Aqueous system-level processes and prokaryote assemblages in the ferruginous and sulfate-rich bottom waters of a post-mining lake

In the aqueous oligotrophic ecosystem of a post-mining lake (Lake Medard, Czechia), reductive Fe(II) dissolution outpaces sulfide generation from microbial sulfate reduction (MSR), and ferruginous conditions occur without quantitative sulfate depletion. An isotopically constrained estimate of the rates of sulfate reduction (SRR) suggests that despite a high genetic potential, this respiration pathway is limited by the rather low amounts of metabolizable organic carbon. This points to substrate competition exerted by iron and nitrogen respiring prokaryotes. Yet, the microbial succession across the nitrogenous and ferruginous zones of the bottom water column also indicates sustained genetic potential for chemolithotrophic sulfur oxidation. Therefore, our isotopic SRR estimates could be rather portraying high rates of anoxic sulfide oxidation to sulfate, probably accompanied by microbially induced disproportionation of S intermediates. Near and at the anoxic sediment-water interface, vigorous sulfur cycling can be fuelled by ferric and manganic particulate matter and redeposited siderite stocks. Sulfur oxidation and disproportionation then appear to prevent substantial stabilization of iron monosulfides as pyrite but can enable the interstitial precipitation of small proportions of equant microcrystalline gypsum. This latter mineral isotopically fingerprints sulfur oxidation proceeding at near equilibrium with the ambient anoxic waters, whilst authigenic pyrite-sulfur displays a 38 to 27 ‰ isotopic offset from ambient sulfate, suggestive of incomplete MSR and likely reflective also of an open sulfur cycling system. Pyrite-sulfur fractionation decreases with increased reducible reactive iron in the sediment. In the absence of ferruginous coastal zones today, the current water column redox stratification in the post-mining Lake Medard has scientific value for (i) testing emerging hypotheses on how a few interlinked biogeochemical cycles operated in nearshore paleoenvironments during redox transitional states; and (ii) to acquire insight on how similar early diagenetic redox proxy signals developed in sediments affected by analogue transitional states in ancient water columns.

Preliminary results of studying the carbon isotope composition of conodont elements at the border of Devonian and Carboniferous periods (Kamenka river sections, Pechora carbonate platform)

Research subject. Changes in the trophic structure of shallow-water pelagic ecosystems at the Devonian/Carboniferous border were investigated by studying the carbon isotope composition of conodont organic matter.Materials and methods. Two Devonian-Carboniferous shallow-water clayey-carbonate sections located in the southern part of the Pechora-Kozhva Uplift (Pechora Plate) were analysed. The Devonian-Carboniferous boundary was detected by the first occurrences of Siphonodella sulcata, S. semichatovae and Patrognathus crassus, as well as by the last occurrence of Pseudopolygnathus graulichi. The carbon isotope composition was investigated both in whole-rock carbonate samples and the conodont organic matter of two dominant species (Polygnathus parapetus and P. communis communis).Results. The distribution of stable carbon isotopes in the organic matter of conodont elements accompanied by the data on carbonate isotope composition allowed us to suggest changes in the food composition of the dominant taxa during the Late Famennian-Early Tournaisian transition. It was assumed that the latest Famennian representatives of Polygnathus parapetus and P. communis communis consumed largely phyto- and zooplankton, which is characterized by a light isotopic composition of organic carbon. The nutrition based on phyto- and zooplankton with a heavier isotopic composition of organic carbon was suggested for the early Tournaisian representatives of these species.Conclusions. The discovered variations in the carbon isotope composition of conodont organic matter in shallow-water facies may correspond to the change from the eutrophic pelagic ecosystem to the oligotrophic ecosystem, and/or global perturbation of the carbon cycle due to climatic changes. Since the available data is limited to two geological sections, it is impossible to unambiguously interpret the scale (local, regional, global) of these variations and their correlation potential.

