bioRxiv (Cold Spring Harbor Laboratory), Jan 12, 2023
With the widespread adoption of barcoding and next-generation sequencing, metabarcoding 2 is emer... more With the widespread adoption of barcoding and next-generation sequencing, metabarcoding 2 is emerging as a potential tool for detecting labelled and unlabelled plant species in herbal 2 products. In this study, newly designed rbcL and ITS2 metabarcode primers were validated 2 for metabarcoding using in-house mock controls of medicinal plant gDNA pools and biomass 3 pools. The applicability of the multi-barcode sequencing approach was evaluated on 17 single 3 drugs and 15 polyherbal formulations procured from the Indian market. The rbcL 3 metabarcode demonstrated detection efficiencies of 86.7% and 71.7% in gDNA plant pools 3 and biomass mock controls, respectively, while the ITS2 metabarcode demonstrated 82.2% 3 and 69.4%. In the gDNA plant pool and biomass pool mock controls, the cumulative 3 detection efficiency increased by 100% and 90%, respectively. A total of 79% cumulative 3 detection efficiency of both metabarcodes was observed in single drugs, while 76.3% was 3 observed in polyherbal formulations. An average fidelity of 83.6% was observed for targeted 3 plant species present within mock controls as well as in herbal formulations. Our results 3 demonstrated the applicability of multilocus strategies in metabarcoding as a potential tool 4 for detecting labelled and unlabelled plant species in herbal formulations.
Microbial heavy metal tolerance in subsurface samples is indicative of long-term ecotoxicological... more Microbial heavy metal tolerance in subsurface samples is indicative of long-term ecotoxicological impact of metals and could also reflect metal contamination of groundwater. However, the heavy metal tolerance characteristics of microbes isolated from subsurface river sediment profiles are still obscure. In the present study, determination of heavy metal tolerance of bacterial strains isolated from two Late Quaternary sediment profiles (~ 28 m and ~25 m deep) located at the Mahi river basin, Western India, was carried out. Identification of bacterial isolates by the 16S rRNA gene sequencing revealed that bacterial isolates affiliated with phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in both sediment profiles. Heavy metal tolerance of bacterial strains as determined by plate diffusion assay revealed order of metal tolerance as follows: Hg(II)<Cd(II)< Ni(II)<Cu(II)=Cr(VI). Chromate removal study in liquid medium suggested that bacterial strains procured from subsurface possessed the ability to remove Cr(VI) with varied magnitude. A packed bed column experiment indicated that bacterial strains obtained from the subsurface have the potential for Cr(VI) removal from different particle size consistencies of the sediments.
BackgroundThe herbal products market is expanding and creating a bottleneck for raw materials. He... more BackgroundThe herbal products market is expanding and creating a bottleneck for raw materials. Hence, economically motivated adulteration has a high prevalence. DNA barcoding and species-specific PCR assays are now revolutionising the molecular identification of herbal products and are included in a number of pharmacopoeias for the identification of raw materials. High-throughput sequencing with barcoding advances toward metabarcoding, which enables the identification of unintentionally or intentionally unlabelled plant material present in herbal products. Brahmi is one of the most commercially significant and nootropic botanicals, with great controversy over the terms “Brahmi” being used to describe both Bacopa monneri (BM) and Centella asiatica (CA) species.PurposeThis study evaluates DNA-based methods for Brahmi herbal products with the traditional HPLC-based analytical approach in order to assess their effectiveness.MethodsWe employed a species-specific PCR assay, DNA metabarcod...
The linkage between sediment physicochemical and microbial parameters within river terrace sedime... more The linkage between sediment physicochemical and microbial parameters within river terrace sedimentary ecosystems of semiarid regions is still in infancy. Here, we investigated microbial enzyme activities involved in C, N, P, and S cycling, and quantitative PCR (qPCR) based gene abundance of two laterally deposited sediment cores (28 and 25 m deep) comprising the Late Quaternary sediments of the Mahi River (Gujarat, India). Gene abundance indicates the presence of a sustainable bacterial population throughout both cores. The stratified subsurface sediments had notable microbial enzyme activities indicating an important role of both cores in biogeochemical cycling. Correlation between microbial and geological parameters revealed that various trace elements, rare earth elements, K2O, P2O5, EC, TDS, and salinity link significantly with microbial parameters. However, the direction and magnitude of the correlation differ in both cores under study. These results emphasize that sediment physicochemical properties influence microbial parameters differently in the laterally deposited subsurface sediments. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00998-4.
