New primers for the class Actinobacteria: application to marine and terrestrial environments

Diversity and Screening of Cellulolytic Microorganisms from Mangrove Forests, Natural Parks, Paddy Field, and Sugarcane Plantation in Panay Island, Philippines

Cellulolytic microorganisms secrete cellulase, which plays a crucial role in the conversion of lignocellulosic biomass into value-added products with diverse applications in industries, such as biofuel, healthcare, and agriculture. As the world transitions to a bioenergy future, cellulase demand is likely to expand. However, the high cost and low catalytic activity of cellulase hinder the commercialization of biorefineries. Searching for cellulase-producing microorganisms in different environments through bioprospecting can aid in broadening the range of cellulases that are currently available. Meanwhile, the cellulolytic activity of marine microorganisms remains largely unexplored, making it difficult to compare the cellulolytic activity of terrestrial and marine environments. Thus, this study aimed to investigate the diversity and activity of culturable cellulolytic microorganisms in four terrestrial and three marine sites within Panay Island, Philippines. The results showed that the cellulolytic microbial load was tenfold higher in the terrestrial sites than in the marine sites, possibly due to the dynamic mangrove environment. Out of the 42 isolates with a high cellulolytic index (CI) of ≥3.0, 36 were from terrestrial and 6 from marine habitats. The CMCase, Avicelase, and FPase activities were then tested on the 18 isolates with the highest CI. It was observed that many isolates had a high CI, but few exhibited high enzyme activities. Marine isolates showed higher CMCase and Avicelase activities, with comparable FPase activity to their terrestrial counterparts. Isolates S1ACP6B from a sugarcane field and MS1OMP2A from a mangrove site exhibited the highest cellulase activities at 0.41 and 0.29 U/mg, respectively, and were identified as Enterobacter roggenkampii and Rhodococcus erythropolis, respectively. Among the 18 identified isolates, three are resistant to chloramphenicol and three isolates are potentially new species of Halomonas sp. MS1ACP1B, Albirhodobacter sp. MP2ACP3B, and Saccharomycetaceae sp. B1CZP10A. Overall, this study provides an insight on the composition of cellulolytic microbial load and their activities among various habitats.

Screening biosurfactant-producing actinomycetes: Identification of Streptomyces sp. RP1 as a potent species for bioremediation

This study aimed to isolate biosurfactant-producing and hydrocarbon-degrading actinomycetes from different soils using glycerol-asparagine and starch-casein media with an antifungal agent. The glycerol-asparagine agar exhibited the highest number of actinomycetes, with a white, low-opacity medium supporting pigment production and high growth. Biosurfactant analyses, such as drop collapse, oil displacement, emulsification, tributyrin agar test, and surface tension measurement, were conducted. Out of 25 positive isolates, seven could utilize both olive oil and black oil for biosurfactant production, and only isolate RP1 could produce biosurfactant when grown in constrained conditions with black oil as the sole carbon source and inducer, demonstrating in situ bioremediation potential. Isolate RP1 from oil-spilled garden soil is Gram-staining-positive with a distinct earthy odor, melanin formation, and white filamentous colonies. It has a molecular size of ~621 bp and 100% sequence similarity to many Streptomyces spp. Morphological, biochemical, and 16 S rRNA analysis confirmed it as Streptomyces sp. RP1, showing positive results in all screenings, including high emulsification activity against kerosene (27.2%) and engine oil (95.8%), oil displacement efficiency against crude oil (7.45 cm), and a significant reduction in surface tension (56.7 dynes/cm). Streptomyces sp. RP1 can utilize citrate as a carbon source, tolerate sodium chloride, resist lysozyme, degrade petroleum hydrocarbons, and produce biosurfactant at 37°C in a 15 mL medium culture, indicating great potential for bioremediation and various downstream industrial applications with optimization.

Biodiversity and Bioactive Potential of Actinomycetes from Unexplored High Altitude Regions of Kargil, India

The effectiveness of currently available antimicrobials and anticancer medications is steadily declining due to the emergence of drug resistance. Since actinobacteria are important producers of bioactive substances, we have isolated them from the soil samples of exotic North-Western Himalayan terrains. Out of 128 isolates, 39 strains were prioritized based on their bioactive potential. The diversity analysis revealed higher abundance distribution of actinomycetes in the soil of an open field (68.7%), followed by the mountainside (34.9%), from which most of the bioactive strains were obtained. The extract of the strain S26-11 was found to be highly active against Gram-positive Staphylococcus aureus and Bacillus subtilis with a MIC of 0.5 μg/mL and 1 μg/mL respectively. A cytotoxicity assay (sulforhodamine B) was performed on a series of cancer cell lines (PC-3, MCF-7, A-549, and HCT-116). The extract of the strain S26-11 showed cytotoxic activity against all cancer cell lines with an IC50 of 2 µg/mL against PC-3, 1.9 µg/mL against MCF-7, 0.52 µg/mL against A-549, and 0.83 µg/mL against HCT-116. Moreover, the antioxidant activity was assessed using a DPPH-based assay and the results revealed that the S17-8 isolate showed the highest antioxidant activity with IC50 of 114.136 μg/mL. The Response Surface Methodology (RSM) had helped to optimize the physical parameters for scaling up of the bioactive strain S26-11. The unexplored soil niches of Kargil (UT, Ladakh), India, is rich in actinomycetes which are having potential bioactivities, would be worth to explore for the discovery of bioactive compounds.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01133-1.

Comparison of gut microbiota profiles between patients suffering from elderly frailty syndrome and non-frail elderly individuals

BACKGROUND

Frailty syndrome is a state of increased vulnerability to stressors, marked by lowered physical strength and increased dependence on others. The well-established changes in gut microbiota associated with old age suggest a probable relationship between gut microbiota and frailty.

METHODS AND RESULTS

This study was aimed at finding the relationship between gut microbiota and frailty syndrome, by comparing the sociodemographic data and the gut microbiota profiles of 23 non-frail and 14 frail elderly individuals. We used the quantitative polymerase chain reaction method (qPCR) to determine the bacterial loads of Bifidobacteria, Lactobacillus, Bacteroidetes, Prevotella, and Escherichia coli in stool samples from test subjects. We discovered a significant increase in the bacterial load of Prevotella in frail elderly individuals aged 70 or above. Other bacterial loads and ratios were not significantly different between the two groups.

