Garden Soil Research Articles

Optimization of Screening Media to Improve Antimicrobial Biodiscovery from Soils in Undergraduate/Citizen Science Research-Engaged Initiatives.

Background/Objectives: Research-engaged academic institutions offer the opportunity to couple undergraduate education/citizen science projects with antimicrobial biodiscovery research. Several initiatives reflecting this ethos have been reported internationally (e.g., Small World, Tiny Earth, MicroMundo, Antibiotics Unearthed). These programs target soil habitats due to their high microbial diversity and promote initial screening with non-selective, nutrient media such as tryptic soy agar (TSA). However, evaluation of published outputs to date indicates that isolate recovery on TSA is consistently dominated by the genera Bacillus, Pseudomonas, and Paenibacillus. In this study, we evaluated the potential of soil extract agar to enhance soil isolate diversity and antibiosis induction outcomes in our undergraduate Antibiotics Unearthed research program. Methods: We comparatively screened 229 isolates from woodland and garden soil samples on both tryptic soy agar (TSA) and soil extract agar (SEA) for antimicrobial activity against a panel of clinically relevant microbial pathogens. Results: On one or both media, 15 isolates were found to produce zones of clearing against respective pathogens. 16S rRNA gene sequencing linked the isolates with three genera: Streptomyces (7), Paenibacillus (6), and Pseudomonas (2). Six of the Streptomyces isolates and one Pseudomonas demonstrated antimicrobial activity when screened on SEA, with no activity on TSA. Furthermore, incorporation of the known secondary metabolite inducer N acetyl-glucosamine (20 mM) into SEA media altered the pathogen inhibition profiles of 14 isolates and resulted in broad-spectrum activity of one Streptomyces isolate, not observed on SEA alone. In conclusion, SEA was found to expand the diversity of culturable isolates from soil and specifically enhanced the recovery of members of the genus Streptomyces. SEA was also found to be a superior media for antibiosis induction among Streptomyces isolates when compared to TSA. It was noted that Paenibacillus isolates' antibiosis induction demonstrated a strain-specific response with respect to the growth media used. Conclusions: The authors propose SEA inclusion of in soil screening protocols as a cost-effective, complementary strategy to greatly enhance outcomes in undergraduate/citizen science-engaged antimicrobial biodiscovery initiatives.

Biochar affects organic carbon composition and stability in highly acidic tea plantation soil

Biochar amendments are effective in stabilizing soil aggregates and improving soil organic carbon (SOC) content. However, the effects of biochar on highly acidic soil and their relation with soil SOC stability remain understudied. The study aimed to investigate the impact of biochar on changes of aggregate distribution and SOC stability in a highly acidic tea plantation soils over an eight-year period. Soil samples were collected from plots with varying biochar application amounts (0, 2.5 t ha−1, 5 t ha−1, 10 t ha−1, 20 t ha−1 and 40 t ha−1). The content of SOC, iron bound organic carbon (OC-Fe), particulate organic carbon (POC), mineral-associated organic carbon (MAOC) and the functional group composition of SOC was analyzed. The results indicated that in the biochar application treatments, the value of soil pH, SOC, POC and MAOC contents were increased from 3.92 to 4.28, 6.68%–187.02%, 8.31%–66.78% and 13.07%–236.47% respectively, compared with CK, while the content of macro-aggregate (particle size>0.25 mm) and soil aggregates mean weight diameter (MWD) significantly increased with higher biochar application amounts. But dissolved organic carbon (DOC) and OC-Fe content exhibited downward trend, decreased from 2.43% to 6.97% and 4.18%–19.91%. Furthermore, aromatic-C levels increased, with increased biochar application amounts. The integration of biochar not only bolstered soil aggregate stability but also amplified the presence of aromatic-C, thereby enhancing the resilience of organic carbon in highly acidic tea garden soil (BC40 > BC20 > BC5>BC2.5 > BC10 > CK), with increases ranging from 6% to 47%. The principal component analysis and structural equation modeling identified soil pH, TN, SOC, POC, MAOC, R > 0.25 and MWD as key factors of soil organic carbon stability. These findings provide crucial insights into the mechanism underlying biochar's efficiency in fortifying organic carbon stability, particularly in the context of highly acidic soil.

Chromobacterium indicum sp. nov., a Pigment-Producing Bacterium Isolated from Soil.