Abstract We carried out textural, petrological, mineralogical and multi-element geochemical inves... more Abstract We carried out textural, petrological, mineralogical and multi-element geochemical investigations of a ∼25 m sediment core from the lower reaches of the Mahi River basin to understand the influence of climate and tectonics in the Gujarat Alluvial Plain (GAP) over the last >115 thousand years (ka) (Marine Isotopic Stage; MIS-5e). Ternary diagrams of texture analysis, A–CN–K, and A–CNK–FM including mafic index of alteration (MIA) and elemental ratios, suggest that most of the sediments are sandy-silt to silty-sand in nature and show incipient to moderate degree of chemical weathering. Additionally, the higher concentrations of lithic fragments (17%), feldspar (9%), and the presence of pyroxene and amphibole are also suggestive of increased physical weathering rather than chemical weathering. An increase in silt, clay and organic carbon contents register an increase in immobile elements (Al2O3, TiO2, FeOt, K2O, REEs, and Al2O3/SiO2), suggesting grain size control in the sediment geochemistry. The increase in sand and secondarily produced carbonates reduces the absolute concentration of all other elements due to the quartz and calcite dilution effect respectively. Four major tectonoclimatic zones, namely 1 to 4 (oldest to youngest), have been identified based on the observed changes. The extrapolated Bayesian-base age model suggests that the bottom zone 1 (∼25-17.6 m depth) was deposited between >115 to 60 ka (MIS-5a-e) during the enhanced phase of the Indian summer monsoon (ISM), as indicated by higher Rb/Sr ratio and dominance of kaolinite-illite over smectite. However, the deposition of gravel/coarser sediment horizons is also linked to base level change due to localized tectonic activities. The terminal part of zone 1 shows relatively drier conditions that continued through zone 2 (∼60-54 ka; MIS-4), represented by lower values of immobile elements and Rb/Sr and kaolinite/smectite ratios. However, during Zone 3 (∼54-39 ka; MIS-3), the sediment became coarser, implying enhanced rainfall or tectonic activity and a higher sedimentation rate. The top-most zone 4 (∼39.0-6.7 ka MIS-3, 1) marks a fluctuating trend as indicated by the presence of gravely sand in the lower part of this zone (at ∼5 m and ∼3 m depth) due to intense rainfall or tectonic activity at ∼37-38 ka. However, the upper part of this zone is dominated by sand and silt as evidenced by the decreasing chemical index of alteration (CIA) values and lower Rb/Sr ratio (
We report the 3.93-Mbp first draft genome sequence of a species of the genus Thalassobacillus, Th... more We report the 3.93-Mbp first draft genome sequence of a species of the genus Thalassobacillus, Thalassobacillus devorans strain MSP14, a moderate but obligate halophile, isolated from a salt crystallizer of the Little Rann of Kutch, India. Exploring the genome of this organism will facilitate understanding the mechanism(s) of its obligate halophilism.
The 4.37-Mbp draft genome of a moderately halophilic Bacillus megaterium strain, MSP20.1, isolate... more The 4.37-Mbp draft genome of a moderately halophilic Bacillus megaterium strain, MSP20.1, isolated from a saltern of the Little Rann of Kutch, India, is reported here. To understand the mechanism(s) of moderate halophilism and to isolate the gene(s) involved in osmotolerance and adaptation, the genome of MSP20.1 was sequenced.
We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain NSP9.3, ... more We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain NSP9.3, a moderate halophile isolated from a seasonal salt marsh of the Great Rann of Kutch, India. Exploring the genome of this organism will facilitate the understanding of the mechanism(s) of osmotolerance and survival in differential osmolarity.
Abstract Different stratigraphic sequences of Late Quaternary sediments present in a vertically e... more Abstract Different stratigraphic sequences of Late Quaternary sediments present in a vertically exposed 29 m deep river cliff were used as a model system to understand geochemical relationships with potential microbial activity in semiarid alluvial sediments. Microbial activities involved in carbon (C) and phosphorus (P) cycling were measured by dehydrogenase, alkaline phosphatase, and microbial respiration activities. We did not observe patterns in microbial activities that could be explained by sample depth. An extensive analysis of the physical and geochemical characteristics of exposed sediments was conducted along with multivariate statistical analysis to determine the influence of geochemical variables on potential microbial activity. Principal component analysis (PCA) and canonical correlation analysis (CCA) together with Pearson correlation analysis indicated that sediment organic carbon, moisture content, palynofacies components (acid-resistant particulate organic matter) such as fungal spores, brown carbon, structured carbon, and concentrations of Al2O3, FeO, MgO, MnO, and Zr were associated significantly with microbial activities in river cliff sediment deposits. These findings highlight drivers of microbial activity with consequences for C and P biogeochemical cycles in semiarid alluvial soils/sediments of river floodplains.
