halomonas ratio decreased with the proximity to the roots from 2.2 in BS to 0.3 at the root surface. Salt screening of the strains showed that species belonging to nine genera were able to grow up to 5.1 M NaCl. Thus, we found that H. strobilaceum exerted a strong effect on the diversity of the recruited microbiota with an affinity strongly attributed to the genus Halomonas.

Marine Biopolymers as Bioactive Functional Ingredients of Electrospun Nanofibrous Scaffolds for Biomedical Applications

Marine biopolymers, abundantly present in seaweeds and marine animals, feature diverse structures and functionalities, and possess a wide range of beneficial biological activities. Characterized by high biocompatibility and biodegradability, as well as unique physicochemical properties, marine biopolymers are attracting a constantly increasing interest for the development of advanced systems for applications in the biomedical field. The development of electrospinning offers an innovative technological platform for the production of nonwoven nanofibrous scaffolds with increased surface area, high encapsulation efficacy, intrinsic interconnectivity, and structural analogy to the natural extracellular matrix. Marine biopolymer-based electrospun nanofibrous scaffolds with multifunctional characteristics and tunable mechanical properties now attract significant attention for biomedical applications, such as tissue engineering, drug delivery, and wound healing. The present review, covering the literature up to the end of 2021, highlights the advancements in the development of marine biopolymer-based electrospun nanofibers for their utilization as cell proliferation scaffolds, bioadhesives, release modifiers, and wound dressings.

Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation

Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.

Biodegradable Polymeric Nanoparticles for Drug Delivery to Solid Tumors

Advances in nanotechnology have favored the development of novel colloidal formulations able to modulate the pharmacological and biopharmaceutical properties of drugs. The peculiar physico-chemical and technological properties of nanomaterial-based therapeutics have allowed for several successful applications in the treatment of cancer. The size, shape, charge and patterning of nanoscale therapeutic molecules are parameters that need to be investigated and modulated in order to promote and optimize cell and tissue interaction. In this review, the use of polymeric nanoparticles as drug delivery systems of anticancer compounds, their physico-chemical properties and their ability to be efficiently localized in specific tumor tissues have been described. The nanoencapsulation of antitumor active compounds in polymeric systems is a promising approach to improve the efficacy of various tumor treatments.

Unraveling bacterial diversity in oil refinery effluents

Oil refinery effluents are among stressful environments, and they are characterized by alkaline pH, high concentrations of dissolved solids, electrical conductivity, and metals (mainly Fe, Al, B, Sr, Mn, Cu, Ni). In this study, bacterial diversity in these habitats was inferred from full-length 16S rRNA gene sequences obtained from the PacBio^® sequencing platform. The results have shown low bacterial diversity in both raw and treated effluents, with sequences representing only two phyla: Firmicutes and Proteobacteria. Sequences from the raw effluents represent four major genera: Bacillus, Wenzhouxiangella, Rhodabaculum, and Halomonas. Whilst bacterial communities from the treated effluents are relatively more diverse as sequences represent five dominant genera: Pseudoxanthomonas, Brevundimonas, Pseudomonas, Rhodobaculum and Rhizobium. Most of the genera represented in the dataset are halophilic or halotolerant microbes known to have the competency to catabolize a broad spectrum of organic and inorganic pollutants. Hypothetically, these bacteria may be relevant for biotechnological and industrial applications, particularly for the remediation of saline industrial wastes.

Combined Microbial Consortium Inoculation and Black Locust Planting Is Effective in the Bioremediation of Waste Drill Cuttings