A purple colony, designated as TRC1.1.SA was isolated from a tea garden soil sample. It was a Gram-negative, rod-shaped, non-spore-forming and motile bacterium. The strain TRC1.1.SAT grew aerobically at temperatures 15-37℃ and pH levels 5.0-9.0. It showed both oxidase and catalase activity. The 16S rRNA gene sequence blast analysis revealed identity with the members of the genus Chromobacterium. The maximum identity was with the type strains of species Chromobacterium piscinae CCM 3329T (99.8%), C. vaccinii MWU205T (99.7%), and C. violaceum ATCC 12472T (98.7%). However, the average nucleotide identity (ANI) of the genome sequence showed less than 96% similarity with all species of the genus Chromobacterium. Further, digital DNA-DNA hybridization (dDDH) revealed the highest identity of 63.4% with its phylogenetic relative C. piscinae CCM 3329T. The G + C content of the strain was 63.9%. The major polar lipids identified were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphoglyceraldehyde (PG). Fatty acid analysis showed C16:0, C16:1ω7c, C17:0 cyclo, and C18:1ω7c as the major fatty acids. RAST and antiSMASH analyses of the genome revealed the presence of a biosynthetic gene cluster (BGC) involved in the production of violacein pigment, as observed for type species C. violaceum ATCC 12472T. Considering the phenotypic differences and genomic identity, strain TRC1.1.SAT is assigned as a novel species of the genus Chromobacterium, for which the name Chromobacterium indicum is proposed. The type strain of prospective species is designated as TRC1.1.SAT (= MTCC 13391T; JCM 36723T; = KCTC 8324T).

Investigating soil physicochemical factors influencing trace element contamination at the semi-urban-rural home gardening interfaces on the Fiji Islands

Due to its ecological and public health implications, home gardening soil pollution is challenging. However, the physicochemical factors of trace element pollution in semi-urban-rural home gardening soil interfaces in Fiji are unclear. Self-organizing map (SOM), chemometrics, compositional data analysis (CDA), and soil quality indices were used to evaluate spatial patterns, contamination characteristics, sources, and factors affecting trace element contamination in 55 soil samples from semi-urban and rural Fiji. The average contents of diethylenetriaminepentaacetic acid (DTPA)-extractable forms of trace element levels (mg/kg) increased in rural areas as Fe (55.7) > Mn (40.4) > Zn (9.4) > Cu (5.9) and semi-urban areas as Fe (55.2) > Zn (35.9) > Mn (37.1) > Cu (16.1). Rural soils have less ecological risks to home gardening than semi-urban soils. SOM and CDA analysis showed four spatial clusters: clusters 1 and 3 are natural geogenic in rural regions while clusters 2 and 4 are human-induced non-point sources in semi-urban areas. Principal component analysis (PCA) and hierarchical cluster analysis showed that semi-urban Cu-Zn was more affected by manufacturing emissions or fertilization, whereas rural Fe-Mn was more likely to be lithogenic. The research found that pH and organic matter significantly affect Cu and Zn pollution in semi-urban soils (p < 0.05). For rural and semi-urban soils, trace element subsets explained 44 %–87 % of soil contamination changes using the stepwise regression model. These findings aid to establishing a primary database of eco-environmental risks and facilitate comprehensive strategies for assessing soil contamination and potential threats to food safety.

Biological monitoring of soil pollution caused by two different zinc species using earthworms.

