Transcriptional Shift and Metabolic Adaptations during Leishmania Quiescence Using Stationary Phase and Drug Pressure as Models

Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavorable conditions. Quiescent cells are characterized by slow or non-proliferation and a deep downregulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival skill is widespread, including in eukaryotic microorganisms. In Leishmania, a digenetic parasitic protozoan that causes a major infectious disease, quiescence has been demonstrated, but the molecular and metabolic features enabling its maintenance are unknown. Here, we quantified the transcriptome and metabolome of Leishmania promastigotes and amastigotes where quiescence was induced in vitro either, through drug pressure or by stationary phase. Quiescent cells have a global and coordinated reduction in overall transcription, with levels dropping to as low as 0.4% of those in proliferating cells. However, a subset of transcripts did not follow this trend and were relatively upregulated in quiescent populations, including those encoding membrane components, such as amastins and GP63, or processes like autophagy. The metabolome followed a similar trend of overall downregulation albeit to a lesser magnitude than the transcriptome. It is noteworthy that among the commonly upregulated metabolites were those involved in carbon sources as an alternative to glucose. This first integrated two omics layers afford novel insight into cell regulation and show commonly modulated features across stimuli and stages.

Extremely Acidic Eukaryotic (Micro) Organisms: Life in Acid Mine Drainage Polluted Environments—Mini-Review

Acid Mine Drainage (AMD) results from sulfide oxidation, which incorporates hydrogen ions, sulfate, and metals/metalloids into the aquatic environment, allowing fixation, bioaccumulation and biomagnification of pollutants in the aquatic food chain. Acidic leachates from waste rock dams from pyritic and (to a lesser extent) coal mining are the main foci of Acid Mine Drainage (AMD) production. When AMD is incorporated into rivers, notable changes in water hydro-geochemistry and biota are observed. There is a high interest in the biodiversity of this type of extreme environments for several reasons. Studies indicate that extreme acid environments may reflect early Earth conditions, and are thus, suitable for astrobiological experiments as acidophilic microorganisms survive on the sulfates and iron oxides in AMD-contaminated waters/sediments, an analogous environment to Mars; other reasons are related to the biotechnological potential of extremophiles. In addition, AMD is responsible for decreasing the diversity and abundance of different taxa, as well as for selecting the most well-adapted species to these toxic conditions. Acidophilic and acidotolerant eukaryotic microorganisms are mostly composed by algae (diatoms and unicellular and filamentous algae), protozoa, fungi and fungi-like protists, and unsegmented pseudocoelomata animals such as Rotifera and micro-macroinvertebrates. In this work, a literature review summarizing the most recent studies on eukaryotic organisms and micro-organisms in Acid Mine Drainage-affected environments is elaborated.

Gut Microbiome Profiles in Colonizations with the Enteric Protozoa Blastocystis in Korean Populations

The influence of unicellular eukaryotic microorganisms on human gut health and disease is largely unexplored. Blastocystis species commonly colonize the gut, but their clinical significance and ecological role are unclear. We evaluated the effect of Blastocystis colonization on the fecal microbiota of Koreans. In total, 39 Blastocystis-positive and -negative fecal samples were analyzed. The fecal microbiome was assessed by targeting the V3–V4 region of the bacterial 16S ribosomal gene. Bacterial diversity was greater in the Blastocystis-positive than in the Blastocystis-negative group. The bacterial community structure and phylogenetic diversity differed according to the presence of Blastocystis. The mean proportions of Faecalibacterium species and Ruminococcaceae were larger in the Blastocystis-positive group, and that of Enterococcus species was larger in the Blastocystis-negative group. Linear discriminant analysis showed that Faecalibacterium, Prevotella 9, Ruminococcaceae UCG-002, Muribaculaceae, Rikenellaceae, Acidaminococcaceae, Phascolarctobacterium, and Ruminococcaceae UCG-005 were highly enriched in the Blastocystis-positive group, whereas Enterococcus hirae, Enterococcus faecalis, Enterococcus durans, Enterococcaceae, Lactobacillales, and Bacilli were highly abundant in the Blastocystis-negative group. Overall, our results enlighten the notion that Blastocystis colonization is associated with a healthy gut microbiota.

