Two compound heterozygous variants in the CLN8 gene are responsible for neuronal cereidolipofuscinoses disorder in a child: a case report.

Background: Neuronal Ceroid Lipofuscinosis (NCL) disorders, recognized as the primary cause of childhood dementia globally, constitute a spectrum of genetic abnormalities. CLN8, a subtype within NCL, is characterized by cognitive decline, motor impairment, and visual deterioration. This study focuses on an atypical case with congenital onset and a remarkably slow disease progression. Methods: Whole-genome sequencing at 30× coverage was employed as part of a national genomics program to investigate the genetic underpinnings of rare diseases. This genomic approach aimed to challenge established classifications (vLINCL and EPMR) and explore the presence of a continuous phenotypic spectrum associated with CLN8. Results: The whole-genome sequencing revealed two novel likely pathogenic mutations in the CLN8 gene on chromosome 8p23.3. These mutations were not previously associated with CLN8-related NCL. Contrary to established classifications (vLINCL and EPMR), our findings suggest a continuous phenotypic spectrum associated with CLN8. Pathological subcellular markers further validated the genomic insights. Discussion: The identification of two previously undescribed likely pathogenic CLN8 gene mutations challenges traditional classifications and highlights a more nuanced phenotypic spectrum associated with CLN8. Our findings underscore the significance of genetic modifiers and interactions with unrelated genes in shaping variable phenotypic outcomes. The inclusion of pathological subcellular markers further strengthens the validity of our genomic insights. This research enhances our understanding of CLN8 disorders, emphasizing the need for comprehensive genomic analyses to elucidate the complexity of phenotypic presentations and guide tailored therapeutic strategies. The identification of new likely pathogenic mutations underscores the dynamic nature of CLN8-related NCL and the importance of individualized approaches to patient management.

Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes.

Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes. IMPORTANCE: Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.

Influence of Salinity on the Extracellular Enzymatic Activities of Marine Pelagic Fungi.

Even though fungi are ubiquitous in the biosphere, the ecological knowledge of marine fungi remains rather rudimentary. Also, little is known about their tolerance to salinity and how it influences their activities. Extracellular enzymatic activities (EEAs) are widely used to determine heterotrophic microbes' enzymatic capabilities and substrate preferences. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). Due to their sensitivity and specificity, fluorogenic substrate analogues were used to determine hydrolytic activity on carbohydrates (ß-glucosidase, ß-xylosidase, and N-acetyl-ß-D-glucosaminidase); peptides (leucine aminopeptidase and trypsin); lipids (lipase); organic phosphorus (alkaline phosphatase), and sulfur compounds (sulfatase). Afterwards, kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were calculated. All fungal species investigated cleaved these substrates, but some species were more efficient than others. Moreover, most enzymatic activities were reduced in the saline medium, with some exceptions like sulfatase. In non-saline conditions, the average Vmax ranged between 208.5 to 0.02 µmol/g biomass/h, and in saline conditions, 88.4 to 0.02 µmol/g biomass/h. The average Km ranged between 1553.2 and 0.02 µM with no clear influence of salinity. Taken together, our results highlight a potential tolerance of marine fungi to freshwater conditions and indicate that changes in salinity (due to freshwater input or evaporation) might impact their enzymatic activities spectrum and, therefore, their contribution to the oceanic elemental cycles.

Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles.

Viruses play an important role in the marine ecosystem. However, our comprehension of viruses inhabiting the dark ocean, and in particular, under the Antarctic Ice Shelves, remains limited. Here, we mine single-cell genomic, transcriptomic, and metagenomic data to uncover the viral diversity, biogeography, activity, and their role as metabolic facilitators of microbes beneath the Ross Ice Shelf. This is the largest Antarctic ice shelf with a major impact on global carbon cycle. The viral community found in the cavity under the ice shelf mainly comprises endemic viruses adapted to polar and mesopelagic environments. The low abundance of genes related to lysogenic lifestyle (<3%) does not support a predominance of the Piggyback-the-Winner hypothesis, consistent with a low-productivity habitat. Our results indicate a viral community actively infecting key ammonium and sulfur-oxidizing chemolithoautotrophs (e.g. Nitrosopumilus spp, Thioglobus spp.), supporting a "kill-the-winner" dynamic. Based on genome analysis, these viruses carry specific auxiliary metabolic genes potentially involved in nitrogen, sulfur, and phosphorus acquisition. Altogether, the viruses under Antarctic ice shelves are putatively involved in programming the metabolism of ecologically relevant microbes that maintain primary production in these chemosynthetically-driven ecosystems, which have a major role in global nutrient cycles.

