Bioconcentration and lethal effects of gas-condensate and crude oil on nearshore copepod assemblages

The progressive establishment of gas platforms and increasing petroleum accidents pose a threat to zooplankton communities and thus to pelagic ecosystems. This study is the first to compare the impacts of gas-condensate and crude oil on copepod assemblages. We conducted microcosm experiments simulating slick scenarios at five different concentrations of gas-condensate and crude oil to determine and compare their lethal effects and the bioconcentration of low molecular weight polycyclic aromatic hydrocarbons (LMW-PAHs) in eastern Mediterranean coastal copepod assemblages. We found that gas-condensate had a two-times higher toxic effect than crude oil, significantly reducing copepod survival with increased exposure levels. The LMW-PAHs bioconcentration factor was 1-2 orders of magnitude higher in copepods exposed to gas-condensate than in those exposed to crude oil. The median lethal concentration (LC50) was significantly lower in calanoids vs. cyclopoid copepods, suggesting that calanoids are more susceptible to gas-condensate and crude oil pollution, with potential trophic implications.

Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.

Tar pollution event (2021) at the Southeastern Levantine oligotrophic basin, short-term impacts and operational oceanography perspectives

The Levantine basin (LB) in the Southeastern Mediterranean Sea is a high-risk oil pollution hot spot owing to its dense maritime traffic and intense oil and gas exploration and exploitation activities. In February 2021 the Israeli LB shorelines were impacted by an exceptional tar pollution event (~550 tons; average distribution: ~3 kg tar m-1 front beach) of an unknown oil spill source. Here we report on the immediate numerical modelling assessment of the oil spill propagation and tar distribution; operational use of underwater gliders for tracking water column anomalies of dissolved polycyclic aromatic hydrocarbons (PAHs) and turbidity signals; the beached tar composition and amounts and the short-term response of the microbial population along the ~180 km shoreline. This pollution event emphasizes the need for improving the early warning systems for oil spills and implementing continuous operational monitoring at high-risk, ecologically sensitive and valuable resource areas like the Israeli LB waters.

Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia

IMPORTANCE

Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.

Tar patties are hotspots of hydrocarbon turnover and nitrogen fixation during a nearshore pollution event in the oligotrophic southeastern Mediterranean Sea

Weathered oil, that is, tar, forms hotspots of hydrocarbon degradation by complex biota in marine environment. Here, we used marker gene sequencing and metagenomics to characterize the communities of bacteria, archaea and eukaryotes that colonized tar patties and control samples (wood, plastic), collected in the littoral following an offshore spill in the warm, oligotrophic southeastern Mediterranean Sea (SEMS). We show potential aerobic and anaerobic hydrocarbon catabolism niches on tar interior and exterior, linking carbon, sulfur and nitrogen cycles. Alongside aromatics and larger alkanes, short-chain alkanes appear to fuel dominant populations, both the aerobic clade UBA5335 (Macondimonas), anaerobic Syntropharchaeales, and facultative Mycobacteriales. Most key organisms, including the hydrocarbon degraders and cyanobacteria, have the potential to fix dinitrogen, potentially alleviating the nitrogen limitation of hydrocarbon degradation in the SEMS. We highlight the complexity of these tar-associated communities, where bacteria, archaea and eukaryotes co-exist, likely exchanging metabolites and competing for resources and space.

Shared ancestry of algal symbiosis and chloroplast sequestration in foraminifera

Foraminifera are unicellular organisms that established the most diverse algal symbioses in the marine realm. Endosymbiosis repeatedly evolved in several lineages, while some engaged in the sequestration of chloroplasts, known as kleptoplasty. So far, kleptoplasty has been documented exclusively in the rotaliid clade. Here, we report the discovery of kleptoplasty in the species Hauerina diversa that belongs to the miliolid clade. The existence of kleptoplasty in the two main clades suggests that it is more widespread than previously documented. We observed chloroplasts in clustered structures within the foraminiferal cytoplasm and confirmed their functionality. Phylogenetic analysis of 18S ribosomal RNA gene sequences showed that H. diversa branches next to symbiont-bearing Alveolinidae. This finding represents evidence of of a relationship between kleptoplastic and symbiotic foraminifera.. Analysis of ribosomal genes and metagenomics revealed that alveolinid symbionts and kleptoplasts belong to the same clade, which suggests a common ancestry.

