Geochemical characterization of clastic sediments sheds light on energy sources and on alleged anthropogenic impacts in cave ecosystems

Caves are usually oligotrophic ecosystems, where the organic matter represents a limiting factor to the hypogeal community and sediments are often a significant energy source. With a view to identifying the energy input influencing the ecological processes occurring in caves, as well as the potential alteration sources of the natural equilibriums, geochemical features of several typologies of clastic sediments from the Pertosa-Auletta Cave (Italy) were investigated. The collected sediments, analyzed for a number of chemical (organic matter, Al, B, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, S, Si, Sr, Ti, V, Zn concentrations) and mineralogical (quartz, calcite, dolomite, clay minerals) characteristics, showed a different composition. Overall, their origin is supposed to be allochthonous, related to the important fluviokarst activities interesting the cave in the past, whereas the abundance of calcitic and dolomitic compounds can be autochthonous, being the carbonate the main host rock. The highest concentrations of organic matter, together with C, Cu, Mo, N, P, Pb, S and Zn, highlighted in one sample composed mainly of bats guano, revealed an important bioavailable energy input as well as a pollutant accumulation, mainly of anthropogenic origin.

Optimization of eDNA metabarcoding methodology for the biomontoring of the ichthyofauna in the Eastern Mediterranean Sea

Environmental DNA (eDNA) metabarcoding is a relatively new methodology for the detection of organisms in an environmental sample, with emerging applications in the fields of ecology, conservation, invasive biology, biomonitoring and more. Several studies are using eDNA nowadays, yet in the Mediterranean marine ecosystems, its use is limited mostly on plankton studies so far. The icthyofauna of the Eastern Mediterranean is undergoing major changes due to biological invasions, mainly form the Red Sea, in combination with the climate change, and a reliable high-throughput biomonitoring tool is essential to monitor these changes. The main goal of this study was to develop a reliable eDNA metabarcoding protocol to study and monitor fish biodiversity in the oligotrophic ecosystems of the Eastern Mediterranean. The study had two parts: a) standardization of the method by testing two different sets of primers in aquaria with known fish species assemblages, and b) estimation of the heterogeneity of fish eDNA distribution in different habitats within a coastal area, in order to determine the most efficient sampling strategy. In both cases, samples were analysed through Next Generation Sequencing on a Illumina MiSeq platform. To standardize the method, we sampled and filtered water from two tanks of the 'Cretaquarium'. We tested two different sets of primers, one for 16S rRNA and the MiFish primers of Miya et al. (2015) for 12S rRNA, in order to estimate their efficiency in assessing species' composition both qualitatively and semi-quantitatively. Both primer sets performed well and most taxa in both tanks were detected up to species level, with 16S marker exhibiting higher resolution. A rather weak correlation was also detected between actual fish biomass and relative abundance as estimated by eDNA metabarcoding. To estimate the eDNA heterogeneity in natural ecosystems, we sampled water in a coastal ecosystem over three distinct types of habitats: hard substrate, soft substrate, Posidonia meadows, as well as in the mid of the water column. Three samples per habitat were collected, two PCRs per DNA extract were performed and results were obtained only for the 16S marker. A total of 69 taxa were detected, with 55 of them distinguished at the species level, while in each sample the number of taxa detected ranged from 13 to 27. Posidonia meadows and the water column samples showed the greatest heterogeneity, in contrast to the hard and soft substrate samples that showed little differentiation both within and between habitat type. Based on these results, an improved protocol should include more technical PCR replicates per sample (at least 3 PCRs), at least one sample per habitat in each area, and a larger volume of water filtered per sample or alternatively, more samples mixed together in order to achieve better representation of the community. Moreover, it was apparent the need of a more complete and curated reference database for the Mediterranean fishes for the aforementioned markers, in order to be able to reliably identify fishes of the Mediterranean ecosystems at species level. In conclusion, the method seems to work well, and with some small improvements, as well as with the complementation of the respective reference databases, it can be used as a reliable tool for the study of biodiversity and biomonitoring of fish communities of the oligotrophic ecosystems of the Eastern Mediterranean Sea.

