Deciphering the black box of microbial community of common effluent treatment plant through integrated metagenomics: Tackling industrial effluent.

Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.

Spatial and halophyte-associated microbial communities in intertidal coastal region of India.

Microbial communities in intertidal coastal soils respond to a variety of environmental factors related to resources availability, habitat characteristics, and vegetation. These intertidal soils of India are dominated with Salicornia brachiata, Aeluropus lagopoides, and Suaeda maritima halophytes, which play a significant role in carbon sequestration, nutrient cycling, and improving microenvironment. However, the relative contribution of edaphic factors, halophytes, rhizosphere, and bulk sediments on microbial community composition is poorly understood in the intertidal sediments. Here, we sampled rhizosphere and bulk sediments of three dominant halophytes (Salicornia, Aeluropus, and Suaeda) from five geographical locations of intertidal region of Gujarat, India. Sediment microbial community structure was characterized using phospholipid fatty acid (PLFA) profiling. Microbial biomass was significantly influenced by the pH, electrical conductivity, organic carbon, nitrogen, and sodium and potassium concentrations. Multivariate analysis of PLFA profiles had significantly separated the sediment microbial community composition of regional sampling sites, halophytes, rhizosphere, and bulk sediments. Sediments from Suaeda plants were characterized by higher abundance of PLFA biomarkers of Gram-negative, total bacteria, and actinomycetes than other halophytes. Significantly highest abundance of Gram-positive and fungal PLFAs was observed in sediments of Aeluropus and Salicornia, respectively than in those of Suaeda. The rhizospheric sediment had significantly higher abundance of Gram-negative and fungal PLFAs biomarkers compared to bulk sediment. The results of the present study contribute to our understanding of the relative importance of different edaphic and spatial factors and halophyte vegetation on sediment microbial community of intertidal sediments of coastal ecosystem.

Rumen protozoa are a hub for diverse hydrogenotrophic functions.

Ciliate protozoa are an integral part of the rumen microbial community involved in a variety of metabolic processes. These processes are thought to be in part the outcome of interactions with their associated prokaryotic community. For example, methane production is enhanced through interspecies hydrogen transfer between protozoa and archaea. We hypothesize that ciliate protozoa are host to a stable prokaryotic community dictated by specific functions they carry. Here, we modify the microbial community by varying the forage-to-concentrate ratios and show that, despite major changes in the prokaryotic community, several taxa remain stably associated with ciliate protozoa. By quantifying genes belonging to various known reduction pathways in the rumen, we find that the bacterial community associated with protozoa is enriched in genes belonging to hydrogen utilization pathways and that these genes correspond to the same taxonomic affiliations seen enriched in protozoa. Our results show that ciliate protozoa in the rumen may serve as a hub for various hydrogenotrophic functions and a better understanding of the processes driven by different protozoa may unveil the potential role of ciliates in shaping rumen metabolism.

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils.

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses. IMPORTANCE: The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.

A systematic review on mitigation of common indoor air pollutants using plant-based methods: a phytoremediation approach.

Environmental pollution, especially indoor air pollution, has become a global issue and affects nearly all domains of life. Being both natural and anthropogenic substances, indoor air pollutants lead to the deterioration of the ecosystem and have a negative impact on human health. Cost-effective plant-based approaches can help to improve indoor air quality (IAQ), regulate temperature, and protect humans from potential health risks. Thus, in this review, we have highlighted the common indoor air pollutants and their mitigation through plant-based approaches. Potted plants, green walls, and their combination with bio-filtration are such emerging approaches that can efficiently purify the indoor air. Moreover, we have discussed the pathways or mechanisms of phytoremediation, which involve the aerial parts of the plants (phyllosphere), growth media, and roots along with their associated microorganisms (rhizosphere). In conclusion, plants and their associated microbial communities can be key solutions for reducing indoor air pollution. However, there is a dire need to explore advanced omics technologies to get in-depth knowledge of the molecular mechanisms associated with plant-based reduction of indoor air pollutants.

Lemon grass essential oil improves Gladiolus grandiflorus postharvest life by modulating water relations, microbial growth, biochemical activity, and gene expression.

