Culturable Bacterial Community Research Articles

Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis.

Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis. Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL-1, and in combination at 50 µg mL-1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones. Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments. Antibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals.

Arbuscular mycorrhizal fungi and Streptomyces: brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction

BackgroundFungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other’s metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown.ResultsHere, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P.ConclusionsThis work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi.3XiVYVBxkNucerLC-WX6ofVideo

Response of Microbial Recovery Rate to Straw Return after Calcium Cyanamide Soil Disinfection

At present, returning vegetable straw in situ is an effective measure to solve environmental pollution and improve soil properties. However, the direct return of straw to the field can reduce the release rate of soil organic matter and cause serious soilborne diseases. The combined application of calcium cyanamide (CaCN2) and straw can solve this problem. The objective of this study was to determine the effect of CaCN2 combined with pepper straw return on cucumber yield, soil physicochemical properties, and soil microbial communities during 2020 to 2021 in Shandong Province, China. The treatments were designed as follows: (1) calcium cyanamide soil disinfection, CC; (2) fresh pepper straw return, LJ; (3) fresh pepper straw return combined with calcium cyanamide disinfection, LJ+CC; and (4) natural soil without straw return treatment, CK. Compared with CK, the LJ+CC treatment significantly improved cucumber production by 20%. The cultivable microbial community in the soil was temporarily inhibited during soil fumigation treatment, and the cultivable bacterial and actinomycete communities in the soil return to their initial levels after the film was removed (harvest period). The numbers of culturable bacteria and actinomycetes in the soil in the LJ+CC treatment were 4.68 × 107 CFU/g and 5.17 × 107 CFU/g, respectively, higher than those in the soil in the CC treatment. The contents of TN and OM in the LJ+CC treatment increased by 13.1% and 13.5%, respectively, compared with that in LJ. Therefore, the LJ+CC treatment enhanced soil fertility and cucumber yields. CaCN2 can promote straw decomposition and straw can promote soil microbial recovery, and their combined application is considered a feasible and sustainable technique for utilizing vegetable residues in the greenhouse. The combination of returning pepper straw to the field and calcium cyanamide technology achieves a win-win situation of resource circulation and economic circulation by converting agricultural waste into fertilizer before being put into production. Based on this, it is recommended that the straw returning technology receives strong policy support, stimulates researchers to explore the feasibility of different vegetable straw returning to the field, promotes the implementation of this technology achievement, and leverages the environmental benefits of the application of straw returning technology.

168 Characterization of the Culturable Fraction of Bovine Ocular Microbiota and Its in Vitro Antimicrobial Activities Against Pinkeye Pathogens

Abstract Pinkeye, clinically known as infectious bovine keratoconjunctivitis (IBK), is considered one of the most important ocular diseases in cattle, causing an estimated $226 million in annual losses to U.S. cow-calf producers. While Moraxella bovis is considered the principal IBK pathogen, Moraxella bovoculi has also been associated with the pathogenesis of IBK. Thus, these Moraxella species are often the target for antibiotic and/or vaccine-based treatment and prevention strategies. Despite extensive use of antibiotics, IBK infections are challenging to treat, highlighting the increased need for an antibiotic-alternative approach to control IBK. Recent evidence suggests that the microbial community associated with the bovine oculus is important for eye health, and that the ocular microbiota can be a target for enhancing disease resistance against IBK in cattle. The objectives of this study were to characterize the ocular microbiota of healthy and IBK infected cattle using sequencing and culturing techniques, and to isolate and screen commensal ocular isolates for their antimicrobial activity against M. bovis and M. bovoculi. Ocular swabs (n = 64) were collected using eSwabs from cattle diagnosed with IBK or without IBK (healthy control) before antibiotic treatment from beef herds across North Dakota. Swabs were plated onto four different agar plates (blood, Columbia blood, MRS and multi-sliced agar plates), and cultured aerobically and anaerobically. A total of 658 bacterial isolates were obtained via culturing and cryopreserved. Taxonomic identification was performed on a subset of banked isolates (n = 277) by near full-length sequencing of the 16S rRNA gene. These isolates taxonomically belong to 6 different bacterial phyla: Bacillus (42%), Firmicutes (27%), Actinomycetota (13%), Pseudomonadota (11%), Actinobacteria (5%), and Proteobacteria (2%). A total of 55 different genera were identified with Bacillus (25%), Streptococcus (13%), Staphylococcus (10%), Moraxella (6%), Macrococcus (5%), Paenibacillus (3%), Caldibacillus (3%), and Rummeliibacillus (3%) being the most dominant genera. Next, a subset of these commensal isolates (n 53) were screened for their growth inhibition against M. bovis and M. bovoculi using an agar slab method. Among the screened isolates, 6 isolates showed inhibition against M. bovis and M. bovoculi with zones of inhibition ranging from 12 mm to 28 mm. Ocular isolates identified as Weizmannia coagulans (43Y-MRSC), Lentillactobacillus buchneri (23D-MRSA) and Paenibacillus polymyxa (785-WCF) exhibited relatively strong inhibition against both Moraxella isolates. Scanning electron microscopy revealed noticeable structural and morphological damages in M. bovis and M. bovoculi cells due to Weizmannia coagulans culture-supernatant treatment. Overall, our results indicate that ocular mucosa of beef cattle is inhabited by relatively rich and diverse culturable bacterial communities, and that some ocular commensals can inhibit IBK pathogens. This suggests the potential for the development of bacterial therapeutics based on commensal ocular bacteria to mitigate IBK in cattle.

