Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India

The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.

Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal

Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.

Current trends in bioremediation and bio-integrated treatment of petroleum hydrocarbons

Petroleum hydrocarbons and their derivatives constitute the leading group of environmental pollutants worldwide. In the present global scenario, petroleum and natural gas production, exploration, petroleum refining, and other anthropogenic activities produce huge amounts of hazardous petroleum wastes that accumulate in the terrestrial and marine environment. Due to their carcinogenic, neurotoxic, and mutagenic characteristics, petroleum pollutants pose severe risks to human health and exert ecotoxicological effects on the ecosystems. To mitigate petroleum hydrocarbons (PHs) contamination, implementing "green technologies" for effective cleanup and restoration of an affected environment is considered as a pragmatic approach. This review provides a comprehensive outline of newly emerging bioremediation technologies, for instance; nanobioremediation, electrokinetic bioremediation, vermiremediation, multifunctional and sustainably implemented on-site applied biotechnologies such as; natural attenuation, biostimulation, bioaugmentation, bioventing, phytoremediation and multi-process hybrid technologies. Additionally, the scope of the effectiveness and limitations of individual technologies in treating the petroleum hydrocarbon polluted sites are also evaluated.

Crystal structure of Synechococcus phycocyanin: implications of light-harvesting and antioxidant properties

Phycobiliproteins is a family of chromophore-containing proteins having light-harvesting and antioxidant capacity. The phycocyanin (PC) is a brilliant blue coloured phycobiliprotein, found in rod structure of phycobilisome and has been widely studied for their therapeutic and fluorescent properties. In the present study, the hexameric assembly structure of phycocyanin (Syn-PC) from Synechococcus Sp. R42DM is characterized by X-ray crystallography to understand its light-harvesting and antioxidant properties. The crystal structure of Syn-PC is solved with 2.15 Å resolution and crystallographic R-factors, Rwork/Rfree, 0.16/0.21. The hexamer of Syn-PC is formed by heterodimer of two polypeptide chains, namely, α- and β-subunits. The structure is analysed at atomic level to reveal the chromophore microenvironment and possible light energy transfer mechanism in Syn-PC. The chromophore arrangement in hexamer, deviation angle and distance between the chromophore contribute to the energy transfer efficiency of protein. The structural attributes responsible for the antioxidant potential of Syn-PC are recognized and annotated on its 3-dimensional structure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03665-1.

Exploring the structural aspects and therapeutic perspectives of cyanobacterial phycobiliproteins

Phycobiliproteins (PBPs) of cyanobacteria and algae possess unique light harvesting capacity which expand the photosynthetically active region (PAR) and allow them to thrive in extreme niches where higher plants cannot. PBPs of cyanobacteria/algae vary in abundance, types, amino acid composition and in structure as a function of species and the habitat that they grow in. In the present review, the key aspects of structure, stability, and spectral properties of PBPs, and their correlation with ecological niche of cyanobacteria are discussed. Besides their role in light-harvesting, PBPs possess antioxidant, anti-aging, neuroprotective, hepatoprotective and anti-inflammatory properties, which can be used in therapeutics. Recent developments in therapeutic applications of PBPs are reviewed with special focus on 'route of PBPs administration' and 'therapeutic potential of PBP-derived peptide and chromophores'.

Crystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema

Phycoerythrin (PE) is green light-absorbing pigment-protein that assists in efficient light harvesting in cyanobacteria and red-algae. PE in cyanobacteria stays less studied so far as compared to that in red algae. In this study, PE from marine cyanobacteria Halomicronema sp. R31DM is purified and subjected for its structural characterisation by X-ray crystallography in order to understand its light-harvesting characteristics. The crystal structure is solved to a resolution-limit of 2.21 Å with reasonable R-factors values, 0.16/0.21 (R_work/ R_free). PE forms hexamer of hetero-dimers made up of two peptide chains, α- and β-subunits containing 2 and 3 phycoerythrobilin (PEB) chromophores covalently attached to them, respectively. Geometry of five chromophores is analysed along with their relative position within the PE hexamer. Also, their interactions with the surrounding microenvironment are analysed. The plausible energy transfer pathways in hexamer structure have been predicted based on relative position and geometry of chromophores. This structure enriches the structural information of cyanobacterial PE in order to understand its light-harvesting capacity.Communicated by Ramaswamy H. Sarma.

