Machine learning methods can be used as robust techniques to provide invaluable information for analyzing biological samples in pharmaceutical industries, such as predicting the concentration of viral particles of interest in biological samples. Here, we utilized both convolutional neural networks and random forests to predict the concentration of the samples containing measles, mumps, rubella, and varicella-zoster viruses (ProQuad®) based on Raman and absorption spectroscopy. We prepared Raman and absorption spectra datasets with known concentration values, then used the Raman and absorption signals individually and together to train RFs and CNNs. We demonstrated that both RFs and CNNs can make predictions with R2 values as high as 95%. We proposed two different networks to jointly use the Raman and absorption spectra, where our results demonstrated that concatenating the Raman and absorption data increases the prediction accuracy compared to using either Raman or absorption spectrum alone. Additionally, we further verified the advantage of using joint Raman-absorption with principal component analysis (PCA). Furthermore, our method can be extended to characterize properties other than concentration, such as the type of viral particles.
DNA extraction and preservation bias is a recurring topic in DNA sequencing-based microbial ecology. Different methodologies can lead to distinct outcomes, which has been demonstrated especially in studies investigating prokaryotic community composition. Eukaryotic microbes are ubiquitous, diverse, and increasingly a subject of investigation in addition to bacteria and archaea. However, little is known about how the choice of DNA preservation and extraction methodology impacts perceived eukaryotic community composition. In this study, we compared the effect of two DNA preservation protocols and 6 DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than prokaryotes. Especially soft-bodied or hard-shelled eukaryotes like nematodes and diatoms were differentially abundant depending on the extraction method. We conclude that careful consideration of DNA preservation and extraction methodology is crucial to achieving representative community profiles of eukaryotes in marine biofilms, and likely all other habitats containing diverse eukaryotic microbial communities.
Geobacter species have great application potential in remediation processes and electrobiotechnology. In all applications, understanding the metabolism will enable target-oriented optimization of the processes. The typical electron donor and carbon source of the Geobacter species is acetate, while fumarate is the usual electron acceptor. Here, we could show that depending on the donor/acceptor ratio in batch cultivation of G. sulfurreducens different product patterns occur. With a donor/acceptor ratio of 1:2.5 malate accumulated as an intermediate product but was metabolized to succinate subsequently. At the end of the cultivation, the ratio of fumarate consumed and succinate produced was approximately 1:1. When fumarate was added in excess, malate accumulated in the fermentation broth without further metabolization. After the addition of acetate to stationary cells, malate concentration decreased immediately and additional succinate was synthesized. Finally, it was shown that also resting cells of G. sulfurreducens could efficiently convert fumarate to malate without an additional electron donor. Overall, it was demonstrated that by altering the donor/acceptor ratio, targeted optimization of the metabolite conversion by G. sulfurreducens can be realized.
Biofilms are intricate communities of microorganisms encapsulated within a self-produced matrix of extra-polymeric substances (EPS), creating complex three-dimensional structures allowing for liquid and nutrient transport through them. These aggregations offer constituent microorganisms enhanced protection from environmental stimuli - like fluid flow - and are also associated with higher resistance to antimicrobial compounds, providing a persistent cause of concern in numerous sectors like the marine (biofouling, aquaculture), medical (infections, antimicrobial resistance), dentistry (plaque on teeth), food safety, as well as causing energy loss and corrosion. Recent studies have demonstrated that biofilms interact with microplastics, often influencing their pathway to higher trophic levels. Previous research has shown that initial bacterial attachment is affected by surface properties. Using a microfluidic flow cell, we have investigated the relationship between both wall shear stress (τw) and surface properties (surface wettability) upon biofilm formation of two species (Cobetia marina and Pseudomonas aeruginosa). We investigated biofilm development on low-density polyethylene (LDPE) membranes, Permanox® slides, and glass slides, using nucleic acid staining and end-point confocal laser scanning microscopy (CLSM). The results show that flow conditions affect biomass, maximum thickness, and surface area of biofilms, with higher τw (5.6 Pa) resulting in thinner biofilms than lower τw (0.2 Pa). In addition, we observed differences in biofilm development across the surfaces tested, with LDPE typically demonstrating more overall biofilm in comparison to Permanox® and glass. Moreover, we demonstrate the formation of biofilm streamers under laminar flow conditions within straight micro-channels.