Waste drill cuttings (WDCs), produced during gas and oil drilling consisting of 80% rock cuttings and 20% drilling muds, are an increasingly potent source of environmental pollution. We studied the efficiency of bioaugmentation and phytoremediation to remediate WDCs in an experiment where WDCs were incubated in a greenhouse for 120 days with and without black locust (Robinia pseudoacacia) plant and with or without bacterial and fungal consortium inoculant. The pollutant removal rates were highest in inoculated and planted treatment, followed by inoculated treatment and planted treatment. The small decrease in contaminant level in the control treatment suggested that indigenous microorganisms in WDCs had little pollutant degradation capability. In the inoculated and planted treatments, after 120 days, the germination rate of red clover seeds was on the same level as in the natural soil, showing a marked decrease in the ecotoxicity of WDC. Both the bacterial and fungal richness and bacterial diversity increased in all the treatments over time, whereas fungal diversity increased only in the not-inoculated treatments. The activity of laccase enzyme played a key role in the bioremediation process. The enzyme activities were mostly governed by inoculated consortium and soil bacterial community, and black locust affected the bioremediation mainly through its effect on N content that further affected bacterial and fungal communities.

Salt tolerance of nitrate reductase in Halomonas sp. B01

A systematic study on the lack of dissimilatory nitrate reductase (NAR) properties in Halomonas strains had been reported so far. The effects of different factors on Halomonas sp. B01 NAR activity were investigated. The salt tolerance of NAR was characterized. The denitrification process under high salt conditions was reported. Halomonas sp. B01 expressed membrane-bound NAR under induced culture by nitrate. The optimum pH of the enzyme reaction system was 8, and the optimum temperature was 30 °C. The mRNA expression abundance of narH in NAR encoding gene was highest in the 60 g/L NaCl inducing matrix. The NaCl concentration of optimum growth and induction of NAR were both 60 g/L. The ectoine added to the NAR vitro enzyme reaction system could maintain NAR activity under high NaCl concentration. In the range of 0-60 g/L NaCl, the NAR activity was stable at 17.7 (± 0.3) U/mg. The denitrification was performed by Halomonas sp. B01 at 60 g/L NaCl, and the denitrification rate reached 97.1% at 24 h. This study reveals for the first time the NAR properties of Halomonas strains, which provides a theoretical and technical basis for the nitrogen removal of high-salt nitrogenous wastewater using this strain.

Effects of Halophyte Root Exudates and Their Components on Chemotaxis, Biofilm Formation and Colonization of the Halophilic Bacterium Halomonas Anticariensis FP35T

Increase in soil salinity poses an enormous problem for agriculture and highlights the need for sustainable crop production solutions. Plant growth-promoting bacteria can be used to boost the growth of halophytes in saline soils. Salicornia is considered to be a promising salt-accumulating halophyte for capturing large amounts of carbon from the atmosphere. In addition, colonization and chemotaxis could play an important role in Salicornia-microbe interactions. In this study, the role of chemotaxis in the colonization of the halophilic siredophore-producing bacteria, Halomonas anticariensis FP35T, on Salicornia hispanica plants was investigated. The chemotactic response of FP35T to Salicornia root exudates showed optimum dependence at a salt concentration of 5 % NaCl (w/v). Oleanolic acid, the predominant compound in the exudates detected by HPLC and identified by UPLC-HRMS Q-TOF, acts as a chemoattractant. In vitro experiments demonstrated the enhanced positive effects of wild-type H. anticariensis strain FP35T on root length, shoot length, germination and the vigour index of S. hispanica. Furthermore, these positive effects partially depend on an active chemotaxis system, as the chemotaxis mutant H. anticariensis FP35 ΔcheA showed reduced plant growth promotion for all the parameters tested. Overall, our results suggest that chemotaxis responses to root exudates play an important role in interactions between Salicornia and halophilic bacteria, enhance their colonization and boost plant growth promotion. Preliminary results also indicate that root exudates have a positive impact on H. anticariensis FP35T biofilm formation under saline conditions, an effect which totally depends on the presence of the cheA gene.