Transcriptional shift and metabolic adaptations during Leishmania quiescence using stationary-phase and drug pressure as models

Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavourable conditions. Quiescent cells are characterized by slow or non-proliferation and deep down-regulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival skill is widespread, including in eukaryotic microorganisms. In Leishmania, a digenetic parasitic protozoan that causes a major infectious disease, quiescence has been demonstrated, but molecular and metabolic features enabling its maintenance are unknown. Here we quantified the transcriptome and metabolome of Leishmania promastigotes and amastigotes where quiescence was induced in vitro either through drug pressure or by stationary phase. Quiescent cells have a global and coordinated reduction in overall transcription, with levels dropping to as low as 0.4% of those in proliferating cells. However, a subset of transcripts did not follow this trend and were relatively upregulated in quiescent populations, including those encoding membrane components such as amastins and GP63 or processes like autophagy. The metabolome followed a similar trend of overall downregulation albeit to a lesser magnitude than the transcriptome. Noteworthy, among the commonly upregulated metabolites were those involved in carbon sources as an alternative to glucose. This first integrated two omics layers affords novel insights into cell regulation and shows commonly modulated features across stimuli and stages.

Overexpression of Shinorhizobium Meliloti Flavohemoglobinefficiently Improved Cell Growth and Fatty Acid Biosynthesis in Oleaginous Fungus Mucor Circinelloides

Oxygen availability is a limiting factor for lipid biosynthesis in eukaryotic microorganisms. Two bacterial hemoglobins from Vitreoscilla sp. (VHb) and Shinorhizobium meliloti (SHb), which could deliver the oxygen to the respiratory chain to produce more ATP, were introduced into Mucor circinelloides to alleviate oxygen limitation, thereby improving cell growth and fatty acid production. VHb and SHb genes were integrated into the M. circinelloides MU402 genome through homologous recombination, and their protein expression was verified by carbon monoxide difference spectrum (CO-difference spectrum)analysis. SHb-expressing strain showed higher biomass than VHb-expressing strain. The biomass of the SHb-expressing strain was increased by about 50% and the total fatty acid (TFA) content was as high as 15.7% of the dry cell weight which was about 40% higher than that of the control strain in flask conditions. In the fermenter, the maximum biomass and TFA content was obtained in SHb-expressing strains, with the biomass being 12.1 g/L and the TFA being 21.1% of the dry cell weight. VHb and SHb expression also affected the fatty acid composition with the proportion of polyunsaturated fatty acids being increased. Over-expression of bacterial hemoglobins, especially SHb increased cell growth and TFA content in M. circinelloides at low and high aeration, suggesting that SHb is better than VHb in improving the fatty acid production in oleaginous microorganisms.

In situ Prokaryotic and Eukaryotic Communities on Microplastic Particles in a Small Headwater Stream in Germany