The Mahi estuary is located at the western fringe of the Gujarat alluvial plain in Mainland Gujar... more The Mahi estuary is located at the western fringe of the Gujarat alluvial plain in Mainland Gujarat and presents an interesting geomorphic set up. Subsurface microbial diversity plays a vital role in maintenance of good soil health, because microorganisms are involved in many essential functions such as soil formation, elemental cycles, contaminant degradation, and the maintenance of groundwater quality. In the Indian subcontinent, subsurface microbial processes and the diversity are not well studied. Understanding of subsurface microbial diversity of Mahi river basin will help to understand microbial ecology of the Indian subcontinent. Here we examined depth related bacterial diversity pattern within different strata of a vertical sediment section of estuarine region of Mahi river basin. Sediment core samples were collected by core drilling method from Chokari (~17 m deep) (CRD). Upper ~8 m part of sediment core comprises of an estuarine sequence (Holocene age) which is underlain by fluvial sequence (pleistocene age) that continues further down the core. We selected two samples from depth 61.25 cm and 187.5 cm (CRD 2 and CRD 6, respectively) which lie within estuarine sequence and one sample (CRD 27) from 1000 cm depth which lies within fluvial sequence for microbial diversity analysis by using Illumina based sequencing of V3-V4 region of 16S rRNA gene. Total 642462 reads (~ length 250 bp) were obtained which comprised of 32763 OTUs (Operational Taxonomic Units). Abundant OTUs were affiliated with Actinobacteria, Bacteroidetes, Proteobacteria, Plancomycetes, Firmicutes, Chloroflexi, Cyanobacteria, Acidobacteria, and candidate division TM7 phyla. Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria and candidate division TM7 decreased significantly as the depth decreases. Within paleosols of late pleistocene age (CRD 27) Bacteroidetes were comprise of 75.32% OTUs while within Holocene samples it comprises of only 19.78% and 1.63% OTUs (CRD 2 and CRD 6, respectively). Taxonomic patterns of OTUs were similar within Holocene samples while pleistocene sediment sample shows different pattern based on pairwise beta-diversity patterns. Conclusively microbial diversity within subsurface sediment core of estuarine region of Mahi river basin are highly diverse indicating availability of different energy source and electron acceptors in microhabitats within the estuarine region of Mahi river basin.
bioRxiv (Cold Spring Harbor Laboratory), Jan 12, 2023
With the widespread adoption of barcoding and next-generation sequencing, metabarcoding 2 is emer... more With the widespread adoption of barcoding and next-generation sequencing, metabarcoding 2 is emerging as a potential tool for detecting labelled and unlabelled plant species in herbal 2 products. In this study, newly designed rbcL and ITS2 metabarcode primers were validated 2 for metabarcoding using in-house mock controls of medicinal plant gDNA pools and biomass 3 pools. The applicability of the multi-barcode sequencing approach was evaluated on 17 single 3 drugs and 15 polyherbal formulations procured from the Indian market. The rbcL 3 metabarcode demonstrated detection efficiencies of 86.7% and 71.7% in gDNA plant pools 3 and biomass mock controls, respectively, while the ITS2 metabarcode demonstrated 82.2% 3 and 69.4%. In the gDNA plant pool and biomass pool mock controls, the cumulative 3 detection efficiency increased by 100% and 90%, respectively. A total of 79% cumulative 3 detection efficiency of both metabarcodes was observed in single drugs, while 76.3% was 3 observed in polyherbal formulations. An average fidelity of 83.6% was observed for targeted 3 plant species present within mock controls as well as in herbal formulations. Our results 3 demonstrated the applicability of multilocus strategies in metabarcoding as a potential tool 4 for detecting labelled and unlabelled plant species in herbal formulations.
Microbial heavy metal tolerance in subsurface samples is indicative of long-term ecotoxicological... more Microbial heavy metal tolerance in subsurface samples is indicative of long-term ecotoxicological impact of metals and could also reflect metal contamination of groundwater. However, the heavy metal tolerance characteristics of microbes isolated from subsurface river sediment profiles are still obscure. In the present study, determination of heavy metal tolerance of bacterial strains isolated from two Late Quaternary sediment profiles (~ 28 m and ~25 m deep) located at the Mahi river basin, Western India, was carried out. Identification of bacterial isolates by the 16S rRNA gene sequencing revealed that bacterial isolates affiliated with phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in both sediment profiles. Heavy metal tolerance of bacterial strains as determined by plate diffusion assay revealed order of metal tolerance as follows: Hg(II)<Cd(II)< Ni(II)<Cu(II)=Cr(VI). Chromate removal study in liquid medium suggested that bacterial strains procured from subsurface possessed the ability to remove Cr(VI) with varied magnitude. A packed bed column experiment indicated that bacterial strains obtained from the subsurface have the potential for Cr(VI) removal from different particle size consistencies of the sediments.
