Marine viruses disperse bidirectionally along the natural water cycle.

Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.

A predicted CRISPR-mediated symbiosis between uncultivated archaea.

CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.

Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.

Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.

Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea.

Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition.

Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.

uBin: A manual refining tool for genomes from metagenomes.

Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high-quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public databases. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was additionally designed for educational purposes. When applied to the public CAMI dataset, refinement of bins using GC content, coverage and taxonomy was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate the active proliferation of microbes in Earth's lower orbit. uBin is an easy to instal software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software and its helper scripts are open source and available under https://github.com/ProbstLab/uBin.

Action-effect knowledge transfers to similar effect stimuli.

The ability to anticipate the sensory consequences of our actions (i.e., action-effects) is known to be important for intentional action initiation and control. Learned action-effects can select the responses that previously have been associated with them. What has been largely unexplored is how learned action-effect associations can aid action selection for effects that have not previously associated with an action but are similar to learned effects. In two studies, we aimed to show that when presented new, unknown action-effects, participants select the responses that have previously been associated with similar action-effects. In the first study (n = 27), action-effect similarity was operationalized via stimuli belonging to the same or different categories as the previously learned action-effects. In the second study (n = 31), action-effect similarity was realized via stimuli that require comparable motor responses in real life. Participants first learned that specific responses are followed by specific visual effect stimuli. In the test phase, learned effect stimuli, new but similar effect stimuli and new but dissimilar effect stimuli were presented ahead of the response. The findings revealed that both learned effect stimuli and new similar effect stimuli affected response times, whereas new dissimilar effects did not. When a learned or a new similar effect was followed by a learned response, compared to an unlearned response, the responses were faster. We interpret these findings in terms of action-effect learning. The action-effect once bound to an action is used to select an action if a similar effect for which no action has been learned yet is presented. However, it is noteworthy that, due to our design, other explanations for the found transfer are conceivable. We address these limitations in the General Discussion.

High fluency can improve recognition sensitivity based on learned metacognitive expectations.

Fluency of processing has shown to influence recognition judgments. Fluency most commonly induces a liberal response bias to judge fluently processed information as well-known because knowledge of a high correlation between the frequency of encounters, memory strength, and thus fluency of processing has been acquired in the past. In this study, we aimed to show that high fluency can increase recognition judgment sensitivity as well if the participants had encountered fluent and non-fluent processing during training. Thirty-three participants have been trained with a 12-element sequence in a serial reaction time task. During training, the response stimulus interval alternated block-wise between constant (fluent) and variable (non-fluent). Participants showed a higher capability of discriminating between old and new test sequences under fluent than under non-fluent test conditions. Furthermore, participants did not show any liberal or conservative bias after they have been trained with alternating fluency.

Label-Free Raman Microspectroscopy for Identifying Prokaryotic Virocells.

Raman microspectroscopy has been used to thoroughly assess growth dynamics and heterogeneity of prokaryotic cells, yet little is known about how the chemistry of individual cells changes during infection with virulent viruses, resulting in so-called virocells. Here, we investigate biochemical changes of bacterial and archaeal cells of three different species in laboratory cultures before and after addition of their respective viruses using single-cell Raman microspectroscopy. By applying multivariate statistics, we identified significant differences in the spectra of single cells with/without addition of virulent dsRNA phage (phi6) for Pseudomonas syringae. A general ratio of wavenumbers that contributed the greatest differences in the recorded spectra was defined as an indicator for virocells. Based on reference spectra, this difference is likely attributable to an increase in nucleic acid versus protein ratio of virocells. This method also proved successful for identification of Bacillus subtilis cells infected with the double-stranded DNA (dsDNA) phage phi29, displaying a decrease in respective ratio, but failed for archaeal virocells (Methanosarcina mazei with the dsDNA methanosarcina spherical virus) due to autofluorescence. Multivariate and univariate analyses suggest that Raman spectral data of infected cells can also be used to explore the complex biology behind viral infections of bacteria. Using this method, we confirmed the previously described two-stage infection of P. syringae's phi6 and that infection of B. subtilis with phi29 results in a stress response within single cells. We conclude that Raman microspectroscopy is a promising tool for chemical identification of Gram-positive and Gram-negative virocells undergoing infection with virulent DNA or RNA viruses. IMPORTANCE Viruses are highly diverse biological entities shaping many ecosystems across Earth. However, understanding the infection of individual microbial cells and the related biochemical changes remains limited. Using Raman microspectroscopy in conjunction with univariate and multivariate statistics, we established a marker for identification of infected Gram-positive and Gram-negative bacteria. This nondestructive, label-free analytical method at single-cell resolution paves the way for future studies geared towards analyzing virus-host systems of prokaryotes to further understand the complex chemistry and function of virocells.

