Trophic and symbiotic links between obligate-glacier water bears (Tardigrada) and cryoconite microorganisms

Insights into biodiversity and trophic webs are important for understanding ecosystem functions. Although the surfaces of glaciers are one of the most productive and biologically diverse parts of the cryosphere, the links between top consumers, their diet and microbial communities are poorly understood. In this study, for the first time we investigated the relationships between bacteria, fungi and other microeukaryotes as they relate to tardigrades, microscopic metazoans that are top consumers in cryoconite, a biologically rich and productive biogenic sediment found on glacier surfaces. Using metabarcoding (16S rDNA for bacteria, ITS1 for fungi, and 18S rDNA for other microeukaryotes), we analyzed the microbial community structures of cryoconite and compared them with the community found in both fully fed and starved tardigrades. The community structure of each microbial group (bacteria, fungi, microeukaryotes) were similar within each host group (cryoconite, fully fed tardigrades and starved tardigrades), and differed significantly between groups, as indicated by redundancy analyses. The relative number of operational taxonomic units (ZOTUs, OTUs) and the Shannon index differed significantly between cryoconite and tardigrades. Species indicator analysis highlighted a group of microbial taxa typical of both fully fed and starved tardigrades (potential commensals), like the bacteria of the genera Staphylococcus and Stenotrophomonas, as well as a group of taxa typical of both cryoconite and fully fed tardigrades (likely part of the tardigrade diet; bacteria Flavobacterium sp., fungi Preussia sp., algae Trebouxiophyceae sp.). Tardigrades are consumers of bacteria, fungi and other microeukaryotes in cryoconite and, being hosts for diverse microbes, their presence can enrich the microbiome of glaciers.

The Coexistence Relationship Between Plants and Soil Bacteria Based on Interdomain Ecological Network Analysis

The relationship between plants and their associated soil microbial communities plays a crucial role in maintaining ecosystem processes and function. However, identifying these complex relationships is challenging. In this study, we constructed an interdomain ecology network (IDEN) of plant–bacteria based on SparCC pairwise associations using synchronous aboveground plant surveys and belowground microbial 16S rRNA sequencing among four different natural forest types along the climate zones in China. The results found that a total of 48 plants were associated with soil bacteria among these four sites, and soil microbial group associations with specific plant species existed within the observed plant–bacteria coexistence network. Only 0.54% of operational taxonomy units (OTUs) was shared by the four sites, and the proportion of unique OTUs for each site ranged from 43.08 to 76.28%, which occupied a large proportion of soil bacterial community composition. The plant–bacteria network had a distinct modular structure (p < 0.001). The tree Acer tetramerum was identified as the network hubs in the warm temperate coniferous and broad-leaved mixed forests coexistence network and indicates that it may play a key role in stabilizing of the community structure of these forest ecosystems. Therefore, IDEN of plant–bacteria provides a novel perspective for exploring the relationships of interdomain species, and this study provides valuable insights into understanding coexistence between above-ground plants and below-ground microorganisms.

Phospholipid fatty acids in soil—drawbacks and future prospects

The current opinion and position paper highlights (1) correct assignation of indicator phospholipid fatty acids (PLFA), (2) specificity and recycling of PLFA in microorganisms, and (3) complete extraction and detection of PLFA. The straight-chain PLFA 14:0, 15:0, 16:0, and 17:0 occur in all microorganisms, i.e., also in fungi and not only in bacteria. If the phylum Actinobacteria is excluded from the group of Gram-positive bacteria, all remaining bacteria belong to the bacterial phylum Firmicutes, which should be considered. The PLFA 16:1ω5 should be used as an indicator for the biomass of arbuscular mycorrhizal fungi (AMF) as there is no experimental evidence that they occur in marked amounts in Gram-negative bacteria. Fungal PLFA should embrace the AMF-specific 16:1ω5. In the presence of plants, ergosterol should be used instead of the PLFA 18:2ω6,9 and 18:1ω9 as fungal indicators for Mucoromycotina, Ascomycota, and Basidiomycota. The majority of indicator PLFA are not fully specific for a certain microbial group. This problem might be intensified by recycling processes during decomposition to an unknown extent. Soil handling and extraction conditions should be further optimized. The reliability and accuracy of gas chromatographic separation need to be regularly checked against unintentional variations. PLFA analysis will still be of interest over the next decades as an important independent control of DNA-based methods.

Microorganisms causing of clinical pathologies in canines and domestic felines in Valledupar, Colombia

The pathologies caused by microbial groups generate health risks in domestic dogs and cats; showing a zoonotic potential and producing affections in humans. According to that background, the purpose of this study was to establish the main microorganisms causing clinical pathologies in domestic dogs and cats by reviewing medical records in a veterinary clinic in Valledupar, Colombia. In order to do that, a retrospective study was conducted with clinical histories of dogs and cats admitted during 2017 and 2018 to the veterinary clinic “Mis Mejores Amigos”. Based on the information, a descriptive, explanatory and statistical analysis was applied, the latter by means of a Sperman correlation to evaluate the relationship between race, sex, age, microbial group and pathology-pathogen. From a total of 462 reports of canines and felines admitted to the clinic, a total of 273 diagnoses were obtained. 4% of the felines and 24% of the canines were affected by some microbial group. The most prevalent microorganisms in canines were Ancylostoma spp. (9 %) Entamoeba histolytica (5%) Ehrlichia spp. (5%), and Isospora sp. (5%) while in felines were Haemobartonella felis (20%) and Haemobartonella spp. (17%). It was determined that there is only correlation between the age of felines and the microbial group that affects them, in addition to the pathology presented with the pathogen. It was observed a high percentage of Ancylostoma sp. (9%) in canines of mongrel and French Poodle breeds whilst in felines was found the bacterium Haemobartonella felis in 20% of the mongrel breeds.

Role of Bifidobacteria on Infant Health

Bifidobacteria are among the predominant microorganisms during infancy, being a dominant microbial group in the healthy breastfed infant and playing a crucial role in newborns and infant development. Not only the levels of the Bifidobacterium genus but also the profile and quantity of the different bifidobacterial species have been demonstrated to be of relevance to infant health. Although no definitive proof is available on the causal association, reduced levels of bifidobacteria are perhaps the most frequently observed alteration of the intestinal microbiota in infant diseases. Moreover, Bifidobacterium strains have been extensively studied by their probiotic attributes. This review compiles the available information about bifidobacterial composition and function since the beginning of life, describing different perinatal factors affecting them, and their implications on different health alterations in infancy. In addition, this review gathers exhaustive information about pre-clinical and clinical studies with Bifidobacterium strains as probiotics in neonates.

Bacterial Community Structure and Dynamic Changes in Different Functional Areas of a Piggery Wastewater Treatment System

Chemicals of emerging concern (CEC) in pig farm breeding wastewater, such as antibiotics, will soon pose a serious threat to public health. It is therefore essential to consider improving the treatment efficiency of piggery wastewater in terms of microorganisms. In order to optimize the overall piggery wastewater treatment system from the perspective of the bacterial community structure and its response to environmental factors, five samples were randomly taken from each area of a piggery’s wastewater treatment system using a random sampling method. The bacterial communities’ composition and their correlation with wastewater quality were then analyzed using Illumina MiSeq high-throughput sequencing. The results showed that the bacterial community composition of each treatment unit was similar. However, differences in abundance were significant, and the bacterial community structure gradually changed with the process. Proteobacteria showed more adaptability to an anaerobic environment than Firmicutes, and the abundance of Tissierella in anaerobic zones was low. The abundance of Clostridial (39.02%) and Bacteroides (20.6%) in the inlet was significantly higher than it was in the aerobic zone and the anoxic zone (p < 0.05). Rhodocyclaceae is a key functional microbial group in a wastewater treatment system, and it is a dominant microbial group in activated sludge. Redundancy analysis (RDA) showed that chemical oxygen demand (COD) had the greatest impact on bacterial community structure. Total phosphorus (TP), total nitrogen (TN), PH and COD contents were significantly negatively correlated with Sphingobacteriia, Betaproteobacteria and Gammaproteobacteria, and significantly positively correlated with Bacteroidia and Clostridia. These results offer basic data and theoretical support for optimizing livestock wastewater treatment systems using bacterial community structures.

Rhizosphere P-Enzyme Activity, Mineral Nutrient Concentrations, and Microbial Community Structure Are Altered by Intra-Hole Cropping of Cowpea With Cereals

In Africa, intercropping and intra-hole cropping systems are common practices used by smallholder farmers to optimize land use and tap the benefits of plant-to-plant interactions. The aim of this study was to evaluate mineral nutrient concentrations, P-enzyme activity and changes in microbial communities in the rhizospheres of sole cropped and intra-hole planted cowpea (cvs. TVu 546 and PAN 311), maize (cv. ZM 521), and sorghum (cv. M48). Cowpea cv. TVu546 intra-hole planted with sorghum (i.e., TVu546+M48) produced the highest rhizosphere acid phosphatase (APase) activity (230.0 μg p-nitrophenol.g−1 soil.h−1). From 16S rRNA Miseq Illumina sequencing, the rhizosphere bacterial community structure was altered by intra-hole cropping, and was dominated by Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Proteobacteria, and Verrucomicrobia, which together accounted for about &gt;95% of the total sequences. The Sphingobacteria phylum was the dominant microbial group in the rhizosphere soil of all the cropping systems. The Proteobacteria phylum was the second most abundant in this study, which included the beneficial bacteria in all the rhizosphere soils studied. In contrast, typical pathogens like Ralsotonia and Agrobacterium were completely absent, indicating that the intra-hole cropping system can provide protection against soil-borne diseases possibly through elimination by antibiotics and/or phytoalexins present in plant and microbial exudates in the rhizosphere. Mucilaginibacter and Flavobacterium were however selectively present with intra-hole cropping.

