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.

Draft genome sequence of Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable garden in Gazipur, Bangladesh.

We announce the sequence of the Escherichia coli MTR_GS_S1457 strain isolated from a soil sample of a vegetable gardening system for the first time in Bangladesh. With a length of 4,918,647 bp, this strain contained one plasmid, two CRISPR arrays, 54 predicted antibiotic resistance genes, and 81 predicted virulence factor genes.

Draft genome sequence of antibiotic-resistant Shigella flexneri MTR_GR_V146 strain isolated from a tomato (Solanum lycopersicum) sample collected from a peri-urban area of Bangladesh.

This study announces the genome sequence of the Shigella flexneri MTR_GR_V146 strain isolated from a tomato (Solanum lycopersicum) sample in Bangladesh. This strain has a 4,624,521 bp genome length (coverage: 73.07×), 2 CRISPR arrays, 1 plasmid, 52 predicted antibiotic resistance genes, and 53 virulence factor genes.

Draft genome sequence of multidrug-resistant Citrobacter freundii MTR_GS_V1777 strain isolated from a spinach (Spinacia oleracea) sample in Gazipur, Bangladesh.

We announce a genome sequence of Citrobacter freundii MTR_GS_V1777 strain isolated from a vegetable sample in Bangladesh. This strain had a genome size of 4,997,753 bp (58.7× genome coverage) and contained two plasmids, typed as sequence type ST124, 38 predicted antibiotic resistance genes, and 77 predicted virulence factor genes.

Draft genome sequences of five multidrug-resistant Escherichia coli strains isolated from vegetable samples in Bangladesh.

Reports indicate that vegetables are becoming a source of multidrug-resistant (MDR) bacteria, including Escherichia coli. Here, we present genome sequences of five MDR E. coli strains to assist future genomic analysis of this bacterium. These E. coli strains were isolated from vegetable samples of different gardening systems in Dhaka, Bangladesh.

Exaptation of I4760M mutation in ryanodine receptor of Spodoptera exigua (Lepidoptera: Noctuidae): Lessons from museum and field samples.

Since 2007, diamide insecticides have been widely used in Korea to control various types of lepidopteran pests including Spodoptera exigua. For nearly a decade, diamide resistance in field populations of S. exigua across 18 localities has been monitored using bioassays. Despite their short history of use, resistance to diamide insecticides has emerged. Based on the LC50 values, some field populations showed a higher level of resistance to chlorantraniliprole, a diamide insecticide, compared to that of the susceptible strain, although regional and temporal variations were observed. To investigate resistance at a molecular level, we examined three mutations (Y4701C, I4790M, and G4946E) in the ryanodine receptor (RyR), which is the primary mechanism underlying diamide insecticide resistance. DNA sequencing showed that only the I4790M mutation was found in most field populations. As resistance levels varied significantly despite the uniform presence of the I4790M mutation, we considered the presence of another resistance factor. Further, the I4790M mutation was also found in S. exigua specimens collected prior to the commercialization of diamide insecticides in Korea as well as in other countries, such as the USA. This finding led us to hypothesize that the I4790M mutation were predisposed in field populations owing to selection factors other than diamide use. For further clarification, we conducted whole-genome sequencing of S. exigua (449.83 Mb) and re-sequencing of 18 individual whole genomes. However, no additional non-synonymous mutations were detected in the RyR-coding region. Therefore, we concluded that the high level of diamide insecticide resistance in Korean S. exigua is not caused by mutations at the target site, RyR, but is attributed to other factors that need to be investigated in future studies.

Genome, host genome integration, and gene expression in Diadegma fenestrale ichnovirus from the perspective of coevolutionary hosts.

