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Salt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora , revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.

Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies.

RNA viruses cause substantial global morbidity, yet their impact prior to the twentieth century remains obscured. While ancient DNA studies have transformed our understanding of past pathogens, ancient RNA (aRNA) isolation is largely restricted to exceptionally preserved samples. Here, we simultaneously recover aDNA and aRNA from non-formalin-fixed human lung specimens and reconstructed an 18th-century Human Rhinovirus (HRV) A genome-the oldest human RNA virus identified to date. The RNA is highly fragmented, with distinctive terminal misincorporations and coverage patterns consistent with double-stranded RNA. Phylogenetic analyses indicate that this historical HRV genome is an extinct lineage related to contemporary genotypes, providing a unique perspective on rhinovirus evolution. These findings demonstrate that centuries-old medical specimens can retain informative aRNA, expanding the temporal scope of paleovirology.

Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remains poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments—bulk sediment, rhizosphere, and root—and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings provide a holistic assessment of plant-associated viral diversity and community composition as well as identifying potential targets for exploring viral modulation of microbially-mediated ecosystem functioning in intertidal wetlands. Salt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartment and phenotype shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.

RNA viruses cause substantial global morbidity, yet their impact prior to the twentieth century remains obscured. While ancient DNA studies have transformed our understanding of past pathogens, ancient RNA (aRNA) isolation is largely restricted to exceptionally preserved samples. Here, we simultaneously recover aDNA and aRNA from non formalin-fixed human lung specimens and reconstructed an 18th-century Human Rhinovirus (HRV) A genome - the oldest human RNA virus identified to date. The RNA is highly fragmented, with distinctive terminal misincorporations and coverage patterns consistent with double-stranded RNA. Phylogenetic analyses indicate that this historical HRV genome is an extinct lineage related to contemporary genotypes, providing a unique perspective on rhinovirus evolution. These findings demonstrate that centuries-old medical specimens can retain informative aRNA, expanding the temporal scope of paleovirology.Competing Interest StatementThe authors have declared no competing interest.Footnotes* https://github.com/BlancoMeloLab/Historical_HRVAFunder Information DeclaredNational Institute of Allergy and Infectious Diseases, https://ror.org/043z4tv69, DP2AI177896Searle Scholars Program, Kingship FoundationImmunology and Vaccine Development Program at the Fred Hutchinson Cancer CenterSecretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI), CF-2023-G-957

Ocean stratification and the vertical extent of the mixed layer influence the rate at which the ocean and atmosphere exchange properties. This process has direct impacts for anthropogenic heat and carbon uptake in the Southern Ocean. Submesoscale instabilities that evolve over space (1–10 km) and time (from hours to days) scales directly influence mixed layer variability and are ubiquitous in the Southern Ocean. Mixed layer eddies contribute to mixed layer restratification, while down-front winds, enhanced by strong synoptic storms, can erode stratification by a cross-frontal Ekman buoyancy flux. This study investigates the role of these submesoscale processes on the subseasonal and interannual variability of the mixed layer stratification using four years of high-resolution glider data in the Southern Ocean. An increase of stratification from winter to summer occurs due to a seasonal warming of the mixed layer. However, we observe transient decreases in stratification lasting from days to weeks, which can arrest the seasonal restratification by up to two months after surface heat flux becomes positive. This leads to interannual differences in the timing of seasonal restratification by up to 36 days. Parameterizing the Ekman buoyancy flux in a one-dimensional mixed layer model reduces the magnitude of stratification compared to when the model is run using heat and freshwater fluxes alone. Importantly, the reduced stratification occurs during the spring restratification period, thereby holding important implications for mixed layer dynamics in climate models as well as physical–biological coupling in the Southern Ocean.