BackgroundThe herbal products market is expanding and creating a bottleneck for raw materials. He... more BackgroundThe herbal products market is expanding and creating a bottleneck for raw materials. Hence, economically motivated adulteration has a high prevalence. DNA barcoding and species-specific PCR assays are now revolutionising the molecular identification of herbal products and are included in a number of pharmacopoeias for the identification of raw materials. High-throughput sequencing with barcoding advances toward metabarcoding, which enables the identification of unintentionally or intentionally unlabelled plant material present in herbal products. Brahmi is one of the most commercially significant and nootropic botanicals, with great controversy over the terms “Brahmi” being used to describe both Bacopa monneri (BM) and Centella asiatica (CA) species.PurposeThis study evaluates DNA-based methods for Brahmi herbal products with the traditional HPLC-based analytical approach in order to assess their effectiveness.MethodsWe employed a species-specific PCR assay, DNA metabarcod...
The linkage between sediment physicochemical and microbial parameters within river terrace sedime... more The linkage between sediment physicochemical and microbial parameters within river terrace sedimentary ecosystems of semiarid regions is still in infancy. Here, we investigated microbial enzyme activities involved in C, N, P, and S cycling, and quantitative PCR (qPCR) based gene abundance of two laterally deposited sediment cores (28 and 25 m deep) comprising the Late Quaternary sediments of the Mahi River (Gujarat, India). Gene abundance indicates the presence of a sustainable bacterial population throughout both cores. The stratified subsurface sediments had notable microbial enzyme activities indicating an important role of both cores in biogeochemical cycling. Correlation between microbial and geological parameters revealed that various trace elements, rare earth elements, K2O, P2O5, EC, TDS, and salinity link significantly with microbial parameters. However, the direction and magnitude of the correlation differ in both cores under study. These results emphasize that sediment physicochemical properties influence microbial parameters differently in the laterally deposited subsurface sediments. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00998-4.
Abstract We carried out textural, petrological, mineralogical and multi-element geochemical inves... more Abstract We carried out textural, petrological, mineralogical and multi-element geochemical investigations of a ∼25 m sediment core from the lower reaches of the Mahi River basin to understand the influence of climate and tectonics in the Gujarat Alluvial Plain (GAP) over the last >115 thousand years (ka) (Marine Isotopic Stage; MIS-5e). Ternary diagrams of texture analysis, A–CN–K, and A–CNK–FM including mafic index of alteration (MIA) and elemental ratios, suggest that most of the sediments are sandy-silt to silty-sand in nature and show incipient to moderate degree of chemical weathering. Additionally, the higher concentrations of lithic fragments (17%), feldspar (9%), and the presence of pyroxene and amphibole are also suggestive of increased physical weathering rather than chemical weathering. An increase in silt, clay and organic carbon contents register an increase in immobile elements (Al2O3, TiO2, FeOt, K2O, REEs, and Al2O3/SiO2), suggesting grain size control in the sediment geochemistry. The increase in sand and secondarily produced carbonates reduces the absolute concentration of all other elements due to the quartz and calcite dilution effect respectively. Four major tectonoclimatic zones, namely 1 to 4 (oldest to youngest), have been identified based on the observed changes. The extrapolated Bayesian-base age model suggests that the bottom zone 1 (∼25-17.6 m depth) was deposited between >115 to 60 ka (MIS-5a-e) during the enhanced phase of the Indian summer monsoon (ISM), as indicated by higher Rb/Sr ratio and dominance of kaolinite-illite over smectite. However, the deposition of gravel/coarser sediment horizons is also linked to base level change due to localized tectonic activities. The terminal part of zone 1 shows relatively drier conditions that continued through zone 2 (∼60-54 ka; MIS-4), represented by lower values of immobile elements and Rb/Sr and kaolinite/smectite ratios. However, during Zone 3 (∼54-39 ka; MIS-3), the sediment became coarser, implying enhanced rainfall or tectonic activity and a higher sedimentation rate. The top-most zone 4 (∼39.0-6.7 ka MIS-3, 1) marks a fluctuating trend as indicated by the presence of gravely sand in the lower part of this zone (at ∼5 m and ∼3 m depth) due to intense rainfall or tectonic activity at ∼37-38 ka. However, the upper part of this zone is dominated by sand and silt as evidenced by the decreasing chemical index of alteration (CIA) values and lower Rb/Sr ratio (
We report the 3.93-Mbp first draft genome sequence of a species of the genus Thalassobacillus, Th... more We report the 3.93-Mbp first draft genome sequence of a species of the genus Thalassobacillus, Thalassobacillus devorans strain MSP14, a moderate but obligate halophile, isolated from a salt crystallizer of the Little Rann of Kutch, India. Exploring the genome of this organism will facilitate understanding the mechanism(s) of its obligate halophilism.