Polydnaviruses (PDVs) exhibit species-specific mutualistic relationships with endoparasitoid wasps. PDVs can be categorized into bracoviruses and ichnoviruses, which have independent evolutionary origins. In our previous study, we identified an ichnovirus of the endoparasitoid Diadegma fenestrale and named it DfIV. Here, DfIV virions from the ovarian calyx of gravid female wasps were characterized. DfIV virion particles were ellipsoidal (246.5 nm × 109.0 nm) with a double-layered envelope. Next-generation sequencing of the DfIV genome revealed 62 non-overlapping circular DNA segments (A1-A5, B1-B9, C1-C15, D1-D23, E1-E7, and F1-F3); the aggregate genome size was approximately 240 kb, and the GC content (43%) was similar to that of other IVs (41%-43%). A total of 123 open reading frames were predicted and included typical IV gene families such as repeat element protein (41 members), cysteine motif (10 members), vankyrin (9 members), polar residue-rich protein (7 members), vinnexin (6 members), and N gene (3 members). Neuromodulin N (2 members) was found to be unique to DfIV, along with 45 hypothetical genes. Among the 62 segments, 54 showed high (76%-98%) sequence similarities to the genome of Diadegma semiclausum ichnovirus (DsIV). Three segments, namely, D22, E3, and F2, contained lepidopteran host genome integration motifs with homologous regions of about 36-46 bp between them (Diadegma fenestrale ichnovirus, DfIV and lepidopteran host, Plutella xylostella). Most of the DfIV genes were expressed in the hymenopteran host and some in the lepidopteran host (P. xylostella), parasitized by D. fenestrale. Five segments (A4, C3, C15, D5, and E4) were differentially expressed at different developmental stages of the parasitized P. xylostella, and two segments (C15 and D14) were highly expressed in the ovaries of D. fenestrale. Comparative analysis between DfIV and DsIV revealed that the genomes differed in the number of segments, composition of sequences, and internal sequence homologies.

Quorum Sensing Inhibitory Potential and Molecular Docking Studies of Phyllanthus emblica Phytochemicals Against Pseudomonas aeruginosa.

Phyllanthus emblica is a traditional medicinal plant that is endowed with curative properties including anti-bacterial, anti-fungal, anti-viral, and analgesic properties. Bacteria make use of cell-cell signaling system known as quorum sensing (QS) and respond to their own population. In most gram-negative bacteria, the transcriptional regulators belonging to the Lux R protein play a crucial role in the QS mechanism by detecting the presence of signaling molecules known as N-acyl homoserine lactones (AHLs). In this present work, the anti-quorum sensing activity of Phyllanthus emblica was evaluated against Pseudomonas aeruginosa. Anti-quorum sensing efficacy of Phyllanthus emblica was estimated with reference to QS bio-monitoring strain Chromobacterium violaceum. The binding efficacy of the phytochemicals of Phyllanthus emblica against CviR protein from Chromobacterium violaceum and LasR protein from Phyllanthus emblica were studied.

Oviposition preference not necessarily predicts offspring performance in the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae) on vegetable crops.

Given the new spread and potential damage of the fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) in Asia, it has become imperative to understand the development biology of this invasive species on selected vegetable crops in newer geographical regions. In this study, we investigated the ovipositional preference of FAW females on different host plants, under choice- and non-choice tests. In addition, using the age-stage, two-sex life table theory, we assessed the performance of immature FAW individuals fed and reared on selected vegetable crops to get information related to development time, survival, reproduction and longevity. Fall armyworm females had an oviposition preference on maize compared to other vegetable crops, including cabbage and soybean, and reluctance for tomato, which was confirmed during the choice and non-choice tests. In contrast to the oviposition preference, our results also suggest that despite low preference for cabbage, soybean, and tomato, these crops seemed to provide a high benefit for an appropriate offspring performance, exceeding in some cases the benefits from a maize-based diet. Information from this study was discussed in terms of FAW ecology and how female's decision affects their reproductive fitness, and the survival and performance of its offspring.

Molecular docking and in vitro analysis of phytoextracts from B. serrata for antibacterial activities.

The bioactives of Boswellia serrata have a role in ulcer healing therapies. Eleven bioactive compounds were obtained by GC-MS among which Cholan-24-oic acid, 3,12-bis (acetyl oxy) has a high molecular weight of 490.6719 with a retention time of 26.729. Twenty wound samples were collected aseptically from the labs and hospitals in and around the Namakkal districts of Tamilnadu, India. The antibacterial potential of E.coli showed a maximum inhibition of 27 mm against Tetracycline at 30µg. The ethanolic extract of the B. serrata shows a susceptibility of 19mm towards E. coli at 60µg concentration in MIC. Molecular docking results show the binding energy of Cholan-24-oic acid, 3,12-bis(acetyloxy) -8.6 (kcal/mol) followed by Pyrene, hexadecahydro- -6.7 (kcal/mol), and 5(1H)- Azulenone, 2,4,6,7,8,8a-hexahydro-3,8-dimethyl-4-(1-methylethylidene)-, (8S-cis)- 6.4 (kcal/mol) for further consideration.

Food system disruption: initial livelihood and dietary effects of COVID-19 on vegetable producers in India.