White Rann of Kachchh harbours distinct microbial diversity reflecting its unique biogeography

The understanding of sub-surface soil microbial diversity is limited at both saline and hypersaline ecosystems, even though salinity is found to affect the microbial community in aqueous and terrestrial environment. In this study, a phylo-taxonomy analysis as well as the functional characteristics of microbial community of flat salt basin of White Rann of Kachchh (WR), Gujarat, India was performed along the natural salinity gradient. The high throughput sequencing approach has revealed the numerical abundance of bacteria relative to the archaea. Salinity, TOC, EC and sulphate concentration might be the primary driver of the community distribution along the transect at WR. The much anticipated effect of salinity gradient on the microbial composition surprisingly turned out to be more speculative, with little variance in the community composition along the spatial distance of WR. The metabolic pathways involved in energy metabolism (like carbon, nitrogen, sulphur) along with environmental adaptive genes (like osmotic and oxidative stress response, heat and cold shock genes clusters) were abundantly annotated from shot-gun metagenomic study. The carbonic anhydrase harbouring bacteria Bacillus sp. DM4CA1 was isolated from WR, having a catalytic ability for converting the gaseous carbon dioxide in presence of calcium carbonate into calcite at 25 % higher rate as compared to non-harbouring strains. The enzyme has a role in multiple alternative pathways in microbial metabolism. With the array of results obtained, the study could become the new reference for understanding the diversity structure and functional characteristics of the microbial community of terrestrial saline environment.

Electroactive bacterial community augmentation enhances the performance of a pilot scale constructed wetland microbial fuel cell for treatment of textile dye wastewater

This study evaluated the effect of bioaugmentation of a newly enriched electroactive bacterial community DC5 on the performance of a pilot scale sequential two-step Horizontal Sub-surface flow Constructed Wetland-Microbial Fuel Cell (HSCW-MFC) system treating textile dye wastewater. The system consisted of CW-MFC-1 planted with Fimbristylis ferruginea and CW-MFC-2 planted with consortium of Fimbristylis ferruginea and Elymus repens plant species. Before bioaugmentation, HSCW-MFC system showed 62 ± 2% Chemical Oxygen Demand (COD) and 90 ± 1.5% American Dye Manufacturer's Institute (ADMI) removal and 177.3 mW/m² maximum power density (CW-MFC-1). After bioaugmentation of DC5 into the HSCW-MFC, COD and ADMI removal was enhanced to 74.10 ± 1.75% and 97.32 ± 1.90% with maximum power density of 197.94 mW/m² (CW-MFC-1). The genera Exiguobacterium, Desulfovibrio and Macellibacteroides of DC5 were significantly enriched at the electrodes of HSCW-MFC after bioaugmentation. These results demonstrate that the performance of the CW-MFC treating textile dye wastewater can be improved by bioaugmentation of electroactive bacterial community.

Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae

A novel bacterial strain designated as ADMK78^T was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78^T grows best at 28 °C. Phylogeny of 16S rRNA gene placed the strain ADMK78^T with the members of genera Ciceribacter and Rhizobium, while the highest sequence similarity was with Rhizobium wuzhouense W44^T (98.7%) and Rhizobium ipomoeae shin9-1 ^T (97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78^T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. We propose re-classification of Rhizobium ipomoeae, R. wuzhouense, R. rosettiformans and R. rhizophilum into the novel genus Peteryoungia. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78^T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78^T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78^T represents a novel species, Peteryoungia desertarenae sp. nov. The type strain is ADMK78^T (= MCC 3400^T; KACC 21383^T; JCM 33657^T). We also proposed the reclassification of Rhizobium daejeonense, R. naphthalenivorans and R. selenitireducens, into the genus Ciceribacter, based on core gene phylogeny and AAI values.

Therapeutic potential of bioactive compounds from Punica granatum extracts against aging and complicity of FOXO orthologue DAF-16 in Caenorhabditis elegans

Some natural fruits have significant importance in improving health which provides many nutritional supplements essential to maintain proper metabolism with the age. In this study, phytochemical screening of extract (methanolic) of Punica granatum arils, outer and inner peels was confirmed by the respective spot tests. Quantification of phytochemical constituents revealed the plentiful of total phenols in the outer peels in comparison to inner peels and juice whereas total flavonoids and vitamin C are abundant in inner peel and juice, respectively. High-performance liquid chromatography, Gas chromatography along with mass spectrometry and Fourier-transform infrared spectroscopy analysis revealed the presence of compound 9, 17-octadecadienal, (Z) in the outer/inner peels. A compound N-hexadecanoic acid was also observed in the outer peels. Extracts from every section of the fruits were comprehensively evaluated for their antioxidant activity. Contrary to fruit aril juice, the extracts of outer and inner peels exhibited significant and dose-dependent in vitro antioxidant and radical-scavenging potentials. The supplementation of P. granatum extracts (PGEs) significantly enhanced the lifespan of C. elegans. The protective effect of PGEs was also observed against oxidative stress in C. elegans. Additionally, the involvement of FOXO orthologue DAF-16 dependent longevity was obtained with PGEs (outer peel and inner peel) fed TJ356 worms. Overall, the results indicate the vital role of PGEs especially the extracts of outer peels in life-saving mechanisms of C. elegans by virtue of their antioxidant asset and life-prolonging effects via daf-16 dependent Insulin signaling pathway. See also Figure 1(Fig. 1).