Release of cell-free enzymes by marine pelagic fungal strains.

Fungi are ubiquitous organisms that secrete different enzymes to cleave large molecules into smaller ones so that can then be assimilated. Recent studies suggest that fungi are also present in the oceanic water column harboring the enzymatic repertoire necessary to cleave carbohydrates and proteins. In marine prokaryotes, the cell-free fraction is an important contributor to the oceanic extracellular enzymatic activities (EEAs), but the release of cell-free enzymes by marine fungi remains unknown. Here, to study the cell-free enzymatic activities of marine fungi and the potential influence of salinity on them, five strains of marine fungi that belong to the most abundant pelagic phyla (Ascomycota and Basidiomycota), were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). The biomass was separated from the medium by filtration (0.2 µm), and the filtrate was used to perform fluorogenic enzymatic assays with substrate analogues of carbohydrates, lipids, organic phosphorus, sulfur moieties, and proteins. Kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were obtained. The species studied were able to release cell-free enzymes, and this represented up to 85.1% of the respective total EEA. However, this differed between species and enzymes, with some of the highest contributions being found in those with low total EEA, with some exceptions. This suggests that some of these contributions to the enzymatic pool might be minimal compared to those with higher total EEA. Generally, in the saline medium, the release of cell-free enzymes degrading carbohydrates was reduced compared to the non-saline medium, but those degrading lipids and sulfur moieties were increased. For the remaining substrates, there was not a clear influence of the salinity. Taken together, our results suggest that marine fungi are potential contributors to the oceanic dissolved (i.e., cell-free) enzymatic pool. Our results also suggest that, under salinity changes, a potential effect of global warming, the hydrolysis of organic matter by marine fungal cell-free enzymes might be affected and hence, their potential contribution to the oceanic biogeochemical cycles.

Complicaciones neurológicas de la prematuridad / Neurological consequences of prematurity

Resumen Los nacimientos prematuros representan un in dicador importante de salud de un país. Estos niños tienen un mayor riesgo de mortalidad y morbilidad. Las principales lesiones encefálicas en los prematuros incluyen lesiones de la sustancia blanca, hemorragias intracraneanas y lesiones cerebelosas, que pueden ser detectadas mediante ecografía encefálica y resonancia magnética, siendo esta última la técnica más sensible. Estas lesiones pueden tener repercusión a largo plazo en el neurodesarrollo de los prematuros, con un mayor riesgo de parálisis cerebral, trastornos cognitivos, con ductuales, sensoriales y del aprendizaje, entre otros. Es fundamental aplicar estrategias de prevención y aten ción temprana para reducir las consecuencias negativas de las lesiones encefálicas asociadas a la prematuridad.

Abstract Premature births are an important health indicator for a country. These children have a higher risk of mor tality and morbidity. The main brain injuries in preterm infants include white matter injuries, intracranial hem orrhages, and cerebellar injuries. These injuries can be detected through brain ultrasound and magnetic reso nance imaging (MRI), with MRI being the most sensitive technique. Perinatal brain injuries may have long-term consequences on the neurodevelopment of preterm infants, with an increased risk of cerebral palsy, cogni tive, behavioral, sensory, and learning disorders, among others. It is key to implement prevention strategies and early intervention to reduce the negative consequences of brain injuries associated with prematurity.

