Global Structuring of Phylogenetic and Functional Diversity of Pelagic Fungi by Depth and Temperature

Fungal contributions to ecosystem processes are well documented for terrestrial systems yet oceans, which account for most of the Earth’s surface, have remained poorly explored with regards to organisms in this kingdom. Here, we demonstrate that, although in low relative abundance (i.e., fungal reads made up 1.4–2.9% of the metagenomes), fungi contribute to both phylogenetic and functional microbial diversity with a conserved fungal presence in global marine samples. Universally distributed taxa and functions implicate them in complex carbon and fatty acid metabolism, with depth stratification along pelagic zones. Functional differences in observed genes between epipelagic and mesopelagic waters indicate changes in UV protection, shift to carbohydrate limited diets, as well as alternative energy sources. Metagenomic data also provided evidence for a latitudinal gradient in fungal diversity linked to temperature shifts. Our results suggest that fungi contribute to multiple biogeochemical cycles in the pelagic ocean, and could be integral for ecosystem functioning through provision of key nutrients

Mesoscale eddies: Hotspots of prokaryotic activity and differential community structure in the ocean

14 pages, 9 figures, 2 tablesTo investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic hotspots of prokaryotic activity (in the epi- and mesopelagic realms)This research was supported by two grants of the Spanish Ministry of Education and Science to JA (Oceanic Eddies and Atmospheric Deposition—RODA, CTM 2004-06842-C03/MAR, and Shelf–Ocean Exchanges in the Canaries– Iberian Large Marine Ecosystem-CAIBEX, CTM 2007- 66498-C02), a grant of the Earth and Life Science Division of the Dutch Science Foundation (ALW-NWO; ARCHIMEDES project, 835.20.023) to GJH, and a predoctoral Fellowship of the Spanish Ministry of Education and Science (AP2005-3932) to FB. IL and JMG were also supported by project MODIVUS (CTM2005-04795/MAR). The work was carried out within the frame of the EU ‘Networks of Excellence’ MarBef and EurOceansPeer Reviewe

Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria

Marine microbes are an important control on the biogeochemical cycling of trace metals, but simultaneously, these metals can control the growth of microorganisms and the cycling of major nutrients like C and N. However, studies on the response/limitation of microorganisms to trace metals have traditionally focused on the response of autotrophic phytoplankton to Fe fertilization. Few reports are available on the response of heterotrophic prokaryotes to Fe, and even less to other biogeochemically relevant metals. We performed the first study coupling dark incubations with next generation sequencing to specifically target the functional and phylogenetic response of heterotrophic prokaryotes to Fe enrichment. Furthermore, we also studied their response to Co, Mn, Ni, Zn, Cu (individually and mixed), using surface and deep samples from either coastal or open-ocean waters. Heterotrophic prokaryotic activity was stimulated by Fe in surface open–ocean, as well as in coastal, and deep open-ocean waters (where Zn also stimulated). The most susceptible populations to trace metals additions were uncultured bacteria (e.g., SAR324, SAR406, NS9, and DEV007). Interestingly, hydrocarbon-degrading bacteria (e.g., Thalassolituus, Marinobacter, and Oleibacter) benefited the most from metal addition across all waters (regions/depths) revealing a predominant role in the cycling of metals and organic matter in the ocean

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.Agencia Estatal de Investigación | Ref. PID2019-110011RB-C3