Extension of life span and stress tolerance modulated by DAF-16 in Caenorhabditis elegans under the treatment of Moringa oleifera extract

The present study was focused to isolate the bioactive compounds present in the leaves of Moringa oleifera which contains a high nutritional value. Furthermore, the research was aimed to evaluate the antioxidant, anti-aging, and anti-neurodegenerative properties of M. oleifera using the experimental model Caenorhabditis elegans. The separation of compounds from the crude extract and its identification was carried out through TLC, Column chromatography, UV absorption spectroscopy, and GC-MS. The compounds identified in most abundant fraction of column chromatography were [Phenol-2,4-bis(1,1-dimethylethyl)- phosphite (3:1)] and Tetratetracontane. The result suggests that the leaves extracts and column fraction were able to significantly extend the life span of the N2 wild-type strain of C. elegans. The most potent life span extending effect was displayed by the dichloromethane extract of leaves which was 21.73 ± 0.142 days compared to the control (16.55 ± 0.02 days). It could also extend the health span through improved physiological functions such as pharyngeal pumping, body bending, and reversal frequency with increased age. The treated worms were also exhibited improved resistance to thermal stress, oxidative stress, and reduced intracellular ROS accumulation. Moreover, the leaves extract could elicit neuroprotection as it could delay the paralysis in the transgenic strain of C. elegans 'CL4176' integrated with Aβ. Interestingly, The RNAi experiment demonstrated that the extended life span under the treatment of extracts and the compound was daf-16 dependent. In transgenic C. elegans TJ356, the DAF-16 transcription factor was localized in the nucleus under the stress conditions, further supported the involvement of the daf-16 gene in longevity. Overall, the study suggests the potential of M. oleifera as a dietary supplement and alternative medicine to defend against oxidative stress and aging.

Polycyclic Aromatic Hydrocarbons: Sources, Toxicity, and Remediation Approaches

Polycyclic aromatic hydrocarbons (PAHs) are widespread across the globe mainly due to long-term anthropogenic sources of pollution. The inherent properties of PAHs such as heterocyclic aromatic ring structures, hydrophobicity, and thermostability have made them recalcitrant and highly persistent in the environment. PAH pollutants have been determined to be highly toxic, mutagenic, carcinogenic, teratogenic, and immunotoxicogenic to various life forms. Therefore, this review discusses the primary sources of PAH emissions, exposure routes, and toxic effects on humans, in particular. This review briefly summarizes the physical and chemical PAH remediation approaches such as membrane filtration, soil washing, adsorption, electrokinetic, thermal, oxidation, and photocatalytic treatments. This review provides a detailed systematic compilation of the eco-friendly biological treatment solutions for remediation of PAHs such as microbial remediation approaches using bacteria, archaea, fungi, algae, and co-cultures. In situ and ex situ biological treatments such as land farming, biostimulation, bioaugmentation, phytoremediation, bioreactor, and vermiremediation approaches are discussed in detail, and a summary of the factors affecting and limiting PAH bioremediation is also discussed. An overview of emerging technologies employing multi-process combinatorial treatment approaches is given, and newer concepts on generation of value-added by-products during PAH remediation are highlighted in this review.

Characterizing the bacterial consortium ASDF capable of catabolic degradation of fluoranthene and other mono- and poly-aromatic hydrocarbons

In this study, a bacterial consortium ASDF was developed, capable of degrading fluoranthene (a non-alternant poly-aromatic hydrocarbon). It comprised of three bacterial strains: Pseudomonas sp. ASDF1, Burkholderia sp. ASDF2 and Mycobacterium sp. ASDF3 capable of degrading 100 mg/L of fluoranthene under experimentally defined and optimum conditions (37 °C, pH 7.0, 150 rpm) within 7 days. Consortium had metabolized fluoranthene as sole source of carbon and energy with maximum degradation rate of 0.52 mg/L/h and growth rate of 0.054/h. Fluoranthene degradation is an aerobic process, therefore with increasing the gyratory shaking from 50 to 150 rpm, degradation was concurrently enhanced by 7.1-fold. The synthetic surfactants SDS and CTAB had antagonistic effect on fluoranthene degradation (decreased up to 2.8-fold). The proficiency of consortium was assessed for its inherent ability to degrade seven other hydrocarbons both individually as well as in mixture. The degradation profile was studied using HPLC and the detection of two degraded intermediates (salicylic acid and derivatives of phthalic acid) suggested that fluoranthene degradation might have occurred via ortho- and meta-cleavage pathways. The competency of consortium was further validated through simulated microcosm studies, which showed 96% degradation of fluoranthene in soil ecosystem under the ambient conditions. Hence, the study suggested that the consortium ASDF has an inherent potential for its wide applicability in bioremediation of hydrocarbon-contaminated sites.

