Biology subjects

Hackl, T.

Publications and source records attributed to Hackl, T..

At least 19 recordsLinked to original sources

bioRxiv2026

An expanded urine culturing workflow to cultivate and characterize diverse urobiome isolates

Despite increased recognition of the diverse resident microbiome of the urinary tract (i.e., the urobiome) in postmenopausal women, the roles and functions of these microbes remain largely unknown. Further empirical research is needed to understand the physiology, interactions, and antibiotic resistance evolution of urobiome members with pathogenic potential. However, experimental work relies on viable, culturable isolates. Standard urine culturing practices are designed for identifying a narrow set of known urinary microbes, and are thus poorly suited for cultivating taxa from the resident urobiome. Here we expand the urine culturing toolkit to reliably recover diverse urobiome taxa for downstream empirical research. Urine samples collected from postmenopausal women with recurrent urinary tract infections were shipped at ambient temperature to a central point for culturing. Microbial viability was maintained using boric acid preservative tubes during multi-day transport of sample aliquots. Selective media incubated under specialized conditions were used to promote recovery of diverse urobiome members, including fastidious taxa. Under 5% CO2 -enriched atmospheric conditions and with longer incubation times, we leveraged a chromogenic agar (UTIC) to further differentiate isolates based on colony color and morphology. We evaluated the workflow for its ability to isolate and characterize urobiome taxa, as determined by morphological differentiation and taxonomic identification. Across 108 urine samples, 6.3 {+/-} 3.2 distinct isolates were recovered, with no detectable relationship between sample shipment duration and isolate richness. On chromogenic agar, colony growth and color intensity was improved with CO2 -enriched atmospheric conditions and extended incubation times. We identified diverse taxa that are typically underrepresented in standard diagnostic culture and provide novel morphological characterizations for members of the genera Actinotignum, Aerococcus, Facklamia, Lactobacillus, Latilactobacillus, Limosilactobacillus, and Streptococcus species, which have not been previously described on UTIC chromogenic agar. Using this novel workflow, we recovered a diverse collection of urobiome isolates from urine samples shipped over multiple days. We also demonstrated the utility of a chromogenic agar for the visual differentiation of key urobiome taxa. While sequencing approaches have enhanced our understanding of urobiome composition, culturing is needed to investigate microbial interactions, virulence mechanisms, and antimicrobial susceptibility. This protocol adds to the growing toolkit for the cultivation of diverse urobiome isolates needed to support downstream empirical studies and advance urinary tract infection research.

microbiology↗

bioRxiv2026

A Tripartite Co-culture System Reveals Defensive Mutualism Between a Nanobdellati Symbiont and Its Host

Archaeal symbioses remain among the least understood cellular interactions. Ultra-small Nanobdellati (initially called DPANN) archaea rely on larger hosts for survival, yet their effects on host eco-physiology and their interactions with infecting viruses have not yet been examined experimentally. Here, we established the first stable tripartite co-culture comprising a Nanobdellales symbiont (YN4), its archaeal host (YN4HA), and a virus (MTIV4). We analyzed this system using physiological, genomic, transcriptomic, glycoproteomic, and cryo-electron tomography (cryoET) approaches. CryoET analysis revealed that the Nanobdellales archaeon formed cone-like structures to contact the host, as has been observed in other Nanobdellati-host systems. In this system, the host is infected by the virus. The Nanobdellales archaeon mitigated virus-induced growth inhibition of the host without any detectable fitness cost, indicating a defensive mutualism rather than a strictly parasitic relationship. This protective effect may involve Nanobdellati-driven remodeling of host cell surface glycans, suggesting a previously unrecognized glycan-mediated defense strategy. Overall, our tripartite system provides new insight into complex archaeal interactions in extreme environments that cannot be captured through conventional binary co-culture systems.

microbiology↗

bioRxiv2025

Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific

Giant DNA viruses are ubiquitous among unicellular eukaryotes and occur in marine, freshwater, and terrestrial environments. Despite intense metagenomic data mining, their strain-level diversity remains largely unexplored. Here we introduce a model system comprising four isolates of a giant virus called ChlorV, which infects marine microalgae of the class Chlorarachniophyceae (Rhizaria) from station ALOHA, Hawaii. The ChlorV genomes are 469 kbp to 493 kbp long and encode approximately 400 proteins, at least 106 of which are present n purified virions. Although the four viral genomes are highly syntenic, they differ by several insertions and deletions that often encode methyltransferases. Interestingly, we found that some of these methyltransferase genes correlated with specific DNA methylation patterns in the ChlorV strain Our study describes the first giant viruses infecting the eukaryotic supergroup Rhizaria and demonstrates how viral strain-level variation in gene content and epigenetic features may affect eco-evolutionary processes in marine microalgae.

