Marine Biological Laboratory

Populations of large pelagic sharks are declining worldwide due to overfishing. Determining the overlap between shark populations and fishing activities is important to inform conservation measures. However, for many threatened sharks the whereabouts of particularly vulnerable life-history stages – such as pregnant females and juveniles – are poorly known. Here, we investigated the spatial distribution of size classes, energy transfer and reproductive states of pregnant females of the endangered shortfin mako, Isurus oxyrinchus, using spatially resolved catch data from a Spanish surface longline vessel (1996 − 2009) in the South-east Pacific Ocean. Our results suggest a general eastward gradient of occurrence of pregnant females of thousands of kilometers from western oceanic feeding grounds towards the eastern Pacific, where we observed an aggregation area of small juveniles. Moreover, the potential nursery likely overlapped a longline fishing hotspot, increasing the vulnerability of juveniles from fisheries. Our results suggest that limiting fishing pressure in this area could reduce mortality of early life stages and contribute to the conservation of this endangered shark species.

Sharks are one the most threatened chondrichthyan taxa in the marine environment comprising high ecological, economic, and cultural significance. In India, a substantial quantity of shark landings occurs as bycatches through trawl and gillnet fisheries. However, there are limited findings about the species composition, size distribution, and levels of shark-gear interactions. The present study aimed to fill this knowledge gap through the estimation of length-weight relationships and condition factors for six shark species, viz., Carcharhinus falciformis, C. limbatus, C. melanopterus, Sphyrna lewini, Alopias vulpinus and A. superciliosus, from the tuna gillnet and trawl net fishery at three major fish landing centers along the southeast coast of India from January to December 2022. The results indicate that the estimated allometric coefficient (b) and the condition factor (Kn) for all six species ranged from 2.66 to 3.26 and 1.02 to 1.28 respectively. Understanding key aspects of biology and ecology is a crucial step toward conserving the declining population of these iconic predators which the study aims to emphasize.

Marine foundation species are increasingly impacted by anthropogenic stressors, driving a loss of diversity within these critical habitats. Prior studies suggest that species diversity within mussel beds has declined precipitously in southern California, USA, but it is unclear whether a similar loss has occurred farther north. Here, we resurvey a mussel bed community in northern California first sampled in 1941 to evaluate changes in diversity after 78 years. More broadly, we explore the value and potential challenges of using imperfect historical data to assess community changes. Our 2019 survey documented 90 species/taxa across 10 phyla. The majority of species (~ 72%) were common to all replicate plots, suggesting that variation in species diversity over small spatial scales was unlikely to mask temporal changes. In contrast to results from southern California, we observed no decline in species diversity between timepoints. However, there were shifts in species composition, with an increase in the abundance of southern species and a decrease in northern species, consistent with warming observed at a nearby shoreline site. Overall, our findings are an encouraging sign for the health of this mussel bed community in northern California and illustrate how non-traditional data can contribute to assessments of long-term ecological change.

A draft genome was generated for a strain of Mycobacterium closely related to Mycobacterium sp. ENV421 isolated in vitro from plants of smooth cordgrass germinated in vitro from seeds collected in a salt marsh in Cape Cod (USA). Genomic DNA was sequenced using paired-end Illumina technologies. Here, we report the classification and genome statistics of Mycobacterium sp. SA01. A strain of Mycobacterium was isolated from seedlings of Sporobolus alterniflorus germinated under in vitro conditions after surface sterilization. The seeds were collected in Little Swippewisett Marsh, Barnstable, MA, USA.

Diversity-generating retroelements (DGRs) create massive protein sequence variation (up to 10³⁰)¹ in ecologically diverse microorganisms. A recent survey identified around 31,000 DGRs from more than 1,500 bacterial and archaeal genera, constituting more than 90 environment types². DGRs are especially enriched in the human gut microbiome2,3 and nano-sized microorganisms that seem to comprise most microbial life and maintain DGRs despite reduced genomes4,5. DGRs are also implicated in the emergence of multicellularity6,7. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for complementary DNA synthesis to be carried out by a complex of the DGR reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Here we show through cryogenic electron microscopy that this RNA envelops bRT and lies over the barrel-shaped Avd, forming an intimate ribonucleoprotein. An abundance of essential interactions in the ribonucleoprotein precisely position an RNA homoduplex in the bRT active site for initiation of reverse transcription. Our results explain how the surrounding RNA primes complementary DNA synthesis, promotes processivity, terminates polymerization and strictly limits mutagenesis to specific proteins through mechanisms that are probably conserved in DGRs belonging to distant taxa.

Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained ‘de-aberration’ networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.