Juncus Bulbosus Tissue Nutrient Concentrations and Stoichiometry in Oligotrophic Ecosystems: Variability with Seasons, Growth Forms, Organs and Habitats

Aquatic plant nutrient concentrations provide important information to characterise their role in nutrient retention and turnover in aquatic ecosystems. While large standing biomass of aquatic plants is typically found in nutrient-rich localities, it may also occur in oligotrophic ecosystems. Juncus bulbosus is able to form massive stands even in very nutrient-dilute waters. Here we show that this may be achieved by tissues with very high carbon-to-nutrient ratios combined with perennial (slow) growth and a poor food source for grazers inferred from plant stoichiometry and tissue nutrient thresholds. We also show that the C, N, P and C:N:P stoichiometric ratios of Juncus bulbosus vary with the time of year, habitats (lakes versus rivers) and organs (roots versus shoots). We found no differences between growth forms (notably in P, inferred as the most limiting nutrient) corresponding to small and large plant stands. The mass development of J. bulbosus requires C, N and P, whatever the ecosystem (lake or river), and not just CO2 and NH4, as suggested in previous studies. Since macrophytes inhabiting oligotrophic aquatic ecosystems are dominated by isoetids (perennial plants with a high root/shoot ratio), attention should be paid to quantifying the role of roots in aquatic plant stoichiometry, nutrient turnover and nutrient retention.

Spiders and Carabid beetles as the elements of arthropod’s diversity in ecosystems of Lva-Stvyga inter-river area (Rivne province, Ukraine)

The series of epigeibiontic Arthropoda communities are investigated in several fo­rest and woodland ecosystems of Lva-Stvyga inter-river area within Volyn Polissia region of Ukraine. This is remoted district with peculiar ecological features as well as dominancy of oligotrophic forest and peat-bog ecosystems. The material of epigeibiontic arthropods was collected in spring and summer 2015 by the method of Barber’s pitfall traps. There are three pilot areas explored: 1) wet oligotrophic pine woodland (Ledo-Pinion); 2) late secondary succession of wet oligotrophic pine woodland cutting area; 3) dry oligotrophic pine woodland on the sands (Dicrano-Pinion). In total, 186 species of epigeibiontic arthropods were explored. There were found 75 species of spiders (Araneae) and 27 species of ground beetles (Coleoptera, Carabidae) among them. Along with that, the ants (Formicidae) have dominancy within related communities with an amount about 82–87 % of total arthropod individual’s number, and Araneae both with Carabidae exceed 6–7 % of this number. Nevertheless, there are nine spider species found for the first time for Ukrainian Polissia region and 1 species – Gnaphosa nigerrima – for the territory of Ukraine. One Carabid beetle species (Cymindis vaporariorum) was found at the first time for West Polissia region of Ukraine. There is also a number of rare and less known Araneae and Carabidae species found. Thus, the species composition and structure of explored Araneae & Carabidae communities show many specific features, which are caused by characteristic ecological and biogeographical peculiarities of oligotrophic ecosystems within investigated area. Following research of related taxonomical groups has to be directed to the wider spectrum of ecosystems covering, especially to peat-bog and mire complexes as unique protected habitats in Ukraine and the European Union.

Leave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core

The hyperarid core of the Atacama Desert is an extremely harsh environment previously thought to be colonized by only a few heterotrophic bacterial species. In addition, carbon and nitrogen cycling in these highly oligotrophic ecosystems are poorly understood. Here we genomically resolved a novel genus of Thaumarchaeota, Ca. Nitrosodesertus, found below boulders of the Atacama hyperarid core, and used comparative genomics to analyze their pangenome and site-specific adaptations. Their genomes contain genes for ammonia oxidation and the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, indicating a chemolithoautotrophic lifestyle. Ca. Nitrosodesertus possesses the capacity for tolerating extensive environmental stress highlighted by the presence of genes against oxidative stress, DNA damage and genes for the formation of biofilms. These features are likely responsible for their dominance in samples with extremely low water content across three different boulder fields and eight different boulders. Genome-specific adaptations of the genomes included the presence of additional genes for UV resistance, heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Our results suggest that Thaumarchaeota mediate important carbon and nitrogen cycling in the hyperarid core of the Atacama and are part of its continuous and indigenous microbiome.