Gladiolus (Gladiolus grandiflorus Andrews) is a high-valued bulbous cut flower. However, the shorter postharvest life of the gladiolus, limits its marketing and commercial value. In the present investigation, the effect of lemon grass (LG) essential oil as an antimicrobial agent was studied towards increasing the vase life of gladiolus. The results revealed that as compared to control (distilled water), treatment with a lower concentration of 5 µL L-1 LG essential oil prolonged the vase life of gladiolus up to 11 days (d). Scanning Electron Microscope (SEM) observation indicated that the sample treated with 5 µL L-1 LG essential oil showed intact vasculature, suggesting reduced microbial blockage at the stem end which was further corroborated by microbial count. Biochemical analysis suggested an increased level of total soluble sugars, carotenoid content, lower MDA accumulation, and higher activity of antioxidant enzymes in LG treated flowers. Moreover, transcripts levels of genes associated with senescence viz., GgCyP1 and GgERS1a were downregulated, while expression of GDAD1 and antioxidant genes such as GgP5C5, GgPOD 1, GgMnSOD, and GgCAT1 were upregulated in LG treated cut spikes as compared to control. Among various treatments we have concluded that, the vase life of the gladiolus cut spike was improved along with the relative fresh flower weight and diameter of flower at the lower dose of 5 µL L-1 LG oil in the vase solution. Thus, LG oil as an eco-friendly agent has the potential to extend the postharvest life of cut flowers.

Cloning and functional characterization of arsenite oxidase (aoxB) gene associated with arsenic transformation in Pseudomonas sp. strain AK9.

Arsenic transforming bacterial strains belong to genus Pseudomonas sp.AK9 (KY569424), were isolated from the middle Gangetic plains of Bihar, India. The Pseudomonas sp. AK9 strains were able to transform toxic arsenite to a less toxic arsenate. In the present work, the presence of different arsenic resistance genes (aoxB, arsB, acr3 and aoxAB) were observed in isolated strain. Furthermore, the aoxB gene was amplified from genomic DNA of AK9, cloned in E.coli/DH5αcells, and sequenced. The BLASTn results and phylogenetic study of the aoxB gene showed 95.32 % and 90.07 % identity with the large subunit of aoxB gene of previous reported Thiomonas arsenivorans strain DSM16361 and Thiomonas arsenivorans strain b6, respectively. Further overhang primers were designed for amplifications of full length aoxB gene (∼1200 bp), and cloned in to the expression vector and host E.coli/BL21 cells. The GST-aoxB gene was expressed in BL21 cells, and a profound expression product of âˆ¼ 72 kDa was observed in SDS PAGE. The detection of a large subunit (aoxB) of arsenate oxidase protein in western blotting assay affirmed the expression of aoxB gene in recombinant E.coli/BL21 clone. Further, the recombinant E.coli/BL21cells showed increased growth than the normal E.coli/BL21 cells against As (III). Thus, this study showed the presence of aoxB gene in Pseudomonas sp. AK9 genome which regulates the resistant ability to arsenic toxicity.

An appraisal of early stage biofilm-forming bacterial community assemblage and diversity in the Arabian Sea, India.

The community composition and distribution of early-stage (24 h) biofilm-forming bacteria on two different surfaces (glass slide and polystyrene plastic slide) at three different locations (Diu, Alang and Sikka) were studied using a culture-dependent and next-generation sequencing (NGS) approach in the Arabian Sea, Gujarat, India. The most dominant phyla observed using the NGS approach were the Proteobacteria among the sampling sites. Gammaproteobacteria class dominated both the surfaces among the sites and accounted for 46.7% to 89.2% of total abundance. The culture-dependent analysis showed Proteobacteria and Firmicutes as the dominant phyla on the surfaces within the sampling sites. During the initial colonization, hydrocarbon-degrading bacterial strains have also attached to the surfaces. The outcome of this study would be of great importance for targeting the early stage biofilm-forming and hydrocarbon-degrading bacterial isolates may help to degrade plastic in the marine environment.

Synergistic effect of graphene oxide and silver nanoparticles as biostimulant improves the postharvest life of cut flower bird of paradise (Strelitzia reginae L.).