Trombosis venosa y de senos cerebrales en recién nacidos y niños / Venous and cerebral sinus thrombosis in newborns and children

Resumen Introducción : La trombosis de venas y senos venosos cerebrales (TVSC) constituye una causa conocida, aun que subestimada de ictus en la infancia. Su diagnóstico requiere un alto índice de sospecha, una correcta in terpretación de la neuroimagen e interrelación entre el clínico y el radiólogo. Objetivo : Analizar las manifestaciones clínicas, fac tores de riesgo y neuroimagen de recién nacidos (RN) y niños menores de 15 años con TVSC. Métodos: Estudio descriptivo, retrospectivo, multi céntrico, de una serie consecutiva de casos de menores de 15 años que ingresaron por TVSC entre el 1 de enero del 2010 y el 1 de marzo de 2022. Resultados : El estudio incluyó 51 pacientes: 39% con síntomas agudos y 59% subagudos. En los RN predomi naron síntomas encefalopáticos y convulsiones, mien tras en los niños elementos de hipertensión endocranea na (HTEC). Se identificaron factores de riesgo en el 90% de los casos. La resonancia magnética con angiografía en tiempo venoso confirmó el diagnóstico en el 80%, siendo el seno recto el más afectado en RN y el seno lateral en niños. Se encontraron complicaciones hemorrágicas en 30.5%, siendo más frecuentes en los RN. Se inició anti coagulación en el 82% sin complicaciones. Las secuelas estuvieron presentes en 44.4% de RN y 37.9% de niños, siendo más frecuentes y graves en los RN. Conclusiones : Para realizar un diagnóstico precoz es fundamental pensar en TVSC en RN con síntomas en cefalopáticos y/o convulsiones y en mayores con clínica de HTEC en presencia de enfermedades predisponentes o desencadenantes.

Abstract Introduction : Cerebral venous sinus thrombosis (CVST) is a well-known, although underestimated, cause of stroke in childhood. Its diagnosis requires a high index of suspicion, a correct interpretation of neuroim aging studies and an interrelation between clinicians and radiologists. The clinical features, risk factors and neuroimaging of children under 15 years of age with CVST were analyzed. Methods : multicenter, retrospective, descriptive, study of a consecutive series of cases of children under 15 years of age, who were admitted due to CVST between January 1st, 2010, and March 1st, 2022. Results : The study included 51 patients: 39% with acute symptoms and 59% with subacute symptoms. Newborns predominantly presented encephalopathic symptoms and seizures, while children exhibited signs of intracranial hypertension (ICH). Risk factors were 96 identified in 90% of the cases. Magnetic resonance with angiography in venous time confirmed the diagnosis in 80% of the patients, with the straight sinus being the most affected in newborns and the lateral sinus in chil dren. Hemorrhagic complications were found in 30.5%, being more frequent in newborns. Anticoagulation was initiated in 82% without complications. Sequelae were present in 44.4% of newborns and 37.9% of children, being more frequent and severe in newborns. Conclusions : To make an early diagnosis, it is essen tial to consider CVST in newborns with encephalopathic symptoms and/or seizures, and in children with signs of ICH in the presence of predisposing or triggering conditions.

[Neurological consequences of prematurity]. / Complicaciones neurológicas de la prematuridad.

Premature births are an important health indicator for a country. These children have a higher risk of mortality and morbidity. The main brain injuries in preterm infants include white matter injuries, intracranial hemorrhages, and cerebellar injuries. These injuries can be detected through brain ultrasound and magnetic resonance imaging (MRI), with MRI being the most sensitive technique. Perinatal brain injuries may have long-term consequences on the neurodevelopment of preterm infants, with an increased risk of cerebral palsy, cognitive, behavioral, sensory, and learning disorders, among others. It is key to implement prevention strategies and early intervention to reduce the negative consequences of brain injuries associated with prematurity. Key words: prematurity, periventricular leukomalacia, intracranial hemorrhage, neurodevelopmental disorders, cerebral palsy.

Los nacimientos prematuros representan un indicador importante de salud de un país. Estos niños tienen un mayor riesgo de mortalidad y morbilidad. Las principales lesiones encefálicas en los prematuros incluyen lesiones de la sustancia blanca, hemorragias intracraneanas y lesiones cerebelosas, que pueden ser detectadas mediante ecografía encefálica y resonancia magnética, siendo esta última la técnica más sensible. Estas lesiones pueden tener repercusión a largo plazo en el neurodesarrollo de los prematuros, con un mayor riesgo de parálisis cerebral, trastornos cognitivos, conductuales, sensoriales y del aprendizaje, entre otros. Es fundamental aplicar estrategias de prevención y atención temprana para reducir las consecuencias negativas de las lesiones encefálicas asociadas a la prematuridad.

