Methanotrophs colonize freshwater and marine sediments, but in the latter the density of methylotrophs is not sufficient to account for the methane consumption. In this work, we studied the composition of methanotrophic communities associated with two marine sediments that differ for the methane levels consumed (1,100 and 200 mg CH4 m−3, respectively). We used the combination of genetic and isotope approaches to demonstrate that an uncultured archaeal Methanosarcina bavarica species is abundant and active in the sediment that consumed more methane. Moreover, as revealed by microsensors, the ex situ incubation experiments indicated that members of this population were metabolically active also in the sediment that consumed less methane. Although uncultured, this Methanosarcina lineage harbored all genes encoding for enzymes needed for both aerobic methanotrophy and methanogenesis, suggesting that this lineage had already diversified along these two pathways. However, the abundance of M. bavarica in both sediment communities could not be explained only by the concentration of the substrate. Furthermore, microsensor measurements revealed that the substrate had to be metabolized for the production of oxygen that, as revealed by genetic analysis, was coupled with the oxidation of the substrate. Therefore, our work is one of the few studies where the presence of this uncultured species was confirmed in situ, thus providing crucial information about the methane cycle in the marine environment. The new findings add to the understanding of the mechanisms of methane oxidation in the sediments and provide important insights on this unique metabolic pathway.
Abstract: The marine iron-sulfur (Fe/S) clusters are used by many organisms to reduce the quinone pool of the electron transport chain, thus contributing to cellular energy conservation and to the energy balance of marine ecosystems. Besides, Fe/S clusters are involved in detoxification of reactive oxygen species (ROS), both in living cells and upon cell death. The high sensitivity of marine organisms to ROS suggests that they have an extremely efficient defense system to counteract free radicals attack, and that the biochemistry of Fe/S clusters plays a key role in protecting organisms from oxidative damage. To fulfill these diverse functions, the biogenesis of Fe/S clusters is an evolutionary highly conserved process that allows, in some phyla (e.g., fungi), a complete absence of Fe/S synthesis and only depends on the uptake of external Fe/S clusters. However, very few organisms, among those that survive in the oxygenated ocean, have developed Fe/S cluster biogenesis capabilities.
The main objective of this work was to get a deeper insight into the biosynthesis of Fe/S clusters in marine phytoplankton, i.e., unicellular eukaryotes and cyanobacteria. To this purpose, the model organism Phaeodactylum tricornutum was analyzed in terms of (1) the presence of homologs of Nfs1 and Isd11/Isd11-like proteins, and (2) the relative transcript abundance of siderophore- and ISC-mediated iron and sulfur mobilization systems.
The results showed that phaeodactylum tricornutum had at least two Nfs1 homologs (NfsA and NfsB) with unique domain organization. Analysis of the expression of both genes by Real-Time RT-PCR indicated that, in P. tricornutum, NfsB appeared to be more expressed during growth than NfsA, which had a lower relative expression. Among ISC-type proteins, Phaeodactylum tricornutum showed a single IscA-like protein with an unusual domain organization, and a homolog of Yfe, known as Isd11/Isd11-like proteins. The results of expression analysis of these genes showed that iscA is more highly expressed than the iscB homolog. Isd11-like and, especially, Yfe were constitutively and highly expressed both under iron limiting conditions and under iron replete conditions.
The results obtained in this study indicated that Nfs1 and Isd11/Isd11-like homologs are present in the genome of the marine centric diatom Phaeodactylum tricornutum. Moreover, both NfsA and NfsB of P. tricornutum share the same organization of the domain organization as those present in other organisms able to grow in iron-depleted environments. These results show that marine diatoms do not only uptake iron and manganese as observed for other cyanobacteria, but that they have developed a specific iron uptake mechanism that allows a constant scavenging of Fe(2+) ions and a slow uptake of Fe(3+) under Fe-limited conditions.
Abstract: Benthic ecosystems are highly relevant for the maintenance and recycling of carbon and other key elements in the ocean. Yet, the role of benthic organisms in carbon cycling is still poorly understood. A major obstacle to this field of research is that benthic organisms are challenging to sample and analyze, so benthic C uptake experiments are difficult to conduct. This review describes the development of a culture system developed to enable the physiological investigation of marine benthic organisms by allowing controlled benthic or pelagic incubations in a stable environment. This chamber, coupled with a flow-through system, allows the incubation of small pieces of sediment, ranging from cm to m in size, under controlled conditions that allow benthic and pelagic incubations. This paper reports the results of incubations with the benthic diatom Heterocapsa pygmaea.
The technique described here enabled the first experimental testing of C uptake by the benthic diatom H. pygmaea, allowing for a physiological analysis of this species under controlled laboratory conditions. In control conditions, we found that H. pygmaea had an average daily CO2 uptake of 1.0 ± 0.2 nmol C cm−2 s−1, with rates that were linearly dependent on light intensity. The benthic diatom showed a net C exchange between the benthic and the pelagic compartments, a feature shared by other benthic diatoms, in particular Thalassiosira pseudonana. H. pygmaea and other phytoplankton species are considered to be efficient C sinks in the marine realm, but recent studies highlighted the plasticity of the uptake mechanisms of this species when responding to environmental stress. The ability of H. pygmaea to control its C uptake via photosynthesis seems to provide protection against stressful conditions. Our study demonstrates that the C efflux from benthic organisms may not be as low as previously considered and that the capacity of H. pygmaea to respond to environmental stress and change its C uptake properties could allow this species to potentially exert a larger influence on ocean C cycling than previously considered.
Abstract: Although many studies have shown a clear relationship between sediment composition and sediment microbial communities in lakes and oceans, little information exists about the link between these two variables in freshwater riverbeds. To provide novel insights into benthic microbial communities associated with sediment, this study combined geochemical measurements, phylogenetic composition, and metagenomic data. Sediment samples were collected in the Piemonte Region (Italy) at 10 different stations, ranging from the headwaters of a pristine river system to downstream areas of urbanized streams, and samples were analyzed for mineralogy, elemental composition and geochemical parameters. The Illumina platform and 16S rRNA gene sequencing showed that the bacterial community in these sediment samples was dominated by Betaproteobacteria (BetaXVIII and BetaXV), especially in downstream areas. Taxonomic analysis revealed a relationship between the microbial community composition and the sediment geochemistry, characterized by high levels of Mn (up to 19.6 g/kg), followed by S (2.7 g/kg), Mg (0.7 g/kg) and Ca (0.5 g/kg). Sequences were identified in known sulfur cycling microorganisms (Desulfobulbaceae and Bacteroidetes), suggesting sulfate as the major electron acceptor for bacterial metabolism. Overall, our results suggest that riverbeds act as a local hot spot of sulfide production and can be considered hotspots for sulfur cycling in freshwater riverbeds.
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