Culturable Diversity Research Articles

A Surveillance Study of Culturable and Antimicrobial-Resistant Bacteria in Two Urban WWTPs in Northern Spain.

Wastewater treatment plants (WWTPs) are hotspots for the spread of antimicrobial resistance into the environment. This study aimed to estimate the proportion of clinically relevant antimicrobial-resistant bacteria in two Spanish urban WWTPs, located in the region of La Rioja (Spain); Methods: Ninety-four samples (48 water/46 sludge) were collected and streaked on ten different selective media, in order to recover the culturable bacterial diversity with relevant resistance phenotypes: Extended-Spectrum β-Lactamase-producing Escherichia coli/Klebsiella pneumoniae (ESBL-Ec/Kp), Carbapenem-resistant Enterobacteriaceae (CR-E), Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin-resistant Enterococcus faecium/faecalis (VR-E. faecium/faecalis). Isolates were identified by MALDI-TOF and were tested for antimicrobial susceptibility using the disk diffusion method. The confirmation of ESBL production was performed by the double-disk test; Results: A total of 914 isolates were recovered (31 genera and 90 species). Isolates with clinically relevant resistance phenotypes such as ESBL-Ec/Kp and CR-E were recovered in the effluent (0.4 × 100-4.8 × 101 CFU/mL) and organic amendment samples (1.0-101-6.0 × 102 CFU/mL), which are discharged to surface waters/agricultural fields. We reported the presence of VR-E. faecium in non-treated sludge and in the digested sludge samples (1.3 × 101-1 × 103 CFU/mL). MRSA was also recovered, but only in low abundance in the effluent (0.2 × 101 CFU/mL); Conclusions: This study highlights the need for improved wastewater technologies and stricter regulations on the use of amendment sludge in agriculture. In addition, regular monitoring and surveillance of WWTPs are critical for early detection and the mitigation of risks associated with the spread of antimicrobial resistance.

Next-generation sequencing-based comparative mapping and culture-based screening of bacterial rhizobiome in Phytophthora capsici-resistant and susceptible Piper species.

Black pepper (Piper nigrum L.), a highly valued spice crop, is economically significant as one of the most widely traded spices in the world. The global yield and quality of black pepper (Piper nigrum L.) are affected by foot rot-causing soil-borne oomycete pathogen Phytophthora capsici. To gain initial insights toward developing an approach that utilizes microbial genetic resources for controlling foot rot disease in black pepper, we mapped the rhizobiome communities in susceptible Piper nigrum L. and wild-resistant Piper colubrinum. The analysis showed compositional differences in the rhizobiome of two Piper species, which revealed higher diversity and the presence of more differentially abundant genera in P. colubrinum. Furthermore, P. colubrinum rhizobiome had a significantly higher abundance of known anti-oomycete genera, such as Pseudomonas, and a higher differential abundance of Janthinobacterium, Variovorax, and Comamonas, indicating their probable contribution to pathogen resistance. Predictive functional profiling in P. colubrinum rhizobiome showed highly enriched functional gene orthologs (KOs), particularly chemotaxis proteins, osmoprotectants, and other transport systems that aid in pathogen resistance. Similarly, pathways such as phenylpropanoid biosynthesis and other antimicrobial synthesis were enriched in P. colubrinum rhizobiome. The culturable diversity of the resistant root endosphere, which harbors efficient biocontrol agents such as Pseudomonas, strengthens the possible role of root microbiome in conferring resistance against soil-borne pathogens. Our results depicted a clear distinction in the rhizobiome architecture of resistant and susceptible Piper spp., suggesting its influence in recruiting bacterial communities that probably contribute to pathogen resistance.

Abundance and diversity of the culturable nectar mycobiome in Rhododendron catawbiense varies with elevation

Abstract The nectar microbiome can influence pollinator choice and plant fitness. Previous research has shown that changes in environmental conditions at large spatial scales can influence nectar microbiome composition. However, little is known about how changes in climate with increasing elevation affect nectar microbiome abundance and composition. Here we describe the culturable nectar mycobiome of Rhododendron catawbiense (Ericaceae) by quantifying colony abundance, identity, and richness of fungal genera. We further evaluate how the culturable nectar mycobiome (CNMB) abundance, diversity, and composition (i.e., the fungal species within the nectar microbiome) varies at two different elevations. Nectar samples were collected from R. catawbiense individuals at a high and low elevation and were cultured on yeast agar with 0.01% chloramphenicol media. Fungal colonies were categorized morphologically, quantified, and then identified using DNA barcoding. In total, 2,822 fungal colonies were recorded belonging to six genera across both elevations. Elevation did not influence CNMB diversity (Simpson’s diversity index) or genera richness per flower, however only three genera were found at the high elevation while six were found at the low elevation. Elevation had a significant effect on colony abundance with a 95% increase in the number of colonies in nectar samples at low compared to the high elevation. Variation in abundance and overall genera composition of fungal colonies across elevations may have the potential to affect nectar quantity and quality and ultimately pollination success. This study adds to our understanding of the drivers of CNMB composition across spatial scales its potential implications for plant-pollinator interactions.