Degradation and Toxicity Analysis of a Reactive Textile Diazo Dye-Direct Red 81 by Newly Isolated Bacillus sp. DMS2

An efficient diazo dye degrading bacterial strain, Bacillus sp. DMS2 was isolated from a long-term textile dye polluted environment. The strain was assessed for its innate ability to completely degrade and detoxify Direct Red 81 (DR81) textile dye under microaerophilic conditions. The degradation ability of strain showed significant results on optimizing the nutritional and environmental parameters. Based on statistical models, maximum efficiency of decolorization achieved within 24 h for 100 mg/l of dye supplemented with glucose (0.02%), MgSO₄ (0.002%) and urea (0.5%) at 30°C and pH (7.0). Moreover, a significant catabolic induction of a laccase and azoreductase suggested its vital role in degrading DR81 into three distinct metabolites (intermediates) as by-products. Further, toxicity analysis of intermediates were performed using seeds of common edible plants, aquatic plant (phytotoxicity) and the nematode model (animal toxicity), which confirmed the non-toxic nature of intermediates. Thus, the inclusive study of DMS2 showed promising efficiency in bioremediation approach for treating industrial effluents.

Cyanobacterial pigment protein allophycocyanin exhibits longevity and reduces Aβ-mediated paralysis in C. elegans: complicity of FOXO and NRF2 ortholog DAF-16 and SKN-1

The allophycocyanin (APC) protein purified from Phormidium sp. A09DM was investigated for its in vivo antioxidant and anti-aging potential in Caenorhabditis elegans. An increased mean lifespan of APC-treated (100 μg/ml) worms (wild type) were observed from 16 ± 0.2 days (control) to 20 ± 0.1 days (treated). APC-treated worms also showed improved physiological marker of aging such as the rate of pharyngeal pumping and higher rate of survival against oxidative and thermal stress. Furthermore, APC was found to moderate the expression of human amyloid beta (Aβ1-42) as well as associated Aβ-induced paralysis in the transgenic C. elegans CL4176 upon increase in temperature. Furthermore, RNA interference (RNAi)-mediated studies revealed the dependence of downstream regulator daf-16, independent of stress-induced resistance gene skn-1 in the APC treated C. elegans. In the present study, we tried to demonstrate the anti-aging activity, longevity and protective effects of APC against cellular stress in C. elegans, which can lead to the use of this biomolecule in drug development for age-related disorders.

Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin

The crystal structure of phycocyanin (pr-PC) isolated from Phormidium rubidum A09DM (P. rubidum) is described at a resolution of 1.17 Å. Electron density maps derived from crystallographic data showed many clear differences in amino acid sequences when compared with the previously obtained gene-derived sequences. The differences were found in 57 positions (30 in α-subunit and 27 in β-subunit of pr-PC), in which all residues except one (β145Arg) are not interacting with the three phycocyanobilin chromophores. Highly purified pr-PC was then sequenced by mass spectrometry (MS) using LC-MS/MS. The MS data were analyzed using two independent proteomic search engines. As a result of this analysis, complete agreement between the polypeptide sequences and the electron density maps was obtained. We attribute the difference to multiple genes in the bacterium encoding the phycocyanin apoproteins and that the gene sequencing sequenced the wrong ones. We are not implying that protein sequencing by mass spectrometry is more accurate than that of gene sequencing. The final 1.17 Å structure of pr-PC allows the chromophore interactions with the protein to be described with high accuracy.

Microaerophilic biodegradation of raw textile effluent by synergistic activity of bacterial community DR4

Treatment of raw textile effluent (RTE) is very difficult, due to its inherent heterogeneous, low-biodegradable and toxic compositions. Pure and mixed microbial cultures have limited metabolic capabilities in effective mineralization of complex RTE. Therefore, in this study a novel bacterial community DR4 was enriched directly into a complex RTE consisting of 27 different dyes using textile dye polluted soil as an inoculum. The rigorous enrichment process resulted in acclimatization of a taxonomically distinct bacterial population, with an abundance of the genus Comamonas in the bacterial community DR4 as compared to the abundance of Pseudomonas in the RTE respectively, as revealed by high-throughput 16S rRNA gene (V3-V4 region) sequencing. Microaerophilic treatment of RTE by enriched bacterial community DR4, in the presence of optimized electron donor (sucrose) and nitrogen source (yeast extract) resulted in 88% of American Dye Manufacturer's Institute (ADMI) removal and 98% of Chemical oxygen demand (COD) reduction within 32 h at 37 °C. In silico prediction of the functional genes within bacterial community DR4 was made by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. The PICRUSt analysis revealed high abundance of xenobiotic degradation and metabolism genes. The predicted functional genes and textile dye degradation pathways were further validated using Ultraviolet-visible spectroscopy (UV-Vis), Fourier transform infrared (FTIR) spectroscopy and High Resolution Liquid Chromatography coupled with Mass Spectrometry (HR-LCMS) based characterization of textile dye degradation metabolites. The activity of azoreductases in the cell-free extracts (CFE) of the enriched bacterial community DR4 was induced by 1.83-7.81 folds in the presence of representative textile dyes as compared to uninduced samples, which confirmed their role in textile effluent decolourization. The degradation of four representative azo dyes present in RTE such as Disperse orange 30, Reactive red 152, Direct blue 2 and Acid brown 15 depicted symmetric degradation of azo bonds by bacterial community DR4.

