A deep learning–based score to evaluate multiple sequence alignments

Abstract. Multiple sequence alignment (MSA) inference is a central task in molecular evolution and comparative genomics, and the reliability of downstream

dx.doi.org

Fructophilic lactic acid bacteria as a window into multi-scale convergent evolution

Fructophilic lactic acid bacteria (FLAB) are a group of lactic acid bacteria with unique growth characteristics, that is, poor growth on glucose. Thei…

sciencedirect.com

Oxic Subseafloor Microbial Communities Retain Anabolic Capacity under both Oxic and Oxygen-depleted Conditions

Access full-text academic articles: J-STAGE is an online platform for Japanese academic journals.

jstage.jst.go.jp

Phage terminase recognition by the bacterial immune sensors Avs2 and Upx - Nature Communications

Direct recognition of viral proteins is key to bacterial immunity. Here, Evans et al. uncover the mechanisms used by two distinct defense proteins to detect the phage DNA packaging motor mechanisms: bridging ATP ligand or binding an unfolded state.

nature.com

Dynamic balance of CRISPR-Cas immunity and resistance plasmid anti-immunity mediated by a bifunctional protein AcrIE10 - Nature Communications

The transmission of plasmids represents a key mechanism for antimicrobial resistance. Here, authors show AcrIE10 inhibits bacterial CRISPR immunity and dynamically regulates self-expression, balancing host immunity and plasmid anti-defense.

nature.com

grafify online: A web app for graphing and statistical analysis

Creating accurate graphs and performing statistical analyses can be challenging for those who lack coding experience. This Community Page introduces grafify online, a free, browser-based app for generating publication-quality graphs and performing statistical tests and post-hoc comparisons.

journals.plos.org

The Origins and Evolution of the RNA Virome in Land Flora

By mining transcriptomes and genomes across 2,402 species, this study discovered ∼35,000 plant-associated RNA viruses, substantially expanding the known plant virosphere. Phylogenomic analyses reveal that plant viruses emerged on numerous independent occasions, primarily driven by horizontal virus transfer from invertebrates and fungi within the holobiont.

cell.com

Fast remote nucleotide sequence alignment with Riboseek

Structure prediction has reached RNA, where generating deep alignments is now the bottleneck. We developed Riboseek, a search and alignment tool for RNA and DNA that represents sequences as overlapping di-mers. Riboseek is more sensitive for homology detection than BLASTN and nhmmer, and generates alignments 250- and 376-fold faster than nhmmer and rMSA. With structure-aware realignment, it approaches rMSA's base-pair recovery, while remaining 29-fold faster. We provide a web server and 1.7 million precomputed alignments for putatively structured RNAs. Riboseek is freely available at https://github.com/steineggerlab/riboseek. ### Competing Interest Statement M.S. acknowledges outside interest in Stylus Medicine. National Research Foundation of Korea, https://ror.org/013aysd81, RS-2024-00396026, RS-2025- 00438101, RS-2026-25549295, RS-2026- 25515455 Novo Nordisk Foundation, NNF24SA0092560

biorxiv.org

Convection injects labile particulate organic carbon to the deep ocean

Autonomous ocean robots and models reveal deep convection as a major pathway for the export of fresh organic carbon.

science.org

Cpf1(Cas12a)-based genome editing in the filamentous cyanobacterium Nostoc punctiforme

The filamentous cyanobacterium Nostoc punctiforme is a key model organism used to study several aspects of cyanobacterial biology, including development, nitrogen-fixing symbioses with plants, and secondary metabolites, among others. While N. punctiforme is amenable to genetic manipulation, traditional approaches for the generation of mutant strains using homologous recombination are slow, requiring prolonged outgrowth under antibiotic selection to ensure isogenic mutant populations. CRISPR-based genome editing using Cpf1 (Cas12a) was recently shown to be an effective means of rapid generation of isogenic mutants in several cyanobacteria. In this study, Cpf1-based genome editing tools were developed for N. punctiforme. A total of 19 unmarked, in-frame deletion mutants were successfully constructed using Cpf1-targeted cleavage along with homology directed repair (HDR). The length of the homology arms (HAs) on the homologous repair template (HRT) used for HDR was found to be a critical factor for successful deletion of target genes, with some requiring up to 4 kb HAs to acquire mutant exconjugants. A strategy for allelic replacement was also developed by introducing an exogenous target site in place of the deleted genes, which could subsequently be targeted for cleavage and repaired with an HRT containing altered alleles of the genes of interest. Additionally, a single-step cloning strategy was devised, allowing for rapid assembly of editing plasmids, and improved conjugation protocols for genetic transfer from E. coli to N. punctiforme were implemented. Collectively, these tools and protocols should enhance the pace and ease of conducting genetic studies in this important model cyanobacterium. ### Competing Interest Statement The authors have declared no competing interest. NSF, 2420339

