Natural Niche Research Articles

Reconstruction of Ultra-thin Alveolar-capillary Basement Membrane Mimics.

Alveolar-capillary basement membrane (BM) is ultra-thin (<2 µm) extracellular matrix that maintains integral epithelial-endothelial cell layers. In vitro reconstructions of alveolar-capillary barrier supported on synthetic scaffolds closely resembling the fibrous and ultra-thin natural BM are essential in mimicking the lung pathophysiology. Although BM topology and dimensions are well known to significantly influence cellular behavior, conventionally used BM mimics fail to recreate this natural niche. To overcome this, electrospun ultra-thin 2 µm poly(caprolactone) (PCL) nanofibrous mesh is used to establish an alveolar-capillary barrier model of lung endothelial/epithelial cells. Transepithelial electrical resistance (TEER) and permeability studies reveal integral tight junctions and improved mass transport through the highly porous PCL meshes compared to conventional dense membranes with etched pores. The chemotaxis of neutrophils is shown across the barrier in presence of inflammatory response that is naturally impeded in confined regions. Conventional requirement of 3 µm or larger pore size can lead to barrier disruption due to epithelial/endothelial cell invasion. Despite high porosity, the interconnected BM mimic prevents barrier disruption and allows neutrophil transmigration, thereby demonstrating the physiological relevance of the thin nanofibrous meshes. It is envisioned that these bipolar cultured barriers would contribute to an organ-level in vitro model for pathological disease, environmental pollutants, and nanotoxicology.

Nutrient Deficiency Promotes the Entry of Helicobacter pylori Cells into Candida Yeast Cells.

Simple SummaryHelicobacter pylori is a pathogenic bacterium which causes several gastric and extra-gastric pathologies in humans. This pathogen is capable of entering eukaryotic cells of humans or of other species, including yeasts of the genus Candida. These yeasts are resistant to stressing environmental conditions (such as pH changes or scarce nutrients) which threaten the viability of H. pylori. Therefore, Candida yeasts may harbor this bacterium when subjected to stressing conditions or become transmission vehicles for it. Further research is required to establish the stressing environmental factors triggering the harboring of H. pylori within yeasts. The present work evaluated if deficiency or absence of the necessary nutrients favors the endosymbiotic relationship between these two microorganisms, facilitating the viability of the bacterium. In fact, a deficiency of nutrients increased the harboring of viable H. pylori cells within the yeast cells. On the contrary, in the complete absence of nutrients, the presence of intra-yeast bacteria was reduced. Therefore, yeast cells may contribute to the subsistence of this pathogenic bacterium when subjected to nutrient deficiency until it may infect an appropriate host, such as humans. The present work may also contribute, with further studies, to elucidate the transmission routes used by the pathogen H. pylori to infect its hosts.Helicobacter pylori, a Gram-negative bacterium, has as a natural niche the human gastric epithelium. This pathogen has been reported to enter into Candida yeast cells; however, factors triggering this endosymbiotic relationship remain unknown. The aim of this work was to evaluate in vitro if variations in nutrient concentration in the cultured medium trigger the internalization of H. pylori within Candida cells. We used H. pylori–Candida co-cultures in Brucella broth supplemented with 1%, 5% or 20% fetal bovine serum or in saline solution. Intra-yeast bacteria-like bodies (BLBs) were observed using optical microscopy, while intra-yeast BLBs were identified as H. pylori using FISH and PCR techniques. Intra-yeast H. pylori (BLBs) viability was confirmed using the LIVE/DEAD BacLight Bacterial Viability kit. Intra-yeast H. pylori was present in all combinations of bacteria–yeast strains co-cultured. However, the percentages of yeast cells harboring bacteria (Y-BLBs) varied according to nutrient concentrations and also were strain-dependent. In conclusion, reduced nutrients stresses H. pylori, promoting its entry into Candida cells. The starvation of both H. pylori and Candida strains reduced the percentages of Y-BLBs, suggesting that starving yeast cells may be less capable of harboring stressed H. pylori cells. Moreover, the endosymbiotic relationship between H. pylori and Candida is dependent on the strains co-cultured.