Activity and Identification of Culturable Methanotrophs from Mangrove Sediments, South East Coast of India

Anthropogenic activities have escalated CH4 emissions, exacerbating global warming, yet specialized bacteria known as Methanotrophs play a key role in mitigating atmospheric CH4 levels by consuming 30-70% of emitted methane. This study focuses on exploring the culturable methanotrophic population within Muthukuda mangrove sediments, an unexplored reservoir of methanotrophic diversity. The sediment sample yielded a methanotrophic bacterial count of 1.5 x 103 CFU/g, leading to the selection of three unique bacterial morphotypes (NCT270, NCT271, and NCT272) for in-depth investigation. Optimal growth was observed at pH 8, with peak growth at 30°C, while extreme temperatures of 4°C and 40°C inhibited growth across all isolates. Salinity levels between 20 and 30 ppt supported optimal growth, with strains displaying tolerance to various stressors. Methane served as the sole carbon source for all experiments, with positive urease production noted after 7 days of incubation. Microscopic and biochemical analyses suggested the classification of strains NCT270, NCT271, and NCT272 within Group I methanotrophic genera: Methylomicrobium, Methyloscarcina, and Methylomonas, respectively. BLASTn analysis of 16S rRNA gene sequences shared high similarities with known methanotrophic species Methyloscarcina fibrate (ON834586) with 99.28%, Methylomicrobium album (ON834587) with 98.77% and Methylomonas methanica (ON834588) with 99.15%. The resulting insights enhance our understanding of culturable methanotrophic diversity and underscore its potential for environmental applications.

Impact of Soil Management Practices on Soil Culturable Bacteriota and Species Diversity in Central European a Productive Vineyard under Warm and Dry Conditions

Sustainable management practices are crucial for the longevity of a monoculture vineyard, especially in the context of a changing climate. Therefore, soil management practices in a vineyard (T: tillage, T+FYM: tillage + farmyard manure, G: grass strips, G+NPK1: grass strips + rational rates of NPK, and G+NPK2: grass strips + higher rates of NPK) were tested in a temperate climate of Slovakia (Central Europe) under specific soil conditions (Rendzic Leptosol). We investigated the influence of continuous cropping on soil chemical properties and microbial communities during the dry and warm year of 2022. The results showed that the soil pH was higher by 19%, 21%, 24% and 13% in T, T+FYM, G and G+NPK1, respectively, compared to G+NPK2. The lowest soil organic matter (SOM) content was found in T, and it increased in the following order: T < T+FYM < G+NPK2 < G+NPK1 < G. Similarly, the lowest abundance of soil culturable bacteriota was found in T and it increased in the following order: T < T+FYM = G+NPK2 < G+NPK1< G. Culturable bacteriota was identified using mass spectrometry (MALDI-TOF MS Biotyper). The most numerous species group was Bacillus, followed by Lactobacillus > Staphylococcus > Pseudomonas. The most frequently isolated species were Bacillus megaterium (16.55%), Bacillus cereus (5.80%), Bacillus thuringiensis (4.87%), and Bacillus simplex (4.37%). Positive relationships between SOM and soil culturable bacteriota were found in the G and G+NPK1 treatments. Temperature also affected soil culturable bacteriota in all soil management practices, most significantly in G+NPK1. Overall, the best scenario for the sustainable management of a productive vineyard is the use of grass strips.