[Venous and cerebral sinus thrombosis in newborns and children]. / Trombosis venosa y de senos cerebrales en recién nacidos y niños.

INTRODUCTION: Cerebral venous sinus thrombosis (CVST) is a well-known, although underestimated, cause of stroke in childhood. Its diagnosis requires a high index of suspicion, a correct interpretation of neuroimaging studies and an interrelation between clinicians and radiologists. The clinical features, risk factors and neuroimaging of children under 15 years of age with CVST were analyzed. METHODS: multicenter, retrospective, descriptive, study of a consecutive series of cases of children under 15 years of age, who were admitted due to CVST between January 1st, 2010, and March 1st, 2022. RESULTS: The study included 51 patients: 39% with acute symptoms and 59% with subacute symptoms. Newborns predominantly presented encephalopathic symptoms and seizures, while children exhibited signs of intracranial hypertension (ICH). Risk factors were identified in 90% of the cases. Magnetic resonance with angiography in venous time confirmed the diagnosis in 80% of the patients, with the straight sinus being the most affected in newborns and the lateral sinus in children. Hemorrhagic complications were found in 30.5%, being more frequent in newborns. Anticoagulation was initiated in 82% without complications. Sequelae were present in 44.4% of newborns and 37.9% of children, being more frequent and severe in newborns. CONCLUSIONS: To make an early diagnosis, it is essential to consider CVST in newborns with encephalopathic symptoms and/or seizures, and in children with signs of ICH in the presence of predisposing or triggering conditions.

Introducción: La trombosis de venas y senos venosos cerebrales (TVSC) constituye una causa conocida, aunque subestimada de ictus en la infancia. Su diagnóstico requiere un alto índice de sospecha, una correcta interpretación de la neuroimagen e interrelación entre el clínico y el radiólogo. OBJETIVO: Analizar las manifestaciones clínicas, factores de riesgo y neuroimagen de recién nacidos (RN) y niños menores de 15 años con TVSC. Métodos: Estudio descriptivo, retrospectivo, multicéntrico, de una serie consecutiva de casos de menores de 15 años que ingresaron por TVSC entre el 1 de enero del 2010 y el 1 de marzo de 2022. RESULTADOS: El estudio incluyó 51 pacientes: 39% con síntomas agudos y 59% subagudos. En los RN predominaron síntomas encefalopáticos y convulsiones, mientras en los niños elementos de hipertensión endocraneana (HTEC). Se identificaron factores de riesgo en el 90% de los casos. La resonancia magnética con angiografía en tiempo venoso confirmó el diagnóstico en el 80%, siendo el seno recto el más afectado en RN y el seno lateral en niños. Se encontraron complicaciones hemorrágicas en 30.5%, siendo más frecuentes en los RN. Se inició anticoagulación en el 82% sin complicaciones. Las secuelas estuvieron presentes en 44.4% de RN y 37.9% de niños, siendo más frecuentes y graves en los RN. CONCLUSIONES: Para realizar un diagnóstico precoz es fundamental pensar en TVSC en RN con síntomas encefalopáticos y/o convulsiones y en mayores con clínica de HTEC en presencia de enfermedades predisponentes o desencadenantes.

Fungal Diversity and Community Composition across Ecosystems.

Fungi have shaped the biosphere since the development of life on Earth. Despite fungi being present in all environments, most of the available fungal research has focused on soils. As a result, the role and composition of fungal communities in aquatic (marine and freshwater) environments remain largely unexplored. The use of different primers to characterise fungal communities has additionally complicated intercomparisons among studies. Consequently, we lack a basic global assessment of fungal diversity across major ecosystems. Here, we took advantage of a recently published 18S rRNA dataset comprising samples from major ecosystems (terrestrial, freshwater, and marine) to attempt a global assessment of fungal diversity and community composition. We found the highest fungal diversities for terrestrial > freshwater > marine environments, and pronounced gradients of fungal diversity along temperature, salinity, and latitude in all ecosystems. We also identified the most abundant taxa in each of these ecosystems, mostly dominated by Ascomycota and Basidiomycota, except in freshwater rivers where Chytridiomycota dominated. Collectively, our analysis provides a global analysis of fungal diversity across all major environmental ecosystems, highlighting the most distinct order and ASVs (amplicon sequencing variants) by ecosystem, and thus filling a critical gap in the study of the Earth's mycobiome.