Cephalopods produce dynamic colors and skin patterns for communication and camouflage via stratified networks of neuronally actuated yellow, red, and brown chromatophore organs, each filled with thousands of pigment granules. While compositional analysis of chromatophore granules in Doryteuthis pealeii reveals the pigments as ommochromes, the ultrastructural features of the granules and their effects on bulk coloration have not been explored. To investigate this, we isolated granules from specific colored chromatophores and imaged them using multiple modalities. The brown granules are largest with smooth surface coatings. Red granules are intermediate in size with irregular surface textures, and yellow granules are smallest, with rough, porous surfaces. Many of the granules contain sub-granular features that also vary in presentation with color. Correlated light and electron microscopy reveal that differences in hue of individual granules are similarly associated with size, shape, and texture, suggesting that granules may be structurally adapted to modify the dominant visible colors presented within the chromatophores. These findings suggest that granule ultrastructure, not just chemical composition, may be significant in producing the range of colors presented in cephalopod chromatophores.

Impact statement The aquifer in the subseafloor igneous basement is a massive, continuous microbial substrate, yet sparingly little is known about life in this habitat. The work to date has focused largely on describing microbial diversity in the young basement (<10 Ma), where the basaltic crust is still porous and fluid flow through it is active. Here, we test the hypothesis that microbial life exists in subseafloor basement >65 Ma using samples collected from the Louisville Seamount Chain via seafloor drilling. Cell biomass was heterogeneous in nature, ranging from below detection to ~10⁴ cells cm⁻³. Bacterial 16S rRNA genes from core samples and enrichment incubations are dominated by lineages putatively carrying out nitrogen, sulfur, and metal redox processes and hydrocarbon oxidation. Taken together, the data indicate that microbial life is indeed present in subseafloor igneous basement >65 Ma, which significantly expands the range of the subseafloor biosphere where microbial life is known to exist.

Marine eastern boundary current ecosystems, such as the California Current System (CCS), involve productive, mesotrophic transition zones. The CCS exhibits highly variable primary production (PP), yet factors driving the variability and underlying phytoplankton communities remain poorly understood. We integrated physicochemical and biological data from surface waters sampled during 10 CCS expeditions, spanning 13 yr, and resolved regimes with distinct phytoplankton communities. Additional to an oligotrophic regime (OR), mesotrophic waters beyond the coastal area partitioned into Meso‐High and Meso‐Low regimes, differing in nitrate concentrations and PP. The OR was dominated by Prochlorococcus High‐Light I (HLI), and eukaryotic phytoplankton were largely predatory mixotrophs. Eukaryotes dominated Meso‐Low and Meso‐High phytoplankton biomass. Within the Meso‐Low, Pelagomonas calceolata was important, and Prochlorococcus Low‐Light I (LLI) rose in prominence. In the Meso‐High, the picoprasinophyte Ostreococcus lucimarinus was abundant, and Synechococcus Clade IV was notable. The Meso‐High exhibited the highest PP (38 ± 16 mg C m⁻³ d⁻¹; p < 0.01) and higher growth rates for photosynthetic eukaryotes (0.84 ± 0.02 d⁻¹) than for Prochlorococcus (0.61 ± 0.01 d⁻¹) and Synechococcus (0.31 ± 0.05 d⁻¹). An experiment simulating seasonal oligotrophic seawater intrusion into the Meso‐High resulted in growth rates reaching 1.18 ± 0.10 d⁻¹ (O. lucimarinus), 0.75 ± 0.21 d⁻¹ (Prochlorococcus LLI), and 0.50 ± 0.04 d⁻¹ (Synechococcus EPC2). Thus, variable PP is underpinned by distinct phytoplankton communities across CCS mesotrophic regimes, and their dynamic nature is influenced by the rapidity with which specific taxa respond to changing environmental conditions or possibly transient nutrient release from viral encounters. Future work should assess whether these dynamics are consistent across eastern boundary current ecosystems and over temporal variations.

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth’s subsurface and surface environments.

The composition of the larval fish assemblages in the Ross Sea is relatively well known, especially in the western sector. One of the most abundant icefish is Dacodraco hunteri (Channichthyidae), although it is considered a rare species as an adult. In the present study, we aimed at assessing aspects of the early life history of this species, such as age, hatching period, growth rate and feeding habits, and comparing samples collected in the eastern and western sectors of the Ross Sea. Individual age estimates were obtained by otolith microincrement counts and body growth was described by an exponential model. Diet composition was inferred from stomach content analysis. Fish samples consisted of yolk-sac and preflexion larval stages of development, with an estimated age range of 49–80 days. Growth rates were similar in both sectors of the Ross Sea ranging between 0.18 and 0.19 mm/day, which corresponded to a daily increase of 1.07–1.08% of body size. Larval hatching took place over a relatively short period (November), at a mean size of 8.2–8.7 mm notochord length. Larval stages of Pleuragramma antarcticum were the only prey items found in the stomachs, though with different frequency of occurrence in the eastern (13%) and western sectors (38%) of the Ross Sea. Consistent with previous data, the early life cycle of D. hunteri was characterized by relatively small larvae hatching in summer and overwintering juveniles with a specialized diet of P. antarcticum. D. hunteri are likely to be one of the main consumers of P. antarcticum within the pelagic realm.