Ammonium is the preferred source of nitrogen for planktonic foraminifer and their dinoflagellate symbionts

The symbiotic planktonic foraminifera Orbulina universa inhabits open ocean oligotrophic ecosystems where dissolved nutrients are scarce and often limit biological productivity. It has previously been proposed that O. universa meets its nitrogen (N) requirements by preying on zooplankton, and that its symbiotic dinoflagellates recycle metabolic ‘waste ammonium’ for their N pool. However, these conclusions were derived from bulk 15 N-enrichment experiments and model calculations, and our understanding of N assimilation and exchange between the foraminifer host cell and its symbiotic dinoflagellates remains poorly constrained. Here, we present data from pulse-chase experiments with 13 C-enriched inorganic carbon, 15 N-nitrate, and 15 N-ammonium, as well as a 13 C- and 15 N- enriched heterotrophic food source, followed by TEM (transmission electron microscopy) coupled to NanoSIMS (nanoscale secondary ion mass spectrometry) isotopic imaging to visualize and quantify C and N assimilation and translocation in the symbiotic system. High levels of 15 N-labelling were observed in the dinoflagellates and in foraminiferal organelles and cytoplasm after incubation with 15 N-ammonium, indicating efficient ammonium assimilation. Only weak 15 N-assimilation was observed after incubation with 15 N-nitrate. Feeding foraminifers with 13 C- and 15 N-labelled food resulted in dinoflagellates that were labelled with 15 N, thereby confirming the transfer of 15 N-compounds from the digestive vacuoles of the foraminifer to the symbiotic dinoflagellates, likely through recycling of ammonium. These observations are important for N isotope-based palaeoceanographic reconstructions, as they show that δ 15 N values recorded in the organic matrix in symbiotic species likely reflect ammonium recycling rather than alternative N sources, such as nitrates.

Microbial regeneration and respiration of Fe(III) outcompetes sulphate respiration in ferruginous, high-sulphate oligotrophic ecosystems

<div> </div><div> <p>In anoxic lacustrine systems, at low-sulphate concentrations, sulphidisation acts as a crucial pathway driving the reductive dissolution of amorphous and nanocrystalline Fe-(oxyhydr)oxides in the presence of dissolved organic matter. The cycling of intermediate sulphur through a disproportionation reaction with the available Fe(III) stocks supports a continued intermediate sulphur-based respiration mechanism often referred to as cryptic. The prevalence of the so-called cryptic mechanism in meromictic, low-sulphate lakes could be attributed to the abundance of crystalline as opposed to more reactive amorphous iron (oxyhyd)roxides, which by immobilizing ferric iron also favour microbial sulphate reduction (MSR) promoting the accumulation of solid phase intermediate sulphur and sulphides<sup>[1]</sup>. In a ferruginous, sulphate-rich and oligotrophic post-mining lake (Lake Medard, Czech Republic) we observed a departure from this condition as dissolved sulphide does not accumulate in the bottom water column nor precipitate in the anoxic sediments.<sup>[2]</sup> Analyses of the bacterioplankton abundance in the hypolimnion indicate a marked niche compartmentalization, with Fe(II)-oxidising microbes, such as <em>Gallionella</em> sp., <em>Rhodopseudomonas</em> sp. and <em>Sideroxydans</em> sp., being important at the dysoxic to anoxic (ferruginous) interface where they drive the regeneration of ferric iron. On the other hand, Fe(III)-reducers, such as <em>Geobacter</em> sp. and<em> Rhodoferax</em> sp. are present at the O<sub>2</sub>-depleted monimolimnion and in the uppermost anoxic sediments. Toward the redox interface, the chemolithotrophic community described above allows for Fe-(re)cycling and drives the oxidation and turnover of the scarcely available volatile fatty acids. Sulphate reducers (e.g. Desulfobulbaceae, <em>Chrostridia, Desulfarculus</em>) and microorganisms capable of anammox, such as <em>Nitrosomonas</em>  and <em>Nitrosospira</em> where found below the redoxcline. However, together these obligate anaerobes account for < 4% of the total bacterial OTUs identified in the monimolimnion. Our observations in this purported modern analogue to ferruginous, relatively sulphate-enriched Precambrian coastal zones raise the possibility that limited dissimilatory sulphate reduction in the Earth’s primitive ferruginous oceans was rather linked to the scarcity of suitable organic substrates and high rates of Fe-(re)cycling than to low levels of dissolved sulphate. The co-precipitation of minor amounts of gypsum/anhydrite and siderite, with Fe(II,III)-(oxyhydr)oxides further support a potential link between the deep Lake Medard precipitation environment and certain mid- to Late-Archean marginal settings, where these phases have been described to be primary and/or early diagenetic in origin. </p> </div><div> <p><sup>[1]</sup> Hansel, C.M., Lentini, C.J., Tang, Y., et al. ISME J. 9, 2400–2412 (2015). </p> </div><div> <p><sup>[2]</sup> Petrash, D.A., Jan, J., Sirová, et al. Environ. Sci. Process. Impacts 20, 1414–1426 (2018). </p> </div><div> <p> </p> </div>