CONCLUSIONS

More comprehensive studies with larger sample sizes and encompassing a wider range of inflammation-related bacteria need to be performed to discover the existence and exact nature of these relations.

Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water

The quantity and quality of DNA isolated from environmental samples are crucial for getting robust high-throughput sequencing data commonly used for microbial community analysis. The differences in the nature and physicochemical properties of environmental samples impact DNA yields, and therefore, an optimisation of the protocols is always recommended. For instance, samples collected from corroded areas contain high concentrations of metals, salts, and hydrocarbons that can interfere with several steps of the DNA extraction protocols, thereby reducing yield and quality. In this study, we compared the efficiency of commercially available DNA extraction kits and laboratory-adopted methods for microbial community analysis of iron incrustations and oilfield-produced water samples. Modifications to the kits manufacturers' protocols were included to maximise the yield and quality. For iron incrustations, the modified protocol for FastDNA Spin Kit for Soil yielded higher DNA and resulted in higher diversity, including the recovery of low-abundant and rare taxa in the samples, compared to DNeasy PowerSoil Pro Kit. The DNA extracted with modified phenol-chloroform methods yielded higher DNA but failed to pass quality control PCR for 16S sequencing with and without purification. The protocols mentioned here can be used to maximise DNA recovery from iron incrustations and oilfield-produced water samples.

Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria

Culturing the gut microbiota in in vitro models that mimic the intestinal environment is increasingly becoming a promising alternative approach to study microbial dynamics and the effect of perturbations on the gut community. Since the mucus-associated microbial populations in the human intestine differ in composition and functions from their luminal counterpart, we attempted to reproduce in vitro the microbial consortia adhering to mucus using an already established three-dimensional model of the human gut microbiota. Electrospun gelatin structures supplemented or not with mucins were inoculated with fecal samples and compared for their ability to support microbial adhesion and growth over time, as well as to shape the composition of the colonizing communities. Both scaffolds allowed the establishment of long-term stable biofilms with comparable total bacterial loads and biodiversity. However, mucin-coated structures harbored microbial consortia especially enriched in Akkermansia, Lactobacillus, and Faecalibacterium, being therefore able to select for microorganisms commonly considered mucosa-associated in vivo. IMPORTANCE These findings highlight the importance of mucins in shaping intestinal microbial communities, even those in artificial gut microbiota systems. We propose our in vitro model based on mucin-coated electrospun gelatin structures as a valid device for studies evaluating the effects of exogenous factors (nutrients, probiotics, infectious agents, and drugs) on mucus-adhering microbial communities.

The administration of Enterococcus faecium SF68 counteracts compositional shifts in the gut microbiota of diet-induced obese mice

Microorganisms with probiotic properties are eliciting an increasing interest as coadjuvants in the prevention and treatment of obesity through modulation of the gut microbiota. In this study, a probiotic formulation based on Enterococcus faecium SF68 was administered to mice fed with a high-fat diet (HFD) to evaluate its efficacy in reducing body mass gain and in modulating the intestinal bacterial composition. Both stool and ileum samples were collected from untreated and treated mice and absolute abundances of specific taxa constituting the gut microbial consortium were evaluated. SF68 administration significantly reduced the HFD-induced weight gain. In these animals, the microbial gut composition shifted toward an enrichment in microbes positively correlated with mucus thickness, lower inflammation, lower glycemia levels, and SCFA production (i.e., Bifidobacterium, Akkermansia, and Faecalibacterium), as well as a depletion in bacterial phyla having a key role in obesity (i.e., Firmicutes, Proteobacteria). Our results demonstrate the efficacy of E. faecium SF68 in adjusting the composition of the dysbiotic microbiota of HFD-fed animals, thus ameliorating clinical conditions and exerting anti-obesity effects.

Effect of Spirulina and Ferrous Fumarate on Intestinal Morphology and the Diversity of Gut Microbiota of Yellow River Carp

The study aimed to investigate the effect of diets supplemented with Spirulina and the mixture of Spirulina and ferrous fumarate on intestinal morphology and the diversity of gut microbiota of Yellow River carp. The results showed that the Spirulina and the mixture of Spirulina and ferrous fumarate could promote the development of intestinal villi, increase the thickness of intestinal muscular layer. Additionally, high-throughput sequencing of 16S rRNA gene revealed that the Spirulina and the mixture of Spirulina and ferrous fumarate could alter the composition, diversity, and richness of intestinal microbial communities. The relative abundances of the predominant phyla Firmicutes and Verrucomicrobia showed significant changes at the phylum level after fed with Spirulina and ferrous fumarate. At the genus level, the predominant genera with marked differences in abundances were Flavobacterium, Aeromonas, and Brevinema. In conclusion, this study indicated the Spirulina and the ferrous fumarate could alter the intestinal microbiota structure and could also cause positive impacts on the health of Yellow River carp. This study provides the valuable information for elucidating the mechanisms of Spirulina and ferrous fumarate in aquatic animals in the future.

Bacterial inoculants as effective agents in minimizing the non-target impact of azadirachtin pesticide and promoting plant growth of Vigna radiata

Microbes regulate soil health by negating ecological disturbances, and improve plant productivity in a sustainable manner. Indiscriminate application of pesticides creates a detrimental impact on the rhizospheric microbiota, thereby affecting soil health. Azadirachtin, earlier believed to be an environment-friendly alternative to chemical pesticides, exhibits a non-target impact on microbial communities. This study aimed to employ potent bacteria to promote the growth of mungbean plant (Vigna radiata), and mitigate the non-target impact of azadirachtin. Bacterial strains were isolated by enrichment from mungbean rhizosphere. A plant growth experiment was performed with mungbean, amended with azadirachtin to assess the impact of bacterial bioinoculants on the rhizospheric microbiota. The impact of azadirachtin on rhizospheric bacterial community was analyzed qualitatively and quantitatively by 16S rRNA PCR-DGGE and qPCR of various markers, respectively. Residual concentration of azadirachtin in the soil was estimated by HPLC. The bacterial inoculants used in combination significantly promoted plant growth and enhanced the diversity and abundance of total bacterial community in the presence of azadirachtin. Further, the abundance of specific bacterial groups (α-Proteobacteria, β-Proteobacteria, Actinobacteria, Acidobacteria, and Firmicutes) were significantly boosted. Compared to the control, the isolates significantly facilitated the reduction in residual concentration of azadirachtin in the mungbean rhizosphere. Bacterial inoculants can serve a tripartite role in reducing the stress imparted by botanical pesticides, together with promoting plant growth and enriching the rhizospheric bacterial community structure.