Hortaea werneckii is a halotolerant black yeast commonly found in hypersaline environments. This yeast is also the causative agent of tinea nigra, a superficial mycosis of the palm of the hand and soles of the feet of humans. In addition to their remarkable halotolerance, this black yeast exhibits an unconventional cell division cycle, alternating between fission and budding cell division. Cell density and the salt concentration in their environment regulate which cell division cycle H. werneckii uses. Although H. werneckii have been extensively studied due to their unique physiology and cell biology, deciphering the underlying mechanisms behind these remarkable phenotypes has been limited due to the lack of genetic tools available. Here, we report a new ectopic integration protocol for H. werneckii using polyethylene glycol-CaCl2 mediated protoplast transformation. This approach relies on a drug (hygromycin B) resistance gene to select for successful integration of the genetic construct. The same construct was used to express cytosolic green fluorescent protein. Finally, we developed a marker-free CRISPR/Cas9 protocol for targeted gene deletion using the melanin synthesis pathway as a visual reporter of successful transformation. These transformation strategies will allow testing hypotheses related to H. werneckii cell biology and physiology. IMPORTANCE Hortaea werneckii is a remarkable yeast capable of growing in high salt concentration, and its cell division cycle alternates between fission-like and budding. For these unique attributes, H. werneckii has gathered interest in research programs studying extremophile fungi and cell division. Most of our understanding of H. werneckii biology comes from genomic analyses, the usage of drugs to target a particular pathway, or the heterologous expression of its genes in S. cerevisiae. Nonetheless, H. werneckii has remained genetically intractable. Here, we report on two strategies to transform H. werneckii: ectopic integration of a plasmid and gene deletion using CRISPR/Cas9. These approaches will be fundamental to expanding the experimental techniques available to study H. werneckii, including live-cell imaging of cellular processes and reverse genetic approaches.

Axons are ultrathin membrane cables that are specialized for the conduction of action potentials. Although their diameter is variable along their length, how their morphology is determined is unclear. Here, we demonstrate that unmyelinated axons of the mouse central nervous system have nonsynaptic, nanoscopic varicosities ~200 nm in diameter repeatedly along their length interspersed with a thin cable ~60 nm in diameter like pearls-on-a-string. In silico modeling suggests that this axon nanopearling can be explained by membrane mechanical properties. Treatments disrupting membrane properties, such as hyper- or hypotonic solutions, cholesterol removal and nonmuscle myosin II inhibition, alter axon nanopearling, confirming the role of membrane mechanics in determining axon morphology. Furthermore, neuronal activity modulates plasma membrane cholesterol concentration, leading to changes in axon nanopearls and causing slowing of action potential conduction velocity. These data reveal that biophysical forces dictate axon morphology and function, and modulation of membrane mechanics likely underlies unmyelinated axonal plasticity.

We review and salute the third edition of E.B. Wilson's “The Cell in Development and Heredity” published a century ago, noting its unique features and placing them in context. Brief commentaries from colleagues convey how they have encountered and have been influenced by The Cell. Although soon to be 100 years old, Wilson's 1925 edition is a hallmark of our profession, reminding us of a time when certain scholars were able to advance knowledge with a singularity of both mind and pen. Our purpose is to acknowledge the accomplishment by the man who brought together so many different facets of understanding cells and who many regard as the founder of cell biology in the United States. We reflect on the volume's admirable success and bring together perspectives on why it still matters.

The mitotic spindle consists of aligned filaments of dynamic microtubules that faithfully segregate mitotic chromosomes. This view of the mitotic spindle was initially established by detecting weak birefringence of the aligned filaments, which was realized by developing polarized light microscopy (Inoué S, Chromosoma 5:487–500. https://doi.org/10.1007/bf01271498, 1953). Inoué et al. developed a centrifuge polarizing microscope (CPM) (Inoué S et al., J Microsc 201:341–356. https://doi.org/10.1046/j.1365-2818.2001.00850.x, 2001; Inoué S et al., Centrifuge microscope capable of realizing polarized light observation (US Patent: US1907803A), 1999) to further understand the structural and physical basis of the functional positioning of centrosome-based structures (including the mitotic spindle) inside living cells. This chapter describes the procedure for observing biological specimens using CPM by focusing on Caenorhabditis elegans embryos.