Halomonas Rhizobacteria of Avicennia marina of Indian Sundarbans Promote Rice Growth Under Saline and Heavy Metal Stresses Through Exopolysaccharide Production

The Halomonas species isolated from the rhizosphere of the true mangrove Avicennia marina of Indian Sundarbans showed enhanced rice growth promotion under combined stress of salt and arsenic in pot assay. Interestingly, under abiotic stress conditions, Halomonas sp. Exo1 was observed as an efficient producer of exopolysaccharide. The study revealed that salt triggered exopolysaccharide production, which in turn, increased osmotic tolerance of the strain. Again, like salt, presence of arsenic also caused increased exopolysaccharide production that in turn sequestered arsenic showing a positive feedback mechanism. To understand the role of exopolysaccharide in salt and arsenic biosorption, purified exopolysaccharide mediated salt and arsenic sequestration were studied both under in vivo and in vitro conditions and the substrate binding properties were characterized through FT-IR and SEM-EDX analyses. Finally, observation of enhanced plant growth in pot assay in the presence of the strain and pure exopolysaccharide separately, confirmed direct role of exopolysaccharide in plant growth promotion.

Effects of Nanoparticles on Plant Growth-Promoting Bacteria in Indian Agricultural Soil

Soil bacteria are some of the key players affecting plant productivity. Soil today is exposed to emerging contaminants like metal engineered nanoparticles. The objective of this study was to evaluate the toxicological effects of silver and zinc oxide nanoparticles on bacteria classified as plant growth-promoting bacteria. Three types of bacteria—nitrogen fixers, phosphate solubilizers, and biofilm formers—were exposed to engineered nanoparticles. Initially, the effect of silver and zinc oxide nanoparticles was determined on pure cultures of the bacteria. These nanoparticles were then applied to soil to assess changes in composition of bacterial communities. Impacts of the nanoparticles were analyzed using Illumina MiSeq sequencing of 16S rRNA genes. In the soil used, relative abundances of the dominant and agriculturally significant phyla, namely, Proteobacteria, Actinobacteria, and Firmicutes, were altered in the presence of silver nanoparticles. Silver nanoparticles changed the abundance of the three phyla by 25 to 45%. Zinc oxide nanoparticles showed negligible effects at the phylum level. Thus, silver nanoparticles may impact bacterial communities in soil, and this in turn may influence processes carried out by soil bacteria.

Advanced microscopic evaluation of parallel type I and type II cell deaths induced by multi-functionalized gold nanocages in breast cancer

Despite aggressive surgical resections and combinatorial chemoradiations, certain highly malignant populations of tumor cells resurrect and metastasize. Mixed-grade cancer cells fail to respond to standard-of-care therapies by developing intrinsic chemoresistance and subsequently result in tumor relapse. Macroautophagy is a membrane trafficking process that underlies drug resistance and tumorigenesis in most breast cancers. Manipulating cellular homeostasis by a combinatorial nanotherapeutic model, one can evaluate the crosstalk between type I and type II cell death and decipher the fate of cancer therapy. Here, we present a multi-strategic approach in cancer targeting to mitigate the autophagic flux with subcellular toxicity via lysosome permeation, accompanied by mitochondrial perturbation and apoptosis. In this way, a nanoformulation is developed with a unique blend of a lysosomotropic agent, an immunomodulating sulfated-polysaccharide, an adjuvant chemotherapeutic agent, and a monoclonal antibody as a broad-spectrum complex for combinatorial nanotherapy of all breast cancers. To the best of our knowledge, this manuscript illustrates for the first time the applications of advanced microscopic techniques such as electron tomography, three-dimensional rendering and segmentation of subcellular interactions, and fate of the multifunctional therapeutic gold nanocages specifically targeted toward breast cancer cells.

Genome analysis provides insights into crude oil degradation and biosurfactant production by extremely halotolerant Halomonas desertis G11 isolated from Chott El-Djerid salt-lake in Tunisian desert

Here, we report the genomic features and the bioremediation potential of Halomonas desertis G11, a new halophilic species which uses crude oil as a carbon and energy source and displays intrinsic resistance to salt stress conditions (optimum growth at 10% NaCl). G11 genome (3.96 Mb) had a mean GC content of 57.82%, 3622 coding sequences, 480 subsystems and 64 RNA genes. Annotation predicted 38 genes involved in osmotic stress including the biosynthesis of osmoprotectants glycine-betaine, ectoine and osmoregulated periplasmic glucans. Genome analysis revealed also the versatility of the strain for emulsifying crude oil and metabolizing hydrocarbons. The ability of G11 to degrade crude oil components and to secrete a glycolipid biosurfactant with satisfying properties was experimentally confirmed and validated. Our results help to explain the exceptional capacity of G11 to survive at extreme desertic conditions, and highlight the metabolic features of this organism that has biotechnological and ecological potentialities.