biorxiv.org

Genomics and biogeography of novel Trichodesmium isolates from the Sargasso Sea

The cyanobacterium Trichodesmium is important in ocean nitrogen (N) and carbon (C) biogeochemistry through fixation of N2 gas and CO2 into NH3, amino acids, and carbohydrates. These essential compounds then fuel primary productivity, bacterial and grazing communities, and upper trophic levels. In the oligotrophic surface oceans, they are one of few taxa capable of utilizing both atmospheric C and N. Trichodesmium fall into 2 diazotrophic phylogenomic clades named "Thieb" and "Tery" after the most well characterized botanical species, Trichodesmium thiebautii and Trichodesmium erythraeum. Thieb is commonly the most abundant clade in all major ocean regions and paradoxically, is also the least characterized in terms of morphology, genomics, and ecophysiology due to underrepresentation in culture collections. In this study, 25 novel strains of Thieb were enriched in culture from the Sargasso Sea, phenotypically characterized, and whole genome sequenced. Cultures were found to belong to four well-supported subclades (i.e., ThiebA, ThiebB, ThiebC, and ThiebD). Trichodesmium subclades were found to have environmentally relevant differences in colony shape, gene content, cell dimensions, and inferred temperature range. Specifically, ThiebD and ThiebC had the largest biovolumes whereas ThiebA and ThiebB had the smallest. Importantly ThiebB also became relatively more abundant only in bulk seawater metagenomes collected at high temperature (>28°C). This finding indicates that as ocean warming continues, there may be shifts in Trichodesmium community structure towards smaller cells, which would affect overall C+N standing stocks. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, https://ror.org/021nxhr62, 2125191

biorxiv.org

Getting over ANOVA: estimation graphics for multi-group comparisons - Nature Methods

nature.com

Dual-inhibitory mechanism of the bacterial retron Ec78 antiphage defense system | PNAS

Retrons are prokaryotic defense modules that protect bacteria from phage infection through abortive infection. The retron Ec78 system employs a two...

pnas.org

Rapid and quantitative measurement of bacteriophage infectivity via fully automated droplet digital PCR - Nature Communications

In this study, the authors present their automated droplet digital PCR workflow, capable of quantifying phage lytic activity.

nature.com

pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences

AbstractMotivation. The increasing number of fully sequenced bacterial plasmids being annotated and catalogued has prompted the development of computationa

dx.doi.org

Calcium isotopes link ocean acidification to Aptian–Albian foraminiferal extinctions

The second-largest extinction event in the evolutionary history of planktic foraminifera occurred at the Aptian–Albian boundary. This extinction may reflect ocean acidification (OA) associated with Oceanic Anoxic Event 1b. As calcium isotope ratios (δ44/...

science.org

Expansion of the Asgard archaeal virome and defensome provides insights into virus-host interactions - Microbiome

Background Asgard archaea, broadly considered as a group of archaea that exhibit the closest evolutionary relationship with eukaryotes, encode diverse defense systems and are infected by distinct viruses. However, the diversity of Asgard archaeal viruses and their interactions with the hosts remain poorly explored. Results Here, using CRISPR spacer-protospacer matching, we predict 23 viruses associated with Asgard archaea from various habitats. Apart from clusters with known viruses, we report three previously undescribed groups of Asgard viruses with predicted head-tailed virions of the realm Duplodnaviria and filamentous virions characteristic of the archaea-specific realm Adnaviria. Mapping of metagenomic reads to viral and host genomes suggested that most Asgard viruses display relatively low virus-to-host ratios, typically below 10. In addition, we considerably expanded the known defensome of Asgard archaea, among others, detecting putative PARIS and Prometheus defense systems. Finally, the diversity of anti-defense proteins and putative archaeal type IV pilins encoded by some Asgard viruses provide additional insights into the interactions between Asgard archaea and their viruses. Conclusions Overall, this work sheds new light on the Asgard archaeal virome and defensome, and virus-host interactions. Video Abstract

link.springer.com

Quantifying phage-host dynamics using droplet microfluidics - Nature Communications

