BISMiS Live, launched on March 20, 2021, emerged as a timely response to the disruption caused by the CoViD-19 pandemic, offering a global virtual platform for discourse in microbial systematics. Spearheaded by the Bergey's International Society for Microbial Systematics (BISMiS), this monthly webinar series hosted renowned experts and engaged thousands of participants across 84 countries. The initiative emphasized inclusivity, scientific depth, and digital accessibility, with sessions archived on YouTube (@BISMiS_) for broader impact. Behind each event lies a dedicated team managing speaker coordination, technical execution, and global outreach. BISMiS Live has grown into an educational resource, integrated into university curricula and inspiring the next generation of microbial taxonomists. With suggestions for future innovation, such as student lightning talks, thematic series, and podcast formats, the platform is poised to evolve further. BISMiS Live stands as a digital bridge connecting systematists worldwide, sustaining knowledge exchange and community through innovation and collaboration.

A Gram-positive, rod-shaped, spore-forming, aerobic bacterium, with biocontrol potential designated as RMG6T, was isolated from the rhizosphere of the mulberry plant located in the mulberry garden of Raiganj University, West Bengal, India. The strain demonstrated significant antimicrobial activity against Enterococcus faecalis MTCC 439 (1.92 cm inhibition zone) and Escherichia coli MTCC 43 (1.62 cm inhibition zone) in agar-well diffusion assays. Scanning electron microscopy (SEM) confirmed bacterial cell lysis and cytoplasmic leakage. Phylogenetic analysis of the 16S rDNA sequence (1545 bp) revealed that RMG6T is closely associated to Bacillus siamensis KCTC 13,613 (99.93% similarity). Additionally, multilocus sequence analysis (MLSA) suggested that RMG6T represents a novel Bacillus species. The morphological characteristics of RMG6T colonies further distinguished it from closely related Bacillus species. RMG6T remained unidentified through Vitek-2 analysis. Fatty acid methyl ester (FAME) profiling revealed the predominant cellular fatty acids in RMG6T were anteiso-C15:0 (28.13%), iso-C15:0 (20.72%), C18:0 (10.72%), iso-C17:0 (7.00%), iso-C16:0 (5.88%), and anteiso-C17:0 (5.87%). MALDI-TOF MS analysis validated that RMG6T belongs to Bacillus genus. RMG6T exhibited optimal growth at 35 °C, pH 6, and up to 14% NaCl tolerance. The strain produced indole-3-acetic acid (IAA) through the indole-3-pyruvic acid pathway, with a maximum yield of 73.4 µg/mL at 0.2% L-tryptophan supplementation. The Vigna radiata seed germination assay validated its plant growth-promoting potential, with significantly enhanced radicle growth compared to control treatments, highlighting the potential of RMG6T for cross-species bioaugmentation. Antibiotic susceptibility profiling revealed that RMG6T was resistance to beta-lactam antibiotics, aligning with the genomic identification of resistance genes. Whole-genome sequencing (3,818,111 bp; G + C content 46.62%) identified 3723 coding sequences, including biosynthetic gene clusters (BGCs) associated with antimicrobial compound biosynthesis. Moreover, the highest recorded values for average nucleotide identity (ANI) and Genome-to-Genome Distance Calculator 3.0 analysis were 94.44 and 56.80%, respectively, with Bacillus siamensis KCTC 13,613. Comparative genomic and phylogenomic analyses confirmed the novelty of RMG6T, leading to its proposed designation as Bacillus ayatagriensis sp. nov., with RMG6T (= MCM-B-1537). We propose Bacillus ayatagriensis RMG6T as a novel species with significant biocontrol potential and plant growth-promoting capabilities, advocating its expanded use in agriculture and industry.

Glaciers are part of the Earth’s cryosphere and harbor diverse microbial life. The microbes living in glaciers have developed incredible adaptations to survive in these challenging conditions. Their icy environments contain distinct layers and habitats, including snow, ice, glacial streams, and the underlying frozen ground. These habitats feature varying nutrient availabilities and chemical compositions, and support microbial communities that have adapted to survive under extreme cold, fluctuating nutrient levels, and exposure to ultraviolet radiation. Some of their extended adaptation features are the ability to make antifreeze proteins, proteins that bind and break up ice, exopolysaccharides, and solutes that work well with each other. Genome plasticity analysis has uncovered and supported the presence of a unique gene pool among glacier-dwelling microbes. Therefore, studies on glaciers remain important to disclose unknown facts about the full extent of potential microbial diversity and metabolic processes within these icy ecosystems. Hence, there is an urgent need for further research to understand and preserve these unique and extreme environments.

Background Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.Results The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.Conclusion Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.

Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample’s microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.