Cyanobacterial diversity in mat sample obtained from hypersaline desert, Rann of Kachchh

Rann of Kachchh (RoK) is a unique geoformation, which is exposed to dynamic environmental changes such as salinity, temperature, and nutrients throughout the year. In this study, the pooled mat sample was examined for the cyanobacterial community structure using culture-dependent and culture-independent approaches. Taxonomic profiling was studied using amplicon sequencing that revealed the enrichment of Pseudanabaenales and Oscillatoriales by QIIME and MG-RAST, respectively. Other abundant orders were represented by Chroococcales, Nostocales, and unclassified cyanobacteria by both approaches. Nine cyanobacterial cultures were isolated from mat samples showing 90-98% similarities with available sequences in GenBank. The culture-dependent study suggested that mat was dominated by cyanobacterial orders such as Oscillatoriales-filamentous and Chroococcales-unicellular. Our results from the culture-dependent approach also indicated that despite high similarities in gene sequences, six cyanobacteria fall into the separate clade in the phylogenetic analysis that could be signs of evolution due to an extreme environment. Cultured isolates are correlated well with abundant taxa from amplicon sequencing. Further, protein profiling was done specifically for phycobiliproteins which will be helpful to elucidate their roles in light harvesting and energy transfer mechanism in the unique environment of RoK.

Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties

The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among α- and β-subunit (3 in α- and 9 in β-subunit). The phylogenetic analysis suggested that molecular evolution of α- and β-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in β-subunit, compared to α-subunit (relative divergence, 7.38 for α-subunit and 9.66 for β-subunit). Crystal structure of N-PC was solved at 2.35 Å resolution to reasonable R-factors (R_work/R_Free = 0.199/0.248). Substitutions congregate near interface of two αβ-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in β-subunit may be involved in maintaining topology of β-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The β153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.

Synergistic biodegradation of phenanthrene and fluoranthene by mixed bacterial cultures

Polycyclic aromatic hydrocarbons (PAHs) are highly recalcitrant compounds and difficult to degrade. Therefore in this work, using a bioremediation approach, mixed bacterial cultures (ASPF) was developed and enriched from polluted marine sediments capable of degrading 400 mg/L of phenanthrene and fluoranthene in Bushnell Hass medium. ASPF consists of 22 bacterial genera dominated by Azoarcus and Chelativorans. The biostimulation effect of three water soluble fertilizers (NPK, urea, and ammonium sulfate) showed that NPK and ammonium sulfate have enhanced the degradation, whereas urea has decreased their degradation. ASPF was also able to degrade phenanthrene and fluoranthene in the presence of petroleum hydrocarbons. But degradation was found to decrease in the presence of pathway intermediates (phthalic acid and catechol) due to enzymatic feedback inhibition. Optimum degradation of both PAHs was observed under room temperature, suggesting the practical applicability of ASPF.

Therapeutic potential of cyanobacterial pigment protein phycoerythrin: in silico and in vitro study of BACE1 interaction and in vivo Aβ reduction

Cyanobacteria are an immense source of innovative classes of pharmacologically active compounds exhibiting various biological activities ranging from antioxidants, antibiotics, anticancer, anti-inflammatory to anti-Alzheimer's disease. In the present study, we primarily targeted the inhibition of Beta-site amyloid precursor protein cleaving enzyme-1 (BACE1) by a naturally occurring cyanobacterial protein phycoerythrin (C-PE). BACE1 cleaves amyloid-β precursor protein (APP) and leads to accumulation of neurotoxic amyloid beta (Aβ) plaques in the brain, as an attribute of Alzheimer's disease (AD). Inhibition of BACE1 was measured in terms of their association and dissociation rate constants, thermodynamics of binding using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). The kinetic parameters for enzyme activity were also measured using synthetic decapeptide as a substrate. We further validated the potential of PE by in-vivo histopathological staining of Aβ aggregate mutant Caenorhabditis elegans CL4176 by Thioflavin-T. The present studies pave the way for the application of naturally occurring C-PE as a putative therapeutic drug for the AD.

Bioproduction and characterization of extracellular melanin-like pigment from industrially polluted metagenomic library equipped Escherichia coli

To explore the potential genes from the industrially polluted Amlakhadi canal, located in Ankleshwar, Gujarat, India, its community genome was extracted and cloned into E. coli EPI300™-T1^R using a fosmid vector (pCC2 FOS™) generating a library of 3,92,000 clones with average size of 40kb of DNA-insert. From this library, the clone DM1 producing brown colored melanin-like pigment was isolated and characterized. For over expression of the pigment, further sub-cloning of the clone DM1 was done. Sub-clone containing 10kb of the insert was sequenced for gene identification. The amino acids sequence of a protein 4-Hydroxyphenylpyruvate dioxygenase (HPPD), which is know to be involved in melanin biosynthesis was obtained from the gene sequence. The sequence-homology based 3D structure model of HPPD was constructed and analyzed. The physico-chemical nature of pigment was further analysed using ¹H and ¹³C NMR, LC-MS, FTIR and UV-visible spectroscopy. The pigment was readily soluble in DMSO with an absorption maximum around 290nm. Based on the genetic and chemical characterization, the compound was confirmed as melanin-like pigment. The present results indicate that the metagenomic library from industrially polluted environment generated a microbial tool for the production of melanin-like pigment.