Zinc oxide nanoparticles (ZnO-NPs) are commonly used in both commercial and agricultural sectors. As a result, ZnO-NPs are extensively discharged into soil ecosystems, creating a significant environmental issue. Therefore, it is crucial to assess their influence on the soil ecology to ensure its secure and enduring utilization in the future. The exact degree of toxicity associated with ZnO-NPs and their ionic form is still uncertain. To address the challenges, the study used the soil bioindicator earthworm species Eudrilus eugeniae as an experimental model to evaluate the effects of two zinc species (ZnO-NPs and ZnCl2) at 100, 250, 500, and 750mgkg-1 and control (0mgkg-1) in garden soil over 28days. The investigation alsoexamined the impact ofexposure on survival, reproduction, neuro-biomarker, avoidance behavior, and accumulation. The highest avoidance rates were 27.5% for ZnO-NP and 37.5% for ZnCl2 at 750mgkg-1. ZnCl2 treatment reduced juvenile production by 3.73 ± 1.73, while ZnO-NPs showed 4.67 ± 1.15. At 750mgkg-1, soils with ZnCl2 (63.3%) demonstrated lower survival rates than those with ZnO-NPs (53.3%), likely because of higher Zn ion levels. After 28days of exposure, ZnCl2 (536.32 ± 11molmin-1) activated AChE enzymes more than ZnO-NPs (497.7 ± 59molmin-1) at the same dose, compared to control (145.88 ± 28 to 149.41 ± 23molmin-1). Nanoparticles and zinc ions bioaccumulated and reacted negatively with the neurotoxic marker AChE, affecting earthworm reproduction and behavior. However, earthworms exposed to ZnCl2 exhibited less intestinal Zn than those exposed to NPs. The present work contradicts the finding that ZnO-NPs have hazardous effects on soil organisms. The results indicate that earthworm E. eugeniae may significantly affect soil metal uptake from metallic nanoparticles (NPs). This may help design NP soil pollution mitigation strategies.The study offers valuable information for establishing a relationship between the environmental toxicity of ZnO-NPs and soil ecosystems.

Efficient and simultaneous immobilization of fluoride and lead in water and tea garden soil by bayberry tannin foam loaded zirconium

Nowadays, human activities intensified the combined pollution of fluoride and lead in acidic tea garden soil. The key to eliminating this combined pollution is to immobilize pollutants simultaneously, thus preventing their migration from tea garden soil to tea trees. In this paper, the natural product bayberry tannin was employed as raw material to fabricate functional materials (TF-Zr) for simultaneous adsorption of fluorine (F) and lead (Pb) in water and soil by the reactivity of tannin with Pb2+ and the affinity of Zr with F. SEM-Mapping, EDS, FT-IR, XPS were utilized to probe the immobilization mechanisms. The results showed that TF-Zr could simultaneously and efficiently adsorb F– and Pb2+ from water with the adsorption capacity of 5.02 mg/g (Pb) and 4.55 mg/g (F). The adsorption processes were both in accordance with the proposed secondary kinetic adsorption model. Besides, the presence of F– promoted the adsorption of Pb2+ by TF-Zr. The materials were applied into tea garden soil to explore its effect on the variation of F and Pb forms in the soil. It was found that the proportion of water-soluble fluorine, exchangeable fluorine and exchangeable lead in the tea garden soil decreased significantly, while the proportion of residual fluorine and lead increased evidently, illustrating TF-Zr possessed eximious fixation effect on the highly reactive fluorine and lead in the soil and facilitated their conversion to the more stable residue state. Therefore, TF-Zr can be used for the efficient and simultaneous immobilization of fluorine and lead in water and tea garden soil.

Exploring the Effects of Intercropping Ornamental Plants on Soil Fertility and Microbial Community in Tea Gardens: Implications for Sustainable Growth and Ecosystem Functioning

Intercropping of ornamental flowering plants like Lycoris radiata Herb. and Cuphea hookeriana Walp. with tea trees can enhance the visibility and esthetic appeal of tea gardens. However, there has been limited research of the impact of intercropping ornamental flowering plants with tea trees on the soil in tea gardens. During this study, our objective was to analyze the effects of intercropping systems on tea garden soil by examining the physicochemical properties of rhizosphere soil samples from tea gardens intercropped with L. radiata and C. hookeriana. We also performed rhizosphere microbial metagenomic sequencing to assess the microbial community structure. The results revealed significant improvements in soil physicochemical indicators, particularly pH. Although intercropping systems had minor impacts on bacterial diversity and abundance, they had more pronounced effects on the community structure of microorganisms at the phylum and genus levels. Furthermore, an analysis of microbial functions using Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed enrichment of carbon and nitrogen cycling pathways in the tea garden soil. Our findings indicated that intercropping practices have the potential to enhance the visual appeal of tea gardens while improving soil fertility and modulating the microbial community structure. These results contribute to our understanding of intercropping strategies and the implications of intercropping for tea tree growth and ecosystem functioning.

