Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia

Enhancing Trypanosomatid Identification and Genotyping with Oxford Nanopore Sequencing: Development and Validation of an 18S rRNA Amplicon-Based Method

Trypanosomatids, including Trypanosoma and Leishmania species, present significant medical and veterinary challenges, causing substantial economic losses, health complications, and even fatalities. Diagnosing and genotyping these species and their genotypes is often complex, involving multiple steps. This study aimed to develop an amplicon-based sequencing (ABS) method using Oxford Nanopore long-read sequencing to enhance Trypanosomatid detection and genotyping. The 18S rDNA gene was targeted for its inter-species conservation. The Trypanosomatid-ABS method effectively distinguished between 11 Trypanosoma species (including Trypanosoma evansi, Trypanosoma theileri, Trypanosoma vivax, and Trypanosoma rangeli) and 6 Trypanosoma cruzi discrete typing units (TcI to TcVI and TcBat), showing strong concordance with conventional methods (κ index of 0.729, P < 0.001). It detected co-infections between Trypanosomatid genera and T. cruzi, with a limit of detection of one parasite per mL. The method was successfully applied to human, animal, and triatomine samples. Notably, TcI predominated in chronic Chagas samples, whereas TcII and TcIV were found in the acute stage. Triatomine vectors exhibited diverse Trypanosomatid infections, with Triatoma dimidiata mainly infected with TcI and occasional TcBat co-infections, and Rhodnius prolixus showing TcI and TcII infections, along with T. rangeli co-infections and mixed TcII infections. Animals were infected with T. vivax, T. theileri, and T. evansi. The ABS method's high resolution, sensitivity, and accuracy make it a valuable tool for understanding Trypanosomatid dynamics, enhancing disease control strategies, and enabling targeted interventions.

Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands

Peatlands, one of the oldest ecosystems, globally store significant amounts of carbon and freshwater. However, they are under severe threat from human activities, leading to changes in water, nutrient and temperature regimes in these delicate systems. Such shifts can trigger a substantial carbon flux into the atmosphere and diminish the water-holding capacity of peatlands. Microbes associated with moss in peatlands play a crucial role in providing these ecosystem services, which are at risk due to global change. Therefore, understanding the factors influencing microbial composition and function is vital. Our study focused on five peatlands along an altitudinal gradient in Switzerland, where we sampled moss on hummocks containing Sarracenia purpurea. Structural equation modelling revealed that habitat condition was the primary predictor of community structure and directly influenced other environmental variables. Interestingly, the microbial composition was not linked to the local moss species identity. Instead, microbial communities varied significantly between sites due to differences in acidity levels and nitrogen availability. This finding was also mirrored in a co-occurrence network analysis, which displayed a distinct distribution of indicator species for acidity and nitrogen availability. Therefore, peatland conservation should take into account the critical habitat characteristics of moss-associated microbial communities.

Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.

Temperature and CO2 interactively drive shifts in the compositional and functional structure of peatland protist communities

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.

An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG

AIMS

The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs).

METHODS AND RESULTS

The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible.

CONCLUSION

NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.

Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event

BACKGROUND

Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island of New Caledonia (South Pacific) after a cyclonic event, which is considered a pulse disturbance at our study site. The variability of coastal microbiomes, studied by the metabarcoding of V4 18S (protists) and V4-V5 16S (bacteria) rDNA genes, after the cyclone passage was associated with key environmental parameters describing the runoff impact (salinity, organic matter proxies, terrestrial rock origin metals) and compared to community structures observed during the dry season.

RESULTS

Microbiome biodiversity patterns of the dry season were destructured because of the runoff impact, and land-origin taxa were observed in the coastal areas. After the rainy event, different daily community dynamics were observed locally, with specific microbial taxa explaining these variabilities. Plume dispersal modeling revealed the extent of low salinity areas up to the coral reef area (16 km offshore), but a rapid (< 6 days) recovery to typical steady conditions of the lagoon's hydrology was observed. Conversely, during the same time, some biological components (microbial communities, Chl a) and biogeochemical components (particulate nickel, terrigenous organic matter) of the ecosystem did not recover to values observed during the dry season conditions.

CONCLUSION

The ecosystem resilience of subtropical ecosystems must be evaluated from a multidisciplinary, holistic perspective and over the long term. This allows evaluating the risk associated with a potential continued and long-term disequilibrium of the ecosystem, triggered by the change in the frequency and intensity of extreme climatic events in the era of planetary climatic changes.

Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen

The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 μm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 μm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.

VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages

Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.

Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil

Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.

Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater

The Materials Corrosion Test (MaCoTe) at the Underground Research Laboratory in Grimsel, Switzerland, assesses the microbiology and corrosion behavior of engineered barrier components of a deep geological repository (DGR) for long-term disposal of high-level nuclear waste. Diversity and temporal changes of bentonite-associated microbial community profiles were assessed under DGR-like conditions for compacted Wyoming MX-80 bentonite (1.25 g/cm3 and 1.50 g/cm3 targeted dry densities) exposed to natural groundwater. Using culture-dependent and molecular techniques, samples taken from the outside layer of 5-year borehole modules revealed up to 66% and 23% of 16S rRNA gene sequences affiliated with Desulfosporosinus and Desulfovibrio, respectively. Putatively involved in sulfate reduction, these taxa were almost undetectable within the bentonite core. Instead, microbial profiles of the inner bentonite core were similar to uncompacted bentonite used to pack modules years earlier, and were consistent with a previously published 1-year time point, revealing no detectable microbial growth. Abundances of culturable aerobic and anaerobic heterotrophic bacteria in the uncompacted bentonite were relatively low, with less than 1,000 and 100 colony-forming units (CFUs) per gram dry weight, respectively. Nearly 5 years after emplacement, culturable heterotrophic bacterial CFUs and sulfate-reducing bacteria did not change significantly inside the bentonite core. Phospholipid fatty acid data indicated similar lipid abundance, and corresponding cell abundance estimates, for inner 5-year MaCoTe bentonite samples compared to those previously obtained for 1-year incubations. Collectively, our results provide complementary evidence for microbial stability inside highly compacted bentonite exposed to conditions that mimic engineered barrier components of a deep geological repository. IMPORTANCE The long-term safety of a deep geological repository for used nuclear fuel is dependent on the performance of the engineered and natural barriers. Microbial activity can produce chemical species that can influence the corrosion of the disposal containers for used nuclear fuel. Although previous studies have evaluated the microbiology of compacted bentonite clay within subsurface environments, these have been limited to relatively short incubations (i.e., 1 year). The current study provides a unique 5-year perspective that reinforces previous findings of growth inhibition for bentonite clay exposed to in situ subsurface conditions.

Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.

Genetic Markers for Metabarcoding of Freshwater Microalgae: Review

The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.

Temperature dependence of parasitoid infection and abundance of a diatom revealed by automated imaging and classification

Diatoms are a group of phytoplankton that contribute disproportionately to global primary production. Traditional paradigms that suggest diatoms are consumed primarily by larger zooplankton are challenged by sporadic parasitic "epidemics" within diatom populations. However, our understanding of diatom parasitism is limited by difficulties in quantifying these interactions. Here, we observe the dynamics of Cryothecomonas aestivalis (a protist) infection of an important diatom on the Northeast U.S. Shelf (NES), Guinardia delicatula, with a combination of automated imaging-in-flow cytometry and a convolutional neural network image classifier. Application of the classifier to >1 billion images from a nearshore time series and >20 survey cruises across the broader NES reveals the spatiotemporal gradients and temperature dependence of G. delicatula abundance and infection dynamics. Suppression of parasitoid infection at temperatures <4 °C drives annual cycles in both G. delicatula infection and abundance, with an annual maximum in infection observed in the fall-winter preceding an annual maximum in host abundance in the winter-spring. This annual cycle likely varies spatially across the NES in response to variable annual cycles in water temperature. We show that infection remains suppressed for ~2 mo following cold periods, possibly due to temperature-induced local extinctions of the C. aestivalis strain(s) that infect G. delicatula. These findings have implications for predicting impacts of a warming NES surface ocean on G. delicatula abundance and infection dynamics and demonstrate the potential of automated plankton imaging and classification to quantify phytoplankton parasitism in nature across unprecedented spatiotemporal scales.

The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton

Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.

Assessing siliceous sinter matrices for long-term preservation of lipid biomarkers in opaline sinter deposits analogous to Mars in El Tatio (Chile)

Subaerial hydrothermal systems are of great interest for paleobiology and astrobiology as plausible candidate environments to support the origin of life on Earth that offer a unique and interrelated atmosphere-hydrosphere-lithosphere interface. They harbor extensive sinter deposits of high preservation potential that are promising targets in the search for traces of possible extraterrestrial life on Hesperian Mars. However, long-term quality preservation is paramount for recognizing biosignatures in old samples and there are still significant gaps in our understanding of the impact and extent of taphonomy processes on life fingerprints. Here, we propose a study based on lipid biomarkers -highly resistant cell-membrane components- to investigate the effects of silicification on their preservation in hydrothermal opaline sinter. We explore the lipid biomarkers profile in three sinter deposits of up to ~3000 years from El Tatio, one of the best Martian analogs on Earth. The lipid profile in local living biofilms is used as a fresh counterpart of the fossil biomarkers in the centuries-old sinter deposits to qualitatively assess the taphonomy effects of silicification on the lipid's preservation. Despite the geological alteration, the preserved lipids retained a depleted stable-carbon isotopic fingerprint characteristic of biological sources, result highly relevant for astrobiology. The data allowed us to estimate for the first time the degradation rate of lipid biomarkers in sinter deposits from El Tatio, and to assess the time preservation framework of opaline silica. Auxiliary techniques of higher taxonomic resolution (DNA sequencing and metaproteomics) helped in the reconstruction of the paleobiology. The lipids were the best-preserved biomolecules, whereas the detection of DNA and proteins dropped considerably from 5 cm depth. These findings provide new insights into taphonomy processes affecting life fingerprints in hydrothermal deposits and serves as a useful baseline for assessing the time window for recovering unambiguous signs of past life on Earth and beyond.

An Environmental DNA Primer for Microbial and Restoration Ecology

Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.

Whey permeate as a phosphorus source for algal cultivation

Microalgal cultivation for biodiesel and feed requires recycled nutrient resources for a sustainable long-term operation. Whey permeate (WP) from dairy processing contains high organic load (lactose, oils, and proteins) and nitrogen (resources tested for microalgal cultivation) and organic phosphorus (P) that has not yet been tested as a P source for microalgal cultivation. We explored the potential of green algae strains (brackish) and polyculture (freshwater) in exploiting P from WP added to a medium based on either seawater (7 psu) or landfill leachate. Both strains showed a capacity of using organic P in WP with equal growth rates (0.94-1.12 d^-1 ) compared with chemical phosphate treatments (0.88-1.07 d^-1 ). The polyculture had comparable growth rate (0.25-0.57 d^-1 ) and biomass yield (152.1-357.5 mg L^-1 ) and similar or higher nutrient removal rate in the leachate-WP medium (1.3-6.4 mg L^-1  day^-1 nitrogen, 0.2-1.1 mg L^-1  day^-1 P) compared with the leachate-chemical phosphate medium (1.2-4.7 mg L^-1  day^-1 nitrogen, 0.3-1.4 mg L^-1  day^-1 P). This study showed that WP is a suitable P source for microalgal cultivation over a range of salinities. To date, this is the first study demonstrating that raw WP can replace mineral P fertilizer for algal cultivation. PRACTITIONERS POINTS: Whey permeate is a comparable phosphorus source to standard fertilizers used in algal cultivation. Green algae removed phosphorus effectively from whey permeate. Microalgal cultivation is a good approach for treatment of whey permeate in combination with a nitrogen-rich wastewater.

High resolution functional analysis and community structure of photogranules

Photogranules are spherical aggregates formed of complex phototrophic ecosystems with potential for “aeration-free” wastewater treatment. Photogranules from a sequencing batch reactor were investigated by fluorescence microscopy, 16S/18S rRNA gene amplicon sequencing, microsensors, and stable- and radioisotope incubations to determine the granules’ composition, nutrient distribution, and light, carbon, and nitrogen budgets. The photogranules were biologically and chemically stratified, with filamentous cyanobacteria arranged in discrete layers and forming a scaffold to which other organisms were attached. Oxygen, nitrate, and light gradients were also detectable. Photosynthetic activity and nitrification were both predominantly restricted to the outer 500 µm, but while photosynthesis was relatively insensitive to the oxygen and nutrient (ammonium, phosphate, acetate) concentrations tested, nitrification was highly sensitive. Oxygen was cycled internally, with oxygen produced through photosynthesis rapidly consumed by aerobic respiration and nitrification. Oxygen production and consumption were well balanced. Similarly, nitrogen was cycled through paired nitrification and denitrification, and carbon was exchanged through photosynthesis and respiration. Our findings highlight that photogranules are complete, complex ecosystems with multiple linked nutrient cycles and will aid engineering decisions in photogranular wastewater treatment.

Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance

Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.

Microbial Interactions Related to N2O Emissions and Temperature Sensitivity from Rice Paddy Fields

The soil microbiome is a driver of nitrous oxide (N₂O) emissions in terrestrial ecosystems. Identifying the core microbiome of N₂O emissions and its temperature sensitivity from trillions of soil microorganisms is a great challenge and is essential to improving the predictability of soil-climate feedback related to increasing temperature. Here, the integrated soil microbiome covering archaeal, bacterial, fungal, algal, and microfaunal communities was studied to disengage the potential linkage with its N₂O emissions and its temperature sensitivity in paddy fields by hunting for core species pairs. The results showed that between-group interactions of core bacterial and archaeal members and the within-group interactions of core bacterial members jointly contributed to the N₂O emissions and its temperature sensitivity. The contribution of between-group interactions (32 to 33%) was greater than that of within groups (10 to 18%). These results suggested that N₂O emissions and their fluctuations related to climate warming are affected by the within- and between-group interactions of the soil microbiome. Our results help advance the knowledge on the importance of microbial keystone species and network associations in controlling N₂O production and their responses to increasing temperature. IMPORTANCE Soil microorganisms drive emissions of nitrous oxide from soils; this is a powerful greenhouse gas and the dominant ozone-depleting agent. N₂O emissions can be partly predicted from soil properties and specific microbial groups, whereas a possible role of below-ground microbial interactions has largely been overlooked. Here, the integrated soil microbiome covering archaeal, bacterial, fungal, algal, and microfaunal communities was studied to disengage the potential linkage with the N₂O emissions and temperature sensitivity of the microbiome in paddy fields by hunting for core species pairs. The results showed that between-group interactions of core bacterial and archaeal members and the within-group interactions of core bacterial members jointly contributed to the N₂O emissions. The contribution of between-group interactions (32 to 33%) was greater than that of within-group interactions (10 to 18%). Our results help advance the knowledge on the importance of microbial keystone species and interactions in controlling N₂O production and their responses to increasing temperature.

The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes

In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.

Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities

Phototrophic biofilms, also known as periphyton, are microbial freshwater communities that drive crucial ecological processes in streams and lakes. Gaining a deep mechanistic understanding of the biological processes occurring in natural periphyton remains challenging due to the high complexity and variability of such communities. To address this challenge, we rationally developed a workflow to construct a synthetic community by co-culturing 26 phototrophic species (i.e., diatoms, green algae, and cyanobacteria) that were inoculated in a successional sequence to create a periphytic biofilm on glass slides. We show that this community is diverse, stable, and highly reproducible in terms of microbial composition, function, and 3D spatial structure of the biofilm. We also demonstrate the ability to monitor microbial dynamics at the single species level during periphyton development and how their abundances are impacted by stressors such as increased temperature and a herbicide, singly and in combination. Overall, such a synthetic periphyton, grown under controlled conditions, can be used as a model system for theory testing through targeted manipulation.

Methodological 'lenses' influence the characterization of phytoplankton dynamics in a coastal upwelling ecosystem

New technologies enable the opportunity to improve our monitoring and understanding of marine phytoplankton communities. However, careful consideration for how different methodological approaches, or 'lenses', influence our interpretation of phytoplankton ecology is important, particularly when drawing conclusions about change over time or space. Using both high-throughput 18S rRNA gene sequencing and microscopy, we explored how phytoplankton community structure varied over the course of a year within a nearshore semi-enclosed coastal embayment along the Central Coast of California. The seasonal shift in the relative community dominance (i.e., diatom vs. dinoflagellate dominance) was captured in the microscopy results but not effectively captured in the molecular-based findings. However, the molecular approach explained more of the variability in composition across seasons relative to the microscopy approach. Temporal dynamics of specific bloom-forming taxa also differed between the molecular and microscopy results. Overall, the observed differences between the molecular- and microscopy-derived characterization of phytoplankton dynamics suggest that the approaches are best suited to answer different research questions. Moreover, the approaches complement each other for a more comprehensive perspective of a coastal phytoplankton ecosystem. Therefore, identifying the biases of each approach within natural communities is necessary to effectively and accurately characterize phytoplankton communities.

Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration

Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.

Wastewater microorganisms impact microbial diversity and important ecological functions of stream periphyton

Effluents of wastewater treatment plants can impact microbial communities in the receiving streams. However, little is known about the role of microorganisms in wastewater as opposed to other wastewater constituents, such as nutrients and micropollutants. We aimed therefore at determining the impact of wastewater microorganisms on the microbial diversity and function of periphyton, key microbial communities in streams. We used a flow-through channel system to grow periphyton upon exposure to a mixture of stream water and unfiltered or ultra-filtered wastewater. Impacts were assessed on periphyton biomass, activities and tolerance to micropollutants, as well as on microbial diversity. Our results showed that wastewater microorganisms colonized periphyton and modified its community composition, resulting for instance in an increased abundance of Chloroflexi and a decreased abundance of diatoms and green algae. This led to shifts towards heterotrophy, as suggested by the changes in nutrient stoichiometry and the increased mineralization potential of carbon substrates. An increased tolerance towards micropollutants was only found for periphyton exposed to unfiltered wastewater but not to ultra-filtered wastewater, suggesting that wastewater microorganisms were responsible for this increased tolerance. Overall, our results highlight the need to consider the role of wastewater microorganisms when studying potential impacts of wastewater on the receiving water body.

High-throughput engineering of cytoplasmic- and nuclear-replicating large dsDNA viruses by CRISPR/Cas9

The application of CRISPR/Cas9 to improve genome engineering efficiency for large dsDNA viruses has been extensively described, but a robust and versatile method for high-throughput generation of marker-free recombinants for a desired locus has not yet been reported. Cytoplasmic-replicating viruses use their own repair enzymes for homologous recombination, while nuclear-replicating viruses use the host repair machinery. This is translated into a wide range of Cas9-induced homologous recombination efficiencies, depending on the virus replication compartment and viral/host repair machinery characteristics and accessibility. However, the use of Cas9 as a selection agent to target parental virus genomes robustly improves the selection of desired recombinants across large dsDNA viruses. We used ectromelia virus (ECTV) and herpes simplex virus (HSV) type 1 and 2 to optimize a CRISPR/Cas9 method that can be used versatilely for efficient genome editing and selection of both cytoplasmic- and nuclear-replicating viruses. We performed a genome-wide genetic variant analysis of mutations located at predicted off-target sequences for 20 different recombinants, showing off-target-free accuracy by deep sequencing. Our results support this optimized method as an efficient, accurate and versatile approach to enhance the two critical factors of high-throughput viral genome engineering: generation and colour-based selection of recombinants. This application of CRISPR/Cas9 reduces the time and labour for screening of desired recombinants, allowing for high-throughput generation of large collections of mutant dsDNA viruses for a desired locus, optimally in less than 2 weeks.

Lipid Profiles From Fresh Biofilms Along a Temperature Gradient on a Hydrothermal Stream at El Tatio (Chilean Andes), as a Proxy for the Interpretation of Past and Present Biomarkers Beyond Earth

Hydrothermal systems and their deposits are primary targets in the search for fossil evidence of life beyond Earth. However, to learn how to decode fossil biomarker records in ancient hydrothermal deposits, we must first be able to interpret unambiguously modern biosignatures, their distribution patterns, and their association with physicochemical factors. Here, we investigated the molecular and isotopic profile of microbial biomarkers along a thermal gradient (from 29 to 72°C) in a hot spring (labeled Cacao) from El Tatio, a geyser field in the Chilean Andes with abundant opaline silica deposits resembling the nodular and digitate structures discovered on Mars. As a molecular forensic approach, we focused on the analysis of lipid compounds bearing recognized resistance to degradation and the potential to reconstruct the paleobiology of an environment on a broader temporal scale than other, more labile, biomolecules. By exploiting the lipid biomarkers’ potential to diagnose biological sources and carbon fixation pathways, we reconstructed the microbial community structure and its ecology along the Cacao hydrothermal transect. The taxonomic adscription of the lipid biomarkers was qualitatively corroborated with DNA sequencing analysis. The forensic capacity of the lipid biomarkers to identify biosources in fresh biofilms was validated down to the genus level for Roseiflexus, Chloroflexus, and Fischerella. We identified lipid biomarkers and DNA of several new cyanobacterial species in El Tatio and reported the first detection of Fischerella biomarkers at a temperature as high as 72°C. This, together with ecological peculiarities and the proportion of clades being characterized as unclassified, illustrates the ecological singularity of El Tatio and strengthens its astrobiological relevance. The Cacao hydrothermal ecosystem was defined by a succession of microbial communities and metabolic traits associated with a high- (72°C) to low-(29°C) temperature gradient that resembled the inferred metabolic sequence events from the 16S rRNA gene universal phylogenetic tree from thermophilic to anoxygenic photosynthetic species and oxygenic phototrophs. The locally calibrated DNA-validated lipidic profile in the Cacao biofilms provided a modern (molecular and isotopic) end member to facilitate the recognition of past biosources and metabolisms from altered biomarkers records in ancient silica deposits at El Tatio analogous to Martian opaline silica structures.

Microbial Interactions - Underexplored Links Between Public Health Relevant Bacteria and Protozoa in Coastal Environments

The co-existence of bacteria and protozoa in aquatic environments has led to the evolution of predation defense mechanisms by the bacteria. Some of the predation-resistant bacteria (PRB) are also pathogenic to humans and other mammals. The links between PRB and protozoa in natural aquatic systems are poorly known, but they are important in predicting outbreaks and determining the long-term consequences of a contamination event. To elucidate co-occurrence patterns between PRB (16S rRNA) and bacterivorous protozoa (18S rRNA), we performed a field study in a coastal area in the northern Baltic Sea. Interactions between bacteria and protozoa were explored by using two complementary statistical tools. We found co-occurrence patterns between specific PRB and protozoa, such as Legionella and Ciliophora, and we also found that the interactions are genotype-specific as, for example, Rickettsia. The PRB sequence diversity was larger in bays and freshwater inlets compared to offshore sites, indicating local adaptions. Considering the PRB diversity in the freshwater in combination with the large spring floods in the area, freshwater influxes should be considered a potential source of PRB in the coastal northern Baltic Sea. These findings are relevant for the knowledge of survival and dispersal of potential pathogens in the environment.

Protists in the Insect Rearing Industry: Benign Passengers or Potential Risk?

Simple Summary

As human populations grow and the climate crisis deepens, humans will need to look to alternative sustainable sources of protein. The insect rearing industry is now rapidly growing to generate more sustainable sources of food and feed, and, as it does so, there will be an urgent need to better understand the role that microorganisms play in both maintaining insect health and generating disease. Protists are microbes that are neither viral, bacterial nor fungal and, therefore, are sometimes overlooked when considering microbial fauna. In this paper, we review the literature on protists that have been uncovered within insects that are being considered for rearing as food and feed. We discuss what is known about how they interact with hosts, how they may affect industrially reared insects in the future and which tools now need to be developed to better study them.

Abstract

As the insects for food and feed industry grows, a new understanding of the industrially reared insect microbiome is needed to better comprehend the role that it plays in both maintaining insect health and generating disease. While many microbiome projects focus on bacteria, fungi or viruses, protists (including microsporidia) can also make up an important part of these assemblages. Past experiences with intensive invertebrate rearing indicate that these parasites, whilst often benign, can rapidly sweep through populations, causing extensive damage. Here, we review the diversity of microsporidia and protist species that are found in reared insect hosts and describe the current understanding of their host spectra, life cycles and the nature of their interactions with hosts. Major entomopathogenic parasite groups with the potential to infect insects currently being reared for food and feed include the Amoebozoa, Apicomplexa, Ciliates, Chlorophyta, Euglenozoa, Ichtyosporea and Microsporidia. However, key gaps exist in the understanding of how many of these entomopathogens affect host biology. In addition, for many of them, there are very limited or even no molecular data, preventing the implementation of molecular detection methods. There is now a pressing need to develop and use novel molecular tools, coupled with standard molecular diagnostic methods, to help unlock their biology and predict the effects of these poorly studied protist parasites in intensive insect rearing systems.

Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring

During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (> 20 μm), nano- (20-5 μm), and pico-size fractions (5-0.2 μm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related-either positively or negatively-to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.

Short- and long-read metabarcoding of the eukaryotic rRNA operon: evaluation of primers and comparison to shotgun metagenomics sequencing

High-throughput sequencing for analysis of microbial diversity has evolved vastly over the last decade. Currently the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics datasets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.

Comprehensive Metabolic and Taxonomic Reconstruction of an Ancient Microbial Mat From the McMurdo Ice Shelf (Antarctica) by Integrating Genetic, Metaproteomic and Lipid Biomarker Analyses

Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.

Predation increases multiple components of microbial diversity in activated sludge communities

Protozoan predators form an essential component of activated sludge communities that is tightly linked to wastewater treatment efficiency. Nonetheless, very little is known how protozoan predation is channelled via bacterial communities to affect ecosystem functioning. Therefore, we experimentally manipulated protozoan predation pressure in activated-sludge communities to determine its impacts on microbial diversity, composition and putative functionality. Different components of bacterial diversity such as taxa richness, evenness, genetic diversity and beta diversity all responded strongly and positively to high protozoan predation pressure. These responses were non-linear and levelled off at higher levels of predation pressure, supporting predictions of hump-shaped relationships between predation pressure and prey diversity. In contrast to predation intensity, the impact of predator diversity had both positive (taxa richness) and negative (evenness and phylogenetic distinctiveness) effects on bacterial diversity. Furthermore, predation shaped the structure of bacterial communities. Reduction in top-down control negatively affected the majority of taxa that are generally associated with increased treatment efficiency, compromising particularly the potential for nitrogen removal. Consequently, our findings highlight responses of bacterial diversity and community composition as two distinct mechanisms linking protozoan predation with ecosystem functioning in activated sludge communities.

Temporal variations of Microsporidia diversity and discovery of new host-parasite interactions in a lake ecosystem

Microsporidia are a large group of obligate intracellular eukaryotic parasites related to Fungi. Recent studies suggest that their diversity has been greatly underestimated and little is known about their hosts other than metazoans, and thus about their impact on the communities at the base of the food web. In this work, we therefore studied the diversity of Microsporidia over one year and identified potential new hosts in small-sized fractions (<150 μm) in a lake ecosystem using a metabarcoding approach coupled with co-occurrence networks and tyramide signal amplification-fluorescent in situ hybridization. Our analysis shows a great Microsporidia diversity (1 472 OTUs), with an important part of this diversity being unknown. Temporal variations of this diversity have been observed, which might follow temporal variations of their potential hosts such as protists and microzooplankton. New hosts among them were identified as well as associations with phytoplankton. Indeed, repeated infections were observed in Kellicottia (rotifers) with a prevalence of 38% (infected individuals). Microsporidia inside a Stentor (ciliate) were also observed. Finally, potential infections of the diatom Asterionella were identified (prevalence <0.1%). The microsporidian host spectrum could be therefore even more important than previously described, and their role in the functioning of lake ecosystems is undoubtedly largely unknown.

A Metabarcoding Protocol to Analyze Coastal Planktic Communities Collected by Desalination Plant Filters: From Sampling to Bioinformatic Exploratory Analyses

The temporal dynamics of coastal planktic communities can be disclosed through DNA metabarcoding on the filters of reverse-osmosis desalination plants. Here, we describe the steps that are necessary to process the filters in order to create the subsamples used for DNA extraction and the bioinformatic pipeline to perform the first exploratory analyses on this kind of dataset.

Depth-structuring of multi-kingdom soil communities in agricultural pastures

The biodiversity and structure of deep agricultural soil communities are poorly understood, especially for eukaryotes. Using DNA metabarcoding and co-occurrence networks, we tested whether prokaryote, fungal, protist, and nematode biodiversity declines with increasing depth (0-0.1,  0.3-0.5,  and 1.1-1.7m) in pastoral soil; whether deep soil organisms are subsets of those at the surface; and whether multi-kingdom networks become more interconnected with increasing depth. Depth-related richness declines were observed for almost all detected fungal classes, protist phyla, and nematode orders, but only 13 of 25 prokaryote phyla, of which nine had increasing richness with depth. Deep soil communities were not simply subsets of surface communities, with 3.8%-12.2% of eukaryotes and 13.2% of prokaryotes detected only in the deepest samples. Eukaryotes mainly occurred in the upper soil layers whereas prokaryotes were more evenly distributed across depths. Plant-feeding nematodes were most abundant in top soil, whereas bacteria feeders were more abundant in deep soil. Co-occurrence network structure differences suggested that deep soil communities are concentrated around scarce niches of resource availability, in contrast to more spatially homogenous and abundant resources at the surface. Together, these results demonstrate effects of depth on the composition, distribution, and structure of prokaryote and eukaryote soil communities.

Glacial Ice Age Shapes Microbiome Composition in a Receding Southern European Glacier

Glaciers and their microbiomes are exceptional witnesses of the environmental conditions from remote times. Climate change is threatening mountain glaciers, and especially those found in southern Europe, such as the Monte Perdido Glacier (northern Spain, Central Pyrenees). This study focuses on the reconstruction of the history of microbial communities over time. The microorganisms that inhabit the Monte Perdido Glacier were identified using high-throughput sequencing, and the microbial communities were compared along an altitudinal transect covering most of the preserved ice sequence in the glacier. The results showed that the glacial ice age gradient did shape the diversity of microbial populations, which presented large differences throughout the last 2000 years. Variations in microbial community diversity were influenced by glacial conditions over time (nutrient concentration, chemical composition, and ice age). Some groups were exclusively identified in the oldest samples as the bacterial phyla Fusobacteria and Calditrichaeota, or the eukaryotic class Rhodophyceae. Among groups only found in modern samples, the green sulfur bacteria (phylum Chlorobi) stood out, as well as the bacterial phylum Gemmatimonadetes and the eukaryotic class Tubulinea. A patent impact of human contamination was also observed on the glacier microbiome. The oldest samples, corresponding to the Roman Empire times, were influenced by the beginning of mining exploitation in the Pyrenean area, with the presence of metal-tolerant microorganisms. The most recent samples comprise 600-year-old ancient ice in which current communities are living.

Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing

Nematodes are abundant metazoans that play crucial roles in nutrient recycle in the pedosphere. Although high-throughput amplicon sequencing is a powerful tool for the taxonomic profiling of soil nematodes, polymerase chain reaction (PCR) primers for amplification of the 18S ribosomal RNA (SSU) gene and preparation of template DNAs have not been sufficiently evaluated. We investigated nematode community structure in copse soil using four nematode-specific (regions 1–4) and two universal (regions U1 and U2) primer sets for the SSU gene regions with two DNAs prepared from copse-derived mixed nematodes and whole soil. The major nematode-derived sequence variants (SVs) identified in each region was detected in both template DNAs. Order level taxonomy and feeding type of identified nematode-derived SVs were distantly related between the two DNA preparations, and the region U2 was closely related to region 4 in the non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarity. Thus, the universal primers for region U2 could be used to analyze soil nematode communities. We further applied this method to analyze the nematodes living in two sampling sites of a sweet potato-cultivated field, where the plants were differently growing. The structure of nematode-derived SVs from the two sites was distantly related in the principal coordinate analysis (PCoA) with weighted unifrac distances, suggesting their distinct soil environments. The resultant ecophysiological status of the nematode communities in the copse and field on the basis of feeding behavior and maturity indices was fairly consistent with those of the copse- and the cultivated house garden-derived nematodes in prior studies. These findings will be useful for the DNA metabarcoding of soil eukaryotes, including nematodes, using soil DNAs.

In Vitro Incubations Do Not Reflect In Vivo Differences Based on Ranking of Low and High Methane Emitters in Dairy Cows

This study evaluated if ranking dairy cows as low and high CH₄ emitters using the GreenFeed system (GF) can be replicated in in vitro conditions using an automated gas system and its possible implications in terms of fermentation balance. Seven pairs of low and high emitters fed the same diet were selected on the basis of residual CH₄ production, and rumen fluid taken from each pair incubated separately in the in vitro gas production system. In total, seven in vitro incubations were performed with inoculums taken from low and high CH₄ emitting cows incubated in two substrates differing in forage-to-concentrate proportion, each without or with the addition of cashew nutshell liquid (CNSL) as an inhibitor of CH₄ production. Except for the aimed differences in CH₄ production, no statistical differences were detected among groups of low and high emitters either in in vivo animal performance or rumen fermentation profile prior to the in vitro incubations. The effect of in vivo ranking was poorly replicated in in vitro conditions after 48 h of anaerobic fermentation. Instead, the effects of diet and CNSL were more consistent. The inclusion of 50% barley in the diet (SB) increased both asymptotic gas production by 17.3% and predicted in vivo CH₄ by 26.2%, when compared to 100% grass silage (S) substrate, respectively. The SB diet produced on average more propionate (+28 mmol/mol) and consequently less acetate compared to the S diet. Irrespective of CH₄ emitter group, CNSL decreased predicted in vivo CH₄ (26.7 vs. 11.1 mL/ g of dry matter; DM) and stoichiometric CH₄ (CH₄VFA; 304 vs. 235 moles/mol VFA), with these being also reflected in decreased total gas production per unit of volatile fatty acids (VFA). Microbial structure was assessed on rumen fluid sampled prior to in vitro incubation, by sequencing of the V4 region of 16S rRNA gene. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) did not show any differences between groups. Some differences appeared of relative abundance between groups in some specific OTUs mainly related to Prevotella. Genus Methanobrevibacter represented 93.7 ± 3.33% of the archaeal sequences. There were no clear differences between groups in relative abundance of Methanobrevibacter.

Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.

Improved high throughput protocol for targeting eukaryotic symbionts in metazoan and eDNA samples

Eukaryote symbionts of animals are major drivers of ecosystems not only because of their diversity and host interactions from variable pathogenicity but also through different key roles such as commensalism and to different types of interdependence. However, molecular investigations of metazoan eukaryomes require minimising coamplification of homologous host genes. In this study we (1) identified a previously published “antimetazoan” reverse primer to theoretically enable amplification of a wider range of microeukaryotic symbionts, including more evolutionarily divergent sequence types, (2) evaluated in silico several antimetazoan primer combinations, and (3) optimised the application of the best performing primer pair for high throughput sequencing (HTS) by comparing one‐step and two‐step PCR amplification approaches, testing different annealing temperatures and evaluating the taxonomic profiles produced by HTS and data analysis. The primer combination 574*F – UNonMet_DB tested in silico showed the largest diversity of nonmetazoan sequence types in the SILVA database and was also the shortest available primer combination for broadly‐targeting antimetazoan amplification across the 18S rRNA gene V4 region. We demonstrate that the one‐step PCR approach used for library preparation produces significantly lower proportions of metazoan reads, and a more comprehensive coverage of host‐associated microeukaryote reads than the two‐step approach. Using higher PCR annealing temperatures further increased the proportion of nonmetazoan reads in all sample types tested. The resulting V4 region amplicons were taxonomically informative even when only the forward read is analysed. This region also revealed a diversity of known and putatively parasitic lineages and a wider diversity of host‐associated eukaryotes.

Impact of wastewater on the microbial diversity of periphyton and its tolerance to micropollutants in an engineered flow-through channel system

Wastewater treatment plants (WWTPs) play an important role in retaining organic matter and nutrients but to a lesser extent micropollutants. Therefore, treated wastewater is recognized as a major source of multiple stressors, including complex mixtures of micropollutants. These can potentially affect microbial communities in the receiving water bodies and the ecological functions they provide. In this study, we evaluated in flow-through channels the consequences of an exposure to a mixture of stream water and different percentages of urban WWTP effluent, ranging from 0% to 80%, on the microbial diversity and function of periphyton communities. Assuming that micropollutants exert a selective pressure for tolerant microorganisms within communities, we further examined the periphyton sensitivity to a micropollutant mixture extracted from passive samplers that were immersed in the wastewater effluent. As well, micropollutants in water and in periphyton were comprehensively quantified. Our results show that micropollutants detected in periphyton differed from those found in water, both in term of concentration and composition. Especially photosystem II inhibitors accumulated in periphyton more than other pesticides. Although effects of other substances cannot be excluded, this accumulation may have contributed to the observed higher tolerance of phototrophic communities to micropollutants upon exposure to 30% and 80% of wastewater. On the contrary, no difference in tolerance was observed for heterotrophic communities. Exposure to the gradient of wastewater led to structural differences in both prokaryotic and eukaryotic communities. For instance, the relative abundance of cyanobacteria was higher with increasing percentage of wastewater effluent, whereas the opposite was observed for diatoms. Such results could indicate that differences in community structure do not necessarily lead to higher tolerance. This highlights the need to consider other wastewater constituents such as nutrients and wastewater-derived microorganisms that can modulate community structure and tolerance. By using engineered flow-through channels that mimic to some extent the required field conditions for the development of tolerance in periphyton, our study constitutes a base to investigate the mechanisms underlying the increased tolerance, such as the potential role of microorganisms originating from wastewater effluents, and different treatment options to reduce the micropollutant load in effluents.

Herpes simplex virus 2 (HSV-2) evolves faster in cell culture than HSV-1 by generating greater genetic diversity

Herpes simplex virus type 1 and 2 (HSV-1 and HSV-2, respectively) are prevalent human pathogens of clinical relevance that establish long-life latency in the nervous system. They have been considered, along with the Herpesviridae family, to exhibit a low level of genetic diversity during viral replication. However, the high ability shown by these viruses to rapidly evolve under different selective pressures does not correlates with that presumed genetic stability. High-throughput sequencing has revealed that heterogeneous or plaque-purified populations of both serotypes contain a broad range of genetic diversity, in terms of number and frequency of minor genetic variants, both in vivo and in vitro. This is reminiscent of the quasispecies phenomenon traditionally associated with RNA viruses. Here, by plaque-purification of two selected viral clones of each viral subtype, we reduced the high level of genetic variability found in the original viral stocks, to more genetically homogeneous populations. After having deeply characterized the genetic diversity present in the purified viral clones as a high confidence baseline, we examined the generation of de novo genetic diversity under culture conditions. We found that both serotypes gradually increased the number of de novo minor variants, as well as their frequency, in two different cell types after just five and ten passages. Remarkably, HSV-2 populations displayed a much higher raise of nonconservative de novo minor variants than the HSV-1 counterparts. Most of these minor variants exhibited a very low frequency in the population, increasing their frequency over sequential passages. These new appeared minor variants largely impacted the coding diversity of HSV-2, and we found some genes more prone to harbor higher variability. These data show that herpesviruses generate de novo genetic diversity differentially under equal in vitro culture conditions. This might have contributed to the evolutionary divergence of HSV-1 and HSV-2 adapting to different anatomical niche, boosted by selective pressures found at each epithelial and neuronal tissue.

Herpesviruses are highly human pathogens that establish latency in neurons of the peripheral nervous system. Colonization of nerve endings is required for herpes simplex virus (HSV) persistence and pathogenesis. HSV-1 global prevalence is much higher than HSV-2, in addition to their preferential tendency to infect the oronasal and genital areas, respectively. How these closely related viruses have been adapting and evolving to replicate and colonize these two different anatomical areas remains unclear. Herpesviruses were presumed to mutate much less than viruses with RNA genomes, due to the higher fidelity of the DNA polymerase and proofreading mechanisms when replicating. However, the worldwide accessibility and development of high-throughput sequencing technologies have revealed the heterogenicity and high diversity present in viral populations clinically isolated. Here we show that HSV-2 mutates much faster than HSV-1, when compared under similar and controlled cell culture conditions. This high mutation rate is translated into an increase in coding diversity, since the great majority of these new mutations lead to nonconservative changes in viral proteins. Understanding how herpesviruses differentially mutate under similar selective pressures is critical to prevent resistance to anti-viral drugs.