Downwind gas condensate volatiles affect phytoplankton communities

We investigated the effects of volatile organic carbons (VOCs) evaporated from gas condensate on the cyanobacteria Synechococcus sp. WH8103, the diatom Asterionellopsis glacialis, and the dinoflagellate Alexandrium minutum. We used custom algal incubation chambers enabling only the gas condensate-derived VOCs to interact with the cell cultures via an atmospheric bridge, without direct contact with the hydrocarbon oil. The exposure to gas condensate VOCs reduced the abundance, growth rate, and photosynthetic efficiency of Synechococcus sp. WH8103. Thiobarbituric acid reactive substances (TBARS) assays hint at oxidative damage to the chloroplasts and/or the thylakoid membranes in this organism. A.glacialis abundance, physiological state and growth rates remained unchanged, whereas A.minutum abundance and photosynthetic efficiency increased relative to their respective controls. Our results demonstrate that the effects of a gas condensate formed due to an oil spill will not be restricted to the polluted area, but may be prominent in downwind locations through atmospheric transport.

Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments

In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.

Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii

Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.

Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels

Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.

Anthropogenic and natural disturbances along a river and its estuary alter the diversity of pathogens and antibiotic resistance mechanisms

Antibiotic resistance (AMR) in pathogens threatens human health worldwide, and antibiotic-resistant bacteria (ARB) are widespread in the environment. In particular, anthropogenically-disturbed rivers became reservoirs of ARBs and hotspots of antibiotic resistance gene (ARG) transmission. However, the diversity and sources of ARB, and the mechanisms of ARG transmission are not fully known. Here, we used deep metagenomic sequencing to study the dynamics of pathogens and their antibiotic resistance mechanisms along the Alexander River (Israel), affected by sewage and animal farm runoffs. Putative pathogens such as Aeromicrobium marinum and Mycobacterium massilipolynesiensis were enriched in western stations, following the inputs of polluted Nablus River. Aeromonas veronii was dominant in eastern stations in Spring. Several AMR mechanisms showed distinct patterns in Summer-Spring (dry season) and Winter (rainy season). We found low abundance beta-lactamases conferring carbapenem resistance: e.g., OXA-912 was linked to A. veronii in Spring; OXA-119 and OXA-205 to Xanthomonadaceae in Winter. We classified 33 % of ARG-containing contigs as putative plasmid sequences, indicating the high potential for resistome transmission. A limited number of ARGs were linked to putative phages. Our results suggest that this model river is a hotspot for AMR activity and transmission, and highlight the merit of deep sequencing for AMR discovery.

Discharge of Polyphosphonate-Based Antiscalants via Desalination Brine: Impact on Seabed Nutrient Flux and Microbial Activity

Desalination brine is a hypersaline byproduct that contains various operational chemicals such as polyphosphonate-based antiscalants. Brine often sinks and flows over the seabed by density currents; therefore, it may affect sediment-water nutrient fluxes and thus microbial activity. We quantified these parameters in brine plumes around two large-scale desalination facilities located in the P-limited Southeastern Mediterranean Sea. The benthic nutrient fluxes and microbial activity were determined using ex-situ core benthocosms, to which we added brine from the dispersion area in excess salinities of ∼3% and 5% above natural levels. A higher influx of dissolved organic phosphorus (∼6-fold) and an efflux of dissolved organic carbon (∼1.7-fold) were measured in the brine-amended cores relative to the controls. This was accompanied by increased oxygen consumption (15%) and increased microbial activity (∼1.5-6.5-fold). Field observations support the results from experimental manipulations, yielding ∼4.5-fold higher microbial activity rates around the brine plume compared to uninfluenced locations. Our results imply that desalination brine can alter sedimentary processes affecting benthic nutrients inventories. Moreover, we show that brine acts as a vector of anthropogenic P, stimulating microbial activity in the sediment-water interface.

Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity

Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). Trichodesmium thiebautii (puffs) and Trichodesmium erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to Trichodesmium nobis and Trichodesmium miru, respectively that likely occurred as single filaments. The hetR gene phylogeny further indicated that the genotype in clade IV could represent the species Trichodesmium contortum. Importantly, we show the presence of hetR paralogs in Trichodesmium, where two copies of the hetR gene were present within T. thiebautii genomes. This may lead to the overestimation of Trichodesmium diversity as one of the copies misidentified T. thiebautii as Trichodesmium aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.

The worm affair: fidelity and environmental adaptation in symbiont species that co-occur in vestimentiferan tubeworms

The symbioses between the vestimentiferan tubeworms and their chemosynthetic partners (Gammaproteobacteria, Chromatiales and Sedimenticolaceae) hallmark the success of these organisms in hydrothermal vent and hydrocarbon seep deep-sea habitats. The fidelity of these associations varies, as both the hosts and the symbionts can be loose in partner choice. Some tubeworms may host distinct symbiont phylotypes, which often co-occur in a single host individual. To better understand the genetic basis for the promiscuity of tubeworm symbioses, we assembled and investigated metagenome-assembled genomes of two symbiont phylotypes (species, based on the average nucleotide identity < 95%) in Lamellibrachia anaximandri, a vestimentiferan endemic to the Mediterranean Sea, in individuals collected from Palinuro hydrothermal vents (Italy) and hydrocarbon seeps (Eratosthenes seamount and Palmahim disturbance). Using comparative genomics, we show that mainly mobilome and genes involved in defence mechanisms distinguish the symbiont genotypes. While many central metabolic functions are conserved in the tubeworm symbionts, nitrate respiration (Nar, Nap and Nas proteins) is modular, yet this modularity is not linked to phylotype, but rather to geographic location, potentially implying adaptation to the local environment. Our results hint that variation in a single moonlighting protein may be responsible for the fidelity of these symbioses.

Dust-borne microbes affect Ulva ohnoi's growth and physiological state

The marine macroalgae Ulva sp. is considered an ecosystem engineer in rocky shores of temperate waters worldwide. Ulva sp. harbors a rich diversity of associated microbial epibionts, which are known to affect the algae's typical morphological development and 'health'. We examined the interaction between airborne microbes derived from atmospheric aerosols and Ulva ohnoi growth and physiological state. Specifically, we measured U. ohnoi growth rates and photosynthetic efficiency (Fv/Fm), alongside its microbial epibionts abundance, activity and diversity following dust (containing nutrients and airborne microorganisms) or UV-treated dust (only nutrients) amendments to filtered seawater. Parallel incubations with epibionts-free U. ohnoi (treated with antibiotics that removed the algae epibionts) were also tested to specifically examine if dust-borne microbes can replenish the epibiont community of U. ohnoi. We show that viable airborne microbes can restore U. ohnoi natural microbial epibionts communities, thereby keeping the seaweed alive and 'healthy'. These results suggest that microbes delivered through atmospheric aerosols can affect epiphyte biodiversity in marine flora, especially in areas subjected to high annual atmospheric dust deposition such as the Mediterranean Sea.

Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges

Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.

First evidence for the presence of iron oxidizing zetaproteobacteria at the Levantine continental margins

During the 2010–2011 E/V Nautilus exploration of the Levantine basin’s sediments at the depth of 300–1300 m, densely patched orange-yellow flocculent mats were observed at various locations along the continental margin of Israel. Cores from the mat and the control locations were collected by remotely operated vehicle system (ROV) operated by the E/V Nautilus team. Microscopic observation and phylogenetic analysis of microbial 16S and 23S rRNA gene sequences indicated the presence of zetaproteobacterial stalk forming Mariprofundus spp. – like prokaryotes in the mats. Bacterial tag-encoded FLX amplicon pyrosequencing determined that zetaproteobacterial populations were a dominant fraction of microbial community in the biofilm. We show for the first time that zetaproteobacterial may thrive at the continental margins, regardless of crustal iron supply, indicating significant fluxes of ferrous iron to the sediment-water interface. In light of this discovery, we discuss the potential bioavailability of sediment-water interface iron for organisms in the overlying water column.