Colonization by the Red Imported Fire Ant, Solenopsis invicta, Modifies Soil Bacterial Communities

The long-standing association between insects and microorganisms has been especially crucial to the evolutionary and ecological success of social insect groups. Notably, research on the interaction of the two social forms (monogyne and polygyne) of the red imported fire ant (RIFA), Solenopsis invicta Buren, with microbes in its soil habitat is presently limited. In this study, we characterized bacterial microbiomes associated with RIFA nest soils and native (RIFA-negative) soils to better understand the effects of colonization of RIFA on soil microbial communities. Bacterial community fingerprints of 16S rRNA amplicons using denaturing gradient gel electrophoresis revealed significant differences in the structure of the bacterial communities between RIFA-positive and RIFA-negative soils at 0 and 10 cm depths. Illumina sequencing of 16S rRNA amplicons provided fine-scale analysis to test for effects of RIFA colonization, RIFA social form, and soil depth on the composition of the bacterial microbiomes of the soil and RIFA workers. Our results showed the bacterial community structure of RIFA-colonized soils to be significantly different from native soil communities and to evidence elevated abundances of several taxa, including Actinobacteria. Colony social form was not found to be a significant factor in nest or RIFA worker microbiome compositions. RIFA workers and nest soils were determined to have markedly different bacterial communities, with RIFA worker microbiomes being characterized by high abundances of a Bartonella-like endosymbiont and Entomoplasmataceae. Cloning and sequencing of the 16S rRNA gene revealed the Bartonella sp. to be a novel bacterium.

The Use of Baikal Psychrophilic Actinobacteria for Synthesis of Biologically Active Natural Products from Sawdust Waste

One of the relevant areas in microbiology and biotechnology is the study of microorganisms that induce the destruction of different materials, buildings, and machines and lead to negative effects. At the same time, the positive ecological effects of degradation can be explained by the detoxication of industrial and agricultural wastes, chemical substances, petroleum products, xenobiotics, pesticides, and other chemical pollutants. Many of these industrial wastes include hard-to-degrade components, such as lignocellulose or plastics. The biosynthesis of natural products based on the transformation of lignocellulosic wastes is of particular interest. One of the world’s unique ecosystems is presented by Lake Baikal. This ecosystem is characterized by the highest level of biodiversity, low temperatures, and a high purity of the water. Here, we studied the ability of several psychrophilic representatives of Baikal Actinobacteria to grow on sawdust wastes and transform them into bioactive natural products. Different strains of both widely spread genus of Actinobacteria and rare genera of Actinobacteria were tested. We used the LC-MS methods to show that Actinobacteria living in sawmill wastes can produce both known and novel natural products with antibiotic activity. We demonstrated that the type of sawmill wastes and their concentration influence the Actinobacteria biosynthetic potential. We have shown for the first time that the use of Baikal psychrophilic microorganisms as a factory for biodegradation is applicable for the transformation of lignocellulosic wastes. Thus, the development of techniques for screening novel natural products leads to an elaboration on the active ingredients for novel drugs.

The Diversity, Metabolomics Profiling, and the Pharmacological Potential of Actinomycetes Isolated from the Estremadura Spur Pockmarks (Portugal)

The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlantic, off the coast of Portugal. A total of 85 marine-derived actinomycetes were isolated and cultured from sediments collected from this ecosystem at a depth of 200 to 350 m. Nine genera, Streptomyces, Micromonospora, Saccharopolyspora, Actinomadura, Actinopolymorpha, Nocardiopsis, Saccharomonospora, Stackebrandtia, and Verrucosispora were identified by 16S rRNA gene sequencing analyses, from which the first two were the most predominant. Non-targeted LC-MS/MS, in combination with molecular networking, revealed high metabolite diversity, including several known metabolites, such as surugamide, antimycin, etamycin, physostigmine, desferrioxamine, ikarugamycin, piericidine, and rakicidin derivatives, as well as numerous unidentified metabolites. Taxonomy was the strongest parameter influencing the metabolite production, highlighting the different biosynthetic potentials of phylogenetically related actinomycetes; the majority of the chemical classes can be used as chemotaxonomic markers, as the metabolite distribution was mostly genera-specific. The EtOAc extracts of the actinomycete isolates demonstrated antimicrobial and antioxidant activity. Altogether, this study demonstrates that the Estremadura Spur is a source of actinomycetes with potential applications for biotechnology. It highlights the importance of investigating actinomycetes from unique ecosystems, such as pockmarks, as the metabolite production reflects their adaptation to this habitat.

Soil actinobacteria inhibit antagonistic fungi of leafcutter ant colonies

Founder females of the leaf-cutting ant species Atta sexdens experience high mortality during the founding and establishment of their colonies. The foundation site is crucial for the success of a new colony. In this study, we isolated and identified actinobacteria from fungus garden chambers of A. sexdens colony growth in soils from (1) forested areas without leafcutter ant nests and (2) open ground areas close to leafcutter ant nests. The inhibitory effect of these isolates on pathogenic fungi and the mutualistic fungus cultivated by leafcutter ants was evaluated. The 16S rRNA gene sequences were employed to identify nine selected actinobacteria species found in the soil: Streptomyces (6), Nocardia (2), and Kitasatospora (1). One Streptomyces and one Kitasatospora isolate inhibited all the tested fungi. Since there is no evidence of actinobacteria cultivation in the workers' cuticle of the Atta genus, our results corroborate the hypothesis that these workers may establish temporary adaptive symbiosis with soil microorganisms that produce antibiotic substances, living in some parts of their nest, or even inside their bodies. Pathogenic fungi are a risk factor that can be controlled by actinobacteria metabolites from soils, with minimal energy cost to the colony.

Bioprospecting for antituberculosis natural products – A review

There has been an increase in the reported cases of tuberculosis, a disease caused by Mycobacterium tuberculosis, which is still currently affecting most of the world’s population, especially in resource-limited countries. The search for novel antitubercular chemotherapeutics from underexplored natural sources is therefore of paramount importance. The renewed interest in studies related to natural products, driven partly by the growing incidence of MDR-TB, has increased the prospects of discovering new antitubercular drug leads. This is because most of the currently available chemotherapeutics such as rifampicin and capreomycin used in the treatment of TB were derived from natural products, which are proven to be an abundant source of novel drugs used to treat many diseases. To meet the global need for novel antibiotics from natural sources, various strategies for high-throughput screening have been designed and implemented. This review highlights the current antitubercular drug discovery strategies from natural sources.