Trophic Partitioning of Cambarus carinirostris, Cambarus robustus, and Faxonius obscurus in Kings Creek, WV by Stable Isotope Analysis

The competitive exclusion principle states that no two species can share the same niche in nature. Partitioning among coexisting species occurs through utilization of various food sources or differences in microhabitat preference. The purpose of this study is to assess potential trophic partitioning between Cambarus carinirostris, Cambarus robustus, and Faxonius obscurus, three species of crayfish present in Kings Creek, Weirton, WV. Analysis and comparison of individual carbon-13 and nitrogen-15 isotope signatures were used to establish organic matter transfer pathways and trophic structures in the ecosystem. Representative trophic groups were sampled, spanning from macro-predators (e.g., smallmouth bass) to primary producers (e.g., macrophytes and algae). All samples were analyzed for carbon-13 and nitrogen-15 by the Stable Isotope Ecology Laboratory at the University of Georgia. Interspecific partitioning within the community was identified. Smallmouth bass were top predators and crayfish were the second highest group. Between the three species of crayfish, interspecific partitioning was suggested. The lowest and highest trophic levels were occupied by C. carinirostris and F. obscurus, respectively. In addition, intraspecific partitioning within each crayfish species suggested that juveniles occupy a lower trophic level than adults, potentially signifying ontogenetic dietary shifts. All analyzed data represent the summer season. Winter results are pending and once available, the two seasons will be compared for any differences in trophic structure.

Environmental Isolation of Candida auris from the Coastal Wetlands of Andaman Islands, India.

Candida auris is a multidrug resistant pathogen that presents a serious global threat to human health. As C. auris is a newly emerged pathogen, several questions regarding its ecological niche remain unexplored. While species closely related to C. auris have been detected in different environmental habitats, little is known about the natural habitat(s) of C. auris Here, we explored the virgin habitats around the very isolated Andaman Islands in the Indian Ocean for evidence of C. auris We sampled coastal wetlands, including rocky shores, sandy beaches, tidal marshes, and mangrove swamps, around the Andaman group of the Andaman & Nicobar Islands, Union Territory, in India. Forty-eight samples of sediment soil and seawater were collected from eight sampling sites representing the heterogeneity of intertidal habitats across the east and west coast of South Andaman district. C. auris was isolated from two of the eight sampling sites, a salt marsh and a sandy beach. Interestingly, both multidrug-susceptible and multidrug-resistant C. auris isolates were found in the sample. Whole-genome sequencing analysis clustered the C. auris isolates into clade I, showing close similarity to other isolates from South Asia. Isolation of C. auris from the tropical coastal environment suggests its association with the marine ecosystem. The fact that viable C. auris was detected in the marine habitat confirms C. auris survival in harsh wetlands. However, the ecological significance of C. auris in salt marsh wetland and sandy beaches to human infections remains to be explored.IMPORTANCECandida auris is a recently emerged multidrug-resistant fungal pathogen capable of causing severe infections in hospitalized patients. Despite its recognition as a human pathogen a decade ago, so far the natural ecological niche(s) of C. auris remains enigmatic. A previous hypothesis suggested that C. auris might be native to wetlands, that its emergence as a human pathogen might have been linked to global warming effects on wetlands, and that its enrichment in that ecological niche was favored by the ability of C. auris for thermal tolerance and salinity tolerance. To understand the mystery of environmental niches of C. auris, we explored the coastal wetland habitat around the very isolated Andaman Islands in the Indian Ocean. C. auris was isolated from the virgin habitats of salt marsh area with no human activity and from a sandy beach. C. auris isolation from the marine wetlands suggests that prior to its recognition as a human pathogen, it existed as an environmental fungus.

Cryptococcus neoformans: Sex, morphogenesis, and virulence.

Cryptococcus neoformans is a dimorphic fungus that causes lethal meningoencephalitis mainly in immunocompromised individuals. Different morphotypes enable this environmental fungus and opportunistic pathogen to adapt to different natural niches and exhibit different levels of pathogenicity in various hosts. It is well-recognized that C. neoformans undergoes bisexual or unisexual reproduction in vitro to generate genotypic, morphotypic, and phenotypic diversity, which augments its ability for adaptation. However, if and how sexual reproduction and the meiotic machinery exert any direct impact on the infection process is unclear. This review summarizes recent discoveries on the regulation of cryptococcal life cycle and morphogenesis, and how they impact cryptococcal pathogenicity. The potential role of the meiotic machinery on ploidy regulation during cryptococcal infection is also discussed. This review aims to stimulate further investigation on links between fungal morphogenesis, sexual reproduction, and virulence.