Effect of Streptomyces costaricanus Strain A-m1 as a Bioinoculant on Tea Garden Soil and Tea Quality

Chemical fertilization is usually associated with some unreasonable problems that affect the sustainable production of tea gardens. The micro-organism fertilizer created from plant growth-promoting microbes (PGPM) integrates the beneficial properties of functional micro-organisms and bioinoculants. Application of PGPM can activate soil nutrients, prevent soil-borne diseases, and promote crop growth, thus improving crop quality and yield. In this study, the effects of bioinoculants composed of Streptomyces costaricanus strain A-m1 on the properties, enzyme activity, and micro-organisms of soil in a tea garden and on the chemical composition and production of tea were investigated. The present results showed that the application of A-m1 bioinoculant could increase the activities of urease, protease and catalase, the content of alkali-hydrolyzable nitrogen, and the number of bacteria, fungi, and actinomycetes in tea garden soil. After application, the free amino acid content, 100-bud weight, and bud density of spring tea were also elevated. In the year of fertilization, the treatment composed of 70% bioinoculant + 30% chemical fertilizer showed the best effects on soil physical and chemical properties, enzyme activity, culturable microbial counts, and tea quality. A high ratio of organic to chemical fertilizer coapplication can significantly improve the growing conditions for tea plants, reduce the use of chemical fertilizers, improve the efficiency of nutrient utilization, and enhance both the yield and quality of tea. One year after fertilization, the 50% bioinoculant + 50% chemical fertilizer was more conducive to enhancing the quality of tea, while the 30% bioinoculant + 70% chemical fertilizer was more beneficial for improving the production of tea. A high ratio of chemical to bioinoculant coapplication is more favorable for maintaining high yield and quality in tea production, achieving healthy and sustainable tea garden management. The application of A-m1 bioinoculant will reduce the use of chemical fertilizers, improve the utilization efficiency of soil nutrients, and increase the production and quality of tea, contributing to the sustainable production of tea gardens.

Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture.

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO2 fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.

Assessment of growth, and ion uptake of plant species, Conocarpus erectus and Dodonaea viscosa, on industrial solid waste

Present study assessed the growth of two plant species and ion uptake by them grown on different proportion of industrial solid waste and garden soil. The industrial waste having high concentration of chemicals were used with garden soil at different proportion i.e. 0% (T0), 5% (T1), 10% (T2), 15% (T3) and 20% (T4). Two species namely Conocarpus erectus (alien plant) and Dodonaea viscosa (indigenous) were used as test plants in pot study. Different parameters including growth, physiology, and anatomy of plants and concentration of cations (Na+, K+, Ca2+, and Mg2+) in the plant shoot and root were measured at different time duration (initial, 1st, 2nd, 3rd and 4th month). The key objective of the study was to use these plants to establish their plantations on the barren lands where industrial solid wastes were being disposed of. C. erectus showed better growth than D. viscosa, as well as more uptake of ions. A significant increase in plant growth was observed in fourth month in T1, where plant height reached 24.5% and 46% for C. erectus and D. viscosa, respectively. At harvest, in C. erectus, no significant difference in the fresh (65–78 g) and dry weight (24–30 g) of the shoot was observed across treatments compared to the control. In D. viscosa, at the time of harvest, the fresh and dry weights of the root and shoot showed a strong, significantly decreasing pattern across T1, T2, and T3, leading to the death of the plant at T3 and T4. Further, optimum ratio of waste soil to garden soil was found as 10:90 and 20:80 to establish the plantations of D. viscosa and C. erectus, respectively in areas where such solid waste from industries are disposed. Findings can be used for the restoration of such solid waste for the sustainable management of industrial areas and their associated ecosystems.

Distribution characteristics of selenium and influencing factors in the plant–soil system of an arid oasis

A total of 323 topsoil samples, 63 profile soil samples, and 55 plant root samples were collected from an oasis area on the eastern margin of the Tarim Basin in China and the selenium content and other physical and chemical indicators were analyzed. The results showed that the average selenium content in the surface soil was 0.15 mg/kg, which was lower than the national background value, and only about 4% of the surveyed land area was classified as rich in selenium. The vertical distribution of selenium was characterized by surface accumulation. The organic carbon and clay content were positively correlated and the pH levels negatively correlated with the selenium content. Soil type had little effect on selenium content, though the selenium levels in Anthrosols and Gleysols were relatively high. The selenium content for cultivated land and garden soil was higher than for other land use types. The enrichment of selenium in plant roots was highest for Apocynum venetum L., followed by Pulicaria dysenterica (L.). Bernh., Populus euphratica Olive, Tamarix chinensis Lour., Phragmites australis (Cav.) Trin. ex Steud, and Pyrus bretschneideri Rehder. Correlation analysis revealed that the enrichment of selenium in the soil was mainly controlled by supergenesis in conjunction with long-distance migration and deposition. Overall, this study provides useful information for the rational development and utilization of regional land resources.