Relação Fitoplâncton - Zooplâncton em Ambiente Oligotrófico(Fitoplankton-Zooplankton Relationship in Oligotrophic Environment)

Ecossistemas lênticos de pequeno porte respondem rapidamente às condições ambientais, influenciando a comunidade planctônica devido às flutuações bióticas e abióticas do corpo d’água. Este estudo teve como objetivo analisar os parâmetros físico-químicos e a identificação da comunidade planctônica (fitoplâncton, zooplâncton e bacterioplâncton) presentes no reservatório, correlacionando esses organismos em um ambiente oligotrófico. As análises foram realizadas mensalmente no período de julho/2014 a junho/2016. A análise de todos os parâmetros físico-químicos e biológicos foi realizados de acordo com metodologia oficial. Empregou-se ferramentas estatísticas multivariadas (ACP) e teste de Pearson para avaliar a correlação entre as variáveis abióticas e a biomassa total de cada grupo planctônico. Nesta pesquisa encontrou-se uma relação positiva entre as biomassas totais da comunidade zooplânctonica e fitoplânctonica, entretanto componentes do bacterioplancton, não foi significativo. Estes resultados indicaram que a predação e/ou competição não são relações ecológicas significativas entre as espécies zooplanctônicas e fitoplanctônicas presentes neste ecossistema oligotrófico, existindo assim uma relação favorável entre os grupos estudados. Desta forma, o desenvolvimento desses organismos foi influenciado pelas mesmas variáveis abióticas (manganês, dureza e temperatura), atuando de forma direta no estabelecimento de suas biomassas. A B S T R A C TSmall lentic ecosystems respond rapidly to environmental conditions, influencing the planktonic community due to the biotic and abiotic fluctuations of the water body. This study aimed to analyze the physicochemical parameters and identification of the planktonic community (phytoplankton, zooplankton, and bacterioplankton) present in the reservoir, correlating these organisms in an oligotrophic environment. The analyses were performed monthly from July/2014 to June/2016. The analysis of all physicochemical and biological parameters was carried out according to the conventional methodology. Multivariate statistical tools (PCA) and Pearson's test were used to evaluate the correlation between the abiotic variables and the total biomass of each planktonic group. In this research was found a positive relation between the total biomasses of the zooplanktonic community and phytoplanktonic. However, components of bacterioplankton were not significant. These results indicate that predation and competition are not significant ecological relationships between zooplanktonic and phytoplanktonic species present in this oligotrophic ecosystem, and there is a favorable relationship between the studied groups. In this way, the development of these organisms was influenced by the same abiotic variables (manganese, hardness, and temperature), acting directly in the establishment of their biomasses.Keywords: plankton, reservoir, abiotic factors.

Genomes of Abundant and Widespread Viruses from the Deep Ocean

ABSTRACT The deep sea is a massive, largely oligotrophic ecosystem, stretched over nearly 65% of the planet’s surface. Deep-sea planktonic communities are almost completely dependent upon organic carbon sinking from the productive surface, forming a vital component of global biogeochemical cycles. However, despite their importance, viruses from the deep ocean remain largely unknown. Here, we describe the first complete genomes of deep-sea viruses assembled from metagenomic fosmid libraries. “ Candidatus Pelagibacter” (SAR11) phage HTVC010P and Puniceispirillum phage HMO-2011 are considered the most abundant cultured marine viruses known to date. Remarkably, some of the viruses described here recruited as many reads from deep waters as these viruses do in the photic zone, and, considering the gigantic scale of the bathypelagic habitat, these genomes provide information about what could be some of the most abundant viruses in the world at large. Their role in the viral shunt in the global ocean could be very significant. Despite the challenges encountered in inferring the identity of their hosts, we identified one virus predicted to infect members of the globally distributed SAR11 cluster. We also identified a number of putative proviruses from diverse taxa, including deltaproteobacteria, bacteroidetes, SAR11, and gammaproteobacteria. Moreover, our findings also indicate that lysogeny is the preferred mode of existence for deep-sea viruses inhabiting an energy-limited environment, in sharp contrast to the predominantly lytic lifestyle of their photic-zone counterparts. Some of the viruses show a widespread distribution, supporting the tenet “everything is everywhere” for the deep-ocean virome. IMPORTANCE The deep sea is among the largest known habitats and a critical cog in biogeochemical cycling but remains underexplored in its microbiology. Even more than is the case for its prokaryotic community, our knowledge of its viral component has remained limited by the paucity of information provided by studies dependent upon short sequence fragments. In this work, we attempt to fill this existing gap by using a combination of classical fosmid libraries with next-generation sequencing and assembly to recover long viral genomic fragments. We have sequenced ca. 6,000 fosmids from two metagenomics libraries made from prokaryotic biomass from the deep Mediterranean Sea and recovered twenty-eight complete viral genomes, all of them novel and quite distinct from all previously described viral genomes. They are preferentially found in deeper waters and are widely distributed all over the oceans. To our knowledge, this is the first report on complete and cosmopolitan viral genomes from the bathypelagic habitat.