Urban waste no replacement for natural foods—Marabou storks in Botswana

Abstract We compared diets of marabou storks Leptoptilos crumenifer foraging from urban landfills and natural areas in northern Botswana using stable isotope analyses and inductively coupled plasma mass spectrometry on moulted feathers. There were significant differences in the diet of marabous foraging from natural areas compared to urban waste sites, reflected by lower δ13C and less enriched δ15N concentrations in those feeding at landfills, suggesting a shift in trophic niche. Feathers from birds foraging at landfills also had significantly higher concentrations of chromium, lead, nickel, and zinc and lower levels of cadmium and potassium than feathers sampled from natural areas. We also analysed marabou regurgitant (42 kg, naturally expelled indigestible food resources) from the Kasane landfill site. More than half was plastic, with single regurgitants weighing up to 125 g. Urban waste stored in open air landfills is altering some marabou diets, affecting their natural trophic niche, resulting in the consumption (and regurgitation) of large amounts of plastic, and exposing marabou to potentially chronic levels of trace metals. Despite the marabou’s apparent resilience to this behavioural shift, it could have long-term effects on the population of the marabou stork, particularly considering Botswana has some of the few regular marabou breeding colonies in southern Africa.

A chondrogenesis induction system based on a functionalized hyaluronic acid hydrogel sequentially promoting hMSC proliferation, condensation, differentiation, and matrix deposition

Hydrogel scaffolds are widely used in cartilage tissue engineering as a natural stem cell niche. In particular, hydrogels based on multiple biological signals can guide behaviors of mesenchymal stem cells (MSCs) during neo-chondrogenesis. In the first phase of this study, we showed that functionalized hydrogels with grafted arginine-glycine-aspartate (RGD) peptides and lower degree of crosslinking can promote the proliferation of human mesenchymal stem cells (hMSCs) and upregulate the expression of cell receptor proteins. Moreover, grafted RGD and histidine-alanine-valine (HAV) peptides in hydrogel scaffolds can regulate the adhesion of the intercellular at an early stage. In the second phase, we confirmed that simultaneous use of HAV and RGD peptides led to greater chondrogenic differentiation compared to the blank control and single-peptide groups. Furthermore, the controlled release of kartogenin (KGN) can better facilitate cell chondrogenesis compared to other groups. Interestingly, with longer culture time, cell condensation was clearly observed in the groups with RGD and HAV peptide. In all groups with RGD peptide, significant matrix deposition was observed, accompanied by glycosaminoglycan (GAG) and collagen (Coll) production. Through in vitro and in vivo experiments, this study confirmed that our hydrogel system can sequentially promote the proliferation, adhesion, condensation, chondrogenic differentiation of hMSCs, by mimicking the cell microenvironment during neo-chondrogenesis.

Isolation and &amp;lt;i&amp;gt; Ex Vivo&amp;lt;/i&amp;gt; Expansion of Human Hematopoietic Stem Cells Derived from Umbilical Cord Blood

Umbilical cord blood (UCB) is a current major source of hematopoietic stem cells (HSCs) for cell transplantation therapy. Cell transplantation with HSCs derived from UCB is advantageous over transplantation with HSCs from adult tissues. However, the low number of HSC derived from a single unit of UCB limits its application. Thus, ex vivo expansion is a good option to create more UCB HSCs for clinical application. The strategies for HSC expansion in vitro focus on mimicking the composition and structure of HSC natural niche by enhancing self-renewal and inhibiting lineage differentiation of HSCs. In the past decade, the mechanisms of the interaction between HSC and the natural niche have been deeply investigated. This great progress in basic research has led to advancements in UCB HSC ex vivo expansion. In addition, the biological characteristics of the originally isolated UCB HSCs correlate with outcome of subsequent ex vivo expansion. In this paper, we summarize the late progress achieved in isolation and ex vivo expansion of UCB HSCs. Importantly, we attempt to provide an impact and practicable procedure to expand UCB HSC in vitro from isolation of original HSCs to identification of expanded HSCs.

Non-specific porins of Gram-negative bacteria as proteins containing intrinsically disordered regions with amyloidogenic potential.