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.

Expression and characterization of a potential exopolysaccharide from a newly isolated halophilic thermotolerant bacteria Halomonas nitroreducens strain WB1

The halophilic bacterial strain WB1 isolated from a hydrothermal vent was taxonomically characterized using multiple proxies, as Halomonas nitroreducens strain WB1. When grown on malt extract/yeast extract (MY) medium, it produced large quantities of exopolysaccharide (EPS). The polymer was synthesized at a higher rate during the log and early stationary phases. The anionic polysaccharide is primarily composed of glucose, mannose, and galactose. The studied EPS was highly viscous and had pseudoplastic nature. The EPS was found to be a mixture of three polysaccharides under FT-IR, which makes it less labile to environmental diagenesis. It also has emulsifying and antioxidant activity along with the binding capacity to heavy metals. The EPS has unique and interesting physical and chemical properties, which are different from earlier reported exo-polysaccharides produced by different bacterial genus. This suggests that the extreme geological niches like hypersaline, hyperthermal, hypothermal, and oligophilic environments, which are not well studied so far, can offer extensive and potential resources for medical, biotechnological and industrial applications. The study clearly showed that the thermal springs from the temperate region can be a potent source of many such industrially important microbial genera and need further detailed studies to be carried out.

Halomonas xiaochaidanensis sp. nov., isolated from a salt lake sediment

A short-rod-shaped moderately halophilic bacterium, designated CUG 00002(T), was isolated from the sediment of Xiaochaidan salt lake in Qinghai Province, China by using R2A medium. The cells were Gram-staining negative, aerobic, forming creamy and circular colonies with diameters of 2-3 mm on R2A agar when incubated at 30 °C for 3 days. 16S rRNA gene-based phylogenetic analysis indicated that strain CUG 00002(T) belonged to the genus Halomonas in the class Gammaproteobacteria, showing highest sequence similarity of 97.1 and 96.7 % to Halomonas mongoliensis Z-7009(T) (=DSM 17332=VKM B2353) and Halomonas shengliensis SL014B-85(T) (=CGMCC 1.6444(T)=LMG 23897(T)), respectively. The predominant isoprenoid quinone was ubiquinone-9 (Q9), and the major fatty acids were C16:0, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (comprising C18:1 ω7c or C18:1 ω6c). The genomic DNA G+C content of strain CUG 00002(T) was 61.8 mol%. The above characteristics were consistent with the placement of the organism in the genus Halomonas. The level of DNA-DNA relatedness between CUG 00002(T) and its most closely related strain H. mongoliensis Z-7009(T) was 41.0 ± 1.6 %. Based on the results of phenotypic, phylogenetic and biochemical analyses, strain CUG 00002(T) represents a novel species of the genus Halomonas, for which the name Halomonas xiaochaidanensis sp. nov. is proposed. The type strain is CUG 00002(T) (=CCTCC AB 2014152(T)=KCTC 42685(T)).

Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers

The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6 m), with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celeribacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms.