Site, trigger, quenching mechanism and recovery of non-photochemical quenching in cyanobacteria: recent updates

Cyanobacteria exhibit a novel form of non-photochemical quenching (NPQ) at the level of the phycobilisome. NPQ is a process that protects photosystem II (PSII) from possible highlight-induced photo-damage. Although significant advancement has been made in understanding the NPQ, there are still some missing details. This critical review focuses on how the orange carotenoid protein (OCP) and its partner fluorescence recovery protein (FRP) control the extent of quenching. What is and what is not known about the NPQ is discussed under four subtitles; where does exactly the site of quenching lie? (site), how is the quenching being triggered? (trigger), molecular mechanism of quenching (quenching) and recovery from quenching. Finally, a recent working model of NPQ, consistent with recent findings, is been described.

Correction to: Site, trigger, quenching mechanism and recovery of non-photochemical quenching in cyanobacteria: recent updates

In the original publication, under the subtitle Recovery: fluorescence recovery protein (FRP), paragraph 4 the text section enclosed in quotation marks does not occur in one of the original publications cited (Sluchanko et al. 2017a, b).

Degradation of Chrysene by Enriched Bacterial Consortium

Chrysene is a high molecular weight (HMW), polycyclic aromatic hydrocarbon (PAH) known for its recalcitrance and carcinogenic properties and sparsely soluble (0.003 mg/L) in aqueous medium. Due to these refractory properties, bioavailability of chrysene is very low and therefore is persistence in the environment escaping the metabolism by microorganisms. However, few bacterial and fungal strains are reported to degrade chrysene, but with lower efficiency, requiring additional/extraneous carbon sources (co-substrates) for it’s complete mineralization. In this study, development, enrichment and characterization of bacterial consortium ASDC, consisting of Rhodococcus sp., ASDC1; Bacillus sp. ASDC2; and Burkholderia sp. ASDC3 were reported. Chrysene was utilized as a sole source of carbon and energy by the consortium, having maximum degradation rate of 1.5 mg/L/day and maximum growth rate of 0.125/h, under optimized conditions of pH 7.0, 37°C under aeration of 150 rpm on gyrating shaking. Chrysene degradation was unaffected in presence of other PAHs like pyrene, fluoranthene, naphthalene, phenanthrene, benzene, toluene and xylene, individually as well as in mixture. The results revealed that peptone, ammonium nitrate, sodium succinate have enhanced the chrysene degradation rate during first 24 h of experimentation, which was later on inhibited with increase in incubation time. The chrysene degradation was inhibited by mercury even at lower concentration (1 mM). The results also revealed that SDS has enhanced its degradation by 5.2-fold for initial 24 h of growth, but with increasing in the incubation period, it decreases by 1.2-fold on 7^th day of experimentation. The HPLC studies suggested that chrysene was degraded through phthalic acid pathway by the consortium ASDC and the stoichiometric measurements indicated the complete mineralization of chrysene. The flask scale results were validated at simulated microcosm models, where enriched consortium ASDC exhibited maximum degradation (96%) in polluted, non-sterile soil sediment, indicating that consortial strains along with indigenous metabolism showed synergistic metabolism for degradation of chrysene. Thus, the above study revealed the useful enrichment of bacterial community for synergistic degradation of PAHs (chrysene) which could be further exploited for in situ remediation of PAH contaminated sites.

Development of mixed bacterial cultures DAK11 capable for degrading mixture of polycyclic aromatic hydrocarbons (PAHs)

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and persistent pollutants having mutagenic and carcinogenic properties. Microbial metabolism is an alternative approach for removal of PAHs from polluted environment. Mixed bacterial cultures DAK11 capable for degrading mixture of PAHs was developed from long term polluted marine sediments. DAK11 was able to degrade 500 mg/L of mixture of four PAHs and their degradation efficiency was enhanced by supplementing commercially available NPK fertilizer (0.1%, w/v). Anionic surfactant SDS has enhanced the degradation of PAHs, but DAK11 growth was inhibited in presence of cationic surfactant CTAB. Heavy metals have decreased the rate of degradation, while it was completely inhibited in the presence of Zn²⁺ and CrO₄^2- (1mM). DAK11 was able to degrade PAHs in the presence of mono-aromatic hydrocarbons, lubricant oil and diesel. Lower molecular weight aromatic and aliphatic compounds were identified using GC-MS during metabolism of mixture of PHAs.