The safety of meat from a microbiological standpoint is of paramount concern to public health, given the potential for bacterial contaminants to grow and persist during processing and storage. To address this issue, a culture-independent approach targeting the V3-V4 region of the 16S rRNA gene was utilized to investigate the inherent bacterial communities present in 10 chicken meat samples obtained from retail markets. Amplicons were sequenced using the Illumina MiSeq platform, and unique amplicon sequence variants (ASVs) were identified using the DADA2 pipeline. Results indicated the presence of 5 phyla, 7 classes, 16 orders, 33 families, 59 genera, and 273 unique ASVs. The dominant families were Flavobacteriaceae, Moraxellaceae, Enterobacteriaceae, Wohlfahrtiimonadaceae, Morganellaceae, and Pseudomonadaceae, comprising 27.03, 22.04, 15.67, 9.40, 7.92, and 5.02

Abstract Pelagic transport causes oil pollution by traversing the open ocean in southern Asia and Indian territory via international tanker routes. The natural flow of ocean water from east to west, which carries pollutants and biohazards into the marine waters belonging to the Indian territory, is what causes the deposition and saturation of oil spills, tar (i.e., hydrocarbons), and wastes in ocean waters. Water currents and tides carry tons of crude oil that has leaked from oil tanker accidents in the open ocean to coastlines. Here we report that marine traffic of sailing flags across oceans causes pollution that results in the formation of algal blooms and has an impact on the production of chlorophyll and the mortality of fauna. The consequences of pollution have mostly affected coastal areas, especially mangroves, and may destroy potential fishing zones. Furthermore, it was recorded that long-term exposure to pollutants may cause the development of antibiotic and hydrocarbon resistance in bacteria. Bacterial taxa like Bacillus, Domibaciluus, Acinetobacter, Brevundimonas, Streptococcus, Mycolibacterium, and Spingomonas, among others, were found, and their identities were confirmed by sequencing the 16S rRNA gene. Antimicrobial resistance in these bacteria may pose a threat to public health.

Microorganisms play a major role in the degradation of organic matter in sediments. However, the spatiotemporal variation and factors affecting these communities are not clearly understood. At the same time, conventional hydrographic and geochemical parameters do not offer an accurate assessment of transitional ecosystems. PLFA biomarkers which are specific to different taxonomic groups of microorganisms are able to provide a detailed assessment of the community composition in an environment and reflect a more direct assessment of the biological health of transitional ecosystems. We, therefore, conducted a comparison of PLFA biomarkers at four stations (Barmouth, B; Vaduthala, V; Munambam, M; and Arookutty, A) during three seasons (pre-monsoon, PRE; monsoon, MON; and post-monsoon, POST) in the Cochin estuary (CE). Each of the stations represented either a reference point (B), high pollution (V), high salinity (M), or low pollution (A). The communities determined using PLFA profiles could be categorized into six major groups with each group capable of reflecting the state of the ecosystem which correlated with the conventional parameters. The six groups were: G + ve Bacillota (formerly Firmicutes) and G-ve anaerobes (G-I), G-ve aerobic prokaryotes (G-II), ectomycorrhizal fungi (G-III), arbuscular mycorrhizae (G-IV), type-I methanotrophs (G-V), and microeukaryotes (G-VI). The prokaryotes were predominant in sediments amounting to over 78% of the total PLFAs detected, followed by the microeukaryotes. The freshwater-influenced stations were partially anaerobic in nature during PRE and MON and were mainly affected by both marine and terrestrial organic matter inputs, at times prominent in sewage matter. During POST season, CE behaves uniformly, especially in station M. Salinity and DO of BW and texture and organic matter of the sediment were the driving forces for microbial community structure. The reduced presence of cyclopropane fatty acids suggested that the CE was not under any stress during the study period. Our results using PLFA-based community profiling not only provide the fundamental information required to quickly access the impact of stress and other environmental inputs on the CE but also offer a more robust and realistic assessment of the nature of microbial communities in the ecosystem. A periodic and systemic assessment of PLFA profiles at these stations in CE throughout the year will enable the generation of enough metadata enabling a better understanding of this ecosystem and its efficient management in the long term.

The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data ( P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia , respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces , Akkermansia , Isosphaera , and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria , Proteobacteria , Viridiplantae , Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.

Abstract Pelagic transport causes oil pollution by traversing the open ocean in southern Asia and Indian territory via international tanker routes. We report that the traffic of sailing flags across oceans causes pollution in the Bay of Bengal and the Arabian Sea, which results in the formation of harmful algal blooms and an increase in chlorophyll productivity. The natural flow of ocean water from east to west, which carries pollutants into the marine waters belonging to the Indian territory, causes the deposition and saturation of oil spills and biohazardous wastes. The consequences of pollution have mostly affected coastal areas and caused the mortality of fauna. Metagenome analysis indicates a reduced microbial load and the presence of fewer microbial features across coastal soil. Long-term exposure to pollutants results in an unusual increase in cell size and the development of hydrocarbon- and antibiotic-resistant profiles. Bacterial taxa such as Brevundimonas, Streptococcus, Mycolibacterium, Sphingomonas, Bacillus spp., Chitinophaga, Priestia, Domibacillus, Rossellomorea, Acinetobacter towneri, etc., were found, and their identities were confirmed by 16S rRNA gene sequencing. These bacteria pose a serious threat to public health.

We report a preliminary study of soil from the Central Deccan Plateau dry tropical deciduous forest in India using 16S rRNA gene amplicon sequencing. We report diverse taxa, e.g., Proteobacteria, Actinobacteria, Acidobacteria, Plactomycetes, Chloroflexi, Bacteroidetes, Verrucomicrobia, Gemmatimonadetes, Firmicutes, Crenarchaeota, Nitrospirae, Armatimonadetes, Elusimicrobia, Cyanobacteria, Chlamydiae, Chlorobi, Parvachaeota, Tenericutes, Euryarchaeota, Fibrobacteres, Calditrix, and Spirochaetes.

Understanding the impact of long-term fertilization in different soil types and its effect on soil bacteria and crop production is critical for designing sustainable agricultural practices across diverse landscapes. Here, we investigated the impact of 25-37 years of continuous fertilizer treatments in three parent materials (Phaeozem, Cambisol, and Acrisol) on crop yield, soil properties, and soil bacteria (i.e., the total 16 S rRNA gene abundance, community structure, and its relationship with soil nutrient) across diverse Chinese agriculture areas. Four consistent treatments were included: unfertilized control (CK), inorganic nitrogen fertilizer (N), manure (M), and manure plus nitrogen (MN). The crop yields were significantly increased under MN treatments at the rates of 147 kg/ rotation (3 years) in Phaeozem and 90.6 kg/ rotation (1 year) in Acrisol, while the crop yields remained constant or decreased for CK and N treatments. The relative abundance of Acidobacteria_Gp6 and Planctomycete were significantly higher in manure treatments than in chemical fertilizer treatment. Through the structural equation model (SEM) analysis, species in module 1 were directly correlated with crop yield, and both module 2 and module 3 species were indirectly correlated with crop yield via SOM and NO3- contents. Proteobacteria, Acidobacteria, and Firmicutes were dominant bacterial groups in the three modules, respectively. This study reveals the complex role of keystone ecological clusters of soil bacteria on crop yields and identifies the common bacterial taxa that respond to long-term fertilization and thereby, as potential targets for improving soil fertility across soil types.

Advances in sequencing technology have played a critical role in our understanding of the microbial diversity on the planet. The qualitative assessment of microbial diversity began with the use of Sanger sequencing-based cloning-dependent approach in the late 20th century. The quantitative assessment of microbial diversity began with LIBSHUFF, which laid the foundation of statistical tools for microbial diversity studies. However, the development of high-throughput sequencing, such as 454 pyrosequencing, Ion Torrent, Illumina, Nanopore posed specific challenges for post-sequencing analysis. Today, researchers widely use Usearch, K-shuff, FLASH, MOTHUR, Quantitative Insights Into Microbial Ecology (QIIME), Rtools, and many others along with many databases like NCBI, RDP, Greengenes, SILVA, and EzBioCloud for accurate taxonomic assignment of Bacteria, Archaea, and Eukarya. In this chapter, the developments in sequencing technology, databases and analyses tools will be discussed. In addition, the current strategy which is used for the assessment of microbial diversity will be discussed briefly.

The determination of organic nitrogen (N) mineralization is crucial for estimating N availability, quantifying exogenous inputs, and estimating associated environmental impacts. The objective of this study was to explore the effect of long-term various fertilization on soil organic N mineralization potential (NMP), which influences plant N accessibility. Treatments from a 26-year long-term field experiment with no fertilization (CK), chemical fertilizer N at 165 kg N ha−1 and P at 82.5 kg P2O5 ha−1 (NP), NP with K fertilizer at 165, 82.5, 82.5 kg ha−1 N, P2O5 and K2O (NPK), NPK at 165, 82.5, 82.5 kg ha−1 N, P2O5 and K2O with manure at 7857.14 kg ha−1 (NPKM), and NPKM at 165, 82.5, 82.5 kg ha−1 N, P2O5 and K2O with manure at 1.5× application rate (11,785.71 kg ha−1) (1.5NPKM) were examined for potentially mineralizable N by aerobic incubation at 35 °C for 30 weeks. Three pools (Pools I, II, and III) of mineralizable N were recognized. Pool I, the mineralization flush on rewetting in the first 2 weeks; Pool II, gross N mineralization between weeks 2 and 30; and Pool III, the potentially mineralizable N, predicted from the fitted curve, that did not mineralize during the incubation period. Soil microbial biomass carbon (SMBC) and N (SMBN) as well as fixed ammonium (NH4+) contents and relationship with N mineralization rate (k) were also studied. Long-term manure application yielded a significantly higher k (0.32 week−1) than other treatments (0.12–0.22 week−1) but not a significantly higher NMP. Nitrogen mineralization during the wheat and maize-growing seasons was predicted to be 8.7–26.3 (mg N kg−1 soil) and 25.9–42.1 (mg N kg−1 soil), respectively. Both labile mineralizable N pools (Pools I and II) followed the same patterns in the treatments: 1.5NPKM > NPKM > NPK > NP > CK, while the reverse was true for stable N (Pool III). The significant positive correlation between k with SMBC and SMBN (R2 = 0.93, p = 0.008 and R2 = 0.94, p = 0.006) suggested that the higher mineralization rate might be contributed by the higher soil microbial biomass in NPKM. The trends of fixed NH4+ and mineralized N were coupled. Long-term manure application significantly improved the N mineralization rate in soil. Manure application is an effective strategy to enhance soil microbial biomass and soil N availability and has the potential to reduce the dependence upon chemical N fertilization.