The bird of paradise (Strelitzia reginae L.) is one of the important tropical cut flowers. Generally, flowers like bird of paradise (BOP) grown for the commercial ornamental market must be of high pre and postharvest quality. Thus, to improve the postharvest longevity and increase marketability, the relative efficacy of two different biologically synthesized nanoparticles (NPs) was evaluated. The novel proprietary stimulants were graphene oxide (GO) and silver nanoparticles (SNPs). The NP treatments were applied as a vase (lower concentrations) solutions. Among all the applied treatments, the synergistic effect of GO + SNPs at 1 µL L-1 vase solution significantly (p =0.05) prolongs the post-harvest life of cut flowers of BOP. Increased vase life over the deionized water (DI) control was associated with better maintenance of relative water uptake, relative fresh weight, suppressed microbial density at stem-end and delay of stem blockage, reduced electrolyte leakage, malondialdehyde (MDA), SOD, and POD activity. In contrast to control, administration of NPs gave better results for all analyzed parameters. Application of biologically synthesized NPs in combination (GO + SNPs at 1 µL L-1) extended the vase life of cut flowers by 6 days compared with control flowers, and overall, showed better results than the control. The findings of the studies revealed that the standardized NPs could have more potential in prolonging the postharvest life of cut flowers in BOP. Thus, this technique can be used as a novel postharvest technology for commercial application in cut flowers.

Landfill microbiome harbour plastic degrading genes: A metagenomic study of solid waste dumping site of Gujarat, India.

Globally, environmental pollution by plastic waste has become a severe ecological and social problem worldwide. The present study aimed to analyse the bacterial community structure and functional potential of the landfill site using high throughput shotgun metagenomic approach to understand plastic degrading capabilities present in the municipal solid waste (MSW) dumping site. In this study, soil, leachate and compost samples were collected from various locations (height and depth) of the Pirana landfill site in Ahmedabad city Gujarat, India. In total 30 phyla, 58 class, 125 order, 278 families, 793 genera, and 2468 species were predicted. The most dominant phyla detected were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria in the soil and compost samples. Whereas, in leachate samples, the predominant phyla belonged to Firmicutes (54.24%) followed by Actinobacteria (43.67%) and Proteobacteria (1.02%). The functional profiling revealed the presence of enzymatic groups and pathways involved in biodegradation of xenobiotics. The results also demonstrated the presence of potential genes that is associated with the biodegradation of different types of plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS). Present study extablishes the relationship between microbial community structure and rich sources of gene pool, which are actively involved in biodegradation of plastic waste in landfill sites.

Bacterial community structure and functional diversity in subsurface seawater from the western coastal ecosystem of the Arabian Sea, India.

The present study revealed the spatial variability of bacteria in relation to physicochemical variations at four different locations (Diu - DIU, Veraval - VER, Porbandar - POR and Okha - OKH) along the Gujarat coast (Arabian Sea, India). The natural habitat was analyzed for temperature, salinity, pH, total dissolved solids, total organic content, total inorganic content, biological oxygen demand, conductivity and total dissolved oxygen. The lowest salinity and conductivity were observed at the VER site, whereas the highest salinity and conductivity were measured with OKH samples. In contrast, the pH was slightly alkaline at all of the sites. The VER site contained the maximum total dissolved solids (TDS), total carbon (TC), total organic carbon (TOC), and total inorganic carbon (TIC), while OKH showed the maximum dissolve oxygen (DO), biological oxygen demand (BOD), pH, temperature, conductivity, and salinity. The physicochemical characteristics showed that the Gujarat coast is alkaline and has a nutrient heterogeneous nature. Average well color development (AWCD) values, calculated using Biolog EcoPlates, showed that the microbial community from VER contained the highest metabolic activities and could metabolize all 31 substrates, followed by DIU > OKH > POR samples. In contrast, the abundance of the bacterial community, determined by qRT-PCR, was maximum in VER samples, followed by OKH > POR > DIU samples. The Shannon and Simpson indices showed that DIU, POR and OKH seawater clone libraries were more diverse. Furthermore, Chao estimator revealed the high diversity of POR and DIU clone libraries. Interestingly, DIU and OKH did not share any common operational taxonomic units (OTUs), and overall, the maximum bacterial diversity was observed with the POR seawater sample. Moreover, these observations were supported by statistical analysis, such as canonical correspondence analysis (CCA) and principal component analysis (PCA). The molecular phylogeny revealed the dominance of Proteobacteria followed by Firmicutes. Within the Proteobacteria phylum, most of the sequences were affiliated with the Gammaproteobacteria class. In total, about 726 OTUs were observed from all four sites which covers 59.79% DIU, 87.5% VER, 50% POR and 98.83% OKH of samples. This study is the first report to describe physicochemical attributes and the bacterial diversity of the coastal area of Gujarat. The study will provide useful insights about bacterial diversity, distribution, and abundance, as well as their relationships with the habitat.