In naturally competent bacteria, DNA transformation through horizontal gene transfer is an evolutionary mechanism to receive extracellular DNA. Bacteria need to maintain a state of competence to accept foreign DNA and this is an energy-driven phenomenon that is tightly controlled. In Streptococcus, competence development is a complex process that is not fully understood. In this study, we used Streptococcus mutans, an oral bacterium, to determine how cell density affects competence development. We found that in S. mutans the transformation efficiency is maximum when the transforming DNA was added at low cell density and incubated for 2.5 h before selecting for transformants. We also found that S. mutans cells remain competent until the mid-logarithmic phase, after which the competence decreases drastically. Surprisingly, we observed that individual components of Clp proteolytic complexes differentially regulate competence. If the transformation is carried out at the early growth phase, both ClpP protease and ClpX ATPase are needed for competence. In contrast, we found that both ClpC and ClpE negatively affect competence. We also found that if the transformation is carried out at the mid-logarithmic growth phase ClpX is still required for competence but ClpP negatively affects competence. While the exact reason for this differential effect of ClpP and ClpX on transformation is currently unknown, we found that both ClpC and ClpE have a negative effect on transformation, which was not reported before.
Subsurface chlorophyll maxima layers (SCML) are ubiquitous features of stratified aquatic systems. Availability of the micronutrient iron is known to influence marine SCML, but iron has not been explored in detail as a factor in the development of freshwater SCML. This study investigates the relationship between dissolved iron and the SCML within the dimictic, ferruginous lake Grosses Heiliges Meer in northern Germany. The occurrence of the SCML under non-ferruginous conditions in the spring and ferruginous conditions in the fall are context to explore temporal changes in the phytoplankton community and indicators of primary productivity. Results indicate that despite more abundant chlorophyll in the spring, the SCML sits below a likely primary productivity maximum within the epilimnion, inferred based on co-located dissolved oxygen, δ13CDIC, and pH maxima. The peak amount of chlorophyll in the SCML is lower in the fall than in the spring, but in the fall the SCML is co-located with elevated dissolved iron concentrations and a local δ13CDIC maximum. Cyanobacteria and Chlorophyta have elevated abundances within the SCML in the fall. Further investigation of the relationship of iron to primary productivity within ferruginous SCML may help to understand the environmental controls on primary productivity in past ferruginous oceans.
Background. Symbioses between Geosmithia fungi and wood-boring and bark beetles seldom result in disease induction within the plant host. Yet exceptions exist such as Geosmithia morbida, the causal agent of Thousand Cankers Disease (TCD) of walnuts and wingnuts, and Geosmithia sp. 41, the causal agent of Foamy Bark Canker disease of oaks. Isolates of G. obscura were recovered from black walnut trees in eastern Tennessee and at least one isolate induced cankers following artificial inoculation. Due to the putative pathogenicity and lack of recovery of G. obscura from natural lesions, a molecular diagnostic screening tool was developed using microsatellite markers mined from the G. obscura genome. Results. A total of 3,256 candidate microsatellite markers were identified (2236, 789, 137 di-, tri-, and tetra- motifs were identified, respectively), with 2011, 703, 101 di-, tri-, and tetra- motifs containing markers with primers. From these, 75 microsatellite markers were randomly selected, screened, and optimized, resulting in 28 polymorphic markers that yielded single, consistently recovered bands which were used in downstream analyses. Five of these microsatellite markers were found to be specific to G. obscura and did not cross-amplify into other, closely related species. Although the remaining tested markers could be useful, they cross-amplified within different Geosmithia species, making them not reliable for G. obscura detection. Conclusion. Five novel microsatellite markers (GOBS9, GOBS10, GOBS41, GOBS43, GOBS50) were developed based on the G. obscura genome. These species-specific microsatellite markers are available as a tool for use in molecular diagnostics and can assist future surveillance studies.
Arsenic is a toxic metalloid that affects human health by causing numerous diseases and by being used in the treatment of acute promyelocytic leukemia. Saccharomyces cerevisiae (budding yeast) has been extensively utilized to elucidate the molecular mechanisms underlying arsenic toxicity and resistance in eukaryotes. In this study, we applied a genomic DNA overexpression strategy to identify yeast genes that provide arsenic resistance in wild-type and arsenic-sensitive S. cerevisiae cells. In addition to known arsenic-related genes, our genetic screen revealed novel genes, including PHO86, VBA3, UGP1, and TUL1, whose overexpression conferred resistance. To gain insights into possible resistance mechanisms, we addressed the contribution of these genes to cell growth, intracellular arsenic, and protein aggregation during arsenate exposure. Overexpression of PHO86 resulted in higher cellular arsenic levels but no additional effect on protein aggregation, indicating that these cells efficiently protect their intracellular environment. VBA3 overexpression caused resistance despite higher intracellular arsenic and protein aggregation levels. Overexpression of UGP1 led to lower intracellular arsenic and protein aggregation levels whilst TUL1 overexpression had no impact on intracellular arsenic or protein aggregation levels. Thus, the identified genes appear to confer arsenic resistance through distinct mechanisms but the molecular details remain to be elucidated.
While plant pathogens are traditionally controlled using synthetic agrochemicals the availability of commercial bactericides is still limited. One potential control strategy could be the use of plant-growth-promoting bacteria (PGPBs) to suppress pathogens via resource competition or the production of antimicrobial compounds. This study aimed to conduct in vitro and in vivo screening of eight Pseudomonas strains against Ralstonia solanacearum (the causative agent of bacterial wilt) and to investigate underlying mechanisms of potential pathogen suppression. We found that inhibitory effects were Pseudomonas strain-specific, with strain CHA0 showing the highest pathogen suppression. Genomic screening identified 2, 4-diacetylphloroglucinol (DAPG), pyoluteorin, and orfamides A and B secondary metabolite clusters in the genomes of the most inhibitory strains, which were investigated further. While all these compounds suppressed R. solanacearum growth, only Orfamide A was produced in the growth media based on mass spectrometry. Moreover, orfamide variants extracted from Pseudomonas cultures showed high pathogen suppression. Using the Micro Tom tomato cultivar, it was found that CHA0 could reduce bacterial wilt disease incidence with one of the two tested pathogen strains. Together, these findings suggest that a better understanding of Pseudomonas-Ralstonia interactions in the rhizosphere is required to successfully translate in vitro findings into agricultural applications.
Grey seals (Halichoerus grypus) can act as sentinel species reflecting the condition of the environment they inhabit. Our previous research identified strains of pathogenic Campylobacter and Salmonella, originating from both human and agricultural animal hosts, on rectal swabs from live grey seal (Halichoerus grypus) pups and yearlings on the Isle of May, Scotland, UK. We examined rectal swabs from the same pup (n=90) and yearling (n=19) grey seals to gain further understanding into the effects of age-related changes (pup versus yearling) and three different natal terrestrial habitats on seal pup fecal microbiota. DNA was extracted from a subset of rectal swabs (pups n=23, yearlings n=9) using an optimized procedure, and the V4 region of the 16S rRNA gene was sequenced to identify each individual’s microbiota. Diversity in pup samples was lower (3.92 ± 0.19) than yearlings (4.66 ± 0.39) although not significant at the p=0.05 level (p = 0.062) but differences in the composition of the microbiota were (p < 0.001). Similarly, differences between the composition of the microbiota from pups from three different terrestrial habitats (PH, RR, and TS) were highly significant (p < 0.001). Pairwise tests showed significant differences between all three habitats: PH vs TS (p = 0.019), PH vs RR (p = 0.042) and TS vs RR (p = 0.020). This preliminary study suggests a general trend, that seal microbiomes are modified by both age and, in pups, different terrestrial habitats. Furthermore, knowledge of the microbiota species present has the potential to be used in determining the environmental quality index.