Integrating Decomposers, Methane-Cycling Microbes and Ecosystem Carbon Fluxes Along a Peatland Successional Gradient in a Land Uplift Region

Peatlands are carbon dioxide (CO2) sinks that, in parallel, release methane (CH4). The peatland carbon (C) balance depends on the interplay of decomposer and CH4-cycling microbes, vegetation, and environmental conditions. These interactions are susceptible to the changes that occur along a successional gradient from vascular plant-dominated systems to Sphagnum moss-dominated systems. Changes similar to this succession are predicted to occur from climate change. Here, we investigated how microbial and plant communities are interlinked with each other and with ecosystem C cycling along a successional gradient on a boreal land uplift coast. The gradient ranged from shoreline to meadows and fens, and further to bogs. Potential microbial activity (aerobic CO2 production; CH4 production and oxidation) and biomass were greatest in the early successional meadows, although their communities of aerobic decomposers (fungi, actinobacteria), methanogens, and methanotrophs did not differ from the older fens. Instead, the functional microbial communities shifted at the fen–bog transition concurrent with a sudden decrease in C fluxes. The successional patterns of decomposer versus CH4-cycling communities diverged at the bog stage, indicating strong but distinct microbial responses to Sphagnum dominance and acidity. We highlight young meadows as dynamic sites with the greatest microbial potential for C release. These hot spots of C turnover with dense sedge cover may represent a sensitive bottleneck in succession, which is necessary for eventual long-term peat accumulation. The distinctive microbes in bogs could serve as indicators of the C sink function in restoration measures that aim to stabilize the C in the peat.

Characterization of a Novel Shewanella algae Arginine Decarboxylase Expressed in Escherichia coli

Arginine decarboxylase (ADC) catalyzes the decarboxylation of arginine to form agmatine, an important physiological and pharmacological amine, and attracts attention to the enzymatic production of agmatine. In this study, we for the first time overexpressed and characterized the marine Shewanella algae ADC (SaADC) in Escherichia coli. The recombinant SaADC showed the maximum activity at pH 7.5 and 40 °C. The SaADC displayed previously unreported substrate inhibition when the substrate concentration was higher than 50 mM, which was the upper limit of testing condition in other reports. In the range of 1-80 mM L-arginine, the SaADC showed the K_m, k_cat, K_i, and k_cat/K_m values of 72.99 ± 6.45 mM, 42.88 ± 2.63 s^-1, 20.56 ± 2.18 mM, and 0.59 s/mM, respectively, which were much higher than the K_m (14.55 ± 1.45 mM) and k_cat (12.62 ± 0.68 s^-1) value obtained by assaying at 1-50 mM L-arginine without considering substrate inhibition. Both the k_cat values of SaADC with and without substrate inhibition are the highest ones to the best of our knowledge. This provides a reference for the study of substrate inhibition of ADCs.

Bioprospecting marine actinomycetes for antileishmanial drugs: current perspectives and future prospects

Revived analysis interests in natural products in the hope of discovering new and novel antileishmanial drug leads have been driven partially by the increasing incidence of drug resistance. However, the search for novel chemotherapeutics to combat drug resistance had previously concentrated on the terrestrial environment. As a result, the marine environment was often overlooked. For example, actinomycetes are an immensely important group of bacteria for antibiotic production, producing two-thirds of the known antibiotics. However, these bacteria have been isolated primarily from terrestrial sources. Consequently, there have been revived efforts to discover new compounds from uncharted or uncommon environments like the marine ecosystem. Isolation, purification and structure elucidation of target compounds from complex metabolic extract are major challenges in natural products chemistry. As a result, marine-derived natural products from actinomycetes that have antileishmanial bioactivity potentials have been understudied. This review highlights metagenomic and bioassay approaches which could help streamline the drug discovery process thereby greatly reducing time and cost of dereplication to identify suitable antileishmanial drug candidates.

Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis

BACKGROUND

The standardized herbal preparation, STW 5, is effective clinically in functional gastrointestinal disorders and experimentally in ulcerative colitis (UC). The present study explores whether the beneficial effect of STW 5 involves influencing the intestinal microbiota.

METHODS

UC was induced in Wistar rats by feeding them 5% dextran sodium sulfate (DSS) in drinking water for 7 days. Rats were treated concurrently with STW 5 and sacrificed 24 h after last drug administration. Fecal samples were used to determine changes in the abundance of selected microbial phyla and genera using real-time PCR.

RESULTS

Induction of UC led to dysbiosis and changes in the gut microbiota. The changes included an increase in some genera of the Firmicutes, namely Enterococcus, and a decrease in others, namely Blautia, Clostridium, and Lactobacillus. DSS further induced a marked increase in the abundance of Bacteroidetes and Proteobacteria as well as in the relative abundance of Actinobacteria and its genus Bifidobacterium. Methanobrevibacter levels (phylum Euryarchaeota) were also increased. Microbial dysbiosis was associated with changes in various parameters of colonic inflammation. STW 5 effectively guarded against those changes and significantly affected the indices of edema and inflammation in the UC model. Changes in colon length, colon mass index, inflammatory and apoptotic markers, and histological changes induced by DSS were also prevented.

CONCLUSIONS

Dysbiosis plays a contributing role in the development of DSS-induced UC. Derangements in the microbial flora and associated inflammatory processes were largely prevented by STW 5, suggesting that this effect might contribute towards its beneficial usefulness in this condition.

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils

BACKGROUND

Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria, one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with 13C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition.

RESULTS

While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and 13C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility.

CONCLUSIONS

This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling. Video abstract.