Disruption to food systems and impacts on livelihoods and diets have been brought into sharp focus by the COVID-19 pandemic. We aimed to investigate effects of this multi-layered shock on production, sales, prices, incomes and diets for vegetable farmers in India as both producers and consumers of nutrient-dense foods. We undertook a rapid telephone survey with 448 farmers in 4 states, in one of the first studies to document the early impacts of the pandemic and policy responses on farming households. We find that a majority of farmers report negative impacts on production, sales, prices and incomes. Over 80% of farms reported some decline in sales, and over 20% of farms reported devastating declines (sold almost nothing). Price reductions were reported by over 80% of farmers, and reductions by more than half for 50% of farmers. Similarly, farm income reportedly dropped for 90% of farms, and by more than half for 60%. Of surveyed households, 62% reported disruptions to their diets. A majority of farm households reported reduced ability to access the most nutrient-dense foods. Around 80% of households reported ability to protect their staple food consumption, and the largest falls in consumption were in fruit and animal source foods other than dairy, in around half of households. Reported vegetable consumption fell in almost 30% of households, but vegetables were also the only food group where consumption increased for some, in around 15% of households. Our data suggest higher vulnerability of female farmers in terms of both livelihoods and diet, and differential effects on smaller and larger farms, meaning different farms may require different types of support in order to continue to function. Farms reported diverse coping strategies to maintain sales, though often with negative implications for reported incomes. The ability to consume one's own produce may be somewhat protective of diets when other routes to food access fail. The impacts of COVID-19 and subsequent policy responses on both livelihoods and diets in horticultural households risk rolling back the impressive economic and nutrition gains India has seen over the past decade. Food systems, and particularly those making available the most nutrient-dense foods, must be considered in ongoing and future government responses.

Pheromone-binding proteins based phylogenetics and phylogeography of Maruca spp. from Asia, Africa, Oceania, and South America.

Variations in the functional response of legume pod borer (Maruca vitrata) populations to sex pheromone blends were observed in Asia and Africa. Hence, this study was carried out to understand the differences in pheromone-binding proteins (PBPs) among Maruca populations in Asia, Africa, Oceania, and South America. A de novo transcriptome assembly was adopted to sequence the entire transcribed mRNAs in M. vitrata from Taiwan. The raw-sequence data were assembled using homologous genes from related organisms in GenBank to detect M. vitrata PBPs (MvitPBPs). Sections of the cDNA of MvitPBP of different length were used to design primers to amplify the full-length cDNA of PBPs. All three PBP sequences comprised three exons interspersed by two introns. In total, 92 MvitPBP1 haplotypes, 77 MvitPBP2 haplotypes, and 64 MvitPBP3 haplotypes were identified in 105, 98, and 68 Maruca individuals, respectively. High pairwise F ST values (0.41-0.73) and phylogenetic analyses distinguished the putative Maruca species in South America from those occurring in rest of the world, and possibly two putative subspecies in Asia and Africa. The haplotype networks and Automatic Barcode Gap Discovery analyses also confirmed these results. The negative Tajima's D and Fu's F S values showed the recent demographic expansion of Maruca populations. Thus, this study confirmed the presence of different Maruca species and/or subspecies in different continents based on the diversity within PBP genes. Additional sampling and studies are suggested for Oceania and South America. The genetic differences among Maruca populations should be carefully considered while using sex pheromone lures and bio-control agents.

The Effects of Pest-Resistant Amaranth Accessions on the Performance of the Solitary Endoparasitoid Apanteles hemara (Hymenoptera: Braconidae) Against the Amaranth Leaf-Webber Spoladea recurvalis (Lepidoptera: Crambidae).

The leaf-webber Spoladea recurvalis F. is the most devastating pest of amaranths in East Africa. Recent collaborative research in Asia and East Africa revealed one highly resistant amaranth accession (VI036227) to the pest and seven moderately resistant ones (RVI00053, VI033479, VI044437-A, VI047555-B, VI048076, VI049698, and VI056563). The solitary koinobiontic endoparasitoid Apanteles hemara Nixon has also been reported as efficient against the pest. Plant resistance to herbivores may have bottom-up effects on their parasitoids. In this study, we assessed the effects of the seven moderately resistant amaranth accessions and one susceptible accession (VI033482) on the performance of A. hemara. Except VI056563 that recorded lower parasitism rates compared to the susceptible accession, A. hemara performed well on all the other moderately resistant accessions. The longevity of the parasitoid was significantly extended on the resistant accessions compared to the susceptible one. While the parasitoid's body size, developmental time, and survival differed significantly between resistant accessions, they were similar to results obtained on the susceptible accession. Furthermore, while the parasitoid's sex ratio was male-biased in the susceptible accession, balanced sex ratios were obtained from accessions RVI00053, VI033479, VI044437-A, VI047555-B, VI048076, and VI049698. Significant nonreproductive host larval mortality was induced by A. hemara on all the tested accessions. These results suggest that the moderately resistant accessions can be used in combination with the endoparasitoid A. hemara to manage S. recurvalis and other amaranth leaf-webbers in the context of integrated pest management.