Ecological Characteristics of Culturable Myxobacteria in the Rhizosphere Soil of Saline-Tolerant Plants in the Ebinur Saline Wetlands

T his study investigated the ecological distribution of myxobacteria in the saline environment of the Ebinur Lake Wetland, in China, which provides a unique microecological environment for their survival. Culturable myxobacteria were isolated using traditional methods including Escherichia coli DH5α, rabbit feces, and filter paper flakes as food sources. Molecular identification along with physiological, biochemical assays and morphological characterization was carried out for the classification and identification of myxobacteria. Associations between soil environmental factors and myxobacterial diversity were analyzed using redundancy analysis. This study involved collecting rhizosphere soil from 15 species of salt-tolerant plants, ultimately yielding 15 strains of myxobacteria from eight of these species. Fifteen strains of myxobacteria were taxonomically placed by analyzing 16S rRNA homology, seven strains were closely related to Myxococcus virescens, six strains were closely related to Myxococcus fulvus and two strains were closely related to Myxococcus xanthus. Myxococcus virescens, the dominant cultivable species of myxobacteria in the Ebinur Lake Wetland, was isolated from various sampling sites using traditional methods. Analysis of antibiotic resistance revealed that myxobacterial strains M2, M6, M9, M13, and M15 are resistant to gentamicin. Furthermore, predation assays demonstrated that myxobacterial strain M14 exhibits the broadest spectrum of predation against both bacterial and fungal prey. The limited culturable myxobacterial diversity observed in the Ebinur Lake Wetland could potentially result from variations in soil physicochemical properties, vegetation type, and employed isolation methods. These findings enhance our comprehension of the myxobacterial resources within this specific salt desert ecosystem.

Different Tillage and Residue Management Practices Affect Soil Biological Activities and Microbial Culturable Diversity in Rice-Wheat Cropping System Under Reclaimed Sodic Soils

Different Tillage and Residue Management Practices Affect Soil Biological Activities and Microbial Culturable Diversity in Rice-Wheat Cropping System Under Reclaimed Sodic Soils

Culturable Diversity of Endophytic and Rhizoplane Colonizing Bacteria of Indian Mustard (Brassica juncea (L.) Czern & Coss), Affected by Soil Types and Assessment of Plant Growth Promoting Attributes

Microbial community in the rhizosphere of plant significantly influences growth and development of a plant. As the soil vary in microbial composition due to interaction of soil with plant roots and its exudates, the role of soil in shaping microbial diversity of a crop rhizosphere is least studied. In present study, Mustard (Brassica juncea cv Pusa Mehak) was grown in three different soil viz. Vertisols, Inceptisols and Alfisols, and the bacteria were isolated form root tissues and rhizoplane to study their plant growth promoting (PGP) attributes and diversity using BOX-Polymerase chain reaction (PCR) fingerprinting technique, as influenced by soil types. Form threes soil orders, total 37 isolates were obtained of which, 19 could grow on nitrogen free medium, 6 solubilized P from tricalcium phosphate, 2 isolate solubilized potassium from glauconite and 8 had zinc solubilizing ability with the highest zinc solubilization index of 3.84 by isolate VRB-7. Based on the fingerprint analysis, differences occurred in the endophytic bacteria of same host grown in different soil types suggesting influence of soil types in colonization of microbes in rhizoplane and endorhizosphere. The common organisms obtained from host grown in different soil types indicating host genotype driven assembly of bacteria. Similarity in the isolates on rhizoplane and endorhizosphere indicated endophytic colonization of the isolates capable of firmly adhering to the rhizoplane. The findings of this study will help in formulation of crop specific bioinoculant for specific soil types and edaphic properties.

Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast.

Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.

Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils.

Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.

Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach.

The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.

Unveiling the culturable bacterial diversity, pathogens and impact of seasonality on microflora of raw goat milk: A phylogenetic outlook

Goat milk can be beneficial in cardiac diseases, mouth ulcers, dengue fever, etc. but ingestion of raw goat milk may have severe side effects as it may comprise pathogenic bacteria. Raw goat milk samples (n-55) were collected from diverse villages of the Udaipur district, Rajasthan, India and analyzed for bacterial diversity and pathogens using biochemical, molecular, and bioinformatic methods. Goat milk samples displayed an incidence of 36.36% for bacterial pathogens and the most prevalent bacteria reported were Listeria spp. and Staphylococcus spp. Bacillus cereus and Staphylococcus xylosus showed high resistance to tested antibiotics followed by Listeria. The dominant phylum found in the raw goat milk was Firmicutes (67.47%) and the dominant genus was Bacillus (28.32%). Listeria sp. was found dominant during the winter season while Staphylococcus spp. was dominant during summer. Three novel species were identified viz. S. xylosus (GM61), Streptomyces sp. C7 (GM2) and Pantoea agglomerans (GM31) can be further explored for their potential applications as bacteriocin producers' which can be used as food preservatives. New antibiotics or any antimicrobial produced by these three novel species can be used for the treatment of diseases. Pseudomonas yangonensis and Streptomyces sp. have not been previously reported in goat milk at the global level while S. xylosus at the National level.