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

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

Seasonal Prokaryotic Community Linkages Between Surface and Deep Ocean Water

Sinking organic particles from surface waters provide key nutrients to the deep ocean, and could serve as vectors transporting microbial diversity to the deep ocean. However, the effect of this seasonally varying connectivity with the surface on deep microbial communities remains unexplored. Here, a three-year time-series from surface and deep (500 m) waters part of the Munida Microbial Observatory Time-Series (MOTS) was used to study the seasonality of epipelagic and mesopelagic prokaryotic communities. The goal was to establish how seasonally dynamic these two communities are, and any potential linkages between them. Both surface and deep prokaryotic communities displayed seasonality with high variation in community diversity. Deep prokaryotic communities mirrored the seasonal patterns in heterotrophic production and bacterial abundance displayed by surface communities, which were related to changes in chlorophyll-a concentration. However, the magnitude of this temporal variability in deeper waters was generally smaller than in the surface. Detection of surface prokaryotes in the deep ocean seemed seasonally linked to phytoplankton blooms, but other copiotrophic or typically algal-associated surface groups were not detected in the mesopelagic suggesting only specific populations were surviving the migration down the water column. We show transfer of organisms across depths is possibly not always unidirectional, with typically deep ocean microbes being seasonally abundant in surface waters. This indicates the main mechanism linking surface and deep communities changes seasonally: sinking of organic particles during productive periods, and vertical convection during winter overturning

Zooplankton-derived dissolved organic matter composition and its bioavailability of natural prokaryotic communities

Research articleZooplankton grazing onphytoplankton promotes the release of particulate and dissolved organic matter (DOM) into the water column and therefore plays a key role in organic matter cycling in aquatic systems. Prokaryotes are the main DOM consumers in the ocean by actively remineralizing and transforming it, contributing to its molecular diversification. To explore the molecular composition of zooplankton-derived DOM and its bioavailability to natural prokaryotic communities, the DOM generated by a mixed zooplankton community in the coastal Atlantic off Spain was used as substrate for a natural prokaryotic community and monitored over a ~ 5-d incubation experiment. The molecular composition of solid-phase extracted DOM was characterized via Fourier-transform ion cyclotron resonance mass spectrometry. After ~ 4 d in the zooplankton-derived DOM amended incubation, the prokaryotic community demonstrated a 17-fold exponential increase in cell number. The prokaryotic growth resulted in a reduction in bulk dissolved organic carbon concentration and the zooplankton-derived DOM was considerably transformed at molecular and bulk elemental levels over the incubation period. The C : N ratio (calculated from the obtained molecular formulae) increased while the functional diversity decreased over the incubation time. In addition, molecular indices pointed to a reduced bioavailability of DOM at the end of the experiment. These findings show that zooplankton excreta are a source of labile organic matter that is quickly metabolized by the prokaryotic community. Therefore, a fraction of carbon is shunted from transfer to secondary consumers similarly to the viral shunt, suggesting that the zooplankton–prokaryotic interactions play an important role in the ocean's carbon cycle.IEO, XUNTA DE GALICIA (INGO7A 2018/2), DFG (CO 2218/2-1 and TRR51

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

21 pages, 6 figures, supplementary information https://doi.org/10.1038/s41564-023-01374-2.-- Data availability: The sequence data generated in this study have been deposited in the EMBL Nucleotide Sequence Database (ENA) database under Bioproject PRJEB35712 (metagenomic and metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies, metagenomic assembled genomes and single-cell amplified genomes) and in the NCBI Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA amplicon reads).-- Code availability: Scripts available at Zenodo (https://doi.org/10.5281/zenodo.7721930.2023)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 oceanThis research was facilitated by the New Zealand Antarctic Research Institute (NZARI)-funded Aotearoa New Zealand Ross Ice Shelf Program. Samples for MICRO-CARD-FISH were collected on several research cruises led by M. Simon (Sonne 248 cruise), B. Quéguiner and I. Obernosterer (MobyDick) and L. J. A. Gerringa (Geotraces-1). F.B. was supported by the Austrian Science Fund (FWF) projects OCEANIDES (P34304-B), ENIGMA (TAI534), EXEBIO (P35248) and OCEANBIOPLAST (P35619-B). G.J.H. was supported by the FWF project ARTEMIS (P28781-B21) and I486-B09 and by the ERC under the European Community’s 7th Framework Programme (FP7/2007-2013)/ERC grant agreement no. 268595 (MEDEA project). R.L. was supported by INTERACTOMICS, CTM2015-69936-P, and J.M.G. by project PID2019-110011RB-C32 (Spanish Ministry of Science and Innovation, Spanish State Research Agency, doi: 10.13039/501100011033)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits