Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its ...relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
Due to industrialization, the contamination of toxic metals in soils is currently one of the major concerns to scientists worldwide. The presence of high concentrations of heavy metals including ...cadmium in the environment is mainly attributed to human activities. Being a highly toxic metal, cadmium can enter plant cell transporters usually used for the uptake of essential cations, such as iron, calcium, and zinc. This study deals with the appraisement of response and tolerance shown by various bacteria in varied cadmium concentrations (100-1,000 ppm). The optical density (OD) of the isolates was measured to determine the minimum inhibitory concentration (MIC) of cadmium. Isolated bacteria have been identified using 16S rRNA gene sequence and Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among the 72 isolates, 07 (
, and
), isolates had efficacy for cadmium tolerance and showed sequestration potential at varying MIC. Furthermore,
was observed to have the highest (900 ppm) tolerance for cadmium and the lowest (600 ppm) was shown by
. Besides,
showed the highest (75.2%) sequestration potential while the least (52.4%) potential was observed for
. These cadmium tolerant species can be implemented in contaminated environments for detoxification and elimination of cadmium from these agricultural fields. Graphical Abstract.
A novel bacterial strain designated as ADMK78
T
was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78
T
grows best at 28 °C. ...Phylogeny of 16S rRNA gene placed the strain ADMK78
T
with the members of genera
Ciceribacter
and
Rhizobium
, while the highest sequence similarity was with
Rhizobium wuzhouense
W44
T
(98.7%) and
Rhizobium ipomoeae
shin9-1
T
(97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78
T
forms a distinct cluster including five species of
Rhizobium
, which is separate from the cluster of the genera
Rhizobium
and
Ciceribacter.
We propose re-classification of
Rhizobium ipomoeae
,
R. wuzhouense
,
R. rosettiformans
and
R. rhizophilum
into the novel genus
Peteryoungia
. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78
T
were less than 82 and 81%, respectively, among all type strains included in the genus
Peteryoungia.
The strain ADMK78
T
showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78
T
represents a novel species,
Peteryoungia desertarenae
sp. nov. The type strain is ADMK78
T
(= MCC 3400
T
; KACC 21383
T
; JCM 33657
T
). We also proposed the reclassification of
Rhizobium daejeonense
,
R. naphthalenivorans
and
R. selenitireducens
, into the genus
Ciceribacter
, based on core gene phylogeny and AAI values.
Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation ...agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the long-term application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a long-term experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of
Rhizobium
,
Pseudomonas
,
Pantoea
,
Nitrobacter
,
Enterobacter
, and
Sphingomonas
were significantly higher in the rhizosphere. At the same time,
Massilia
,
Paenibacillus
, and
Planomicrobium
were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.
Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore ...of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon’s and Simpson’s alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.
Accurate taxonomy is essential for microbial biological resource centers, since the microbial resources are often used to support new discoveries and subsequent research. Here, we used genome ...sequence data, alongside matrix-assisted laser desorption/ionization time-of-flight mass spectrometer biotyper-based protein profiling, to accurately identify six
complex strains. This approach effectively identified distinct species within the
complex, including
, "
," and
. Moreover, the study revealed the existence of a novel species within the
genus, for which we proposed the name
sp. nov. In summary, this study demonstrates the significance of adopting a genome sequence-driven taxonomy approach for the precise identification of bacterial strains in a biological resource center and expands our understanding of the
complex.
Biologically active secondary metabolites, essential oils, and volatile compounds derived from medicinal and aromatic plants play a crucial role in promoting human health. Within the large family ...Asteraceae, the genus
consists of approximately 500 species.
species have a rich history in traditional medicine worldwide, offering remedies for a wide range of ailments, such as malaria, jaundice, toothache, gastrointestinal problems, wounds, inflammatory diseases, diarrhoea, menstrual pains, skin disorders, headache, and intestinal parasites. The therapeutic potential of
species is derived from a multitude of phytoconstituents, including terpenoids, phenols, flavonoids, coumarins, sesquiterpene lactones, lignans, and alkaloids that serve as active pharmaceutical ingredients (API). The remarkable antimalarial, antimicrobial, anthelmintic, antidiabetic, anti-inflammatory, anticancer, antispasmodic, antioxidative and insecticidal properties possessed by the species are attributed to these APIs. Interestingly, several commercially utilized pharmaceutical drugs, including arglabin, artemisinin, artemether, artesunate, santonin, and tarralin have also been derived from different
species. However, despite the vast medicinal potential, only a limited number of
species have been exploited commercially. Further, the available literature on traditional and pharmacological uses of
lacks comprehensive reviews. Therefore, there is an urgent need to bridge the existing knowledge gaps and provide a scientific foundation for future
research endeavours. It is in this context, the present review aims to provide a comprehensive account of the traditional uses, phytochemistry, documented biological properties and toxicity of all the species of
and offers useful insights for practitioners and researchers into underutilized species and their potential applications. This review aims to stimulate further exploration, experimentation and collaboration to fully realize the therapeutic potential of
in augmenting human health and well-being.
Isolation and characterization of fluorescent pseudomonads with high phosphate-solubilizing ability is reported from the alkaline and calcium-rich soils with low P availability in the cold desert ...region of Lahaul and Spiti in the trans-Himalayas of India. Of 216 phosphate-solubilizing isolates, 12 exhibiting high solubilization of tricalcium phosphate (TCP) in NBRIP liquid culture were identified as Pseudomonas trivialis, P. poae, P. fluorescens, and Pseudomonas spp. on the basis of phenotypic features, whole-cell fatty acids methyl ester (FAME) profiles, and 16S rDNA sequencing. These isolates also showed relatively high solubilization of North Carolina rock phosphate (NCRP) in comparison to the solubilization of Mussoorie rock phosphate (MRP) and Udaipur rock phosphate (URP). The solubilization of phosphate substrates by P. trivialis and P. poae is reported for the first time.
A substantial majority of global population owns cellular phones independently to demographic factors like age, economic status, and educational attainment. In this study, we investigated the ...diversity of microorganisms associated with cellular phones of 27 individuals using cultivation-based methods. Cellular phones were sampled using cotton swabs and a total of 554 isolates representing different morphotypes were obtained on four growth media. Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry could generate protein profiles for 527 isolates and species-level identification was obtained for 415 isolates. A dendrogram was constructed based on the protein profiles of the remaining isolates, to group 112 isolates under 39 different proteotypes. The representative strains of each group were selected for 16S rRNA gene and ITS region sequencing based identification.
,
,
, and
were the most frequently encountered bacteria, and
,
,
, and
were in case of fungi. At species-level the prevalence of
,
,
,
,
, and
was observed, most of these species are commensal microorganisms of human skin. UPGMA dendrogram and PCoA biplot generated based on the microbial communities associated with all cellular phones exhibited build-up of specific communities on cellular phones and the prevalence of objectionable microorganisms in some of the cellular phones can be attributed to the poor hygiene and sanitary practices. The study also revealed the impact of MALDI-TOF MS spectral quality on the identification results. Overall MALDI-TOF appears a powerful tool for routine microbial identification and de-replication of microorganisms. Quality filtering of MALDI-TOF MS spectrum, development of better sample processing methods and enriching the spectral database will improve the role of MALDI-TOF MS in microbial identifications.
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