In most countries, genetically modified microorganisms are not approved for use for fermentation in the food industry. Therefore, random mutagenesis and subsequent screening are performed to improve the productivities of valuable metabolites and enzymes as well as other specific functions in an industrial microbial strain. In addition, targeted gene knockout is performed by genetic recombination using its enzyme genes as selectable markers to maintain self-cloning status. However, random mutagenesis has a drawback as it does not guarantee improvement of the targeted function. Conversely, self-cloning is rarely used to breed an industrial microbial strain. This is probably because a self-cloning strain is similar to a genetically modified strain, as both undergo homologous recombination, although exogenous genes are not introduced. In this article, I discuss the usefulness of genome editing technology as a substitute for conventional techniques to breed filamentous fungal strains. This article particularly focusses on “genome co-editing,” a genome editing technology used for knocking out two genes concomitantly, as reported in Magnaporthe grisea and Aspergillus oryzae. Especially, when genome co-editing is applied to a target gene and a membrane transporter gene that aid the entry of toxic compounds into cells, the resulting clone can be categorized as an autotrophic and non-genetically modified clone. Such a clone should easily apply to industrial fermentation without being restricted by a genetically modified status. Genome co-editing will also be used to construct mutant strains with multiple target gene knockouts by eliminating multiple membrane transporter genes. This could substantially improve the productivities of valuable metabolites and enzymes in a stepwise manner. Thus, genome co-editing is considered a potentially powerful method to knock out single or multiple target genes that can contribute to the breeding of filamentous fungal strains in the food industry.
Laccases belong to a family of multicopper enzymes able to oxidize a broad spectrum of organic compounds. Despite the well-known property of laccases to carry out bleaching and degradation of industrial dyes and polyphenolic compounds, their industrial use is often limited by the high cost, low efficiency, or instability of these enzymes. To look for new microorganisms which produce laccases that are potentially suitable for industrial applications, we have isolated several fungal strains from a cave in northern Spain. Their phenotypic analysis on agar plates supplemented with ABTS (2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) disclosed two laccase-positive strains. Further genotyping revealed that they belonged to the Gliomastix murorum and Conidiobolus thromboides species. The secretion of G. murorum and C. thromboides laccase-like enzymes was then confirmed by zymography. Further identification of these polypeptides by mass-spectroscopy revealed the nature of the laccases and made it possible to predict their functional domains and other features. In addition, plate assays revealed that the laccases secreted by both G. murorum and C. thromboides were capable of degrading industrial dyes (Congo Red, Indigo, and Eriochrome Black T). Homology modeling and substrate docking predicted the putative structure of the currently uncrystallized G. murorum enzyme as well as its amino acid residues potentially involved in interactions with these dyes. In summary, new biochemical and structural insights into decolorization mediated by G. murorum laccase as well as identification of laccase-like oxidase in C. thromboides point to a promising future for these enzymes in biotechnology.
Given the increasing eutrophication of water bodies in Africa due to increasing anthropogenic pressures, data are needed to better understand the responses of phytoplankton communities to these changes in tropical lakes. These ecosystems are used by local human populations for multiple purposes, including fish and drinking water production, potentially exposing these populations to health threats if, for example, an increase in toxic cyanobacterial blooms is associated with increasing eutrophication. To test the short-term response of the phytoplankton community to the addition of nutrients (phosphorus and nitrogen, alone or in combination) and Nile tilapia, we developed an in situ mesocosm experiment in a freshwater lagoon located near Abidjan (Ivory Coast). We found that phytoplankton growth (estimated by chlorophyll-a quantification) was highly stimulated when both nitrogen and phosphorus were added, while there was no clear evidence for such colimitation by these two nutrients when considering their concentrations in the lagoon. Phytoplankton growth was accompanied by significant changes in the diversity and composition of this community and did not lead to an increase in the proportions of cyanobacteria. However, the addition of fish to some mesocosms resulted in a drastic decrease in phytoplankton biomass and a dominance of chlorophytes in this community. Finally, these experiments showed that the addition of nitrogen, alone or combined with phosphorus, stimulated microcystin production by cyanobacteria. In addition, no evidence for microcystin accumulation in the fish was found. Taken together, these data allow us to discuss strategies for controlling cyanobacterial blooms in this tropical ecosystem.