microbiology↗

bioRxiv2025

Genomic insights into antiviral defense systems in haloarchaea and their impact on virus susceptibility

The ongoing evolutionary arm race between archaea and their viruses has led to the development of diverse defense systems against viruses. While recent computational approaches have uncovered many bacterial antiviral defense systems, the viral infection strategies and antiviral responses of archaea remain poorly explored. In this study, we identified antiviral defense systems encoded in the genomes of 20 recently sequenced haloarchaeal strains. These systems were found to be representative of the broader repertoire of defense systems present across all 253 complete sequenced Halobacteria (class) genomes in the RefSeq database. Detailed analysis showed that these haloarchaea usually harbor multiple different defense systems, with a particularly high abundance of uncharacterized predicted defense systems against viruses (Phage Defense Candidates (PDCs)). To further explore the impact of anti-viral defense mechanisms on host range, an extensive virus-host pair screening was performed using a panel of known virulent viruses. By correlating the genomic defense profiles with observed viral infectivity and adsorption profiles, a weak correlation between the number of encoded defense systems and viral susceptibility was detected. Specifically, hosts infected by fewer viruses tended to encode a broader repertoire of antiviral defense systems, whereas those with fewer defense systems were frequently infected. It was found that the host range of haloarchaeal viruses is majorly determined by the availability of viral receptors, whereas the presence of anti-viral defense systems plays a smaller but significant role. These findings offer valuable insights into the evolutionary pressure shaping archaeal antiviral strategies and lay the groundwork for future functional studies of archaeal defense systems. ImportanceArchaeal viruses are understudied, compared to viruses infecting bacteria and eukaryotes. Haloarchaea have evolved as model organisms for the study of virus-host interaction in archaea, as they harbor the highest number of isolated archaeal viruses. Salt-loving haloarchaea dominate microbial communities in hypersaline environments, where they face constant viral threats. To survive, they have evolved a diverse array of antiviral defense systems. Until now, the relevance of these defense systems for susceptibility to viruses had not been tested in archaea. The findings of this study show that strains with a broader repertoire of defense systems tend to be less susceptible to viral infection, while those with fewer systems are more frequently targeted, suggesting an advantage for the accumulation of different defense systems. In addition, it was found that the major determinant of host range is the availability of viral receptors on the host cell. These insights provide a foundation for future research into the molecular mechanisms and ecological roles of archaeal defense systems.

microbiology↗

bioRxiv2025

Curated high-quality genomes of 39 diverse halophilic archaea

Archaea are widespread and ecologically important microorganisms, yet our understanding of their physiology and evolution is constrained by the limited number of complete genome assemblies available. Haloarchaea have emerged as model organisms for archaeal cell biology, virus-host interactions, and biotechnology. Despite their prominence in hypersaline environments and their potential for industrial applications, high-quality reference genomes remain scarce. Here, we present chromosome-level assemblies for 39 cultivable haloarchaeal strains for which no complete genomes were previously available. Using Oxford Nanopore sequencing, we obtained near-complete assemblies, with 38 strains resolving into single closed chromosomes and additional replicons such as plasmids captured largely in full. These genomes expand the available genomic resources for five haloarchaeal genera and provide a framework for comparative analyses of archaeal metabolism, genome organization, and mobile genetic elements. Given that many of these strains are natural hosts to diverse archaeal viruses, the genomes also represent a critical resource for advancing studies of virus-host interactions in archaea. Beyond fundamental insights into archaeal cell biology and evolution, this dataset will support the development of haloarchaeal model systems and facilitate the exploration of their biomolecules for biotechnological applications.