Taxonomic and functional characteristics of xerotolerant culturable bacterial community of Negev desert soil

Despite the significant expansion of the geography of soil microorganisms studies in various, including extreme natural environments, research on the biodiversity and metabolic activity of soil microbial communities under conditions of moisture deficiency are few. Biodiversity of culturable bacteria isolated from the surface horizon of the Negev desert soil (Aridic Calcisol) after pre-incubation of soil samples under the conditions of low water availability has been studied. An increase in the diversity of culturable bacteria after pre-incubation was revealed in comparison with the community isolated from the native soil. From the native and pre-incubated samples, 153 phenotypically unique pure cultures of bacteria from 22 genera belonging to the phyla Actinomycetota, Pseudomonadota, Bacillota, and Bacteroidota were isolated and identified. The taxonomic diversity of culturable bacteria isolated from the sample pre-incubated at a water activity (Aw) of 0.90 was two times higher than that obtained from the native soil. The strain of the genus Pedobacter has been identified, which may be a representative of a previously undescribed bacterial species. Bacteria of the genera Aerococcus, Bacillus, Brevibacterium, Staphylococcus, and Stenotrophomonas capable of growing at Aw 0.91 were found. One strain of the genus Microlunatus has been identified that is capable of growing on a nitrogen-free medium, exhibiting amylase and protease activity, and capable to growth on a medium with Aw down to 0.96. The obtained results confirm the hypothesis that arid ecosystems, in particular, desert soils and sediments, are a depository of a previously unexplored taxonomic diversity of bacteria with unique physiological properties that are promising for study and potential implementation in biotechnological processes.

Assessing the functional diversity of rhizobacteria from cacao by partitioning root and shoot biomasses.

Plant-microbe interactions are critical for the sustainability of agricultural production. In this study, our aims were to characterize the genetic and functional diversity of the culturable bacterial community associated with the cacao rhizosphere and access their potential for growth promotion of cacao seedling. Culture-dependent and molecular methods were used to characterize the population densities and diversity of bacterial communities from soil and cacao plants at two locations and two plant ages. A total of 63 strains were identified through hsp60 sequencing. Pseudomonas and Enterobacter were the most abundant genera in association with the cacao rhizosphere, whereas Bacillus was more numerous in soil. Parameters of seedling growth promotion were evaluated 60days after inoculation of seeds, with partition of the assessments into root and shoot weight. Each isolate showed beneficial, neutral or deleterious effects on plant growth, depending on the isolate and on the parts of plant assessed. Interestingly, although an apparent overall decrease in total biomass of seedlings (roots + shoots dry matters) was observed for the majority of isolates (89%), 94% of all isolates, in fact, revealed an increase in plant roots/shoots dry biomass ratio. Despite that part of the isolates (35%) appeared to significantly decrease plant height, and that 65% did not influence plant height (neutral effect), 18 had significantly increased root dry biomass; nevertheless, seven of these root growth-increasing isolates simultaneously decreased shoots-related growth parameters. The results of this study evidentiated the functional diversity of culturable cacao rhizobacteria and how the partitioning of roots and shoots in the assessment of plant growth parameters could reveal the biotechnological potential of these isolates for promoting growth of clones for rehabilitation of commercial cacao plantations. KEY POINTS: • The most common culturable bacteria in cacao roots were Pseudomonas and Enterobacter • Most culturable bacteria from cacao roots increased the root/shoot ratio • Roots and shoots should be examined separately to detect cacao beneficial bacteria.

Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina.

We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.

In vitro biochemical characterization and identification of hemolytic bacteria associated with life history of Culicoides peregrinus (Diptera: Ceratopogonidae), a vector of bluetongue virus.

Gut bacterial communities in insects provide several beneficial roles like nutrition, digestion, fecundity, and survival of the host. The microbial communities of Culicoides spp. (Diptera: Ceratopogonidae) vary with parity, developmental stages, and environmental factors. Previous studies have revealed the presence of hemolytic bacteria in adult Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae), an important vector of bluetongue virus (BTV). Our objectives were (i) to identify bacterial communities with hemolytic activities associated with all life stages and (ii) to compare between reared and field-collected adults including age graded females. Bacterial identification followed Sanger sequencing of 16S rRNA. In vitro biochemical characterizations including antibiotic sensitivity tests were also done. The majority of bacterial species were beta hemolytic with one, Alcaligenes faecalis, showing alpha hemolysis. Most bacterial species were observed in field-collected adults except Proteus spp. Throughout the life history of the vector, Bacillus cereus (CU6A, CU1E) and Paenibacillus sp. (CU9G) were detected indicating their possible role in blood digestion within the gut of this vector species. In vivo hemolytic activities of these culturable bacterial communities within this vector may be addressed in future. These hemolytic bacterial communities may be targeted to develop novel and effective strategies for vector control.

16S rRNA gene‐based identification and plant growth‐promoting potential of cultivable endophytic bacteria

AbstractEndophytic bacteria play essential roles in plant growth and fitness through nitrogen fixation, nutrient solubilization, and phytohormone production. However, the plant growth‐promoting (PGP) potential of endophytic microorganisms inhabiting vegetables is underexplored. Thus, this study investigated the endophytic bacteria of vegetable crops for their PGP properties using the culture‐dependent technique. Recovered isolates were identified by sequencing the partial 16S rRNA gene using Sanger sequencing. The isolated endophytic bacteria belonged to 15 genera and 39 different species. Bacillus, Enterobacter, Pantoea, and Pseudomonas were the predominant genera and had high phosphate solubilization and siderophore production potential. The isolates differentially produced indole‐3‐acetic acid and ammonium in the range 0.14–44.48 μg mL–1 and 0.77–93.24 mg L–1, respectively. Pseudomonas azotoformans, Stenotrophomonas maltophilia, and Serratia liquefaciens showed a high level of siderophore production, which was not significantly (p > 0.05) different across the plant and organ types. More than 21% of endophytes could produce gelatinase, protease, amylase, and cellulase, contributing to their diverse ecosystem functions. Bacterial density and species composition varied across the vegetable species, organs, and farm locations but were higher in the stems compared with other organs. However, the vegetable organ had no significant (p > 0.05) influence on the bacterial population density, except for the interaction of plant species and organs. Overall, this study provides basic knowledge about the cultivable endophytic bacterial community of vegetables and reveals diverse endophytic bacteria useful in bioinoculant formulations for improving crop productivity.