Features of the structure and functional activity of bacterial outer membrane porins, coupled with their dynamic "behavior," suggests that intrinsically disordered regions (IDPRs) are contained in their structure. Using bioinformatic analysis, the quantitative content of amyloidogenic regions in the amino acid sequence of non-specific porins inhabiting various natural niches was determined: from terrestrial bacteria of the genus Yersinia (OmpF and OmpC proteins of Y. pseudotuberculosis and Y. ruckeri) and from the marine bacterium Marinomonas primoryensis (MpOmp). It was found that OmpF and OmpC porins can be classified as moderately disordered proteins, while MpOmp can be classified as highly disordered protein. Mapping of IDPRs, performed using 3D structures of monomers of the proteins, showed that the regions of increased conformational plasticity fall on the regions, the functional importance of which has been reliably confirmed as a result of numerous experimental studies. The revealed correlation made it possible to explain the differences in the physicochemical characteristics and properties of not only porins from terrestrial and marine bacteria, but also non-specific porins of different types, OmpF and OmpC proteins. First of all, this concerns the flexible outer loops that form the pore vestibule, as well as regions of the barrel with an increased "ability" for aggregation, the so-called "hot spots" of aggregation. The abnormally high content of IDPRs in the MpOmp structure made it possible to suggest that the high adaptive potential of bacteria may correlate with an increase in the number of IDPRs and/or regions with increased conformational variability.

ЦЕНТРАЛЬНЫЙ КАВКАЗ КАК ПРОСТРАНСТВО СОЦИАЛЬНО-ПОЛИТИЧЕСКИХ ВЗАИМОДЕЙСТВИЙ: ИСТОРИОГРАФИЧЕСКИЕ ИТОГИ И ПЕРСПЕКТИВЫ ИЗУЧЕНИЯ

Part of the preparatory work for writing a generalizing history of the Kabardin-Balkaria is summing up the results of a scientific study of its key problems, which include the interpretation of the traditional system of socio-political or inter-social interactions in the Central Caucasus. In the previous publication, the formation of the historiographical tradition in the 18th – early 20th centuries was considered. The proposed article aims to continue the study of this topic using the material of Soviet and post-Soviet historiography. The material considered in the article shows that the construction of a generalized concept of the traditional system of inter-social interactions in the Central Caucasus is a complex problem that touches upon the fundamental issues of the study of regional history. The first of them is the question of the applicability of categories developed in other social sciences or on historical material from other eras and regions to the North Caucasian reality of the 16th – 18th centuries. In this case, individual elements and relationships are identified with the structure of the system as a whole. Inter-social interactions that unfold both in space and in time receive a static, exclusively spatial representation. The second question is related to the need to differentiate ethnic and socio-political nomenclature in the representation of the Central Caucasus as a space of inter-social interactions. Contemporary historiography explicitly or implicitly places the social interactions of the owners and societies of the region in an “interethnic” and / or “ethnopolitical” context. Historical concepts to a certain extent are divorced from the sources of data of the 16th – 18th centuries, in which ethnic communities – "peoples" are never the subjects of inter-social interactions. A generalized interpretation of the historical experience of inter-social interactions in the Central Caucasus is possible on the basis of combining a “narrative”, descriptive approach with a “supra-ethnic” representation of the region as a space with a complex natural and social landscape. The most stable general function of the traditional system of inter-social interactions is the maintenance of order that is understandable to all their participants and ensured the reproduction of each ethno-social unit that occupies its own natural-ecological niche.

A Review Study on Textile Effluent Treatments of Agricultural Soil near Textile Industry

At present many of the man-made compounds are released in soil by various ways. These compounds might be pesticides and other hazardous chemicals. Through food chain these compounds increased day by day at particular trophic level and also affect the soil biodiversity. Microbial cultures and associated biotechnology can be helpful to reduce such types of pollution from soil without affecting their natural habitat or niche. Soils polluted with heavy metals have become common across the globe due to increase in geologic and anthropogenic activities. Plants growing on these soils show a reduction in growth, performance, and yield. Bioremediation and phytoremediation are an effective method of treating heavy metal polluted soils. The heavy metals have potent cumulative properties and toxicity due to which they have a potential hazardous effect not only on crop plants but also on human health. The metal contaminants can be reduced by immobilization of contaminants using macrophytes and also by using genetically engineered microorganisms.

Priming mesenchymal stem cells with uric acid enhances neuroprotective properties in parkinsonian models

Mesenchymal stem cells (MSCs) are a potential source of cell-based disease-modifying therapy in Parkinsonian disorders. A promising approach to develop in vitro culture methods that mimic natural MSC niche is cell priming. Uric acid (UA), a powerful antioxidant, scavenges reactive oxygen species, which has a vital role in maintaining self-renewal and differentiation potential of MSCs. Here, we demonstrated that UA treatment in naïve MSCs stimulated glycolysis and upregulated transcriptional factors responsible for regulation of stemness, leading to increase in the expression levels of osteogenesis-, adipogenesis-, and chondrogenesis-related genes. UA-primed MSCs had more enhanced neuroprotective properties in cellular and parkinsonian animal models compared to naïve MSCs by inhibiting apoptotic signaling pathways. Additionally, expression of miR-137 and miR-145 was decreased in UA-treated MSCs. Our data demonstrated that priming MSCs with UA augment neuroprotective properties through enhanced self-renewal and differentiation potential, suggesting a practical strategy for improving the application of MSCs in parkinsonian disorders.