microbiology↗

bioRxiv2025

De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing

Invasive species are rapidly reshaping aquatic ecosystems worldwide at an accelerating pace, with profound ecological and economic impacts. Many crustacean species have demonstrated invasive potential or are already well-established invaders. The green shore crab, Carcinus maenas, native to Europe and North Africa, is one of the most successful global marine invaders and is now present on six continents. Although the role of genomics in invasion science is increasingly recognized, genomic resources for brachyuran crabs remain limited, including the notable absence of a reference genome for C. maenas. Here we report on a de novo whole genome assembly of C. maenas via long-read Oxford Nanopore Technology sequencing. The assembly spans 1.09 Gbp across 21,887 scaffolds (N50 = 15 Mbp) with a BUSCO completeness of 98.4%, providing a high-quality resource for future genomic analyses. Additionally, we provide a detailed protocol for obtaining high-quality DNA to successfully sequence brachyuran crabs using a long-read approach, including strategies to address nanopore blockage issues. This new resource expands available genomic data for the species-rich infraorder Brachyura, and provides a valuable foundation for understanding the genetic factors underlying the global invasion success of C. maenas, supporting future research in marine invasion genomics.

genomics↗

bioRxiv2025

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution

Background and objectivesAntimicrobial resistance is a major global health threat, driven in part by the rapid evolution of resistance in pathogens, which undermines the effectiveness of antimicrobial treatment. In infections, pathogens rarely live in a well-mixed, single species environment. It is an open question how microbial interactions in contrasting environmental structures affect plasmid mediated antibiotic resistance evolution. MethodologyThis study investigates how a spatially structured versus a well-mixed liquid environment, together with microbial interactions, affect antibiotic resistance evolution in uropathogenic Escherichia coli. We conducted a serial transfer experiment under increasing concentrations of trimethoprim-sulfamethoxazole comparing resistance evolution in the well-mixed and spatially structured environments, both in the presence and absence of a polymicrobial community. ResultsOur results revealed that E. coli in community context displayed parallel evolutionary trajectories, leading to higher final antibiotic tolerance, while the spatial structure allowed for prolonged resistance evolution. Copy number variation of the plasmid-borne resistance locus varied significantly across conditions; E. coli evolved in the well-mixed, monoculture conditions, exhibited the greatest increases in copy number, whereas lineages evolved in the presence of the community showed minimal changes relative to the ancestor. Conclusions and implicationsThese findings underscore the complex interplay between the genetic basis of resistance, the environmental structure and microbial ecology in shaping plasmid-mediated antimicrobial resistance evolution. Lay summaryAntibiotic resistance depends on environmental context, microbial interactions, and genetics. This study shows that E. coli evolved resistance differently in mixed versus structured environments, with changes in plasmid-borne resistance gene copy number. Community interactions led to similar evolutionary paths and higher tolerance, while well-mixed, single-species conditions drove larger genetic changes.

microbiology↗

bioRxiv2024

Effective metabarcoding of endophytic fungi through host-exclusive primer design for nanopore long-read sequencing

Metabarcoding is a powerful tool to simultaneously identify multiple taxa within a habitat. However, its application to host-associated microbiomes is challenged by substantial co-amplification of host DNA. Here we developed a host-exclusive primer design workflow, to selectively generate amplicons from target taxa while excluding the host. This workflow is centered around a new computational tool, mbc-prime, that can generate a list of discriminative candidate primers and score them. We showcase the use of this tool in the design of primers for long-read metabarcoding of endophytic fungi in Vinca minor. Mbc-prime streamlines the design of fungus-specific primers, enabling efficient and plant-free amplification of fungal rDNA from mixed DNA samples. Our workflow can be used to study the composition of complex host-associated microbiomes. It should be universally applicable for the design of discriminative primers in a user-friendly and practical manner and thus be of use for various researchers in microbiome research.

molecular biology↗

bioRxiv2024

Unravelling the functional diversity of type III polyketide synthases in fungi

Type III polyketide synthases (T3PKSs) are enzymes that produce diverse compounds of ecological and clinical importance. While well-studied in plants and bacteria, only a handful of T3PKSs from fungi have been characterised to date. Here, we developed a comprehensive workflow for kingdom-wide characterisation of T3PKSs. Using publicly available genomes, we mined more than 1000 putative enzymes and analysed their active site architecture and genomic neighbourhood. From there, we selected 37 representative PKS candidates for cell-free expression and prototyping with a diverse set of Coenzyme A activated substrates, revealing unique patterns in substrate and cyclisation specificity, as well as the preferred number of malonyl-Coenzyme A extensions. Using the 341 enzyme-substrate pairs generated in this study, we trained a machine learning model to predict T3PKS substrate specificity and experimentally validated it with an extended panel of non-natural substrates. We anticipate that the model will be useful for in silico screening of T3PKSs, while the insight into the product scope of these enzymes offers interesting starting points for further exploration.