Diversity of actinobacteria in sediments of Qaidam Lake and Qinghai Lake, China

Using 16S rRNA gene analysis and high-throughput, the diversity and community structure of actinobacteria in the sediments of Qaidam Lake and Qinghai Lake with different salinity and alkalinity in Qinghai-Xizang Plateau were studied, and the differences of actinobacteria community structure and their relationship with environmental factors were discussed. A total of 77 genera belonging to actinobacteria were found in the samples, of which 31 genera were found in the sediment samples of Qaidam Lake with 19 genera being dominant genera, such as Actinomycetes, Corynebacterium, Morella, Bifidobacterium, and 69 genera were found in the sediment samples of Qinghai Lake with 17 genera becoming dominant, such as Ilumattalaer, Actinotalea, Aquihaans and so on. The correlation analysis of environmental factors and community showed that the community structure of the two salt lakes was mainly affected by total salinity, total organic carbon) (TOC) and CO₃^2-, among which TOC was the most influential factor. The functional differences of metabolic pathway enrichment analysis (KEGG) showed that there was a high abundance of metabolic-related functions in the two salt lakes. There were significant differences in the biosynthesis of energy metabolism and other secondary metabolites between the two salt lakes, which may be the main reason for the difference of actinomycete community. The results show that the actinobacteria diversity was rich in the plateau salt lakes, and affected by a variety of physicochemical factors. In addition, there were a large number of unculturable actinobacteria in the sediment, which provides a theoretical basis for the excavation and utilization of actinobacteria resources in salt lakes.

Isolation of Actinomycetes with Cellulolytic and Antimicrobial Activities from Soils Collected from an Urban Green Space in the Philippines

Actinomycetes are one of the most important groups of soil bacteria that are recognized as sources of commercially important enzymes and antimicrobials. Actinomycetes, however, are largely underestimated and uncharacterized in underexplored habitats such as green spaces in urban areas. This study aimed to isolate actinomycetes from soils in the University of the Philippines Diliman campus and determine their cellulolytic and antimicrobial activities. A total of 235 isolates were purified from the soil samples collected. Cellulolytic and antimicrobial activities were observed in 114 and 18 isolates, respectively. The cell-free supernatants of 31 isolates exhibited high cellulolytic activities. Two isolates, in particular EWLG2 and EPNA9, had 0.596 FPU and 0.885 FPU cellulolytic activity, respectively. Seven isolates exhibited antimicrobial activities in the screening methods used. The crude extracts of isolates AWLG9, AWLG8, AWLG10, AULG1, APLG2, and AWLG13 had minimum inhibitory concentrations (MIC) values ranging from 31.25 µg/mL to 500 µg/mL against Candida spp. Isolates AULG1 and EPLG5 were active against the bacterial test microorganisms and had MIC values ranging from 250 µg/mL to 500 µg/mL. DNA sequencing identified the isolates which exhibited high cellulolytic and antimicrobial activities as Bacillus sp. and Streptomyces sp., with percent identities ≥98%. This study shows that green spaces are rich sources of soil microorganisms that have cellulolytic and antimicrobial activities. It is recommended that the isolates obtained in this study be examined further for possible applications in bioethanol production and pharmacology.

Biodegradation and Characterization of Streptomyces sp. (JMCACA3) from Acid Corroded Iron Plate

From acid corroded iron plates five different types of actinobacteria were isolated. Among the five, JMCACA3 strain was selected for the present study. In ISP media, JMCACA3 strain showed well-developed aerial and substrate mycelia were observed. This strain showed good growth in 12 different carbon and 4 different nitrogen sources. The 16S rRNA sequence of phylogenetic analysis by neighbor-joining method identified the studied strain belongs to Streptomyces sp. The biodegradation activity of the strain analyzed by UV and FTIR analysis, which revealed that the various concentrations of Benzimidazole inhibitor with JMCACA3 culture showed slightly varied results. For weight loss method, mild steel coupons incubated with JMCACA3 culture, Benzimidazole inhibitor + JMCACA3 culture and mixed sample showed that JMCACA3 strain utilized the inhibitor as their energy source and the weight the coupons were slightly varied, evidenced by XRD spectra and showed Fe₂O₃ corrosion products. Our study concluded that the JMCACA3 strain, an iron-reducing actinobacteria which utilizes and converted the corrosion inhibitor Benzimidazole as their energy source. So, it is very urgent to develop more powerful corrosion inhibitor from green biocide or microbial-based biocide and their analog which incorporated into the pre-existing Benzimidazole to increase the corrosion inhibitor level against the biofilm of actinobacterial influenced corrosion.

Exposure of lead on intestinal structural integrity and the diversity of gut microbiota of common carp

Lead is an environmental toxicant that has toxicity effect to the health of aquatic organisms. Gut microbiota has been reported to be closely related to human health. The aim of this study was to investigate the effects of lead exposure on the composition of gut microbiota. The composition of gut microbiota alteration was detected by 16S rRNA gene sequencing, following a 42-day exposure of lead (1 mg/L). The results showed that compared with the normal control group, the carp of lead group showed severe intestinal tissues injury and decreased Zona Occludens 1 (ZO-1) and occludin expression. The production of LPS in serum was increased by the treatment of lead exposure. Our results showed gut bacterial diversity in lead-treated common carp was lower than the control group. At the phylum level, the abundance of Bacteroidetes (LPS producing bacteria) and Fusobacteria in lead-treated carp were much higher than the control carp. And the abundance of Actinobacteria decreased by lead exposure. At the genus level, we found the abundance of Bacteroides (LPS producing bacteria) and Plesiomonas (an important pathogenic bacteria), increased significantly by lead exposure. And the abundance of Akkermansia, a critical probiotics, was markedly inhibited by lead exposure. In conclusion, this study indicated exposure of carp to lead causes gut microbiota alterations and intestinal structural integrity destruction.

CeMbio - The Caenorhabditis elegans Microbiome Resource

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.

Cultivable Actinobacteria First Found in Baikal Endemic Algae Is a New Source of Natural Products with Antibiotic Activity

Inadequate use of antibiotics has led to spread of microorganisms resistant to effective antimicrobial compounds for humans and animals. This study was aimed to isolate cultivable strains of actinobacteria associated with Baikal endemic alga Draparnaldioides baicalensis and estimate their antibiotic properties. During this study, we isolated both widespread and dominant strains related to the genus Streptomyces and representatives of the genera Saccharopolyspora, Nonomuraea, Rhodococcus, and Micromonospora. For the first time, actinobacteria belonging to the genera Nonomuraea and Saccharopolyspora were isolated from Baikal ecosystem. Also, it was the first time when actinobacteria of the genus Nonomuraea were isolated from freshwater algae. Some rare strains demonstrated activity inhibiting growth of bacteria and yeasts. Also, it has been shown that the strains associated with Baikal alga D. baicalensis are active against both Gram-positive and Gram-negative bacteria. According to this study and previously published materials, diversity of cultivable actinobacteria and rare strains isolated from D. baicalensis is comparable to that of cultivable actinobacteria previously isolated from plant sources of Lake Baikal. Also, it exceeds the cultivable actinobacteria diversity previously described for macroinvertebrates, water, or sediments of Lake Baikal. The large number of rare and active strains associated with the endemic alga D. baicalensis could be the promising sources for biopharmaceutical and biotechnological developments and discovery of new natural compounds.