Extracellular products-mediated interspecific interaction between Pseudomonas aeruginosa and Escherichia coli.

The Gram-negative pathogen Pseudomonas aeruginosa adopts several elaborate strategies to colonize a wide range of natural or clinical niches and to overcome the neighboring bacterial competitors in polymicrobial communities. However, the relationship and interaction mechanism of P. aeruginosa with other bacterial pathogens remains largely unexplored. Here we explore the interaction dynamics of P. aeruginosa and Escherichia coli, which frequently coinfect the lungs of immunocompromised hosts, by using a series of on-plate proximity assays and RNA-sequencing. We show that the extracellular products of P. aeruginosa can inhibit the growth of neighboring E. coli and induce a large-scale of transcriptional reprogramming of E. coli, especially in terms of cellular respiration-related primary metabolisms and membrane components. In contrast, the presence of E. coli has no significant effect on the growth of P. aeruginosa in short-term culture, but causes a dysregulated expression of genes positively controlled by the quorum-sensing (QS) system of P. aeruginosa during subsequent pairwise culture. We further demonstrate that the divergent QS-regulation of P. aeruginosa may be related to the function of the transcriptional regulator PqsR, which can be enhanced by E. coli culture supernatant to increase the pyocyanin production by P. aeruginosa in the absence of the central las-QS system. Moreover, the extracellular products of E. coli promote the proliferation and lethality of P. aeruginosa in infecting the Caenorhabditis elegans model. The current study provides a general characterization of the extracellular products-mediated interactions between P. aeruginosa and E. coli, and may facilitate the understanding of polymicrobial infections.

A comparative UHPLC-Q/TOF\u2013MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species

Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories.

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients’ specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

Design process of a water reclamation garden: from natural niches to urban environment

Water reclamation gardens have existed for more than 20 years, combining wastewater process technology and botany to provide wastewater treatment. In these facilities, the boundary between functional gardening and sanitation/water reuse infrastructure is blurred. They use lower footprints than engineered wetlands and can be constructed in urban areas as they do not look or smell like conventional industrial facilities, while providing water treatment on the same scale. These gardens produce treated wastewater, while at the same time provide green and blue access to the community. Treatment can be more effective and adaptive using decentralized systems, where facilities are closer to the waste origin, in this case municipal areas, thereby minimizing costly infrastructure (piping network). For this to work, the treatment units must gain far more public acceptance, and a well-designed and functioning water reclamation garden helps this purpose greatly.There are three main considerations in designing garden facilities; one is climate. It is necessary to determine whether the local climate can support a reclamation garden or whether an artificial microclimate is needed. The species arrangement is primarily defined by the wastewater treatment process. Plants rooted in the wastewater encounter different environments as the treatment process advances. This phenomenon further delimits available species. Selection is based on equivalence of the original plant habitat to the designed treatment phase and conditions. Considering the needs of the community, the local garden and architectural style defines what a community sees as acceptable or pleasing, sometimes even on a subconscious level. Knowledge of the local gardening trends and cultures helps creating gardens which will then be an integral part of a city’s urban fabric.Based on the aspects described above, a methodology for a three-layered comparative design practice is introduced, linking wastewater process knowledge, ecological knowledge and information on stylistic trends. Utilizing these tools provides a solid foundation to answer all these demands and builds a foundation for long-term sustainability.

Prospects of biodiversity and distribution of mushroom fungi in India

Mushrooms are precious fungi, which exists as an important and integral component of the ecosystem. They are the macro or larger fungi which possess fleshy, subfleshy, or sometimes leathery, umbrella like fructifications, which bear their spore producing surface either on lamellae (gills) or lining the tubes, opening out by means of pores. Usually the lamellate members are called ‘mushrooms’ or “toadstools’ depending upon whether or not they are edible or poisonous and therefore the tube bearing poroid members, as boletes. Mushrooms are seasonal fungi, which occupy diverse niches in nature within the forest ecosystem. Different types of edible mushrooms are cultivated on large scale for commercial use and many more species of mushrooms grow wildly in nature which has much nutritional and medicinal value. They predominantly occur during the season and also during spring when the snow melts. In the globe, biodiversity includes not only many species that exist, but also the range of populations that makeup a species and the genetic diversity among individual life forms. Macrofungi are important economically due to their importance in food, medicine, biocontrol, chemical, biological and other industries. Macrofungi are diverse in their uses as food and medicine and a number of other species function as decomposers and also form mycorrhizal associations.

Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata.

Marine hydrocarbon-degrading bacteria play an important role in natural petroleum biodegradation processes and were initially associated with man-made oil spills or natural seeps. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Few studies pointed at some marine microalgae that produce oleophilic compounds (alkanes, long-chain fatty acids, and alcohols) as potential natural hosts of these bacteria. We established Dansk crude oil-based enrichment cultures with photobioreactor-grown marine microalgae cultures Pavlova lutheri and Nannochloropsis oculata and analyzed the microbial succession using cultivation and SSU (16S) rRNA amplicon sequencing. We found that petroleum enforced a strong selection for members of Alpha- and Gamma-proteobacteria in both enrichment cultures with the prevalence of Alcanivorax and Marinobacter spp., well-known hydrocarbonoclastic bacteria. In total, 48 non-redundant bacterial strains were isolated and identified to represent genera Alcanivorax, Marinobacter, Thalassospira, Hyphomonas, Halomonas, Marinovum, Roseovarius, and Oleibacter, which were abundant in sequencing reads in both crude oil enrichments. Our assessment of public databases demonstrated some overlaps of geographical sites of isolation of Nannochloropsis and Pavlova with places of molecular detection and isolation of Alcanivorax and Marinobacter spp. Our study suggests that these globally important hydrocarbon-degrading bacteria are associated with P. lutheri and N. oculata.

Efflux Pump-Driven Antibiotic and Biocide Cross-Resistance in Pseudomonas aeruginosa Isolated from Different Ecological Niches: A Case Study in the Development of Multidrug Resistance in Environmental Hotspots.

Pseudomonas aeruginosa is an opportunistic pathogen displaying high intrinsic antimicrobial resistance and the ability to thrive in different ecological environments. In this study, the ability of P. aeruginosa to develop simultaneous resistance to multiple antibiotics and disinfectants in different natural niches were investigated using strains collected from clinical samples, veterinary samples, and wastewater. The correlation between biocide and antimicrobial resistance was determined by employing principal component analysis. Molecular mechanisms linking biocide and antimicrobial resistance were interrogated by determining gene expression using RT-qPCR and identifying a potential genetic determinant for co- and cross-resistance using whole-genome sequencing. A subpopulation of P. aeruginosa isolates belonging to three sequence types was resistant against the common preservative benzalkonium chloride and showed cross-resistance to fluoroquinolones, cephalosporins, aminoglycosides, and multidrug resistance. Of these, the epidemiological high-risk ST235 clone was the most abundant. The overexpression of the MexAB-OprM drug efflux pump resulting from amino acid mutations in regulators MexR, NalC, or NalD was the major contributing factor for cross-resistance that could be reversed by an efflux pump inhibitor. This is the first comparison of antibiotic-biocide cross-resistance in samples isolated from different ecological niches and serves as a confirmation of laboratory-based studies on biocide adapted isolates. The isolates from wastewater had a higher incidence of multidrug resistance and biocide-antibiotic cross-resistance than those from clinical and veterinary settings.

Exploring metal availability in the natural niche of Streptococcus pneumoniae to discover potential vaccine antigens

ABSTRACT Nasopharyngeal colonization by Streptococcus pneumoniae is a prerequisite for pneumococcal transmission and disease. Current vaccines protect only against disease and colonization caused by a limited number of serotypes, consequently allowing serotype replacement and transmission. Therefore, the development of a broadly protective vaccine against colonization, transmission and disease is desired but requires a better understanding of pneumococcal adaptation to its natural niche. Hence, we measured the levels of free and protein-bound transition metals in human nasal fluid, to determine the effect of metal concentrations on the growth and proteome of S. pneumoniae. Pneumococci cultured in medium containing metal levels comparable to nasal fluid showed a highly distinct proteomic profile compared to standard culture conditions, including the increased abundance of nine conserved, putative surface-exposed proteins. AliA, an oligopeptide binding protein, was identified as the strongest protective antigen, demonstrated by the significantly reduced bacterial load in a murine colonization and a lethal mouse pneumonia model, highlighting its potential as vaccine antigen.