Environmental factors and individual attributes, and their interactions, impact survival, growth and reproduction of an individual throughout its life. In the clonal rotifer Brachionus, low food conditions delay reproduction and extend lifespan. This species also exhibits maternal effect senescence; the offspring of older mothers have lower survival and reproductive output. In this paper, we explored the population consequences of the individual‐level interaction of maternal age and low food availability. We built matrix population models for both ad libitum and low food treatments, in which individuals are classified both by their age and maternal age. Low food conditions reduced population growth rate (Δλ=−0.0574) and shifted the population structure to older maternal ages, but did not detectably impact individual lifetime reproductive output. We analysed hypothetical scenarios in which reduced fertility or survival led to approximately stationary populations that maintained the shape of the difference in demographic rates between the ad libitum and low food treatments. When fertility was reduced, the populations were more evenly distributed across ages and maternal ages, while the lower‐survival models showed an increased concentration of individuals in the youngest ages and maternal ages. Using life table response experiment analyses, we compared populations grown under ad libitum and low food conditions in scenarios representing laboratory conditions, reduced fertility and reduced survival. In the laboratory scenario, the reduction in population growth rate under low food conditions is primarily due to decreased fertility in early life. In the lower‐fertility scenario, contributions from differences in fertility and survival are more similar, and show trade‐offs across both ages and maternal ages. In the lower‐survival scenario, the contributions from decreased fertility in early life again dominate the difference in λ. These results demonstrate that processes that potentially benefit individuals (e.g. lifespan extension) may actually reduce fitness and population growth because of links with other demographic changes (e.g. delayed reproduction). Because the interactions of maternal age and low food availability depend on the population structure, the fitness consequences of an environmental change can only be fully understood through analysis that takes into account the entire life cycle.

Fresh submarine groundwater discharge (FSGD) can deliver significant fluxes of water and solutes from land to sea. In the Arctic, which accounts for ∼34% of coastlines globally, direct observations and knowledge of FSGD are scarce. Through integration of observations and process‐based models, we found that regardless of ice‐bonded permafrost depth at the shore, summer SGD flow dynamics along portions of the Beaufort Sea coast of Alaska are similar to those in lower latitudes. Calculated summer FSGD fluxes in the Arctic are generally higher relative to low latitudes. The FSGD organic carbon and nitrogen fluxes are likely larger than summer riverine input. The FSGD also has very high CO2 making it a potentially significant source of inorganic carbon. Thus, the biogeochemistry of Arctic coastal waters is potentially influenced by groundwater inputs during summer. These water and solute fluxes will likely increase as coastal permafrost across the Arctic thaws.

Introduction In the context of Litopenaeus vannamei aquaculture, the incorporation of oyster shells has proven beneficial for enhancing water quality and the growth conditions of the shrimp. Nonetheless, the specific effects of in-situ water treatment using oyster shells on water quality and shrimp growth, along with the composition and succession dynamics of the microbial community within oyster shell biofilms, have yet to be thoroughly investigated. Methods This study established control, low-concentration, and high-concentration oyster shell addition groups to emulate the in-situ water treatment environment with oyster shells, with the objective of elucidating the impacts of oyster shell addition on the aquaculture setting. Results The results showed that the addition of oyster shells could significantly improve the length (F = 12.248, P = 0.005), weight(F = 138.234, P < 0.001), and survival rate (F = 15.248, P < 0.001) of shrimp, while there were no significant differences in the length (F = -1.233, P = 0.267) and survival rate (F = -2.143, P = 0.076) between the high and low concentration groups. Additionally, oyster shell addition resulted in elevated phosphate levels (F = 74.92, P < 0.001 in Day 70), diminished nitrite levels (F = 5.276, P = 0.031 in Day 56), and increased nitrate concentrations (F = 9.421, P = 0.006 in Day 70). Within the biofilms, the relative abundances of Ruegeria, Tenacibaculum, BD2- 11_terrestrial_group, and Kapabacteriales exhibited significant declines over time, whereas the relative abundance of Nitrospira demonstrated a marked increase, ultimately emerging as the predominant bacterium (Relative abundance 31.8%) in the biofilms during the latter stages of the experiment. Nitrospira also exhibited a notably higher relative abundance in the microbial community of the experimental water group relative to the control group (F = 2.265, P = 0.001). Discussion The biofilm provided conditions for the proliferation of Nitrospira, thereby accelerating the transformation of nitrite into nitrate in the aquaculture system, which subsequently improved the shrimp farming conditions. This research offers valuable insights for the application of oyster shells in shrimp farming and contributes to the theoretical underpinnings necessary for advancing our understanding of the mechanisms through which oyster shell biofilms enhance water quality and foster shrimp health.