Identification of a persisting bacterial contamination of cell culture as Brevibacterium.. [DOI: 10.1101/2020.05.20.107698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Cell culture is an important prerequisite for many of the basic and applied researches in life sciences and contamination is a major problem faced by the researchers in maintaining healthy cell lines. We noted a dot like contamination in our THP1 cell line, which does not make the culture medium turbid as fast as other common contaminants and remains in the culture for many days before it makes the culture unusable. The contaminant was identified as a member of the genus Brevibacterium and we could find that the antibiotic rifampicin effectively suppresses the growth of the bacterium.

Bioactive properties of streptomyces may affect the dominance of Tricholoma matsutake in shiro

Tricholoma matsutake is known to be the dominant fungal species in matsutake fruitbody neighboring (shiro) soil. To understand the mechanisms behind matsutake dominance, we studied the bacterial communities in matsutake dominant shiro soil and non-shiro soil, isolated the strains of Streptomyces from matsutake mycorrhizal root tips both from shiro soil and from the Pinus densiflora seedlings cultivated in shiro soil. Further, we investigated three Streptomyces spp. for their ability to inhibit fungal growth and Pinus densiflora seedling root elongation as well as two strains for their antifungal and antioxidative properties.

Our results showed that Actinobacteria was the most abundant phylum in shiro soil. However, the differences in the Actinobacterial community composition (phylum or order level) between shiro and non-shiro soils were not significant, as indicated by PERMANOVA analyses. A genus belonging to Actinobacteria, Streptomyces, was present on the matsutake mycorrhizas, although in minority. The two antifungal assays revealed that the broths of three Streptomyces spp. had either inhibitory, neutral or promoting effects on the growth of different forest soil fungi as well as on the root elongation of the seedlings. The extracts of two strains, including one isolated from the P. densiflora seedlings, inhibited the growth of either pathogenic or ectomycorrhizal fungi. The effect depended on the medium used to cultivate the strains, but not the solvent used for the extraction. Two Streptomyces spp. showed antioxidant activity in one out of three assays used, in a ferric reducing antioxidant power assay. The observed properties seem to have several functions in matsutake shiro soil and they may contribute to the protection of the shiro area for T. matsutake dominance.

Metabolomic Diversity and Identification of Antibacterial Activities of Bacteria Isolated From Marine Sediments in Hawai'i and Puerto Rico

Antibiotic resistance is a growing concern worldwide and consequently metabolomic tools are being applied increasingly in efforts aimed at identifying new antimicrobial compounds. Marine bacteria-derived compounds have shown great promise in this area. A metabolomics-based study was undertaken to study the diversity of secondary metabolites from marine sediment bacteria isolated from different locations of Hawai’i and Puerto Rico. This effort included characterizing the biodiversity in the sediment samples and searching for antibacterial activity and associated compounds. Bacterial strains were isolated using several different nutrient agars and culture conditions. DNA sequencing (16s rDNA) was used for phylogenetic characterization. Antibacterial activity was assessed against antibiotic-resistant strains of Escherichia coli, Salmonella enterica, Acinetobacter baumannii, Staphylococcus aureus, and Enterococcus faecalis. Ethyl acetate extracted bacterial secondary metabolites were measured by ultra-performance liquid chromatography-mass spectrometry, processed in Progenesis QI and further analyzed by partial least squares-discriminant analysis using MetaboAnalyst 3. Among the strains (n = 143) that were isolated from these two geographical areas and tested for antibiotic activity, 19 exhibited antibacterial activity against at least one antibiotic-resistant human pathogen. One strain from Hawai’i possessed broad-spectrum activity against all five pathogens. Metabolite profiles were diverse and separated the strains into two clusters in PCA analysis that mirrored geographical origin of the isolated strains. A diversity of bacteria and potential antibacterial compounds were observed in this study. Marine environments represent an opportunity to discover a rich diversity of antibacterial compounds for which resistance mechanisms may be uncommon in human pathogens.

Construction of a new integrating vector from actinophage ϕOZJ and its use in multiplex Streptomyces transformation

Streptomyces and other closely-related actinobacteria are important sources of bioactive molecules. Streptomyces synthetic biology and genetics empower therapeutic and agrichemical development through strain improvement and biosynthetic understanding. Such efforts rely on the availability of developed molecular toolsets. Among these tools, vectors that enable combinatorial chromosomal manipulations are particularly desirable. Towards developing tools for facile multiplex engineering, we herein describe the development of new integrating vectors derived from BD1 subgroup actinophage OzzyJ (ϕOZJ). By demonstrating the transformation of several Streptomyces spp. using ϕOZJ-derived vectors, we reveal their potential for strain engineering. We further report the development of new ϕC31 and ϕBT1-based vectors having orthogonal resistance, replication and integration features for concomitant transformation with our ϕOZJ-derived vectors. Importantly, the resulting compatible vector panel enabled us to demonstrate the transfer of up to three plasmids each into Streptomyces venezuelae, Streptomyces roseosporus and Streptomyces pristinaespiralis during a single conjugation experiment. To our knowledge this is the first documentation of conjugation-mediated multiplex plasmid transformation, a useful approach for rapid combinatorial strain development.