The largely neglected ecological role of oceanic pelagic fungi.

Most investigations into ocean ecology and biogeochemistry have tended to focus on marine bacteria, archaea, and protists, while pelagic fungi (mycoplankton) have traditionally been neglected and considered to reside only in association with benthic solid substrates. Nevertheless, recent studies have revealed that pelagic fungi are distributed ubiquitously throughout the water column in every ocean basin and play an active role in the degradation of organic matter and the cycling of nutrients. We review the current status of knowledge on the ecology of mycoplankton and highlight knowledge gaps and challenges. These findings underscore the need to recognize this neglected kingdom as significant contributors to the organic matter cycling and ecology of the oceans.

Respiration, Production, and Growth Efficiency of Marine Pelagic Fungal Isolates.

Despite recent studies suggesting that marine fungi are ubiquitous in oceanic systems and involved in organic matter degradation, their role in the carbon cycle of the oceans is still not characterized and fungal respiration and production are understudied. This study focused on determining fungal growth efficiencies and its susceptibility to temperature differences and nutrient concentration. Hence, respiration and biomass production of three fungal isolates (Rhodotorula mucilaginosa, Rhodotorula sphaerocarpa, Sakaguchia dacryoidea) were measured in laboratory experiments at two temperatures and two nutrient concentrations. We found that fungal respiration and production rates differed among species, temperature, and nutrient concentration. Fungal respiration and production were higher at higher temperatures, but higher fungal growth efficiencies were observed at lower temperatures. Nutrient concentration affected fungal respiration, production, and growth efficiency, but its influence differed among species. Altogether, this study provides the first growth efficiency estimates of pelagic fungi, providing novel insights into the role of fungi as source/sink of carbon during organic matter remineralization. Further research is now needed to unravel the role of pelagic fungi in the marine carbon cycle, a topic that gains even more importance in times of increasing CO2 concentrations and global warming.

Physiological Properties of Three Pelagic Fungi Isolated from the Atlantic Ocean.

Oceanic fungi are widely understudied compared to their terrestrial counterparts. However, they have been shown to be important degraders of organic matter in the global pelagic oceans. By examining the physiological characteristics of fungi isolated from the pelagic waters of the ocean it is possible to infer specific functions of each species in the biogeochemical processes that occur in the marine ecosystem. In this study, we isolated three pelagic fungi from different stations and depths across a transect in the Atlantic Ocean. We identified two yeasts [(Scheffersomyces spartinae (Debaryomycetaceae, Saccharomycetes, Ascomycota) and Rhodotorula sphaerocarpa (Sporidiobolaceae, Microbotryomycetes, Basidiomycota)], and the hyphae-morphotype fungus Sarocladium kiliense (Hypocreales, Sordariomycetes, Ascomycota), and conducted physiological experiments to investigate their preferred carbon uptake as well as their growth patterns under different environmental conditions. Despite their taxonomic and morphological differences, all species exhibited a high tolerance towards a wide range of salinities (0-40 g/L) and temperatures (5-35 °C). Furthermore, a shared metabolic preference for oxidizing amino acids was found among all fungal isolates. Collectively, this study provides relevant information on the physiological properties of oceanic pelagic fungi, revealing a high tolerance towards salinity and temperature changes, ultimately contributing to understanding their ecology and distribution in the oceanic water column.

A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean.

The deep ocean (>200 m depth) is the largest habitat on Earth. Recent evidence suggests sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. Here we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements on samples collected beneath the Ross Ice Shelf in Antarctica to characterize a ubiquitous mixotrophic bacterial group (UBA868) that dominates expression of RuBisCO genes and of key sulfur oxidation genes. Further analyses of the gene libraries from the 'Tara Oceans' and 'Malaspina' expeditions confirmed the ubiquitous distribution and global relevance of this enigmatic group in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes across the global mesopelagic ocean. Our study also underscores the unrecognized importance of mixotrophic microbes in the biogeochemical cycles of the deep ocean.

Molecular hydrogen in seawater supports growth of diverse marine bacteria.

Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.