Bacteriophages are key tools in molecular biology and promising agents against antibiotic-resistant bacteria. Here, the authors present a high-throughput droplet microfluidics platform that co-encapsulates single phages and bacteria to quantify individual infection events and lysis kinetics under precisely controlled conditions.

nature.com

Evolution of a core ribosomal innovation in octopus

Mitra, Han, Scott, et al. discovered a unique structural adaptation in octopus ribosomes that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems.

cell.com

Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature

Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.

nature.com

Diatoms maintain metabolic activity in deep ocean twilight zones

Phytoplankton are primarily confined to the sunlit epipelagic zone, yet intact algal cells persist in the ocean's mesopelagic twilight zone where light is minimal. However, their survival strategies in the deeper ocean remain unknown. Here, we isolate Chaetoceros sp. DS1 from 1000 m depth and reveal its survival mechanisms under prolonged darkness and high pressure, including membrane lipid remodeling and enhanced antioxidant defenses. Importantly, DS1 maintains a latent photosynthetic reserve that activates upon exposure to dim blue light and higher pressure typical of the twilight zone, enabling photosynthesis and nutrient uptake. It exhibits metabolic flexibility by utilizing stored carbon in darkness and assimilating organic carbon under dim light. Global meta-omics data show widespread, transcriptionally active Chaetoceros-like diatoms in the twilight zone, expressing blue-light sensors and protein synthesis genes. These findings identify the ocean twilight zone as a previously overlooked niche for metabolically active phytoplankton, expanding understanding of deep-ocean microbial ecology and carbon cycling. ### Competing Interest Statement The authors have declared no competing interest. Natural Science Foundation of China, 42188102, 42476116, 42476115, 42576100 Global Ocean Negative Carbon Emissions (ONCE) Project Fundamental Research Funds for the Central Universities

biorxiv.org

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature Microbiology

An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.

nature.com

Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences - Nature Microbiology

The phage-encoded protein PptA enables its DNA to masquerade as the host and evade cleavage, providing a potential foundation for engineering therapeutic phages that could bypass this widespread defence system.

nature.com

Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system

Bacterial reverse transcriptases defend against viruses, yet how their DNA products stop infection remains unknown. Bacteriophage inhibition of a host recombination enzyme activates the DRT3 defense system, which employs RNA- and protein-templated reverse transcriptases to synthesize antiviral double-stranded DNA.

cell.com

Rapid microbial production of long-lived dissolved organic carbon in the global ocean | PNAS

Marine microbes have long been regarded as central to replenishing the ocean’s reservoir of recalcitrant dissolved organic matter (RDOM). However, ...

pnas.org

The free-living wellspring of symbiotic nitrogen fixation in Bradyrhizobium | PNAS

The evolutionary origin of nitrogen-fixing symbiosis has been a long-standing question. To address this, we focused on Bradyrhizobium, a globally a...

pnas.org

First Evidence of Dicistroviruses Infecting Protists

Molecular surveys suggest that RNA viruses are abundant and diverse in the ocean, but the hosts for most of these viruses are unknown because so few have been cultivated. Here, we present the genomes of five positive-sense, single-stranded RNA (+ssRNA) viruses isolated from tropical seawater that infect green algae in the genus Tetraselmis (order Chlorodendrales). Phylogenetic analyses of multiple genes placed these closely related viruses within the family Dicistroviridae (order Picornavirales) making them the first viruses within the bounds of the Dicistroviridae family demonstrated to infect an organism other than arthropods. The RNA-dependent and capsid gene sequences of the Tetraselmis RNA viruses (TetRNAV01-05) cluster with others recovered from diverse environmental water samples or aquatic invertebrate tissues, and together they form a strongly supported sister clade to those of viruses in the genus Triatovirus. The TetRNAVs harbor a unique intergenic internal ribosome entry site (IRES), suggesting a translation strategy distinct from that described in arthropod-infecting dicistroviruses. Our results suggest that many uncultivated viruses presumed to infect invertebrates, because they were detected in invertebrate-derived samples and their genes cluster within the family Dicistroviridae, may instead be protist-infecting viruses. ### Competing Interest Statement The authors have declared no competing interest.

biorxiv.org