Cow, Bos taurus, and female buffalo, Bubalus bubalis, are considered sacred animals that are a part of rural livelihood in India. The purity of products from these bovine species has significant sentimental implications in the dairy and meat industry. Therefore, the mitochondrial DNA and the sex origin, targeting the X and Y chromosomes from these bovine species, were selected to design three multiplex real-time probe PCR assays: HiPCR (R) Cow Detection Kit (MBPCR184), Hi-PCR (R) Buffalo Detection Kit (MBPCR185) and Hi-PCR (R) Cattle Sex Determination Kit (MBPCR186). Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines were followed to perform different studies using reference control DNAs. An Internal Reagent Control (IRC) was part of every assay, thus ensuring a successful reaction. The assays were 100% specific, with no crossamplification of the two bovine species. The amplification of the X chromosomal target was observed for male and female DNAs, whereas Y chromosome amplification was observed only for the male DNA. The assays were 100% specific to the target genes in these organisms with no non-specificity towards any other targets or organisms. The limit of detection for sex determination was 0.01 ng/mu l, whereas the differential capability of the assay was 3 copies/mu l and 30 copies/mu l for Bos taurus and Bubalus bubalis, respectively. The assays were reproducible at 1 ng/mu l genomic DNA with 95% CI. The assays are open and compatible with other brands of RealTime PCR systems used in forensic labs. The experiments presented here verify that the developed real-time PCR assays are robust, produce reliable and reproducible results for detection and differentiation of Bos taurus and Bubalus bubalis and their sex even at low DNA concentrations.

Indian arid regions recently witnessed large scale mortality in the Indian mesquite {Prosopis cineraria Druce}, locally known as Khejri tree, due to root rot caused by Ganoderma lucidum. Use of biological control agents offers an attractive alternative to manage Ganoderma induced diseases in Khejri tree, without any negative impact on the environment. Therefore, efforts were made to isolate antagonistic bacterial isolates from infected trees of P. cineraria. Several soil samples were analysed and two bacterial isolates: strains AZAC-1and AZ-11were selected as potential antagonists against G.lucidum from arid soils. Taxonomic identity of the two strains was ascertained using 16S rRNA in EzBioCloud. The strains showed over 99.7% similarity and were identified as Streptomyces sp.strain AZAC-1 (MK459414) and Bacillus sp.strain AZ-11(MH304296).

EDITORIAL article Front. Microbiol., 19 September 2019Sec. Antimicrobials, Resistance and Chemotherapy Volume 10 - 2019 | https://doi.org/10.3389/fmicb.2019.02173

Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and diversity change as a result of local environmental gradients that develop during pedogenesis. Geographic factors were studied between and within locations spanning two scales: (1) regionally between 0.1 and 50 and (2) ∼1700 km apart. The diversity was surveyed using high-throughput pyrosequencing, and variance partitioning was used to describe the effects of spatial, environmental, and spatio-environmental factors on bacterial community composition. At the local scale, variation in bacterial communities was most closely related to environmental factors (rM = 0.59, p = 0.0001). There were differences in bacterial communities between the two locations, indicating spatial biogeography. Estimates of bacterial diversity were much greater in MI (numbers of OTU, ACE, and Chao1) and remained 2–3× greater in MI than GA after removing the effect of soil properties. The large differences in diversity between geographically separated bacterial communities in different climates need further investigation. It is not known if the rare members of the community, which contributed to greater bacterial diversity in GA relative to MI, play an important role in ecosystem function but has been hypothesized to play a role in ecosystem resiliency, resistance, and stability. Further research on the link between bacterial diversity and spatial variability related to climate needs further investigation.

To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50–70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50–70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.