Inopinatus corneliae sp. nov. gen. nov. isolated from human skin: A newly discovered keratinophilic hyphomycete, order Onygenales.

Fungi clinically relevant to human skin comprise prevalent commensals and well-known pathogens. Only rarely human skin harbours fungi that evade identification. To characterise an enigmatic specimen isolated from a skin lesion. A comprehensive clinical and mycological workup including conventional methods for phenotypic characterisation and sequencing based on internal transcribed spacer (ITS) and large subunit (LSU) regions to infer a phylogenetic tree. Cultures on common solid media were macroscopically inconspicuous initially until mycelial tufts developed on the surface, notably on potato dextrose agar. Polymorphous chlamydospores were detected but no aleurospores and ascomata. At 26°C, the isolate grew on standard agars, plant materials and garden soil and utilised peptone, keratins, lipids, inulin, erythrocytes and cellulose. It also grew at 5°C and at 37°C. Nucleotide sequences of its ITS region showed 93% similarity to sequences of different Malbranchea species. The closest matches among LSU rRNA sequences were obtained with the genera Amauroascus, Arthroderma, Auxarthronopsis and Malbranchea (93%-95%). A combined phylogenetic analysis placed the fungus in a sister clade to Neogymnomycetaceae, classified as incertae sedis in Onygenales, on a large distance to either Diploospora rosea or 'Amauroascus' aureus. The genus Inopinatus gen. nov. (MB854685) with the species Inopinatus corneliae sp. nov. (MB854687) is introduced to accommodate our isolate (holotype: DSM 116806; isotypes: CBS 151104, IHEM 29063). Probably Inopinatus corneliae is a geophilic species that, although potentially harmful, was no relevant pathogen in our case. Its ecology, epidemiology and pathogenicity need to be further clarified.

Effect of Zinc on Germination, Growth Yield of (Solanum melongena L.)

Eggplant (Solanum melongena L.) is an economically significant crop, valued for its culinary versatility and nutritional content. Understanding the factors that influence its growth is crucial for optimizing agricultural practices and improving yield. Zinc, an essential micronutrient, plays a vital role in various physiological processes within plants, including enzyme activation, photosynthesis, and hormone regulation. This study investigated the effect of zinc supplementation on the growth parameters of eggplant. The experiment was conducted in Botany Lab of Maharishi University of Information Technology, Lucknow in earthen Pots filled with garden soil. Where eggplant seedlings were subjected to different levels of zinc supplementation. Parameters such as plant height, leaf area, root development, and biomass accumulation were measured at regular intervals over the growth period. Results indicated a significant positive correlation between zinc concentration and various growth parameters of eggplant. Seedlings treated with higher zinc concentrations, enhanced leaf expansion, and more extensive root systems compared to those with lower or no zinc supplementation. Furthermore, zinc-treated eggplants displayed improved resistance to certain environmental stressors, suggesting a potential role of zinc in enhancing plant resilience. These findings underscore the importance of adequate zinc supply in promoting the growth and development of eggplant crops, thereby contributing to higher yields and improved agricultural sustainability. Further research is warranted to elucidate the underlying mechanisms of zinc-mediated growth enhancement in eggplant and optimize zinc application strategies for maximum benefit.

Spatial Heterogeneity Analysis and Risk Assessment of Potentially Toxic Elements in Soils of Typical Green Tea Plantations

The spatial heterogeneity of potentially toxic elements (PTEs) in a typical green tea-producing area in Zhejiang was investigated with application of geostatistics. The positive matrix factorization (PMF) was conducted for analysis of pollution sources and risk assessment of the soil of the tea garden. The results revealed that 93.52% of the study area did not exceed the PTEs risk screening value in the soil pollution risk control standard of agricultural land. The results of the spatial heterogeneity analysis showed that Cd and Pb had moderate spatial auto-correlation, exhibiting similar spatial distribution patterns. The high-value locations were distributed in the southeast of the study area, while low-value locations were distributed in the southwest of the study area. The Cr, As, and Hg had strong spatial auto-correlation, while Cr and As had similar spatial distribution patterns whose high-value areas and low-value areas were concentrated in the west and center of the study area, respectively. The Cd, Pb, and As originated from the agricultural source, transportation source, and industrial source, respectively, while Cr and Hg were from the natural source on the basis of the results of the PMF model. The results of a potential ecological risk assessment revealed that five PTEs in the study area were of low potential risk. The single-factor ecological risk ranking was Cd &gt; As &gt; Hg &gt; Cr &gt; Pb. The overall ecological risk in the study area was slight. The human health risk model indicates that there was a non-carcinogenic risk for children in the study area, and the high-value area was concentrated in the northwest of the study area. It is concluded that emphasis shall be given to excessive Cd caused by agricultural sources in the southeast of the study area, and control and monitoring will be strengthened in the northwestern part of the study area. The relevant measures for prevention of soil pollution must be conducted.