Saccharomyces cerevisiae produces a multicellular phenotype, known as a mat, on a semi-solid medium. This biofilm phenotype was first described in the lab strain 1278b and has been analyzed mostly in this same background. Yeast cells form a mat by spreading across the medium and adhering to each other and the surface, in part through the variegated expression of the cell adhesin, FLO11. This process creates a characteristic floral pattern and generates pH and glucose gradients outward from the center of the mat. Mats are encapsulated in a liquid which may aid in surface spreading and diffusion. Here, we examine thirteen environmental isolates that vary visually in the phenotype. We predicted that mat properties were universal and increased morphological complexity would be associated with more extreme trait values. Our results showed that pH varied significantly among strains, but was not correlated to mat complexity. Only two isolates generated significant liquid boundaries and neither produced visually complex mats. In five isolates, we tracked the initiation of FLO11 using GFP under the control of the endogenous promoter. Strains varied in when and how much GFP was detected, with increased signal associated with increased morphological complexity. Generally, the signal was strongest in the center of the mat and absent at the expanding edge. Our results show that traits discovered in one background vary and exist independently of mat complexity in natural isolates. The environment may favor different sets of traits, which could have implications for how this yeast adapts to its many ecological niches.
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization-related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas-1, Passage, Apse, Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65-related taxonomic database was constructed for identification of Actinobacteria to the species level by Illumina-MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% OTU cutoff) versus 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database (https://zenodo.org/record/5576074) was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species-level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
The use of an adequate protocol that accurately extracts microbial DNA from bovine milk samples is of importance for downstream analysis such as 16S rRNA gene sequencing. Although sequencing platforms such as Illumina are very common, there are reservations concerning reproducibility in challenging samples that combine low bacterial loads with high amounts of host DNA. The objective of this study was to evaluate six different DNA extraction protocols applied to four different prototype milk samples (low/high level of colony-forming units (cfu) and somatic cells). DNA extracts were sequenced on Illumina MiSeq with primers for the hypervariable regions V1V2 and V3V4. The different protocols were evaluated by analyzing the yield and purity of DNA extracts and the number of clean reads after sequencing. Three protocols with the highest median number of clean reads were selected. To assess reproducibility, these extraction replicates were re-sequenced in triplicates (n=120). The most reproducible results for alpha- and beta-diversity were obtained with the modified DNeasy Blood & Tissue kit after a chemical pre-treatment plus resuspension of the cream fraction. The unmodified QIAamp DNA Mini kit performed particularly weak in the sample representing unspecific mastitis. These results suggest that pre-treatment in combination with the modified DNeasy Blood & Tissue kit is useful in extracting microbial DNA from challenging milk samples. To increase reproducibility, we recommend that duplicates, if not triplicates, should be sequenced. We showed that high counts of somatic cells challenged DNA extraction, which shapes the need to apply modified extraction protocols.
The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for eleven bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.
The CRISPR-Cas system of Prokaryotes is an adaptive immune defense mechanism to protect themselves from invading genetic elements (e.g. phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order Enterobacteriales). For some genera, data on CRISPR-Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high-quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotic, and ureilytica. Apart from subtypes I-E and I-F1, which had previously been identified in marcescens, we report that of I-C and the variants I-ES1, I-ES2 and I-F1S1. Analysis of the genomic contexts for CRISPR loci revealed mdtN-phnP as the region mostly shared (grimesii, inhibens, marcescens, nematodiphila, plymuthica, rubidaea, and Serratia sp.). Three new contexts detected in genomes of rubidaea and fonticola (puu genes-mnmA) and rubidaea (osmE-soxG and ampC-yebZ) were also found. Plasmid and/or phage origin of spacers was also established.