Development of an ecotoxicological test procedure for soil microalgae

Since the 80s, ISO and OECD organizations have been developing guidelines for assessing the toxicity of new and existing chemical substances to soil biota. Up to now, any of these guidelines had soil algae as test organisms. Nevertheless, microalgae are relevant components of soil microbial communities and soil biological crusts (BSC) with a great contribution to different soil functions and ecosystem services. In an attempt to bridge the gap, the present work aimed to develop, describe and validate a standard operating procedure for an ecotoxicological test with soil microalgae. Three phases were performed, each one with specific objectives. First, soil microalgae and cyanobacteria were isolated from BSC and then genetically and morphologically characterized. The green microalga Micractinium inermum was selected because it is a species with a wide geographic distribution. Secondly, M. inermum growth curves were obtained in liquid (BG₁₁ and Woods-Hole MBL) and solid media (OECD artificial soil) to determine test duration. The growth curves were also used to analyze the reproducibility of the test's endpoint and to propose a validation criterion. Ultimately, a range of concentrations of two reference substances (glyphosate and copper) were tested, both in soil and liquid media, to assess procedure's reproducibility. The tests made in liquid medium followed the standard guideline for ecotoxicological tests with freshwater microalgae and cyanobacteria (OECD 201:2011). The results obtained prove that when the artificial soil is used, as a test substrate, the sensitivity of M. inermum increases. The tests performed with both reference substances demonstrate that the procedure described for testing in soil was reproducible. Additionally, it will be relevant to test with other reference substances and adjust the procedure for natural soils. It will be also interesting to validate the test procedure with soil cyanobacteria.

Inventory of the benthic eukaryotic diversity in the oldest European lake

We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth's systems with eukaryotes in freshwater sediments being among the least known. In this study, we used high-throughput sequencing of the 18S rRNA gene to investigate the entire diversity of benthic eukaryotes in three distinct habitats (littoral sediment and hard substrate, profundal sediment) of Lake Ohrid, the oldest European lake. Eukaryotic sequences were dominated by annelid and arthropod animals (54% of all eukaryotic reads) and protists (Ochrophyta and Ciliophora; together 40% of all reads). Eukaryotic diversity was 15% higher in the deep profundal than on either near-surface hard substrates or littoral sediments. The three habitats differed in their taxonomic and functional community composition. Specifically, heterotrophic organisms accounted for 92% of the reads in the profundal, whereas phototrophs accounted for 43% on the littoral hard substrate. The profundal community was the most homogeneous, and its network was the most complex, suggesting its highest stability among the sampled habitats.

pr2-primers: An 18S rRNA primer database for protists

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR² version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R-based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set (https://app.pr2-primers.org). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.

Combination of long- and short-read sequencing fully resolves complex repeats of herpes simplex virus 2 strain MS complete genome

Herpes simplex virus serotype 2 (HSV-2) is a ubiquitous human pathogen that causes recurrent genital infections and ulcerations. Many HSV-2 strains with different biological properties have been identified, but only the genomes of HSV-2 strains HG52, SD90e and 333 have been reported as complete and fully characterized sequences. We de novo assembled, annotated and manually curated the complete genome sequence of HSV-2 strain MS, a highly neurovirulent strain, originally isolated from a multiple sclerosis patient. We resolved both DNA ends, as well as the complex inverted repeats regions present in HSV genomes, usually undisclosed in previous published partial herpesvirus genomes, using long reads from Pacific Biosciences (PacBio) technology. Additionally, we identified isomeric genomes by determining the alternative relative orientation of unique fragments in the genome of the sequenced viral population. Illumina short-read sequencing was crucial to examine genetic variability, such as nucleotide polymorphisms, insertion/deletions and sequence determinants of strain-specific virulence factors. We used Illumina data to fix two disrupted open reading frames found in coding homopolymers after PacBio assembly. These results support the combination of long- and short-read sequencing technologies as a precise and effective approach for the accurate de novo assembly and curation of complex microbial genomes.

A phylogenetic framework to investigate the microsporidian communities through metabarcoding and its application to lake ecosystems

Microsporidia are obligate intracellular eukaryotic parasites known to parasitize many species of the animal kingdom as well as some protists. However, their diversity is underestimated, in part as a consequence of the failure of 'universal' primers to detect them in metabarcoding studies. Besides, due to the inconsistency between taxonomy and phylogenetic data, available databases may assign incorrectly sequences obtained with high-throughput sequencing. In this work, we developed a comprehensive reference database which positions microsporidian SSU rRNA gene sequences within a coherent ranked phylogenetic framework. We used this phylogenetic framework to study the microsporidian diversity in lacustrine ecosystems, focusing on < 150 μm planktonic size fractions. Our analysis shows a high diversity of Microsporidia, with the identification of 1531 OTUs distributed within seven clades, of which 76% were affiliated to clade IV2 and 20% to clade I (nomenclature presented hereby). About a quarter of the obtained sequences shared less than 85% identity to the closest known species, which might represent undescribed genera or families infecting small hosts. Variations in the abundance of Microsporidia were recorded between the two lakes sampled and across the sampling period, which might be explained by spatio-temporal variations of their potential hosts such as microeukaryotes and metazooplankton.

Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System

Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we present a 3-year outdoor production of mixed consortia of locally adapted microalgae and bacteria in cold temperate latitude. Microalgal consortia were cultivated in flat panel photobioreactors using brackish Baltic Sea water and CO₂ from a cement factory (Degerhamn, Cementa AB, Heidelberg Cement Group) as a sustainable CO₂ source. To evaluate the ability of the microbial consortia to maintain stable biomass production while exposed to seasonal changes in both light and temperature, we tracked changes in the microbial community using molecular methods (16S and 18S rDNA amplicon sequencing) and monitored the biomass production and quality (lipid, protein, and carbohydrate content) over 3 years. Despite changes in environmental conditions, the mixed consortia maintained stable biomass production by alternating between two different predominant green microalgae (Monoraphidium and Mychonastes) with complementary tolerance to temperature. The bacterial population was few taxa co-occured over time and the composition did not have any connection to the shifts in microalgal taxa. We propose that a locally adapted and mixed microalgal consortia, with complementary traits, can be useful for optimizing yield of commercial scale microalgal cultivation.