Excision of endosymbiotic bacteria from yeast under aging and starvation stresses

Although infrequent in our laboratory, growth of bacterial colonies has been observed on top of the purified cultures of yeasts. In this study, the likelihood of bacterial excision from yeast under aging and starvation stresses was assessed using 10 gastric and 10 food-borne yeasts. Yeasts were identified as members of Candida or Saccharomyces genus by amplification and sequencing of D1/D2 region of 26S rDNA. For aging stress, yeasts were cultured on brain heart infusion agar supplemented with sheep blood and incubated at 30 °C for 3-4 weeks. For starvation stress, yeasts were inoculated into distilled water and incubated similarly. After seven days, starved yeasts were cultured on yeast extract glucose agar, incubated similarly and examined daily for appearance of bacterial colonies on top of the yeast's growth. Outgrowth of excised bacteria was observed on top of the cultures of 4 yeasts (Y1, Y3, Y13 and Y18) after 3-7 days. The excised bacteria (B1, B3, B13 and B18) were isolated and identified at the genus level according to their biochemical characteristics as well as amplification and sequencing of 16S rDNA. B1 (Arthrobacter) were excised from Y1 (Candida albicans) upon aging and B3 (Staphylococcus), B13 (Cellulomonas) and B18 (Staphylococcus) were excised from their respective yeasts; Y3 (Candida tropicalis), Y13 (Saccharomyces cerevisiae) and Y18 (Candida glabrata) upon starvation. DNA from yeasts was used for detection of 16S rDNA of their intracellular bacteria and sequencing. Amplified products from yeasts showed sequence similarity to those of excised bacteria. Under normal conditions, yeast exerts tight control on multiplication of its intracellular bacteria. However, upon aging and starvation the control is no longer effective and bacterial outgrowth occurs. Unlimited multiplication of excised bacteria might provide yeast with plenty of food in close vicinity. This could be an evolutionary dialogue between yeast and bacteria that ensures the survival of both partners.

Succession of Microbial Decomposers Is Determined by Litter Type, but Site Conditions Drive Decomposition Rates

Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.

Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

Bioinformatic and Functional Evaluation of Actinobacterial Piperazate Metabolism

Piperazate (Piz) is a nonproteinogenic amino acid noted for its unusual N-N bond motif. Piz is a proline mimic that imparts conformational rigidity to peptides. Consequently, piperazyl molecules are often bioactive and desirable for therapeutic exploration. The in vitro characterization of Kutzneria enzymes KtzI and KtzT recently led to a biosynthetic pathway for Piz. However, Piz anabolism in vivo has remained completely uncharacterized. Herein, we describe the systematic interrogation of actinobacterial Piz metabolism using a combination of bioinformatics, genetics, and select biochemistry. Following studies in Streptomyces flaveolus, Streptomyces lividans, and several environmental Streptomyces isolates, our data suggest that KtzI-type enzymes are conditionally dispensable for Piz production. We also demonstrate the feasibility of Piz monomer production using engineered actinobacteria for the first time. Finally, we show that some actinobacteria employ fused KtzI-KtzT chimeric enzymes to produce Piz. Our findings have implications for future piperazyl drug discovery, pathway engineering, and fine chemical bioproduction.

Anticancer potential of metabolic compounds from marine actinomycetes isolated from Lagos Lagoon sediment

Thirty-two actinomycetes strains were isolated from sediment samples from 12 different sites at Lagos Lagoon and identified using standard physiological and biochemical procedures as well as 16S rDNA gene sequence analysis. Secondary metabolites were extracted from the strains and their anticancer activity on the K562 (Human acute myelocytic leukemia), HeLa (cervical carcinoma), AGS (Human gastric), MCF-7 (breast adenocarcinoma) and HL-60 (Human acute promyelocytic leukemia) cell lines was determined. The metabolic extracts exhibited cytotoxicity with IC₅₀ values ranging from 0.030 mg/mL to 4.4 mg/mL. The Streptomyces bingchenggensis ULS14 extract was cytotoxic against all the cell lines tested. The bioactivity-guided extraction and purification of the metabolic extracts from this strain yielded two purified anticancer compounds: ULDF4 and ULDF5. The structures of the extracted compounds were determined using spectroscopic analyses, including electrospray ionization mass spectrophotometer and nuclear magnetic resonance (1 Dimensional and 2 Dimensional), and were shown to be structurally similar to staurosporine and kigamicin. The IC₅₀ of ULDF4 and ULDF5 against the HeLa cell line was 0.034 μg/mL and 0.075 μg/mL, respectively. This study is the first to reveal the anticancer potential of actinomycetes from Lagos Lagoon, which could be exploited for therapeutic purposes.

Response of microbial communities to different organochlorine pesticides (OCPs) contamination levels in contaminated soils

Understanding microbial community structure and diversity in contaminated soils helps optimize the bioremediation strategies and performance. This study investigated the roles of environmental variables and contamination levels of organochlorine pesticides (OCPs) in shaping microbial community structure at an abandoned aged insecticide plant site. In total, 28 bacterial phyla were identified across soils with different physiochemical properties and OCPs levels. Proteobacteria, Bacterioidetes and Firmicutes represented the dominant lineages, and accounted for 60.2%-69.2%, 5.6%-9.7% and 6.7%-9.4% of the total population, respectively. The overall microbial diversities, in terms of phylogenetic diversity and phylotype richness, were correlated with the contents of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) in soils, as well as other soil properties including total nitrogen, dissolved organic carbon, pH and vegetation. The multivariate regression tree (MRT) analysis revealed that the soil microbial diversity was significantly impacted by vegetation, which explained 31.8% of the total variation, followed by OCPs level (28.3%), total nitrogen (12.4%), dissolved organic carbon (6.3%) and pH (2.4%). Our findings provide new insights and implications into the impacts on soil microbial community by OCPs contamination and other environmental variables, and offer potential strategic bioremediation for the management of OCPs contaminated sites.

Influence of microbiota in the susceptibility of parasitic wasps to abamectin insecticide: deep sequencing, esterase and toxicity tests

BACKGROUND

The parasitic wasps Eretmocerus mundus, Eretmocerus eremicus and Encarsia formosa are important natural enemies of whiteflies. A broad understanding of their biology, ecology and behavior has been achieved, but the composition and role of their microbiota is not fully determined. The knowledge of the bacteria present in insects might be useful to manage species of human concern such as natural enemies or pests. Here, we performed a residual contact test to study a possible change in the susceptibility of E. mundus adults to abamectin insecticide after antibiotic treatment. Moreover, we assessed the microbiota present in adults of E. eremicus, E. formosa and two strains of E. mundus by MiSeq 16S rRNA amplicon sequencing. Finally, enzymatic tests were done to determine the influence of Arthrobacter species in the susceptibility of E. mundus to pesticides.

RESULTS

The assays showed that when E. mundus adults were pretreated with antibiotic, the toxicity of abamectin was significantly higher. Among the different bacteria associated with parasitic wasps, Arthrobacter has been shown to be involved in the degradation of several kinds of pesticides. Four Arthrobacter species were detected in all the studied insects and the presence of esterases in this bacterial species was confirmed.

CONCLUSIONS

The results suggest that the microbiota can modify the susceptibility of E. mundus to pesticides, which in turn supports the importance of the microbial community in natural enemies that it should be considered as a factor in risk assessment tests of pesticides. © 2018 Society of Chemical Industry.