Salp blooms drive strong increases in passive carbon export in the Southern Ocean.

The Southern Ocean contributes substantially to the global biological carbon pump (BCP). Salps in the Southern Ocean, in particular Salpa thompsoni, are important grazers that produce large, fast-sinking fecal pellets. Here, we quantify the salp bloom impacts on microbial dynamics and the BCP, by contrasting locations differing in salp bloom presence/absence. Salp blooms coincide with phytoplankton dominated by diatoms or prymnesiophytes, depending on water mass characteristics. Their grazing is comparable to microzooplankton during their early bloom, resulting in a decrease of ~1/3 of primary production, and negative phytoplankton rates of change are associated with all salp locations. Particle export in salp waters is always higher, ranging 2- to 8- fold (average 5-fold), compared to non-salp locations, exporting up to 46% of primary production out of the euphotic zone. BCP efficiency increases from 5 to 28% in salp areas, which is among the highest recorded in the global ocean.

Prokaryotic Life in the Deep Ocean's Water Column.

The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.

Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.

Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 µm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05-0.27) of FL bacteria (defined as the size-fraction <3.0 µm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.

Global contribution of pelagic fungi to protein degradation in the ocean.

BACKGROUND: Fungi are important degraders of organic matter responsible for reintegration of nutrients into global food chains in freshwater and soil environments. Recent evidence suggests that they are ubiquitously present in the oceanic water column where they play an active role in the degradation of carbohydrates. However, their role in processing other abundant biomolecules in the ocean in comparison with that of prokaryotes remains enigmatic. Here, we performed a global-ocean multi-omics analysis of all fungal-affiliated peptidases (main enzymes responsible for cleaving proteins), which constitute the major fraction (> 50%) of marine living and detrital biomass. We determined the abundance, expression, diversity, taxonomic affiliation, and functional classification of the genes encoding all pelagic fungal peptidases from the epi- and mesopelagic layers. RESULTS: We found that pelagic fungi are active contributors to protein degradation and nitrogen cycling in the global ocean. Dothideomycetes are the main fungi responsible for protease activity in the surface layers, whereas Leotiomycetes dominate in the mesopelagic realm. Gene abundance, diversity, and expression increased with increasing depth, similar to fungal CAZymes. This contrasts with the total occurrence of prokaryotic peptidases and CAZymes which are more uniformly distributed in the oceanic water column, suggesting potentially different ecological niches of fungi and prokaryotes. In-depth analysis of the most widely expressed fungal protease revealed the potentially dominating role of saprotrophic nutrition in the oceans. CONCLUSIONS: Our findings expand the current knowledge on the role of oceanic fungi in the carbon cycle (carbohydrates) to the so far unknown global participation in nitrogen (proteins) degradation, highlighting potentially different ecological niches occupied by fungi and prokaryotes in the global ocean. Video Abstract.

Extracellular Enzymatic Activities of Oceanic Pelagic Fungal Strains and the Influence of Temperature.

Although terrestrial and aquatic fungi are well-known decomposers of organic matter, the role of marine fungi remains largely unknown. Recent studies based on omics suggest that marine fungi potentially play a major role in elemental cycles. However, there is very limited information on the diversity of extracellular enzymatic activities performed by pelagic fungi in the ocean and how these might be affected by community composition and/or critical environmental parameters such as temperature. In order to obtain information on the potential metabolic activity of marine fungi, extracellular enzymatic activities (EEA) were investigated. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown at 5 °C and 20 °C, and fluorogenic enzymatic assays were performed using six substrate analogues for the hydrolysis of carbohydrates (ß-glucosidase, ß-xylosidase, and N-acetyl-ß-D-glucosaminidase), amino acids (leucine aminopeptidase), and of organic phosphorus (alkaline phosphatase) and sulfur compounds (sulfatase). Remarkably, all fungal strains were capable of hydrolyzing all the offered substrates. However, the hydrolysis rate (Vmax) and half-saturation constant (Km) varied among the fungal strains depending on the enzyme type. Temperature had a strong impact on the EEAs, resulting in Q10 values of up to 6.1 and was species and substrate dependent. The observed impact of temperature on fungal EEA suggests that warming of the global ocean might alter the contribution of pelagic fungi in marine biogeochemical cycles.