Microbiological quality and cultivable bacterial community of fresh and ripened Minas cheeses made from raw and pasteurised milk

The microbiological and physicochemical characteristics of 56 samples of Brazilian fresh (Minas frescal cheese, MFC) and ripened (Minas padrão cheese, MPC; Minas artisanal cheese, MAC) cheeses produced from pasteurised (MFC and MPC) or raw milk (MAC) were evaluated. Significant differences were observed between samples, with a positive emphasis on microbiological quality for MPC. MALDI-TOF MS identified a diverse bacterial community from the 808 colonies isolated from different culture media. Staphylococcus aureus (34.32%) and Escherichia coli (35.59%) were the most isolated species. The eae gene, which confers virulence on E. coli strains, was observed in 23 samples (41.07%), and in 21.05%, 27.78%, and 73.68% of MFC, MPC and MAC samples, respectively. There was no correlation between the evaluated indicators and the presence of eae-positive cheese samples. The choice of the ideal microbiological indicator must be specific, considering the physicochemical characteristics and the raw milk of the different types of cheese.

Vertical profile of culturable bacteria from the Makassar Strait, Indonesia

Abstract. Siallagan ZL, Kristianti T, Dwivany FM, Nugrahapraja H, Fretes CED, Fadli M, Trinugroho JP, Radjasa OK, Susanto RD. 2023. Vertical profile of culturable bacteria from the Makassar Strait, Indonesia. Biodiversitas 24: 1356-1365. Indonesia's extensive maritime background is a rich biological and chemical diversity source. This diversity has become as source of unique chemical compounds with the potential for industrial development as enzymes, molecular probes, chemicals, pharmaceuticals, cosmetics, nutritional supplements, and agrochemicals. The present study aimed to analyze the community composition of culturable bacteria from three different layers of depth from Makassar Strait using high throughput DNA Illumina sequencing of 16S rRNA. Bioinformatic analysis has rendered 140336 high-quality sequences with an average of 124127 sequences per sample and a mean read length of 428 bp. Results showed that Firmicutes and Proteobacteria were the two most abundant phyla. Taxonomic analysis showed that Firmicutes dominated all samples. Genus Streptomycetes and Psychrobacter occurred mainly in the culture from the surface layer. Species richness and diversity for the bacterial communities at 100 m were higher than those at 5 m and 200 m. PCA plot, NMDS plot, and UPGMA clustering demonstrated that the culturable bacterial community compositions of 100 and 200 ms were highly similar and distinct from those in 5 m. This research discovered microbes with potential as sources of marine natural products, including Streptomyces, Paenibacillus, Bacillus, Psychrobacter, Arthrobacter, Bradyrhizobium, Gemmatimonas, and Acidobacteria.

Further Bacteriological Analysis of Annual Pheasantshell (Actinonaias Pectorosa) Mussel Mortality Events in the Clinch River (Virginia/Tennessee), USA, Reveals a Consistent Association with Yokenella Regensburgei

Pheasantshell (Actinonaias pectorosa) mussels in the Clinch River (Tennessee/Virginia, USA) have declined dramatically in recent years. The bacterium Yokenella regensburgei was first isolated with high prevalence from Pheasantshells during the peak of a 2017 mortality event, but it was not identified after mortality subsided a few months later. Since 2017, Pheasantshell mortality in the Clinch River has occurred each autumn. We extended the investigation of culturable bacterial communities in the Clinch River during mussel mortality events in 2018, 2019, and 2020 and examined the spatial and temporal distribution of bacterial genera among Pheasantshells, as well as among other unionid mussels. We identified Y. regensburgei each year, almost exclusively during active mortality events. The significance of Y. regensburgei remains unclear, but the continued association of this bacterium with mussel mortality events warrants further study.

Composition of the culturable bacterial community associated with the water column and soft tissues from oysters of the mangrove ecosystem at Honda Swamp, Colombian Caribbean

