Florian Kokoszka

Bio: Florian Kokoszka is an academic researcher from Stazione Zoologica Anton Dohrn. The author has contributed to research in topics: Environmental science & Oceanography. The author has an hindex of 2, co-authored 3 publications receiving 1414 citations. Previous affiliations of Florian Kokoszka include École Normale Supérieure.

Structure and function of the global ocean microbiome

Abstract: Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

Linking mixing processes and climate variability to the heat content distribution of the Eastern Mediterranean abyss

Abstract: The heat contained in the ocean (OHC) dominates the Earth’s energy budget and hence represents a fundamental parameter for understanding climate changes. However, paucity of observational data hampers our knowledge on OHC variability, particularly in abyssal areas. Here, we analyze water characteristics, observed during the last three decades in the abyssal Ionian Sea (Eastern Mediterranean), where two competing convective sources of bottom water exist. We find a heat storage of ~1.6 W/m2 – twice that assessed globally in the same period – exceptionally well-spread throughout the local abyssal layers. Such an OHC accumulation stems from progressive warming and salinification of the Eastern Mediterranean, producing warmer near-bottom waters. We analyze a new process that involves convectively-generated waters reaching the abyss as well as the triggering of a diapycnal mixing due to rough bathymetry, which brings to a warming and thickening of the bottom layer, also influencing water-column potential vorticity. This may affect the prevailing circulation, altering the local cyclonic/anticyclonic long-term variability and hence precondition future water-masses formation and the redistribution of heat along the entire water-column.

Coastal mesozooplankton respond to decadal environmental changes via community restructuring

Abstract: Long-term ecological research has revealed the impact of climate on marine ecosystems at multiple time scales. Changes in the pelagic system have been detected at the LTER-MC site in the Gulf of Naples (Tyrrhenian Sea, western Mediterranean) since 1984. Here we analyzed the time series to determine whether zooplankton had significantly changed over the three decades 1984–2015. In addition to the seasonal cycle as the main mode of temporal variability, we observed long-term trends in the functional groups and species. Copepods, the most abundant group, declined over the years owing to a decrease in the abundance of Acartia clausi, Centropages typicus, the Paracalanus parvus complex, and Oithona spp. Increasing trends were observed for strict carnivores (chaetognaths) and typical filter feeders (cladocerans, appendicularians, and thaliaceans); the latter may be linked to a higher density of <5 μm phytoplankton. Two main temporal shifts were detected: (i) in 1985–87, similarly to the regime shifts registered in other basins of the Northern Hemisphere, and (ii) after 2011, likely related to local atmospheric forcing. The disappearance or decrease in some neritic copepods and the increased abundance of typical offshore species seem to reflect the enhanced influence of the open Tyrrhenian waters at the sampling site. Despite these changes, no significant trends were detected in the total zooplankton abundance and overall composition, which indicates restructuring within the whole community. These results underline the need to examine the entire zooplankton diversity spectrum and improve our knowledge of their ecological traits to detect and interpret long-term variability.

Gulf of Naples Advanced Model (GNAM): A Multiannual Comparison with Coastal HF Radar Data and Hydrological Measurements in a Coastal Tyrrhenian Basin

Abstract: High-resolution modelling systems have increasingly become an essential requirement to investigate ocean dynamics over a wide range of spatial and temporal scales, and to integrate the punctual ocean observations. When applied in coastal areas, they also have the potential to provide a detailed representation of transport and exchange processes at the sub-basin scale. This paper presents a validation exercise between the surface fields generated by the regional ocean modeling system (ROMS), developed for the Tyrrhenian Sea and downscaled for the Gulf of Naples (GNAM Gulf of Naples advanced model), and a 4 year-long (2009–2012) record of high-frequency radar (HFR) data. The comparison between hourly and seasonal model results and HFR surface fields is focused on the Gulf of Naples (GoN), where an observational network of three HFR sites has been operational since 2004, and on a specific subdomain characterized by the presence of the Sarno river, a long-term ecological research station (LTER-MC) and one important canyon area. An evaluation on a transect delimiting inshore–offshore zones in the GoN is also presented. The GNAM model was also compared with in situ hydrological parameters of temperatures and salinities retrieved at the LTER-MC fixed monitoring station. According to the skill metrics, basic circulation features are accurately reproduced by the circulation model, despite some model drawbacks in terms of increment of energy content in the surface current field occurring during specific seasonal events. The results allow us to identify potential model errors and to suggest useful improvements, the outcome also confirms the unique capability of HF radar systems to provide fine-scale measurements for the validation of numerical models and to counterbalance the lack of high-resolution measurements in coastal areas.

KEGG: integrating viruses and cellular organisms.

Abstract: KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. The network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database. The KO database for functional orthologs continues to be improved and virus KOs are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.

The microbial nitrogen-cycling network

Abstract: Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications

The biomass distribution on Earth

Abstract: A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life. We find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals (≈2 Gt C) are mainly marine, and bacteria (≈70 Gt C) and archaea (≈7 Gt C) are predominantly located in deep subsurface environments. We show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 Gt C of marine biota, doubling the previous estimated quantity. Our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. Finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Abstract: eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de.

Decoupling function and taxonomy in the global ocean microbiome

Abstract: Microbial metabolism powers biogeochemical cycling in Earth’s ecosystems. The taxonomic composition of microbial communities varies substantially between environments, but the ecological causes of this variation remain largely unknown. We analyzed taxonomic and functional community profiles to determine the factors that shape marine bacterial and archaeal communities across the global ocean. By classifying >30,000 marine microorganisms into metabolic functional groups, we were able to disentangle functional from taxonomic community variation. We find that environmental conditions strongly influence the distribution of functional groups in marine microbial communities by shaping metabolic niches, but only weakly influence taxonomic composition within individual functional groups. Hence, functional structure and composition within functional groups constitute complementary and roughly independent “axes of variation” shaped by markedly different processes.