What triggers explicit awareness in implicit sequence learning? Implications from theories of consciousness.

This article aims to continue the debate on how explicit, conscious knowledge can arise in an implicit learning situation. We review hitherto existing theoretical views and evaluate their compatibility with two current, successful scientific concepts of consciousness: The Global Workspace Theory and Higher-Order Thought Theories. In this context, we introduce the Unexpected Event Hypothesis (Frensch et al., Attention and implicit learning, John Benjamins Publishing Company, 2003) in an elaborated form and discuss its advantage in explaining the emergence of conscious knowledge in an implicit learning situation.

The interplay between unexpected events and behavior in the development of explicit knowledge in implicit sequence learning.

Some studies in implicit learning investigate the mechanisms by which implicitly acquired knowledge (e.g., learning a sequence of responses) becomes consciously aware. It has been suggested that unexpected changes in the own behavior can trigger search processes, of which the outcome then becomes aware. A consistent empirical finding is that participants who develop explicit knowledge show a sudden decrease in reaction times, when responding to sequential events. This so called RT-drop might indicate the point of time when explicit knowledge occurs. We investigated whether an RT-drop is a precursor for the development of explicit knowledge or the consequence of explicit knowledge. To answer this question, we manipulated in a serial reaction time task the timing of long and short stimulus-onset asynchronies (SOA). For some participants, the different SOAs were presented in blocks of either long or short SOAs, while for others, the SOAs changed randomly. We expected the participants who were given a blocked presentation to express an RT-drop because of the predictable timing. In contrast, randomly changing SOAs should hamper the expression of an RT-drop. We found that more participants in the blocked-SOA condition than in the random-SOA condition showed an RT-drop. Furthermore, the amount of explicit knowledge did not differ between the two conditions. The findings suggest that the RT-drop does not seem to be a presupposition to develop explicit knowledge. Rather, it seems that the RT-drop indicates a behavioral strategy shift as a consequence of explicit knowledge.

Virus-associated organosulfur metabolism in human and environmental systems.

Viruses influence the fate of nutrients and human health by killing microorganisms and altering metabolic processes. Organosulfur metabolism and biologically derived hydrogen sulfide play dynamic roles in manifestation of diseases, infrastructure degradation, and essential biological processes. Although microbial organosulfur metabolism is well studied, the role of viruses in organosulfur metabolism is unknown. Here, we report the discovery of 39 gene families involved in organosulfur metabolism encoded by 3,749 viruses from diverse ecosystems, including human microbiomes. The viruses infect organisms from all three domains of life. Six gene families encode for enzymes that degrade organosulfur compounds into sulfide, whereas others manipulate organosulfur compounds and may influence sulfide production. We show that viral metabolic genes encode key enzymatic domains, are translated into protein, and are maintained after recombination, and sulfide provides a fitness advantage to viruses. Our results reveal viruses as drivers of organosulfur metabolism with important implications for human and environmental health.

Lytic archaeal viruses infect abundant primary producers in Earth's crust.

The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

Feature codes in implicit sequence learning: perceived stimulus locations transfer to motor response locations.

An important question in implicit sequence learning research is how the learned information is represented. In earlier models, the representations underlying implicit learning were viewed as being either purely motor or perceptual. These different conceptions were later integrated by multidimensional models such as the Dual System Model of Keele et al. (Psychol Rev 110(2):316-339, 2003). According to this model, different types of sequential information can be learned in parallel, as long as each sequence comprised only one single dimension (e.g., shapes, colors, or response locations). The term dimension, though, is underspecified as it remains an open question whether the involved learning modules are restricted to motor or to perceptual information. This study aims to show that the modules of the implicit learning system are not specific to motor or perceptual processing. Rather, each module processes an abstract feature code which represents both response- and perception-related information. In two experiments, we showed that perceiving a stimulus-location sequence transferred to a motor response-location sequence. This result shows that the mere perception of a sequential feature automatically leads to an activation of the respective motor feature, supporting the notion of abstract feature codes being the basic modules of the implicit learning system. This result could only be obtained, though, when the task instructions emphasized the encoding of the stimulus-locations as opposed to an encoding of the color features. This limitation will be discussed taking into account the importance of the instructed task set.

Action-effects enhance explicit sequential learning.