The study of bacterial communities is highly relevant in relation to the knowledge of global biological biodiversity and the biogeochemical cycles of the planet. Microbiological activity is the basis of ecosystems functioning, among these are the mangroves, which offer a wide variety of goods and services to humanity. Nevertheless, they have been severely impacted by anthropogenic activities such as felling, heavy metal pollution, water enrichment, overexploitation of resources, among others. This research aimed to characterize the culturable bacterial community from the water column and the oyster Crassostrea rhizophorae muscle tissue in a mangrove ecosystem from the Cartagena Bay, Colombian Caribbean as a baseline for future studies on bioremediation treatments. To accomplish this, four samplings were conducted over the course of a year, including contrasting climatic seasons (e.g., windy and rainy), collecting oyster individuals from mangroves and samples from superficial water. The bacterial community comprised 25 species, from which 9 were exclusive for the oyster tissue, 7 for the water column, and 9 generalists isolated from both types of samples. Enterobacter cloacae was the most frequent species during the year, followed by Escherichia coli and Erwinia sp.There were significant differences in the species composition between the sampling months (ANOSIM, R = 0:492; p=D 0:001), because of the presence of a higher number of exclusive species in December than in the other months. Furthermore, the physicochemical variables that presented a major influence on the bacterial community composition were the wind velocity and the dissolved oxygen. The review of this research findings will allow to detect if any of the identified species could be exploited for bioremediation treatments, and it will contribute to the preservation of marine-coastal water bodies biodiversity.

Community Composition and Antibiotic Resistance of Tap Water Bacteria Retained on Filtration Membranes

Community composition and antibiotic resistance of tap water bacteria are still not known well enough. This study fills the gaps in knowledge regarding this matter. To provide representativeness of collected samples, tap water bacteria were concentrated from huge amounts of water, using filtration membranes monthly during the continuous, semi-annual study, covering winter and spring seasons. Biomass was investigated both using a culture-based method (for total and antibiotic-resistant culturable bacteria counts) and metagenomic DNA sequencing (for taxonomic identification of bacteria). The results showed that bacteria resistant to ceftazidime were the most prevalent among the studied resistance phenotypes, whereas bacteria resistant to amoxicillin, ciprofloxacin, and tetracycline were scarce. On average, 20,059 and 26,200 CFU/mL per month was counted in the winter and spring season, respectively, whereas in terms of antibiotic-resistant bacteria, average counts were 14,270 and 9435 CFU/mL per month in the winter and spring season, respectively. In terms of bacterial community composition, Cyanobacteria, Proteobacteria and Actinobacteria were the most abundant phyla, reaching up to 77.71%, 74.40% and 21.85%, respectively, which is supported by previous studies conducted on the same water supply network and other drinking water distribution systems across the world. No season-dependent variations were observed for culturable antibiotic-resistant bacteria or bacterial community composition. The prevalence of culturable antibiotic-resistant bacteria was not correlated with any of the identified taxa.

Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland.

Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey's air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site's nature and location.

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla Periphylla

The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose-yeast-malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC50 values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.

Bacterial diversity associated with Millepora alcicornis and Phyllogorgia dilatata corals and prospection for genes encoding bioactive molecules

Coral reefs are marine environments with notable biodiversity, considered rich in organisms that produce active molecules. The microorganisms present in coral tissue play different roles that are not yet fully understood. The study of the microbiota can explain how microorganisms influence the health of corals and their participation in defense mechanisms. In this study, the cultivable bacterial communities of Millepora alcicornis and Phyllogorgia dilatata corals were analyzed following the steps of isolation, morphological characterization, and molecular identification by amplification of the gene encoding 16S rRNA. Of the 135 bacterial isolates, 121 of which were from M. alcicornis and 14 from P. dilatata, most belonged to the phyla Proteobacteria and Firmicutes, with the majority from the genera Vibrio and Bacillus. Coral metagenomic DNA was extracted and the gene encoding 16S rRNA was analyzed. The isolates were evaluated, in vitro, for antimicrobial activity against ATCC strains of Escherichia coli and Staphylococcus aureus, and 29 isolates from M. alcicornis showed activity against at least one of the bacteria evaluated. Using specific pairs of primers, 27 isolates showed amplification for at least one pair of primers designed for amplification of genes involved in the synthesis of non-ribosomal peptides (NRPs) and polyketides (PKs). However, only in some cases was a relationship detected between the isolates that showed antimicrobial activity in vitro and the isolates where amplification of genes involved in the synthesis of NRPs and PKs was observed.