An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM

C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94-103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB's spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17-28, 2016).

Picosecond excitation energy transfer of allophycocyanin studied in solution and in crystals

Cyanobacteria perform photosynthesis with the use of large light-harvesting antennae called phycobilisomes (PBSs). These hemispherical PBSs contain hundreds of open-chain tetrapyrrole chromophores bound to different peptides, providing an arrangement in which excitation energy is funnelled towards the PBS core from where it can be transferred to photosystem I and/or photosystem II. In the PBS core, many allophycocyanin (APC) trimers are present, red-light-absorbing phycobiliproteins that covalently bind phycocyanobilin (PCB) chromophores. APC trimers were amongst the first light-harvesting complexes to be crystallized. APC trimers have two spectrally different PCBs per monomer, a high- and a low-energy pigment. The crystal structure of the APC trimer reveals the close distance (~21 Å) between those two chromophores (the distance within one monomer is ~51 Å) and this explains the ultrafast (~1 ps) excitation energy transfer (EET) between them. Both chromophores adopt a somewhat different structure, which is held responsible for their spectral difference. Here we used spectrally resolved picosecond fluorescence to study EET in these APC trimers both in crystallized and in solubilized form. We found that not all closely spaced pigment couples consist of a low- and a high-energy pigment. In ~10% of the cases, a couple consists of two high-energy pigments. EET to a low-energy pigment, which can spectrally be resolved, occurs on a time scale of tens of picoseconds. This transfer turns out to be three times faster in the crystal than in the solution. The spectral characteristics and the time scale of this transfer component are similar to what have been observed in the whole cells of Synechocystis sp. PCC 6803, for which it was ascribed to EET from C-phycocyanin to APC. The present results thus demonstrate that part of this transfer should probably also be ascribed to EET within APC trimers.

Antioxidant activity and associated structural attributes of Halomicronema phycoerythrin

In the present study, blue light absorbing pigment protein phycoerythrin (PE) is purified up to molecular grade purity from marine Halomicronema sp. R31DM. The purification method is based on the use of non-ionic detergent Triton-X 100 in ammonium sulphate precipitation. The purified PE is characterized for its antioxidant activity in vitro and in vivo. PE is noted to show substantial in vitro antioxidant activity probed by various biochemical assays. The PE moderated rise in the intracellular-ROS (reactive oxygen species) in wild type Caenorhabditis elegans upon heat and oxidative stress. Further, the antioxidant asset of PE is noted an expedient in averting the ROS associated abnormalities, i.e. impaired physiological behaviour (health span) and aging in C. elegans. The structural attributes of PE contributing to its antioxidant virtue are analysed; the presence of ample residues having antioxidant activity and chromophore-PEB in PE are identified as a source of its antioxidant activity. Furthermore, the stability of PE is assessed under three physico-chemical stresses, temperature, pH and oxidative stress.

Purification and antioxidant activity of phycocyanin from Synechococcus sp. R42DM isolated from industrially polluted site

The cyanobacterium Synechococcus sp. R42DM, isolated from an industrially polluted site Vatva, Gujarat, India was recognized to produce phycocyanin (PC) as major phycobiliprotein. In present study, the combinatorial approach of chemical and physical methods i.e. Triton-X 100 treatment and ultra-sonication was designed for extraction of PC. From cell extract, the intact and functional-PC was purified up to purity 4.03 by ammonium sulphate fractionation and ion-exchange chromatography. The PC displayed considerable in vitro antioxidant and radical-scavenging activity. This PC was further noticed to scavenge intracellular-ROS and to increase tolerance against thermal and oxidative stress in Caenorhabditis elegans. Moreover, the PC was noticed to improve the physiological behaviour and longevity of C. elegans. In addition, the PC showed remarkable stability under physico-chemical stressors, which is desirable for their use in biomedical applications. In conclusion, present paper added up evidence in support of the prospective use of PC as an antioxidant nutraceutical.

Microalgal hydrogen production - A review

Bio-hydrogen from microalgae including cyanobacteria has attracted commercial awareness due to its potential as an alternative, reliable and renewable energy source. Photosynthetic hydrogen production from microalgae can be interesting and promising options for clean energy. Advances in hydrogen-fuel-cell technology may attest an eco-friendly way of biofuel production, since, the use of H₂ to generate electricity releases only water as a by-product. Progress in genetic/metabolic engineering may significantly enhance the photobiological hydrogen production from microalgae. Manipulation of competing metabolic pathways by modulating the certain key enzymes such as hydrogenase and nitrogenase may enhance the evolution of H₂ from photoautotrophic cells. Moreover, biological H₂ production at low operating costs is requisite for economic viability. Several photobioreactors have been developed for large-scale biomass and hydrogen production. This review highlights the recent technological progress, enzymes involved and genetic as well as metabolic engineering approaches towards sustainable hydrogen production from microalgae.