Role of Bacterial Exopolysaccharides as Agents in Counteracting Immune Disorders Induced by Herpes Virus

Extreme marine environments, such as the submarine shallow vents of the Eolian Islands (Italy), offer an almost unexplored source of microorganisms producing unexploited and promising biomolecules for pharmaceutical applications. Thermophilic and thermotolerant bacilli isolated from Eolian vents are able to produce exopolysaccharides (EPSs) with antiviral and immunomodulatory effects against Herpes simplex virus type 2 (HSV-2). HSV-2 is responsible for the most common and continuously increasing viral infections in humans. Due to the appearance of resistance to the available treatments, new biomolecules exhibiting different mechanisms of action could provide novel agents for treating viral infections. The EPSs hinder the HSV-2 replication in human peripheral blood mononuclear cells (PBMC) but not in WISH (Wistar Institute Susan Hayflic) cells line, indicating that cell-mediated immunity was involved in the antiviral activity. High levels of Th1-type cytokines were detected in PBMC treated with all EPSs, while Th2-type cytokines were not induced. These EPSs are water soluble exopolymers able to stimulate the immune response and thus contribute to the antiviral immune defense, acting as immunomodulators. As stimulants of Th1 cell-mediated immunity, they could lead to the development of novel drugs as alternative in the treatment of herpes virus infections, as well as in immunocompromised host.

Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters

The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir.

Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome

Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.

Characterization of an extremely halotolerant Staphylococcus arlettae HPSSN35C isolated from Dwarka Beach, India

An extremely halotolerant bacterium designated as HPSSN35C was isolated from saline soil of Dwarka beach, India. It exhibited growth over a wide range of NaCl in medium varying from 0 to 6 M. The isolate produced peach-pink pigment above ∼1.3 M NaCl. The culture was characterized using biochemical tests, bioMerieux Staph identification kit, API ID32 Staph system, and Biolog. Due to slow growth and extreme salt tolerance no ID was obtained in Biolog. Antibiotic sensitivity to various antibiotics was tested. Phenotypic characterization showed that it belonged to the novobiocin resistant staphylococci group. Analysis of 16S rRNA gene sequence comparison of 1452 base pairs showed that isolate is closely related to Staphylococcus saprophyticus group with close relationship to Staphylococcus arlettae (99% similarity). The halotolerant S. arlettae described in literature till date have been reported to tolerate 4.5 M NaCl and produce white to yellow pigment. The present study reports for the first time extremely halotolerant S. arlettae exhibiting growth up to ∼6 M NaCl and producing peach-pink pigment above ∼1.3 M NaCl.

Characterization of Halomonas sp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA

Background

Halomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions.

Results

The analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOB_V family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family.

Conclusions

This study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.

Bacterial exopolysaccharide based nanoparticles for sustained drug delivery, cancer chemotherapy and bioimaging

Introduction of a novel biocompatible, stable, biomaterial for drug delivery application remains always challenging. In the present study, we report the synthesis of an extremophilic bacterial sulfated polysaccharide based nanoparticle as a stable biocompatible material for drug delivery, evaluation of anticancer efficacy and bioimaging. Mauran (MR), the sulfated exopolysaccharide extracted from a moderately halophilic bacterium, Halomonas maura was used for the synthesis of nanoparticles along with chitosan (CH). MR/CH nanoparticles were synthesized by simple polyelectrolyte complexation of anionic MR and cationic CH. The MR/CH hybrid nanoparticles formed were ranging between 30 and 200 nm in diameter with an overall positive zeta potential of 27.5±5 mV and was found to be stable under storage in solution for at least 8 weeks. In vitro drug release studies showed a sustained and prolonged delivery of 5-fluorouracil (5FU) for 10-12 days from MR/CH nanoparticles under three different pHs of 4.5, 6.9 and 7.4 respectively. Cytotoxicity assay revealed that MR/CH nanoparticles were non-cytotoxic towards normal cells and toxic to cancer cells. Also, 5FU loaded MR/CH nanoparticles were found more effective than free 5FU in its sustained and controlled manner of killing breast adenocarcinoma cells. Fluorescein isothiocyanate (FITC) labeled MR/CH nanoparticles were used for cell binding and uptake studies; thereby demonstrating the application of dye tagged MR/CH nanoparticles for safe and nontoxic mode of live cellular imaging. We report the introduction of an extremophilic bacterial polysaccharide, MR, for the first time as a novel biocompatible and stable biomaterial to the world of nanotechnology, pharmaceutics and biomedical technology.