Determining the Effect of Rooting Media and Different Polythene Wrappers on Air Layering of Grape Fruit (Citrus paradisi)

The present study aims to investigate the “EFFECT OF ROOTING MEDIA AND DIFFERENT POLYTHENE WRAPPERS ON AIR LAYERING OF GRAPE FRUIT (Citrus paradisi’)”at The Department of Horticulture, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, during the period 2023-24. The experiment was laid in completely randomized block design with three replications and ten treatment combinations. viz, T1 (BA1000PPM + BLACK POLYTHENE + SPHAGNUM MOSS) ,T2 (IBA1000PPM + BLACK POLYTHENE + SAWDUST), T3 (IBA1000PPM + BLACK POLYTHENE + GARDEN SOIL+ SPHAGNUM MOSS),T4 (IBA1000PPM + BLACK POLYTHENE + SPHAGNUM MOSS+ SAWDUST), T5(IBA1000PPM + BLACK POLYTHENE + GARDEN SOIL+ SAWDUST), T6 (IBA1000PPM + WHITE POLYTHENE + SPHAGNUM MOSS), T7 (IBA1000PPM + WHITE POLYTHENE + SAWDUST),T8(IBA1000PPM + WHITE POLYTHENE + GARDEN SOIL + SPHAGNUMMOSS), T9(IBA1000PPM + WHITE POLYTHENE + GARDEN SOIL + SAWDUST),T10(IBA1000PPM + WHITE POLYTHENE + SPHAGNUM MOSS + SAWDUST). On the basis of present experimental findings, it is concluded that treatmentT4(IBA1000PPM + BLACK POLYTHENE + SPHAGNUM MOSS+ SAWDUST) was found to be best in terms of Number of days to root formation (initial rooting), Root length(cm), Root thickness(mm), Number of roots per layer, Survival percentage, Number of new sprouts per layered plant, Number of new leaves per layered plant and length of new shoot(cm) in Grape fruit.Whereas T9(IBA1000PPM + WHITE POLYTHENE + GARDEN SOIL + SAWDUST) was found to be least in terms of Number of days to root formation (initial rooting), Root length(cm), Survival percentage, Number of new sprouts per layered plant, Number of new leaves per layered plant and Length of new shoots(cm) whereas in Root thickness(mm) and number of roots per layer in Grape fruit.

Genome sequencing, annotation and application of a strain of Microbacterium paraoxydans – A bacterium with arsenic bioremediation and plant growth promoting potential

A heavy metal hypertolerant plant growth-promoting bacterium was isolated from the arsenic-contaminated garden soil of Bhagobangola I block (Murshidabad district). Metagenomic classification identified the bacterial isolate as a member of the genus Microbacterium. Taxonomic assessment of the isolated strain revealed its maximum average nucleotide identity (89.99 %) with the Microbacterium paraoxydans strain DSM 15019. Prokaryotic genome annotation was performed by Prokka, DFAST and RAST. The entire genome consisted of 3365911 bases with 69.90 % GC content. Prokka detected 3216 coding sequences (1461 hypothetical sequences), 3283 genes, 10 miscellaneous RNAs, 3 rRNAs, 53 tRNAs and 1 tmRNA in the bacterial genome. DFAST detected 3257 coding sequences (1217 hypothetical sequences), 3 rRNA sequences and 53 tRNA sequences in the bacterial genome. RAST detected 3285 coding sequences and 49 RNAs in the genome. Only 25 % of these coding sequences could be categorised in the RAST subsystems. In RAST, 789 and 32 coding sequences were considered as non-hypothetical and hypothetical, respectively. The genes and gene clusters responsible for arsenic resistance (arsR, arsB, arsC, acr1, acr2 and acr3), tolerance to other heavy metals (copper, manganese, zinc, etc.) and plant growth promotion (auxin biosynthesis, siderophore-mediated iron acquisition, phosphate and polyphosphate metabolism, trehalose biosynthesis, etc.) were also identified in the Microbacterium paraoxydans genome. The bioremediation potential and plant growth-promoting nature of the bacterium were confirmed by silver diethyl dithio carbamate (SDDC) method and pot experiments, respectively. The aforementioned traits point towards potential of the bacterium as a bioremediation tool and biofertilizer for reducing arsenic toxicity and promoting plant growth.

Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh.

Soil microbiome science, rapidly evolving, predominantly focuses on field crop soils. However, understanding garden soil microbiomes is essential for enhancing food production sustainability in garden environments. This study aimed to unveil the bacteriome diversity and composition in rooftop garden soils (RGS) and surface garden soils (SGS) across urban (Dhaka North and Dhaka South City Corporations) and peri-urban (Gazipur City Corporation) areas of Dhaka Division, Bangladesh. We analyzed 11 samples, including six RGS and five SGS samples from 11 individual gardens using 16S rRNA (V3-V4 region) gene-based amplicon sequencing. A total of 977 operational taxonomic units (OTUs), including 270 and 707 in RGS and SGS samples, respectively, were identified. The observed OTUs were represented by 21 phyla, 45 classes, 84 orders, 173 families, and 293 genera of bacteria. Alpha diversity indices revealed significantly higher bacterial diversity in SGS samples (p = 0.01), while beta diversity analyses indicated distinct bacteriome compositions between RGS and SGS samples (p = 0.028, PERMANOVA). Despite substantial taxonomic variability between sample categories, there was also a considerable presence of shared bacterial taxa. At the phylum level, Bacilliota (61.14%), Pseudomonadota (23.42%), Actinobacteria (6.33%), and Bacteroidota (3.32%) were the predominant bacterial phyla (comprising > 94.0% of the total abundances) in both types of garden soil samples. Of the identified genera, Bacillus (69.73%) and Brevibacillus (18.81%) in RGS and Bacillus (19.22%), Methylophaga (19.21%), Acinetobacter (6.27%), Corynebacterium (5.06%), Burkholderia (4.78%), Paracoccus (3.98%) and Lysobacter (2.07%) in SGS were the major bacterial genera. Importantly, we detected that 52.90% of genera were shared between RGS and SGS soil samples. Our data reveal unique and shared bacteriomes with probiotic potential in soil samples from both rooftop and surface gardens. Further studies should explore the functional roles of shared bacterial taxa in garden soils and how urban environmental factors affect microbiome composition to optimize soil health and sustainable food production.

Characterization of protease-producing bacteria from garden soil and antagonistic activity against pathogenic bacteria

Bacteria play an essential role in various industrial processes, including food, medicine, and detergents, due to their ability to produce protease, a hydrolytic enzyme. This study aimed to identify and characterize protease-producing bacterial strains isolated from garden soil, evaluate their antibiotic susceptibility, and optimize conditions for enhanced protease production. Using skimmed milk agar medium and the gelatin hydrolysis method, 7 bacterial strains (S1, S2, S3, S4, S5, S6, and S7, respectively) were identified for protease production in garden soil. The bacteria were identified based on morphological studies, biochemical characterization, and the BIOLOG™ system, and the isolates were determined to be Bacillus cereus (S1), B. thuringiensis (S2), B. subtilis (S3), B. amyloliquefaciens (S4), Pseudomonas aeruginosa (S5), Macrococcus brunensis (S6), and B. schlegelii (S7). The antibiotic susceptibility test, performed using the Kirby-Bauer agar disc diffusion method, revealed that all isolates were resistant to penicillin, nitrofurantoin, and metronidazole. Additionally, B. subtilis and P. aeruginosa demonstrated antagonistic activity against pathogens. Optimal conditions for protease production were found to be a temperature range of 30°C to 40°C and a pH range of 6.5–7.5. Under these conditions, B. cereus (2.19 U/ml) and B. thuringiensis (2.12 U/ml) exhibited the highest protease activity. Further characterization of protease activity in B. cereus, P. aeruginosa, and M. brunensis under different physiological parameters revealed that maximum activity occurred within a pH range of 5.0–6.0 and temperatures between 30°C and 40°C. Protease activity increased in the presence of calcium (CaCl2) but decreased with the addition of urea. These findings underscore the significant industrial applications of proteases produced by these bacterial strains.