The 4.37-Mbp draft genome of a moderately halophilic Bacillus megaterium strain, MSP20.1, isolate... more The 4.37-Mbp draft genome of a moderately halophilic Bacillus megaterium strain, MSP20.1, isolated from a saltern of the Little Rann of Kutch, India, is reported here. To understand the mechanism(s) of moderate halophilism and to isolate the gene(s) involved in osmotolerance and adaptation, the genome of MSP20.1 was sequenced.
We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain NSP9.3, ... more We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain NSP9.3, a moderate halophile isolated from a seasonal salt marsh of the Great Rann of Kutch, India. Exploring the genome of this organism will facilitate the understanding of the mechanism(s) of osmotolerance and survival in differential osmolarity.
Abstract Different stratigraphic sequences of Late Quaternary sediments present in a vertically e... more Abstract Different stratigraphic sequences of Late Quaternary sediments present in a vertically exposed 29 m deep river cliff were used as a model system to understand geochemical relationships with potential microbial activity in semiarid alluvial sediments. Microbial activities involved in carbon (C) and phosphorus (P) cycling were measured by dehydrogenase, alkaline phosphatase, and microbial respiration activities. We did not observe patterns in microbial activities that could be explained by sample depth. An extensive analysis of the physical and geochemical characteristics of exposed sediments was conducted along with multivariate statistical analysis to determine the influence of geochemical variables on potential microbial activity. Principal component analysis (PCA) and canonical correlation analysis (CCA) together with Pearson correlation analysis indicated that sediment organic carbon, moisture content, palynofacies components (acid-resistant particulate organic matter) such as fungal spores, brown carbon, structured carbon, and concentrations of Al2O3, FeO, MgO, MnO, and Zr were associated significantly with microbial activities in river cliff sediment deposits. These findings highlight drivers of microbial activity with consequences for C and P biogeochemical cycles in semiarid alluvial soils/sediments of river floodplains.
The Mahi estuary is located at the western fringe of the Gujarat alluvial plain in Mainland Gujar... more The Mahi estuary is located at the western fringe of the Gujarat alluvial plain in Mainland Gujarat and presents an interesting geomorphic set up. Subsurface microbial diversity plays a vital role in maintenance of good soil health, because microorganisms are involved in many essential functions such as soil formation, elemental cycles, contaminant degradation, and the maintenance of groundwater quality. In the Indian subcontinent, subsurface microbial processes and the diversity are not well studied. Understanding of subsurface microbial diversity of Mahi river basin will help to understand microbial ecology of the Indian subcontinent. Here we examined depth related bacterial diversity pattern within different strata of a vertical sediment section of estuarine region of Mahi river basin. Sediment core samples were collected by core drilling method from Chokari (~17 m deep) (CRD). Upper ~8 m part of sediment core comprises of an estuarine sequence (Holocene age) which is underlain by fluvial sequence (pleistocene age) that continues further down the core. We selected two samples from depth 61.25 cm and 187.5 cm (CRD 2 and CRD 6, respectively) which lie within estuarine sequence and one sample (CRD 27) from 1000 cm depth which lies within fluvial sequence for microbial diversity analysis by using Illumina based sequencing of V3-V4 region of 16S rRNA gene. Total 642462 reads (~ length 250 bp) were obtained which comprised of 32763 OTUs (Operational Taxonomic Units). Abundant OTUs were affiliated with Actinobacteria, Bacteroidetes, Proteobacteria, Plancomycetes, Firmicutes, Chloroflexi, Cyanobacteria, Acidobacteria, and candidate division TM7 phyla. Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria and candidate division TM7 decreased significantly as the depth decreases. Within paleosols of late pleistocene age (CRD 27) Bacteroidetes were comprise of 75.32% OTUs while within Holocene samples it comprises of only 19.78% and 1.63% OTUs (CRD 2 and CRD 6, respectively). Taxonomic patterns of OTUs were similar within Holocene samples while pleistocene sediment sample shows different pattern based on pairwise beta-diversity patterns. Conclusively microbial diversity within subsurface sediment core of estuarine region of Mahi river basin are highly diverse indicating availability of different energy source and electron acceptors in microhabitats within the estuarine region of Mahi river basin.
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Papers by Abhi Shah