Culturable yeast diversity in urban topsoil influenced by various anthropogenic impacts.

In urban ecosystems, processes associated with anthropogenic influences almost always lead to changes in soil micromycete complexes. The taxonomic structure of soil micromycete complexes is an important informative parameter of soil bioindication in the ecological control of urban environments. Unicellular fungi, such as culturable yeasts, are a very suitable and promising object of microbiological research for monitoring urban topsoil. This review aims to give an overview of the yeast communities in urban topsoil in different areas of Moscow (heating main area, household waste storage and disposal area, highway area) and to discuss the changes in the taxonomic structure of culturable yeast complexes depending on the type and intensity of anthropogenic impact.

Unearthing diverse culturable fungal communities associated with Ophiocordyceps indica sp. nov. from Indian Western Himalaya.

Fungal communities colonizing Ophiocordyceps spp. plays a crucial ecological role in their natural habitat, contributing to infect the host larvae, and influencing their occurrence. Although associated fungi with the newly described Ophiocordyceps indica, from the Indian Western Himalaya remains unclear. Therefore, we untangled the culturable fungal communities associated with O. indica and soil adhered to it, collected from low-height areas of Himachal Pradesh, India. The study resulted in the identification of 111 fungal isolates representing 17 families, with maximum fungal isolates (36.03%) within Cordycipitaceae. Interestingly, a total of 24 genera were found associated with O. indica and adhered soil, of which 12 were common, 8 were exclusive to O. indica and4 were only limited to soil. Additionally, the influence of soil physicochemical parameters on fungal diversity indices revealed a positive correlation with humidity and available nitrogen and a negative correlation with pH and available phosphorus. These findings provide insights into the culturable fungal diversity of O. indica and the soil adhering to it, thus can contribute to the understanding of host-microbial interactions. Furthermore, these associations can be explored as a source of bioactive metabolites to combat the unending industrial demands.

Bacteria associated with carminic acid metabolism in the intestinal tract of three predators of Dactylopius opuntiae

AbstractDactylopius spp. produce carminic acid as part of defence against predation. The average carminic acid concentration varies depending on the species, e.g., for prickly pear cochineal, Dactylopius opuntiae (Cockerell), and cochineal, Dactylopius coccus Costa (Hemiptera: Dactylopiidae), it is 3–5 and 19–25%, respectively. Generalist predators such as Laetilia coccidivora Comstock (Lepidoptera: Pyralidae) and specialist predators such as Leucopis bellula Williston (Diptera: Chamaemyiidae) and Hyperaspis trifurcata Schaeffer (Coleoptera: Coccinellidae) require detoxification mechanisms, which could be provided by gut bacteria. We determined the diversity of gut‐associated cultivable bacteria in these three predators and their ability to metabolize carminic acid. The bacteria were identified morphologically and by partial sequencing of the 16S rRNA gene. In vitro assays were done to determine their ability to metabolize carminic acid. The greatest culturable bacterial diversity was found in L. coccidivora larvae and H. trifurcata adults, followed by H. trifurcata larvae. The lowest diversity was found in L. bellula larvae. DNA sequencing revealed the presence of Bacillus cereus Frankland & Frankland, Enterococcus gallinarum (Bridge & Sneath) Collins et al., and Enterococcus casseliflavus Collins et al. in L. coccidivora larvae, Enterobacter spec. in larvae of H. trifurcata, Lactococcus lactis (Lister) Schleifer in adults of H. trifurcata, and Staphylococcus spec. in larvae and adults of H. trifurcata. Bacillus pumilus Meyer & Gottheil was only found in L. bellula larvae. In vitro assays showed that all isolates evaluated could metabolize carminic acid, suggesting they play an important role in the predators' ability to metabolize carminic acid. Presence of E. gallinarum, which had the most efficient metabolism of carminic acid, might allow L. coccidivora to feed on the two Dactylopius species regardless of carminic acid concentration.

Insights into Some Onygenalean Fungi from Freshwater Sediments in Spain and Description of Novel Taxa.