The 2013 Intergovernmental Panel on Climate Change report, using CMIP5 and EMIC model outputs suggests that the Atlantic Meridional Overturning Circulation (MOC) is very likely to weaken by 11–34% over the next century, with consequences for global rainfall and temperature patterns. However, these coupled, global climate models cannot resolve important oceanic features such as the Agulhas Current and its leakage around South Africa, which a number of studies have suggested may act to balance MOC weakening in the future. To properly understand oceanic changes and feedbacks on anthropogenic climate change we need to substantially improve global ocean observations, particularly within boundary current regions such as the Agulhas Current, which represent the fastest warming regions across the world’s oceans. The South African science community, in collaboration with governing bodies and international partners, has recently established one of the world’s most comprehensive observational networks of a western boundary current system, measuring the Greater Agulhas Current System and its inter-ocean exchanges south of Africa. This observational network, through its design for long-term monitoring, collaborative coordination of resources and skills sharing, represents a model for the international community. We highlight progress of the new Agulhas System Climate Array, as well as the South African Meridional Overturning Circulation programme, which includes the Crossroads and GoodHope hydrographic transects, and the South Atlantic MOC Basin-wide Array. We also highlight some of the ongoing challenges that the programmes still face. Significance: • Large mooring arrays have been successfully deployed to monitor the Greater Agulhas Current system. • Capacity development is ongoing, although established, in marine science around South Africa. • Challenges exist with regard to retention of skilled staff, resources and funding.

Underwater gliders have become widely used in the last decade. This has led to a proliferation of data and the concomitant development of tools to process the data. These tools are focused primarily on converting the data from its raw form to more accessible formats and often rely on proprietary programming languages. This has left a gap in the processing chain for glider data, specifically academics, who often need to perform secondary quality control, calibrate, correct, interpolate and visualise data. Here, we present GliderTools, an open-source Python package that addresses these needs of the glider user community. The tool is designed to change the focus from the processing to the data. In this paper, we present a set of tools, that includes: secondary cleaning and calibration, calibration procedures for bottle samples, fluorescence quenching correction, photosynthetically available radiation corrections and data interpolation in the vertical and horizontal dimensions. Many of these processes have been described in several other studies, but do not exist in a collated package designed for underwater glider data. Importantly, we provide potential users with guidelines on how these tools are used so that they can be easily and rapidly accessible to a wide range of users that span the student to the experienced researcher. We recognise that this package may not be all-encompassing for every user and we thus welcome community contributions and promote GliderTools as a community-driven project for scientists.

The Department of Science and Technology's (DST's) 10-year Global Change Grand Challenge programme requires platforms to 'attract young researchers to the region and retain them by exciting their interest in aspects of global change; while developing their capacity and professional skills in the relevant fields of investigation' (1). In addition, in July 2014, President Zuma officially launched Operation Phakisa and announced that a key target of this Oceans Economy initiative would be 'for the Department of Higher Education and Training to drive alignment between theoretical and workplace learning' (2). SEAmester–South Africa's recently established Class Afloat–achieves just that. SEAmester introduces marine science as an applied and cross-disciplinary field to students who have shown an affinity for core science disciplines. It identifies with government's National Development Plan (3) on education, training and innovation–critical to South Africa's long-term development and investment in this sector. SEAmester has a long-term vision aimed at building capacity within the marine sciences by coordinating and fostering cross-disciplinary research projects and achieving this goal through a highly innovative programme. The strength of SEAmester is that postgraduate students combine theoretical classroom learning with the application of this knowledge through ship-based, and more importantly, hands-on research. The state-of-the-art research vessel, SA Agulhas II, provides an ideal teaching and research platform for this programme; its size, comfort and shipboard facilities allow large groups of students and lecturers to productively interact over a period of 10 days. KEYWORDS: marine science; National Development Plan; SA Agulhas II; postgraduates; teaching and research platform

The Department of Science and Technology's (DST's) 10-year Global Change Grand Challenge programme requires platforms to 'attract young researchers to the region and retain them by exciting their interest in aspects of global change; while developing their capacity and professional skills in the relevant fields of investigation'. In addition, in July 2014, President Zuma officially launched Operation Phakisa and announced that a key target of this Oceans Economy initiative would be 'for the Department of Higher Education and Training to drive alignment between theoretical and workplace learning'. SEAmester - South Africa's recently established Class Afloat - achieves just that. SEAmester introduces marine science as an applied and cross-disciplinary field to students who have shown an affinity for core science disciplines. It identifies with government's National Development Plan on education, training and innovation - critical to South Africa's long-term development and investment in this sector. SEAmester has a long-term vision aimed at building capacity within the marine sciences by coordinating and fostering cross-disciplinary research projects and achieving this goal through a highly innovative programme. The strength of SEAmester is that postgraduate students combine theoretical classroom learning with the application of this knowledge through ship-based, and more importantly, hands-on research. The state-of-the-art research vessel, SA Agulhas II, provides an ideal teaching and research platform for this programme; its size, comfort and shipboard facilities allow large groups of students and lecturers to productively interact over a period of 10 days.