Antibacterial and Antioxidant Activities of Novel Actinobacteria Strain Isolated from Gulf of Khambhat, Gujarat.

Bacterial secondary metabolites possess a wide range of biologically active compounds including antibacterial and antioxidants. In this study, a Gram-positive novel marine Actinobacteria was isolated from sea sediment which showed 84% 16S rRNA gene sequence (KT588655) similarity with Streptomyces variabilis (EU841661) and designated as Streptomyces variabilis RD-5. The genus Streptomyces is considered as a promising source of bioactive secondary metabolites. The isolated novel bacterial strain was characterized by antibacterial characteristics and antioxidant activities. The BIOLOG based analysis suggested that S. variabilis RD-5 utilized a wide range of substrates compared to the reference strain. The result is further supported by statistical analysis such as AWCD (average well color development), heat-map and PCA (principal component analysis). The whole cell fatty acid profiling showed the dominance of iso/anteiso branched C15-C17 long chain fatty acids. The identified strain S. variabilis RD-5 exhibited a broad spectrum of antibacterial activities for the Gram-negative bacteria (Escherichia coli NCIM 2065, Shigella boydii NCIM, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas sp. NCIM 2200 and Salmonella enteritidis NCIM), and Gram-positive bacteria (Bacillus subtilis NCIM 2920 and Staphylococcus aureus MTCC 96). Extract of S. variabilis strain RD-5 showed 82.86 and 89% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and metal chelating activity, respectively, at 5.0 mg/mL. While H2O2 scavenging activity was 74.5% at 0.05 mg/mL concentration. Furthermore, polyketide synthases (PKSs types I and II), an enzyme complex that produces polyketides, the encoding gene(s) detected in the strain RD-5 which may probably involve for the synthesis of antibacterial compound(s). In conclusion, a novel bacterial strain of Actinobacteria, isolated from the unexplored sea sediment of Alang, Gulf of Khambhat (Gujarat), India showed promising antibacterial activities. However, fractionation and further characterization of active compounds from S. variabilis RD-5 are needed for their optimum utilization toward antibacterial purposes.

Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities.

Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO2 concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.

Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach.

Diazotrophs are key players of the globally important biogeochemical nitrogen cycle, having a significant role in maintaining ecosystem sustainability. Saline soils are pristine and unexplored habitats representing intriguing ecosystems expected to harbour potential diazotrophs capable of adapting in extreme conditions, and these implicated organisms are largely obscure. Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach. Four nifH gene clone libraries were constructed from different soil niches, that is saline soils (low and high salinity; EC 3.8 and 7.1 ds m(-1) ), and agricultural and rhizosphere soil. Additionally, the abundance of diazotrophic community members was assessed using quantitative PCR. Results showed environment-dependent metabolic versatility and the presence of nitrogen-fixing bacteria affiliated with a range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Cyanobacteria and Firmicutes. The analyses unveiled the dominance of Alphaproteobacteria and Gammaproteobacteria (Pseudomonas, Halorhodospira, Ectothiorhodospira, Bradyrhizobium, Agrobacterium, Amorphomonas) as nitrogen fixers in coastal-saline soil ecosystems, and Alphaproteobacteria and Betaproteobacteria (Bradyrhizobium, Azohydromonas, Azospirillum, Ideonella) in agricultural/rhizosphere ecosystems. The results revealed a repertoire of novel nitrogen-fixing bacterial guilds particularly in saline soil ecosystems.