During the course of a project investigating culturable Ascomycota diversity from freshwater sediments in Spain, we isolated 63 strains of cycloheximide-resistant fungi belonging to the order Onygenales. These well-known ascomycetes, able to infect both humans and animals, are commonly found in terrestrial habitats, colonizing keratin-rich soils or dung. Little is known about their diversity in aquatic environments. Combining morphological features and sequence analyses of the ITS and LSU regions of the nrDNA, we identified 14 species distributed in the genera Aphanoascus, Arachniotus, Arthroderma, Arthropsis, Emmonsiellopsis, Gymnoascoideus, Leucothecium, Malbranchea, and Myriodontium. Furthermore, three novel species for the genus Malbranchea are proposed as M. echinulata sp. nov., M. irregularis sp. nov., and M. sinuata sp. nov. The new genera Albidomyces and Neoarthropsis are introduced based on Arachniotus albicans and Arthropsis hispanica, respectively. Neoarthropsis sexualis sp. nov. is characterized and differentiated morphologically from its counterpart by the production of a sexual morph. The novel family Neoarthropsidaceae is proposed for the genera Albidomyes, Apinisia, Arachnotheca, Myriodontium, and Neoarthropsis, based on their phylogenetic relationships and phenotypic and ecological traits. Pseudoamaurascopsis gen. nov. is introduced to accommodate P. spiralis sp. nov., a fungus with unclear taxonomy related to Amaurascopsis and Polytolypa. We traced the ecology and global distribution of the novel fungi through ITS environmental sequences deposited in the GlobalFungi database. Studying the fungal diversity from freshwater sediments not only contributes to filling gaps in the relationships and taxonomy of the Ascomycota but also gives us insights into the fungal community that might represent a putative risk to the health of animals and humans inhabiting or transient in aquatic environments.

Unraveling the genomic diversity and ecological potential of the genus Demequina: insights from comparative analysis of different saline niche strains

During an investigation of the culturable microbial diversity of sediments with salinity from tidal flats and saline lake, seven strains of the genus Demequina were harvested. The genomic analysis and physiological characteristics of strains of this genus have unveiled their significant potential in degrading complex carbon source such as lignin, hemicellulose, chitin, and oligosaccharides. In addition, these strains show potential abilities in nitrite ammonification and sulfide oxidation. These findings not only improved our understanding of their metabolic model, but also provided valuable insights into their ecological roles. Four new species of the genus Demequina are described: Demequina litoralis sp. nov., with SYSU T00192T designated as the type species; Demequina zhanjiangensis sp. nov., with SYSU T00b26T as the type species; Demequina lignilytica sp. nov., with SYSU T00068T as the type species; and Demequina muriae sp. nov., with EGI L300058T as the type species. Additionally, strains SYSU T0a273, SYSU T00039-1, and SYSU T00039 are identified as different strains of Demequina lignilytica. Our study thus sheds light on the diversity, biological significance, and ecological contribution of the Demequina genus in different habitats.

Changes of microbiome in response to supplements with silver nanoparticles in cotton rhizosphere.

The current study focuses on analyzing the effects of supplements containing silver nanoparticles (AgNPs) on plant growth and rhizospheric bacterial communities. Specifically, the impact of AgNP supplements was assessed on both plant growth promoting traits and bacterial communities in the soil. To do this, a screening process was conducted to select bacteria capable of synthesizing AgNPs through extracellular biosynthesis. UV-Visible spectrophotometer, Fourier transform infrared, X-ray diffraction, scanning electron microscope, and field emission scanning electron microscopy all confirmed, produced AgNPs is in agglomerates form. The resulting AgNPs were introduced into soil along with various supplements and their effects were evaluated after 10 days using next generation sequencing (Illumina-16S rDNA V3-V4 region dependent) to analyze changes in bacterial communities. Seed germination, root-shoot biomass and chlorophyll content were used to assess the growth of the cotton plant, whereas the bacterial ability to promote growth was evaluated by measuring its culturable diversity including traits like phosphate solubilization and indole acetic acid production. The variance in Bray-Curtis β diversity among six selected combinations including control depends largely on the type of added supplements contributing to 95%-97% of it. Moreover, seed germination improves greatly between 63% and 100% at a concentration range of 1.4 to 2.8 mg/L with different types of supplements. Based on the results obtained through this study, it is evident that using AgNPs along with fructose could be an effective tool for promoting Gossypium hirsutum growth and enhancing plant growth traits like profiling rhizospheric bacteria. The results that have been obtained endorse the idea of boosting the growth of rhizospheric bacteria in a natural way when AgNPs are present. Using these supplements in fields that have been contaminated will lead to a better understanding of how ecological succession occurs among rhizospheric bacteria, and what effect it has on the growth of plants.

The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean

To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles.

More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.