Expression of Resistance in Amaranthus spp. (Caryophyllales: Amaranthaceae): Effects of Selected Accessions on the Behaviour and Biology of the Amaranth Leaf-Webber, Spoladea recurvalis (Lepidoptera: Crambidae).

Spoladea recurvalis F. is a major pest moth of amaranth (Amaranthus spp.) flowers worldwide, with a potential of causing complete foliage loss under severe outbreaks. Chemical insecticides are uneconomical for resource-poor farmers and pose health and environmental risks. Host plant resistance (HPR) to insects is an effective, economical and environmentally friendly alternative that is poorly understood and largely unexploited among traditional leafy vegetables. A total of 35 amaranth accessions were evaluated for the expression of their antixenotic and antibiotic traits against S. recurvalis, focusing on their effects on the biology of the pest in comparison with a susceptible accession. The accession VI036227 was found to be highly resistant against the pest, exhibiting exemplary antibiosis by causing 100% larval mortality within the first 36 h, despite not being deterrent for oviposition. The accessions VI048076, VI056563 and VI047555-B demonstrated moderate resistance against the pest for specific parameters including low oviposition, moderate early stage larval mortality and reduced adult longevity. Total mortality and weight gain in these three accessions were, however, not significantly different from the susceptible control. Higher numbers of eggs were laid in no-choice compared to choice situations. The implications of these findings in the management of S. recurvalis on amaranths are discussed.

Transcriptome analysis in the beet webworm, Spoladea recurvalis (Lepidoptera: Crambidae).

The beet webworm, Spoladea recurvalis Fabricius, is a destructive pest on vegetable crops in tropics and subtropics; its main host plant is amaranth. It has become imperative to develop non-chemical methods to control S. recurvalis on amaranth. However, the lack of molecular information about this species has hindered the development of novel pest management strategies. In this study, high-throughput RNA sequencing covering de novo sequence assemblies, functional annotation of transcripts, gene function classification and enrichment was performed on S. recurvalis. Illumina sequencing generated a total of 120 435 transcript contigs ranging from 201 to 22 729 bases with a mean length of 688 bases. The assembled transcripts were subjected to Basic Local Alignment Search Tool-X (BLASTX) to obtain the annotations against non-redundant, Swiss-Prot, Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases. A subset of 58 225 transcript sequences returned hits from known proteins in the National Center for Biotechnology Information database, and the majority of the transcript sequences had the highest number of hits for Danaus plexippus (50.43%). A total of 1217 Gene Ontology-level 3 annotations were assigned to 51 805 transcripts, while 39 650 transcripts were predicted as functional protein-coding genes in the COG database and 20 037 transcripts were enriched to KEGG pathways. We identified 40 putative genes related to pheromone production and reception in S. recurvalis, with the expression of one gene between 0.29 and 1141.79 fragments per kilo base per million (FPKM) reads. The transcriptome sequence of S. recurvalis is a first step toward offering a comprehensive genomic resource which would enable better understanding of molecular mechanisms to enable development of effective pest management practices for this species.

Phylogeographical structure in mitochondrial DNA of whitefly, Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae) in southern India and Southeast Asia.

South and Southeast Asia endure high vegetable production losses due to begomovirus diseases mainly transmitted by the insect vector, whitefly (Bemisia tabaci). Control over the spread of virus infection can be achieved through a better understanding of genetic diversity among B. tabaci. A total of 64 populations of B. tabaci collected from Tamil Nadu (India), Vietnam, Thailand, and Indonesia were investigated based on mitochondrial cytochrome c oxidase I (coxI) sequences. Populations from Tamil Nadu are distributed into three clades (Asia I, Asia II 7, and Asia II 8), whereas Indonesian populations settle along with Asia I population of India in the phylogenetic tree. Vietnam populations align with the Middle East-Asia Minor 1 (MEAM1) clade, and interestingly MEAM1 invades northern Vietnam quite recently. Samples from Thailand made a unique clade between the outgroup and the remaining B. tabaci, representing the possibility of a new subspecies. AMOVA analysis among populations from various districts in Tamil Nadu exhibits significant differences, which represent each district's individuality. This study proves that the use of coxI as a marker for molecular identification of B. tabaci can provide a better estimate of diversity. We provide important clues for developing insight into the genetic structure of B. tabaci, and suggest strategies for control.

Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis.

BACKGROUND: Bruchid beetles are an important storage pest of grain legumes. Callosobruchus sp. infect mungbean (Vigna radiata) at low levels in the field, multiply during grain storage and can destroy seed stocks in a few months. Resistance against bruchid beetles has been found in wild mungbean V. radiata var. sublobata TC1966 and in cultivated mungbean line V2802. RESULTS: Bruchid resistance data were obtained from recombinant inbred line populations TC1966 (V. radiata var. sublobata) × NM92 (F12) and V2802 (V. radiata) × NM94 (F7). More than 6,000 single nucleotide polymorphic markers were generated through genotyping by sequencing (GBS) for each of these populations and were used to map bruchid resistance genes. One highly significant quantitative trait locus (QTL) associated with bruchid resistance was mapped to chromosome 5 on genetic maps of both populations, suggesting that TC1966 and V2802 contain the same resistance locus. Co-segregation of all markers associated with resistance indicated the presence of only one major resistance QTL on chromosome 5, while QTL analysis based on physical map positions of the markers suggested the presence of multiple QTLs on different chromosomes. The diagnostic capacity of the identified molecular markers located in the QTL to correctly predict resistance was up to 100 %. CONCLUSIONS: Molecular markers tightly linked to bruchid resistance loci of two different mungbean resistance sources were developed and validated. These markers are highly useful for developing resistant lines.

Management of Oehler's Type III Dens Invaginatus Using Cone Beam Computed Tomography.

Dens Invaginatus is a dental malformation that poses diagnostic difficulties in the clinical context. This anomaly may increase the risk of pulp disease and can potentially complicate endodontic procedure due to the aberrant root canal anatomy. Compared to conventional radiographs, three-dimensional images obtained with Cone Beam Computed Tomography (CBCT) are invaluable in the diagnosis of the extent of this anomaly and in the appropriate treatment planning. Oehler's classification (1957) for Dens Invaginatus (DI) into three types depending on the depth of the invagination has been used for treatment planning. Of the three types Type III DI is characterized by infolding of the enamel into the tooth up to the root apex and is considered as the most severe variant of DI and hence the most challenging to treat endodontically, due to the morphological complexities. This report describes a case of Oehler's Type III DI in a necrotic permanent maxillary lateral incisor in which CBCT images played a key role in diagnosis and treatment planning. The case was managed successfully by a combination of nonsurgical and surgical endodontic therapy with orthograde and retrograde thermoplastic gutta percha obturation.

Novel family of terpene synthases evolved from trans-isoprenyl diphosphate synthases in a flea beetle.

Sesquiterpenes play important roles in insect communication, for example as pheromones. However, no sesquiterpene synthases, the enzymes involved in construction of the basic carbon skeleton, have been identified in insects to date. We investigated the biosynthesis of the sesquiterpene (6R,7S)-himachala-9,11-diene in the crucifer flea beetle Phyllotreta striolata, a compound previously identified as a male-produced aggregation pheromone in several Phyllotreta species. A (6R,7S)-himachala-9,11-diene-producing sesquiterpene synthase activity was detected in crude beetle protein extracts, but only when (Z,E)-farnesyl diphosphate [(Z,E)-FPP] was offered as a substrate. No sequences resembling sesquiterpene synthases from plants, fungi, or bacteria were found in the P. striolata transcriptome, but we identified nine divergent putative trans-isoprenyl diphosphate synthase (trans-IDS) transcripts. Four of these putative trans-IDSs exhibited terpene synthase (TPS) activity when heterologously expressed. Recombinant PsTPS1 converted (Z,E)-FPP to (6R,7S)-himachala-9,11-diene and other sesquiterpenes observed in beetle extracts. RNAi-mediated knockdown of PsTPS1 mRNA in P. striolata males led to reduced emission of aggregation pheromone, confirming a significant role of PsTPS1 in pheromone biosynthesis. Two expressed enzymes showed genuine IDS activity, with PsIDS1 synthesizing (E,E)-FPP, whereas PsIDS3 produced neryl diphosphate, (Z,Z)-FPP, and (Z,E)-FPP. In a phylogenetic analysis, the PsTPS enzymes and PsIDS3 were clearly separated from a clade of known coleopteran trans-IDS enzymes including PsIDS1 and PsIDS2. However, the exon-intron structures of IDS and TPS genes in P. striolata are conserved, suggesting that this TPS gene family evolved from trans-IDS ancestors.