Transfer of diazotroph-derived nitrogen towards non-diazotrophic planktonic communities: a comparative study between <i>Trichodesmium</i> <i>erythraeum</i>, <i>Crocosphaera watsonii</i> and <i>Cyanothece</i> sp.

Biological dinitrogen (N2) fixation is the major source of new nitrogen (N) for the open ocean, and thus promotes marine productivity, in particular in the vast N-depleted regions of the surface ocean. Yet, the fate of the diazotroph-derived N (DDN) in marine ecosystems is poorly understood, and its transfer to auto- and heterotrophic surrounding plankton communities is rarely measured due to technical limitations. Moreover, the different diazotrophs involved in N2 fixation (Trichodesmium spp. vs. UCYN) exhibit distinct patterns of N2 fixation and inhabit different ecological niches, thus having potentially different fates in the marine food webs that remain to be explored. Here we used nanometer scale secondary ion mass spectrometry (nanoSIMS) coupled with 15N2 isotopic labelling and flow cytometry cell sorting to examine the DDN transfer to specific groups of natural phytoplankton and bacteria during artificially induced diazotroph blooms in New Caledonia (southwestern Pacific). The fate of the DDN was compared according to the three diazotrophs: the filamentous and colony-forming Trichodesmium erythraeum (IMS101), and the unicellular strains Crocosphaera watsonii WH8501 and Cyanothece ATCC51142. After 48 h, 7–17 % of the N2 fixed during the experiment was transferred to the dissolved pool and 6–12 % was transferred to non-diazotrophic plankton. The transfer was twice as high in the T. erythraeum bloom than in the C. watsonii and Cyanothece blooms, which shows that filamentous diazotrophs blooms are more efficient at promoting non-diazotrophic production in N-depleted areas. The amount of DDN released in the dissolved pool did not appear to be a good indicator of the DDN transfer efficiency towards the non-diazotrophic plankton. In contrast, the 15N-enrichment of the extracellular ammonium (NH4+) pool was a good indicator of the DDN transfer efficiency: it was significantly higher in the T. erythraeum than in unicellular diazotroph blooms, leading to a DDN transfer twice as efficient. This suggests that NH4+ was the main pathway of the DDN transfer from diazotrophs to non-diazotrophs. The three simulated diazotroph blooms led to significant increases in non-diazotrophic plankton biomass. This increase in biomass was first associated with heterotrophic bacteria followed by phytoplankton, indicating that heterotrophs took the most advantage of the DDN in this oligotrophic ecosystem.

Introduction to the project VAHINE: VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific

On the global scale, N2 fixation provides the major external source of reactive nitrogen to the surface ocean, surpassing atmospheric and riverine inputs, and sustains ∼ 50 % of new primary production in oligotrophic environments. The main goal of the VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific (VAHINE) project was to study the fate of nitrogen newly fixed by diazotrophs (or diazotroph-derived nitrogen) in oceanic food webs, and how it impacts heterotrophic bacteria, phytoplankton and zooplankton dynamics, stocks and fluxes of biogenic elements and particle export. Three large-volume ( ∼ 50 m3) mesocosms were deployed in a tropical oligotrophic ecosystem (the New Caledonia lagoon, south-eastern Pacific) and intentionally fertilized with ∼ 0.8 µM of dissolved inorganic phosphorus (DIP) to stimulate diazotrophy and follow subsequent ecosystem changes. VAHINE was a multidisciplinary project involving close collaborations between biogeochemists, molecular ecologist, chemists, marine opticians and modellers. This introductory paper describes in detail the scientific objectives of the project as well as the implementation plan: the mesocosm description and deployment, the selection of the study site (New Caledonian lagoon), and the logistical and sampling strategy. The main hydrological and biogeochemical conditions of the study site before the mesocosm deployment and during the experiment itself are described, and a general overview of the papers published in this special issue is presented.