The presence of Pseudogymnoascus destructans, a fungal pathogen of bats, correlates with changes in microbial metacommunity structure

Metacommunity theory provides a framework for how community patterns arise from processes across scales, which is relevant for understanding patterns in host-associated microbial assemblages. Microbial metacommunities may have important roles in host health through interactions with pathogens; however, it is unclear how pathogens affect host microbial metacommunities. Here, we studied relationships between a fungal pathogen and a host-associated microbial metacommunity. We hypothesized that a fungal pathogen of bats, Pseudogymnoascus destructans, correlates with a shift in metacommunity structure and changes in relationships between community composition, and factors shaping these assemblages, such as ecoregion. We sampled bat cutaneous microbial assemblages in the presence/absence of P. destructans and analyzed microbial metacommunity composition and relationships with structuring variables. Absence of P. destructans correlated with a metacommunity characterized by a common core microbial group that was lacking in disease positive bats. Additionally, P. destructans presence correlated with a change in the relationship between community structure and ecoregion. Our results suggest that the fungal pathogen intensifies local processes influencing a microbial metacommunity and highlights the importance of cutaneous microbial assemblages in host–pathogen interactions.

Differential Antimicrobial Effect of Essential Oils and Their Main Components: Insights Based on the Cell Membrane and External Structure

The biological activity of essential oils and their major components is well documented. Essential oils such as oregano and cinnamon are known for their effect against bacteria, fungi, and even viruses. The mechanism of action is proposed to be related to membrane and external cell structures, including cell walls. This study aimed to evaluate the biological activity of seven essential oils and eight of their major components against Gram-negative and Gram-positive bacteria, filamentous fungi, and protozoans. The antimicrobial activity was evaluated by determination of the Minimal Inhibitory Concentration for Bacillus cereus, Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Salmonella Typhimurium, Shigella sonnei, Aspergillus niger, Aspergillus ochraceus, Alternaria alternata, and Fusarium oxysporium, the half-maximal inhibitory concentration (IC50) for Trypanosoma cruzi and Leishmania mexicana, and the median lethal dose (LD50) for Giardia lamblia. Results showed that oregano essential oil showed the best antibacterial activity (66–100 µg/mL), while cinnamon essential oil had the best fungicidal activity (66–116 µg/mL), and both showed excellent antiprotozoal activity (22–108 µg/mL). Regarding the major components, thymol and carvacrol were also good antimicrobials (23–200 µg/mL), and cinnamaldehyde was an antifungal compound (41–75 µg/mL). The major components were grouped according to their chemical structure as phenylpropanoids, terpenoids, and terpinenes. The statistical analysis of the grouped data demonstrated that protozoans were more susceptible to the essential oils, followed by fungi, Gram-positive bacteria, and Gram-negative bacteria. The analysis for the major components showed that the most resistant microbial group was fungi, which was followed by bacteria, and protozoans were also more susceptible. Principal Component Analysis for the essential oils demonstrated the relationship between the biological activity and the microbial group tested, with the first three components explaining 94.3% of the data variability. The chemical structure of the major components was also related to the biological activity presented against the microbial groups tested, where the three first principal components accounted for 91.9% of the variability. The external structures and the characteristics of the cell membranes in the different microbial groups are determinant for their susceptibility to essential oils and their major components

Physico-chemical Parameters with Direct Influence on the Dynamism of the Indigenous Microflora of the Traditional Cheese “J’ben Elgafs”

Background: The microbial evolution of the J’ben Elgafs prepared with raw milk from local cows, was studied during the manufacturing and maturating process in order to characterize this variety of cheese from the Algerian terroir.Methods: The microbial activity and physical-chemical parameters were tested during the three dairy seasons of the year. Total, lactics and alteration floras were counted on their selective environments.Result: Lactic germs multiply considerably during the first days and only stabilize towards the end of maturation. The low presence of alteration floras is the result of the continuous modification of the physico-chemical parameters of Aw and pH from one stage to the other of the j’ben production and the respect of good processing practices. These different proportions of variation are induced by the biochemical reactions and microbial interactions that take place responsible for the sequential growth of one microbial group compared to another.