Phycoerythrin averts intracellular ROS generation and physiological functional decline in eukaryotes under oxidative stress

In vitro antioxidant virtue and life-prolonging effect of phycoerythrin (PE; a pigment protein isolated from Phormidium sp. A09DM) have been revealed in our previous reports (Sonani et al. in Age 36:9717, 2014a; Sonani et al. in Process Biochem 49:1757-1766, 2014b). It has been hypothesized that the PE expands life span of Caenorhabditis elegans (bears large resemblance with human aging pathways) due to its antioxidant virtue. This hypothesis is tested in present study by checking the effect of PE on intracellular reactive oxygen species (ROS) generation and associated physiological deformities using mouse and human skin fibroblasts, C. elegans, and Drosophila melanogaster Oregon R ⁺ and by divulging PE's structural attributes responsible for its antioxidant asset. PE treatment displayed noteworthy decrease of 67, 48, and 77 % in ROS level in mouse fibroblast (3T3-L1), human fibroblast, and C. elegans N2, respectively, arisen under chemical-induced oxidative stress. PE treatment delayed the development of paraquat-induced Alzheimer phenotype by 14.5 % in C. elegans CL4176. Furthermore, PE improved the locomotion of D. melanogaster Oregon R ⁺ under oxidative stress with simultaneous up-regulation in super-oxide dismutase and catalase activities. The existence of 52 Glu + Asp + His + Thr residues (having metal ion sequestration capacity), 5 phycoerythrobilin chromophores (potential electron exchangers) in PE's primary structure, and significant hydrophobic patches on the surface of its α- and β-subunits are supposed to collectively contribute in the antioxidant virtues of PE. Altogether, results support the hypothesis that it is the PE's antioxidant asset, which is responsible for its life-prolonging effect and thus could be exploited in the therapeutics of ROS-associated abnormalities including aging and neurodegeneration in eukaryotes.

Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM

The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the β-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 Å resolution, respectively. In both the structures, heterodimers of α- and β- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of π-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to α-subunit and amino acid at position 73 of β-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates

Background

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation.

Results

Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum “Proteobacteria” and genus “Chromobacterium,” respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions.

Conclusion

To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0669-8) contains supplementary material, which is available to authorized users.

Recent advances in production, purification and applications of phycobiliproteins

An obligatory sunlight requirement for photosynthesis has exposed cyanobacteria to different quantity and quality of light. Cyanobacteria can exhibit efficient photosynthesis over broad region (450 to 650 nm) of solar spectrum with the help of brilliantly coloured pigment proteins called phycobiliproteins (PBPs). Besides light-harvesting, PBPs are found to involve in several life sustaining phenomena including photoprotection in cyanobacteria. The unique spectral features (like strong absorbance and fluorescence), proteineous nature and, some imperative properties like hepato-protective, anti-oxidants, anti-inflammatory and anti-aging activity of PBPs enable their use in food, cosmetics, pharmaceutical and biomedical industries. PBPs have been also noted to show beneficial effect in therapeutics of some disease like Alzheimer and cancer. Such large range of applications increases the demand of PBPs in commodity market. Therefore, the large-scale and coast effective production of PBPs is the real need of time. To fulfil this need, many researchers have been working to find the potential producer of PBPs for the production and purification of PBPs. Results of these efforts have caused the inventions of some novel techniques like mixotrophic and heterotrophic strategies for production and aqueous two phase separation for purification purpose. Overall, the present review summarises the recent findings and identifies gaps in the field of production, purification and applications of this biological and economically important proteins.

Crystal structure analysis of phycocyanin from chromatically adapted Phormidium rubidum A09DM

Structural and sequence analyses of Phormidium phycocyanin revealed three co-evolving residues that determine the conformation of a phycocyanobilin chromophore believed to play role in alternate pathways for intra and inter-rod energy transfer.

Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India

The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY.

Bloom Dynamics of Cyanobacteria and Their Toxins: Environmental Health Impacts and Mitigation Strategies

Cyanobacteria are ecologically one of the most prolific groups of phototrophic prokaryotes in both marine and freshwater habitats. Both the beneficial and detrimental aspects of cyanobacteria are of considerable significance. They are important primary producers as well as an immense source of several secondary products, including an array of toxic compounds known as cyanotoxins. Abundant growth of cyanobacteria in freshwater, estuarine, and coastal ecosystems due to increased anthropogenic eutrophication and global climate change has created serious concern toward harmful bloom formation and surface water contamination all over the world. Cyanobacterial blooms and the accumulation of several cyanotoxins in water bodies pose severe ecological consequences with high risk to aquatic organisms and global public health. The proper management for mitigating the worldwide incidence of toxic cyanobacterial blooms is crucial for maintenance and sustainable development of functional ecosystems. Here, we emphasize the emerging information on the cyanobacterial bloom dynamics, toxicology of major groups of cyanotoxins, as well as a perspective and integrative approach to their management.