Laboratory studies of movement and microenvironment choices of engorged adult female Amblyomma maculatum (Acari: Ixodidae).

Microenvironmental factors affect ovipositional choices and behavior in ticks. In this study, engorged female Amblyomma maculatum Koch were released in an observation arena covered with garden soil. The arena was evenly split into wet and dry sides, each containing 5 different types of structures (totaling 10). Upon release, observations at particular time points were made over 2 days as to speed, distance, actual paths traveled, and ultimate site selection, presumably for oviposition. In addition, time-lapse videography was utilized to record the track of each individual tick. This scenario was replicated 3 times with different cohorts of ticks (n = 5 per replicate). Of the total 15 ticks released in the arena, all attained a final site selection by 24 h. These final sites were 7/15 (47%) edge of arena; 2/15 (13%) under bark; 2/15 (13%) open soil; 2/15 (13%) at or near release point; 1/15 (7%) tunnel with animal fur; and 1/15 (7%) tunnel with chicken feathers. At final site selection, 11/15 (73%) subsequently burrowed into the soil, 3 of which were completely buried. Time-lapse videography revealed that most ticks (80%) explored the arena in a "looping back" fashion. Overall, engorged Gulf Coast ticks moved at an average speed of 0.09 mm/s, and the total distance traversed by the ticks averaged 2.37 m.

Termite mound soil based potting media: a better approach towards sustainable agriculture.

Termite mound soils are known to possess unique physico-chemical and biochemical properties, making them highly fertile. Considering their rich nutrient content, the objective of the current experiment is to assess the physico-chemical properties and enzyme activities of termite mound based potting media and evaluate theirperformance for further exploration in floriculture. Potting media consisting of termite mound soil (TS) of a subterranean termite, Odontotermes obesus were prepared in 7 different combinations with garden soil (GS), sand (S) and farmyard manure (FYM) and a control (without termite mound soil), i.e., T1 (TS, GS, S, FYM (v:v:v:v /1:2:1:1)), T2 (TS, GS, S, FYM (v:v:v:v / 2:1:1:1)), T3 (TS, S, FYM (v:v:v / 2:1:1)), T4 (TS, GS, FYM (v:v:v / 2:1:1)), T5 (TS, GS, S (v:v:v / 2:1:1)), T6 (TS, S, FYM (v:v:v / 3:1:1)), T7 (TS, S, FYM (v:v:v / 1:1:2)) and control (GS, S, FYM (v:v:v / 2:1:1)). The samples were then analysed in laboratory. Experimental analysis on physico-chemical and biological parameters revealed superiority of T7 (TS, S, FYM (v:v:v / 1:1:2)) in terms of pH (7.15), organic carbon (2.13%), available nitrogen (526.02 kg ha-1), available phosphorus (56.60 kg ha-1), available potassium (708.19 kg ha-1), dehydrogenase activity (18.21 μg TTF g-1 soil day-1), Phosphomonoesterase (PME) activity (46.68 54 μg p-nitrophenol/gsoil/h) and urease activity (3.39 μg NH4-N g-1 soil h-1). Whereas T4 (TS, GS, FYM (v:v:v /2:1:1)) registered superiority in terms of PME activity (50.54 μg p-nitrophenol/gsoil/h), Fluorescein diacetate (FDA) activity (11.01 μgfluorescein/gsoil/h) and Soil Microbial Biomass Carbon (SMBC) (262.25 μg/g). Subsequent to the laboratory analysis, two best potting mixtures (T7 & T4) were selected and their performance was assessed by growing a test crop, Tagetes erecta cv. Inca Orange. Considering the growth parameters, the potting media: T7 was found to be significantly superior in terms of plant spread (39.64 cm), leaf area index (4.07), fresh weight (37.72 g), yield (317.81 g/plant), and diameter (9.38 cm) of flower over T4 & control. The Benefit:Cost (B:C) ratio meaning the ratio of net returns to total cost of cultivation was determined. The B:C ratio of raising marigold flower as potted plant in T7 was 1.10 whereas the B:C ratio of the potting mixture of T7 was 2.52. This shows that T7 potting media is also economically viable choice for commercial purposes.