Different studies have shown that action-effect associations seem to enhance implicit learning of motor sequences. In a recent study (Haider et al., Conscious Cognit 26:145-161, 2014), we found indications that action-effect learning might play a special role in acquiring explicit knowledge within an implicit learning situation. The current study aims at directly manipulating the action-effect contingencies in a Serial Reaction Time Task and examining its impact on explicit sequence knowledge. For this purpose, we created a situation in which the participants' responses led to a melodic tone sequence. For one group, these effect tones were contingently bound to the sequential responses and immediately followed the key press; for the second group, the tones were delayed by 400 ms. For a third group, the tones also followed the response immediately and resulted in the same melody but were not contingently bound to the responses. A fourth control group received no effect tones at all. Only the group that experienced contingent effect tones that directly followed the response showed an increase in explicit sequence knowledge. The results are discussed in terms of the multi-modal structure of action-effect associations and the ideomotor principle of action control.

The Emergence of Explicit Knowledge in a Serial Reaction Time Task: The Role of Experienced Fluency and Strength of Representation.

The Serial Reaction Time Task (SRTT) is an important paradigm to study the properties of unconscious learning processes. One specifically interesting and still controversially discussed topic are the conditions under which unconsciously acquired knowledge becomes conscious knowledge. The different assumptions about the underlying mechanisms can contrastively be separated into two accounts: single system views in which the strengthening of associative weights throughout training gradually turns implicit knowledge into explicit knowledge, and dual system views in which implicit knowledge itself does not become conscious. Rather, it requires a second process which detects changes in performance and is able to acquire conscious knowledge. In a series of three experiments, we manipulated the arrangement of sequential and deviant trials. In an SRTT training, participants either received mini-blocks of sequential trials followed by mini-blocks of deviant trials (22 trials each) or they received sequential and deviant trials mixed randomly. Importantly the number of correct and deviant transitions was the same for both conditions. Experiment 1 showed that both conditions acquired a comparable amount of implicit knowledge, expressed in different test tasks. Experiment 2 further demonstrated that both conditions differed in their subjectively experienced fluency of the task, with more fluency experienced when trained with mini-blocks. Lastly, Experiment 3 revealed that the participants trained with longer mini-blocks of sequential and deviant material developed more explicit knowledge. Results are discussed regarding their compatibility with different assumptions about the emergence of explicit knowledge in an implicit learning situation, especially with respect to the role of metacognitive judgements and more specifically the Unexpected-Event Hypothesis.

Abstract feature codes: The building blocks of the implicit learning system.

According to the Theory of Event Coding (TEC; Hommel, Müsseler, Aschersleben, & Prinz, 2001), action and perception are represented in a shared format in the cognitive system by means of feature codes. In implicit sequence learning research, it is still common to make a conceptual difference between independent motor and perceptual sequences. This supposedly independent learning takes place in encapsulated modules (Keele, Ivry, Mayr, Hazeltine, & Heuer 2003) that process information along single dimensions. These dimensions have remained underspecified so far. It is especially not clear whether stimulus and response characteristics are processed in separate modules. Here, we suggest that feature dimensions as they are described in the TEC should be viewed as the basic content of modules of implicit learning. This means that the modules process all stimulus and response information related to certain feature dimensions of the perceptual environment. In 3 experiments, we investigated by means of a serial reaction time task the nature of the basic units of implicit learning. As a test case, we used stimulus location sequence learning. The results show that a stimulus location sequence and a response location sequence cannot be learned without interference (Experiment 2) unless one of the sequences can be coded via an alternative, nonspatial dimension (Experiment 3). These results support the notion that spatial location is one module of the implicit learning system and, consequently, that there are no separate processing units for stimulus versus response locations. (PsycINFO Database Record

Implicit visual learning: how the task set modulates learning by determining the stimulus-response binding.

Implicit learning is one of the most fundamental learning mechanisms that enables humans to adapt to regularities inherent in the environment. Despite its high flexibility, it depends on constraints, such as selective attention. Here, we focused on the stimulus-to-response binding which defines the dimensions of the stimuli and the responses participants attend to. In a serial reaction time task with a visual sequence, we investigated whether this stimulus-response binding influences the amount of sequence learning. The results of Experiments 1 and 2 showed that visual sequence learning is reduced when participants do not attend to the relevant response dimension. Furthermore, the findings of Experiment 3 suggest that attention to the relevant response dimension increased the development of explicit knowledge without affecting implicit knowledge. This latter finding is difficult to reconcile with the assumption that explicit learning results from the gradual strengthening of sequence representations.