The ubiquitous use of plastic products in our daily life is often accompanied by improper disposal. The first interactions of plastics with organisms in the environment occur by overgrowth or biofilm formation on the particle surface, which can facilitate the ingestion by animals. In order to elucidate the colonization of plastic particles by prokaryotic and eukaryotic microorganisms in situ, we investigated microbial communities in biofilms on four different polymer types and on mineral particles in a small headwater stream 500 m downstream of a wastewater treatment plant in Germany. Microplastic and mineral particles were exposed to the free-flowing water for 4 weeks in spring and in summer. The microbial composition of the developing biofilm was analyzed by 16S and 18S amplicon sequencing. Despite the expected seasonal differences in the microbial composition of pro- and eukaryotic communities, we repeatedly observed polymer type-specific differentiation in both seasons. The order of polymer type-specific prokaryotic and eukaryotic community distances calculated by Robust Aitchison principal component analysis (PCA) was the same in spring and summer samples. However, the magnitude of the distance differed considerably between polymer types. Prokaryotic communities on polyethylene particles exhibited the most considerable difference to other particles in summer, while eukaryotic communities on polypropylene particles showed the most considerable difference to other spring samples. The most contributing bacterial taxa to the polyethylene-specific differentiation belong to the Planctomycetales, Saccharimonadales, Bryobacterales, uncultured Acidiomicrobia, and Gemmatimonadales. The most remarkable differences in eukaryotic microorganism abundances could be observed in several distinct groups of Ciliophora (ciliates) and Chlorophytes (green algae). Prediction of community functions from taxonomic abundances revealed differences between spring and summer, and – to a lesser extent – also between polymer types and mineral surfaces. Our results show that different microplastic particles were colonized by different biofilm communities. These findings may be used for advanced experimental designs to investigate the role of microorganisms on the fate of microplastic particles in freshwater ecosystems.

Interactions with Arsenic: Mechanisms of Toxicity and Cellular Resistance in Eukaryotic Microorganisms

Arsenic (As) is quite an abundant metalloid, with ancient origin and ubiquitous distribution, which represents a severe environmental risk and a global problem for public health. Microbial exposure to As compounds in the environment has happened since the beginning of time. Selective pressure has induced the evolution of various genetic systems conferring useful capacities in many microorganisms to detoxify and even use arsenic, as an energy source. This review summarizes the microbial impact of the As biogeochemical cycle. Moreover, the poorly known adverse effects of this element on eukaryotic microbes, as well as the As uptake and detoxification mechanisms developed by yeast and protists, are discussed. Finally, an outlook of As microbial remediation makes evident the knowledge gaps and the necessity of new approaches to mitigate this environmental challenge.

Adaptive Role of Cell Death in Yeast Communities Stressed with Macrolide Antifungals

Eukaryotic microorganisms harbor elements of programmed cell death (PCD) mechanisms that are homologous to the PCD of multicellular metazoa. However, it is still debated whether microbial PCD has an adaptive role or whether the processes of cell death are an aimless operation in self-regulating molecular mechanisms.

High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem

The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.

Filamentous Fungi Producing l-Asparaginase with Low Glutaminase Activity Isolated from Brazilian Savanna Soil

l-asparaginase is an enzyme used as treatment for acute lymphoblastic leukemia (ALL) due to its ability to hydrolyze l-asparagine, an essential amino acid synthesized by normal cells unlike neoplastic cells. The adverse effects of l-asparaginase formulations are associated with its glutaminase activity and bacterial origin; therefore, it is important to find new sources of l-asparaginase-producing eukaryotic microorganisms with low glutaminase activity. This work evaluated the biotechnological potential of filamentous fungi isolated from Brazilian Savanna soil and plants for l-asparaginase production. Thirty-nine isolates were screened for enzyme production using the plate assay, followed by measuring enzymatic activity in cells after submerged fermentation. The variables influencing l-asparaginase production were evaluated using Plackett–Burman design. Cell disruption methods were evaluated for l-asparaginase release. Penicillium sizovae 2DSST1 and Fusarium proliferatum DCFS10 showed the highest l-asparaginase activity levels and the lowest glutaminase activity levels. Penicillium sizovae l-asparaginase was repressed by carbon sources, whereas higher carbon concentrations enhanced l-asparaginase by F. proliferatum. Maximum enzyme productivity, specific enzyme yield and the biomass conversion factor in the enzyme increased after Plackett–Burman design. Freeze-grinding released 5-fold more l-asparaginase from cells than sonication. This study shows two species, which have not yet been reported, as sources of l-asparaginase with possible reduced immunogenicity for ALL therapy.