Exploring the nexus between the composition of essential oil and the bacterial phytobiome associated with different compartments of the medicinal plants Origanum vulgare ssp. vulgare, O. vulgare ssp. hirtum, and O. heracleoticum

The emergence of new multidrug-resistant (MDR) pathogens brought attention to the need for new antimicrobial compounds. One of the advances in addressing the global issue of antibiotic resistance is the discovery that microorganisms residing inside medicinal plants (i.e., the endophytes) may contribute to the production of metabolites of pharmaceutical interest. In this work, the composition of the essential oil (EO) and the cultivable bacterial communities isolated from three different species belonging to the genus Origanum , i.e., O. vulgare ssp . vulgare, O. vulgare ssp . hirtum and O. heracleoticum were analyzed, to check the possible nexus existing between them. The three species exhibited different EO aroma profiles, revealing two trans -sabinene hydrate chemotypes and a carvacrol chemotype. The composition of the bacterial endophytic cultivable microbiome isolated from flowers, leaves, and stems and the bacterial communities isolated from bulk soil were characterized at the genus, species, and/or strain level. The analyses revealed a high degree of biodiversity and a low number of strains shared between the three plant species and compartments of the same plant, suggesting the existence of one or more forces responsible for the distribution of the endophytes in the different microenvironments of the plant. Data obtained also suggested that the composition of the EO might be involved in the structuring of the microbial community and that bacteria might be able to colonize the plant since they are resistant to the antimicrobial activity exhibited by the EO itself and/or able to utilize some compounds as a carbon and energy source. Lastly, the composition of microbial communities might enhance or influence the EO composition. Schematic representation of the experimental strategy used in the present work . • Three Origanum plants exhibited different essential oil aroma profiles. • Cultivable bacterial endophytes were isolated and molecularly characterized. • A very low number of bacterial strains was shared between plants. • Different plant compartments were inhabited by different endophytic communities. • Essential oil composition might be involved in the structuring of the microbiome.

Culturable bacteria diversity in stem liquid and resina from Populus euphratica and screening of plant growth-promoting bacteria

BackgroundPopulus euphratica Olivier is a kind of tree capable of growing in extremely arid desert and semi-desert environments. In this study, a culture-dependent method was used to analyze the bacterial diversity of stem liquid of P. euphratica and resina of P. euphratica, and to further evaluate plant growth promoting (PGP) activity.ResultsA total of 434 bacteria were isolated from stem fluid and resina of P. euphratica in Ebinur Lake Wetland Nature Reserve and Mulei Primitive forest. The results of taxonomic composition analysis shows that Gammaproteobacteria, Firmicutes, and Actinobacteria_c are the three dominant groups in all the communities, and the representative genera are Bacillus, Nesterenkonia and Halomonas. The diversity analysis shows that the culturable bacterial community diversity of P. euphratica in Ebinur Lake Wetland Nature Reserve is higher than that in Mulei Primitive forest, and the bacterial community diversity of P. euphratica stem fluid is higher than that of resina. According to PGP activity evaluation, 158 functional bacteria with plant growth promoting potential were screened. Among them, 61 strains havephosphorus solubilizing abilities, 80 strains have potassium solubilizing abilities, 32 strains have nitrogen fixation abilities, and 151 strains have iron ammonia salt utilization abilities. The germination rate, plant height, and dry weight of the maize seedlings treated with strains BB33-1, TC10 and RC6 are significantly higher than those of the control group.ConclusionIn this study, a large number of culturable bacteria were isolated from P. euphratica, which provides new functional bacteria sources for promoting plant growth.

Bacterial diversity on stained glass windows

In order to explore the role of bacteria in the alteration of stained glass windows, and especially on the browning phenomenon, it is necessary to have an overview of the microbial inhabitants likely to be found on this kind of material. In this study, biological samples were collected on stained glass of different colours, both on site and stored in a conservation workshop. Cultivable bacterial communities were identified by 16S rDNA sequencing. Similarity values ranged from 99 to 100% to known bacteria. Sequence analysis showed different bacterial communities depending on the sampling site. The more represented genera were Arthrobacter, Micrococcus, Paenibacillus and Bacillus. Some of the identified bacteria are known for their weathering potential.