biochemistry↗

bioRxiv2024

detectEVE: fast, sensitive and precise detection of endogenous viral elements in genomic data

SummaryEndogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs due to their genomic integration during their life cycle, however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr)EVEs. Detecting nrEVEs poses challenges due to their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, due to its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs. Availability and ImplementationdetectEVE is implemented as snakemake workflow, available with detailed documentation at https://github.com/thackl/detectEVE and can be easily installed using conda.

bioinformatics↗

bioRxiv2023

Novel isolates expand the physiological diversity of Prochlorococcus and illuminate its macroevolution

Prochlorococcus is a diverse picocyanobacterial genus and the most abundant phototroph on Earth. Its photosynthetic diversity divides it into high- or low-light adapted groups representing broad phylogenetic grades - each composed of several monophyletic clades. Here we physiologically characterize four new Prochlorococcus strains isolated from below the deep chlorophyll maximum in the North Pacific Ocean and combine this information with genomic and evolutionary analyses. The isolates belong to deeply-branching low-light adapted clades that have no other cultivated representatives and display some unusual characteristics. For example, despite its otherwise low-light adapted physiological characteristics, strain MIT1223 has low chl b2 content similar to high-light adapted strains. Isolate genomes revealed that each strain contains a unique arsenal of pigment biosynthesis and binding alleles that have been horizontally acquired, contributing to the observed physiological diversity. Comparative genomic analysis of all picocyanobacteria reveals that Pcb, the major pigment carrying protein in Prochlorococcus, greatly increased in copy number and diversity per genome along a branch that coincides with the loss of facultative particle attachment. Collectively, these observations add support to the current macroevolutionary model of picocyanobacteria, where niche constructing radiations allowed ancestral lineages to transition from a particle-attached to planktonic lifestyle and broadly colonize the water column, followed by adaptive radiations near the surface that pushed ancestral lineages deeper in the euphotic zone resulting in modern depth-abundance profiles. Originality-Significance StatementThe marine cyanobacterium, Prochlorococcus, is among the Earths most abundant organisms, and much of its genetic and physiological diversity remains uncharacterized. While field studies help reveal the scope of diversity, cultured isolates allow us to link genomic potential to physiological processes, illuminate eco-evolutionary feedbacks, and test theories arising from comparative genomics of wild cells. Here, we report the isolation and characterization of novel low-light (LL) adapted Prochlorococcus strains that fill in multiple evolutionary gaps. These new strains are the first cultivated representatives of the LLVII and LLVIII paraphyletic grades of Prochlorococcus, which are broadly distributed in the lower regions of the ocean euphotic zone. Each of these grades is a unique, highly diverse section of the Prochlorococcus tree that separates distinct ecological groups: the LLVII grade branches between monophyletic clades that have facultatively particle-associated and constitutively planktonic lifestyles, while the LLVIII grade lies along the branch that leads to all high-light (HL) adapted clades. Characterizing strains and genomes from these grades yields insights into the large-scale evolution of Prochlorococcus. The new LLVII and LLVIII strains are adapted to growth at very low irradiance levels and possess unique light-harvesting gene signatures and pigmentation. The LLVII strains represent the most basal Prochlorococcus group with a major expansion in photosynthetic antenna genes. Further, a strain from the LLVIII grade challenges the paradigm that all LL-adapted Prochlorococcus exhibit high ratios of chl b:a2. These findings provide insights into major transitions in Prochlorococcus evolution, from the benthos to a fully planktonic lifestyle and from growth at low irradiances to the rise of the HL-adapted clades that dominate the modern ocean.

microbiology↗

bioRxiv2023

Diverse rhizosphere-associated Pseudomonas genomes isolated along the marine-terrestrial transition zone of a Wadden island salt march

Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would not only advance our understanding of Pseudomonas role in natural soil ecosystems but also provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.