Industrial and environmental applications of halophilic microorganisms

In comparison with the thermophilic and the alkaliphilic extremophiles, halophilic microorganisms have as yet found relatively few biotechnological applications. Halophiles are involved in centuries-old processes such as the manufacturing of solar salt from seawater and the production of traditional fermented foods. Two biotechnological processes involving halophiles are highly successful: the production of beta-carotene by the green alga Dunaliella and the production of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid), used as a stabilizer for enzymes and now also applied in cosmetic products, from moderately halophilic bacteria. The potential use of bacteriorhodopsin, the retinal protein proton pump of Halobacterium, in optoelectronic devices and photochemical processes is being explored, and may well lead to commercial applications in the near future. Demand for salt-tolerant enzymes in current manufacturing or related processes is limited. Other possible uses of halophilic microorganisms such as treatment of saline and hypersaline wastewaters, and the production of exopolysaccharides, poly-beta-hydroxyalkanoate bioplastics and biofuel are being investigated, but no large-scale applications have yet been reported.

Isolation and characterisation of bacteria from the haloalkaline Lake Elmenteita, Kenya

Culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. In this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from Lake Elmenteita. Different media were prepared using filter-sterilised water from the lake. The isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. Phylogenetic analysis of 181 partial 16S rRNA gene sequences with excellent quality showed that the majority of the isolates were affiliated to the class Gammaproteobacteria and to the genus Bacillus. Isolates from the genus Halomonas and Bacillus constituted 37 and 31% of the total sequenced isolates, respectively. Other groups recovered were related to Marinospirillum, Idiomarina, Vibrio, Enterococcus, Alkalimonas, Alkalibacterium, Amphibacillus, Marinilactibacillus and the actinobacteria Nocardiopsis and Streptomyces. Fifty-one different genera were represented with 31 and 15 cultures scoring with their nearest neighbour similarities below 98 and 97%, respectively. Some novel taxa were identified which had not been isolated previously from the soda environment. The results show that the use of different media with varying compositions can help retrieve novel bacterial diversity from the soda lake environment.

Drop-size soda lakes: transient microbial habitats on a salt-secreting desert tree

We describe a hitherto unrecognized bacterial community, inhabiting the leaf surfaces of the salt-excreting desert tree Tamarix. High temperatures, strong radiation, and very low humidity dictate a daytime existence in complete desiccation, but damp nights allow the microbial population to proliferate in a sugar-rich, alkaline, and hypersaline solution, before drying up again after sunrise. The exclusively bacterial population contains many undescribed species and genera, but nevertheless appears to be characterized by relatively limited species diversity. Sequences of 16S rRNA genes from either isolates or total community DNA place the identified members of the community in five bacterial groups (Actinobacteria, Bacteroidetes, Firmicutes, alpha-, and gamma-Proteobacteria); in each of these, they concentrate in a very narrow branch that in most cases harbors organisms isolated from unrelated halophilic environments.

A membrane-bound nitrate reductase encoded by the narGHJI operon is responsible for anaerobic respiration in Halomonas maura

The halophilic bacterium Halomonas maura is capable of anaerobic respiration on nitrates. By insertional mutagenesis with the minitransposon Tn-5 we obtained the mutant Tc62, which was incapable of anaerobic respiration on nitrates. An analysis of the regions adjacent to the transposon allowed us to characterize the membrane-bound anaerobic-respiratory nitrate reductase narGHJI gene cluster in H. maura. We identified consensus sequences for fumarate and nitrate reductase regulator (FNR)-like protein-binding sites in the promoter regions of the nar genes and consensus sequences corresponding to the NarL binding sites upstream of the nar genes. RT-PCR analysis showed that the narGHJI operon was expressed in response to anaerobic conditions when nitrate was available as electron acceptor. This membrane-bound nitrate reductase is the only enzyme responsible for anaerobic respiration on nitrate in H. maura. In this article we discuss the possible relationship between this enzyme and a dissimilatory nitrate-reduction-to-ammonia process (DNRA) in H. maura and its role in the colonization of the rhizosphere.