A Short-Term Response of Soil Microbial Communities to Cadmium and Organic Substrate Amendment in Long-Term Contaminated Soil by Toxic Elements

Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of Actinobacteria determined by phylum specific qPCR increased and also the proportion of Actinobacteria and Chloroflexi increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly Actinobacteria withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil.

Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia

Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Actinobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against bacteria and fungi. It was shown that representatives of the genera Nocardia and Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic properties. However, despite the lack of antimicrobial and fungicidal activity of Nocardia extracts, those strains are specific in terms of their fatty acid spectrum. When assessing fatty acid profile, we found that polyunsaturated fatty acids were quantitatively dominant in extracts of Nocardia sp. and Streptomyces sp. grown in different media. Saturated fatty acids were the second most abundant type in the fatty acid profile. It was due to palmitic acid. Also, a few monounsaturated fatty acids were detected. The obtained materials can become a basis for development of approaches to use bacteria isolated from caves as a biological sources of bioactive compounds to create medical and veterinary drugs.

Long-term effects of environmentally relevant concentrations of silver nanoparticles on major soil bacterial phyla of a loamy soil

BACKGROUND

The growing production and use of engineered AgNP in industry and private households make increasing concentrations of AgNP in the environment unavoidable. Although we already know the harmful effects of AgNP on pivotal bacterial driven soil functions, information about the impact of silver nanoparticles (AgNP) on the soil bacterial community structure is rare. Hence, the aim of this study was to reveal the long-term effects of AgNP on major soil bacterial phyla in a loamy soil. The study was conducted as a laboratory incubation experiment over a period of 1 year using a loamy soil and AgNP concentrations ranging from 0.01 to 1 mg AgNP/kg soil. Effects were quantified using the taxon-specific 16S rRNA qPCR.

RESULTS

The short-term exposure of AgNP at environmentally relevant concentration of 0.01 mg AgNP/kg caused significant positive effects on Acidobacteria (44.0%), Actinobacteria (21.1%) and Bacteroidetes (14.6%), whereas beta-Proteobacteria population was minimized by 14.2% relative to the control (p ≤ 0.05). After 1 year of exposure to 0.01 mg AgNP/kg diminished Acidobacteria (p = 0.007), Bacteroidetes (p = 0.005) and beta-Proteobacteria (p = 0.000) by 14.5, 10.1 and 13.9%, respectively. Actino- and alpha-Proteobacteria were statistically unaffected by AgNP treatments after 1-year exposure. Furthermore, a statistically significant regression and correlation analysis between silver toxicity and exposure time confirmed loamy soils as a sink for silver nanoparticles and their concomitant silver ions.

CONCLUSIONS

Even very low concentrations of AgNP may cause disadvantages for the autotrophic ammonia oxidation (nitrification), the organic carbon transformation and the chitin degradation in soils by exerting harmful effects on the liable bacterial phyla.

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood^®-kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates corroborated enormous endophytic bacteria. This study elucidates a vast diversity of cultivation-recalcitrant endophytic bacteria prevailing in grapevine field shoots, their in vitro introduction, and unsuspecting sustenance with possible silent participation in tissue culture processes.

Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity

Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of Actinobacteria and Saccharibacteria were gradually increased. Using LEfSe analyses, we found that Saccharibacteria was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to Actinobacteria, and one belonged to Bacteroidetes. The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and Saccharibacteria played a potential role in evaluating the biological effects of continuous fumigation.

Biodiversity of Actinobacteria from the South Pacific and the Assessment of Streptomyces Chemical Diversity with Metabolic Profiling

Recently, bioprospecting in underexplored habitats has gained enhanced focus, since new taxa of marine actinobacteria can be found, and thus possible new metabolites. Actinobacteria are in the foreground due to their versatile production of secondary metabolites that present various biological activities, such as antibacterials, antitumorals and antifungals. Chilean marine ecosystems remain largely unexplored and may represent an important source for the discovery of bioactive compounds. Various culture conditions to enrich the growth of this phylum were used and 232 bacterial strains were isolated. Comparative analysis of the 16S rRNA gene sequences led to identifying genetic affiliations of 32 genera, belonging to 20 families. This study shows a remarkable culturable diversity of actinobacteria, associated to marine environments along Chile. Furthermore, 30 streptomycete strains were studied to establish their antibacterial activities against five model strains, Staphylococcus aureus, Listeria monocytogenes, Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa, demonstrating abilities to inhibit bacterial growth of Gram-positive bacteria. To gain insight into their metabolic profiles, crude extracts were submitted to liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis to assess the selection of streptomycete strains with potentials of producing novel bioactive metabolites. The combined approach allowed for the identification of three streptomycete strains to pursue further investigations. Our Chilean marine actinobacterial culture collection represents an important resource for the bioprospection of novel marine actinomycetes and its metabolites, evidencing their potential as producers of natural bioproducts.

Short-duration hydrothermal fermentation of food waste: preparation of soil conditioner for amending organic-matter-impoverished arable soils

Soil conditioners can be used to compensate for the insufficient soil nutrition and organic matter (OM) of arable soils. However, the traditional preparation method for soil conditioners is lengthy and requires facilities that occupy large tracts of land. In this study, a short-duration hydrothermal fermentation (SHF) method was developed for the preparation of soil conditioners from food waste. The SHF method required only 18 h to produce soil conditioners with physicochemical characteristics that were similar to those of soil conditioners obtained through traditional fermentation (TF), which takes 20 days to complete. Inoculation and dynamic SHF significantly affected the distribution of different molecular weight fractions in the prepared soil conditioners. The results of spectral analysis revealed that a large amount of soluble microbial byproducts and carbohydrate C formed in the SHF soil conditioner. This effect indicated that the SHF soil conditioner supplied not only immediately available nutrients, which can stimulate the growth of soil microbial communities, but also provided sustained-release nutrients for the long-term cultivation of crops on OM-impoverished soils. Cyanobacteria were present in the SHF soil conditioner at a relative abundance of 6.29%, which was 28.6 and 314.5 times those in the raw material and TF soil conditioner, respectively. Amending OM-impoverished soil with the SHF soil conditioner enhanced the carbon pool management index of the resulting SHF soil by 1.50 and 1.12 times those of unfertilized soil and TF soil, respectively. These results indicated that the SHF soil exhibited a high capacity to supply nutrients for crop growth.