genomics↗

bioRxiv2023

Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites

BackgroundFilamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified as Anthostomella pinea. The fungus belongs to a complex polyphyletic genus in the family of Xylariaceae, which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that, Anthostomella is largely understudied and only two species have been fully sequenced and characterized at a genomic level. ResultsIn this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome of A. pinea encodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti-Gram-positive effect of the extracts that we observed in antibacterial plate assays. ConclusionsTaken together, our results provide a first glimpse into the potential of Anthstomella pinea to provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites.

microbiology↗

bioRxiv2023

Community coalescence altered the potential of horizontal gene transfers within the native soil microbiome

Microbial community coalescence, which refers to the mixing of microbial communities, frequently shapes the assemblage of soil microbiomes in natural ecosystems. It can exert selective pressure on the coalescent taxa, leading to ecological changes in microbial community structure or microbial evolutionary changes via horizontal gene transfer (HGT). However, the influence of community coalescence on the potential of HGTs within native communities, particularly in soil ecosystems, remains poorly understood. Here, we experimentally quantified the potential evolutionary consequences of soil coalescence. We achieved that by subjecting microcosms containing natural soil to invasion by several microbial communities and profiling mobile genetic elements (MGEs) and adaptive genes of microbial communities up to 60 days after coalescence. Our findings revealed both specific and common responses of MGEs to coalescences over time. Specific effects differed across invasive communities and were particularly pronounced in the early stages. Common effects were associated with an increased abundance of insertion sequences (ISs) across different treatments, suggesting that ISs played a crucial role in promoting diversification at the community level. In summary, we showed that changing MGE profiles are an intrinsic response of the soil microbial community to coalescence-imposed pressure. Our study provides new insights into the modulation of adaptability in soil microbial communities by utilizing community coalescences to address global challenges.

ecology↗

bioRxiv2023

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs or exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key to enhancing our ability to capture the full spectrum of viral diversity.

microbiology↗

bioRxiv2022

Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle

Marine picocyanobacteria (Prochlorococcus and Synechococcus), the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, we find that genes for breaking down chitin - an abundant source of organic carbon that primarily exists as particles - are widespread in this group. We further show that cells with a chitin degradation pathway display chitin degradation activity, attach to chitin particles and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated form of chitin. Marine chitin is largely derived from arthropods, whose roots lie in the early Phanerozoic, 520-535 million years ago, close to when marine picocyanobacteria began colonizing the ocean. We postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Transitioning to a constitutive planktonic life without chitin associations along a major early branch within the Prochlorococcus tree led to cellular and genomic streamlining. Our work highlights how coevolution across trophic levels creates metabolic opportunities and drives biospheric expansions.

ecology↗

bioRxiv2021

Siderophores as an iron source for Prochlorococcus in deep chlorophyll maximum layers of the oligotrophic ocean

Prochlorococcus is one of the most abundant photosynthesizing organisms in the oligotrophic oceans. Gene content variation among Prochlorococcus populations in separate ocean basins often mirrors the selective pressures imposed by the regions distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in low-light adapted Prochlorococcus populations from iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower iron flux). Prochlorococcus siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, particularly at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of Prochlorococcus.

ecology↗

bioRxiv2021

proovframe: frameshift-correction for long-read (meta)genomics

Long-read sequencing technologies hold big promises for the genomic analysis of complex samples such as microbial communities. Yet, despite improving accuracy, basic gene prediction on long-read data is still often impaired by frameshifts resulting from small indels. Consensus polishing using either complementary short reads or to a lesser extent the long reads themselves can mitigate this effect but requires universally high sequencing depth, which is difficult to achieve in complex samples where the majority of community members are rare. Here we present proovframe, a software implementing an alternative approach to overcome frameshift errors in long-read assemblies and raw long reads. We utilize protein-to-nucleotide alignments against reference databases to pinpoint indels in contigs or reads and correct them by deleting or inserting 1-2 bases, thereby conservatively restoring reading-frame fidelity in aligned regions. Using simulated and real-world benchmark data we show that proovframe performs comparably to short-read-based polishing on assembled data, works well with remote protein homologs, and can even be applied to raw reads directly. Together, our results demonstrate that protein-guided frameshift correction significantly improves the analyzability of long-read data both in combination with and as an alternative to common polishing strategies. Proovframe is available from https://github.com/thackl/proovframe.

bioinformatics↗