The geochemical fingerprint of microbial long-distance electron transport in the seafloor

Recently, a novel “electrogenic” type of sulfur oxidation has been documented in marine sediments, whereby long filamentous cable bacteria are generating electrical currents over centimeter-scale distances. Here we propose a numerical model description that is capable of quantitatively simulating the solute depth profiles and biogeochemical transformations in such electro-active marine sediments. The model is based on a conventional reactive transport description of marine sediments, which is extended with a new model formulation for the long-distance electron transport induced by the cable bacteria. The mechanism of electron hopping is implemented to describe the electron transport along the longitudinal axis of the microbial filaments. We demonstrate that this model is capable of reproducing the observed geochemical fingerprint of electrogenic sulfur oxidation, which consists of a characteristic set of O2, pH and H2S depth profiles. Our simulation results suggest that the cable bacteria must have a high affinity for both oxygen and sulfide, and that intensive cryptic sulfur cycling takes place within the suboxic zone. A sensitivity analysis shows how electrogenic sulfur oxidation strongly impacts the biogeochemical cycling of sulfur, iron, carbon and calcium in marine sediments

Foraminiferal species responses to in situ, experimentally induced anoxia in the Adriatic Sea

Anoxia was successfully induced in four benthic chambers installed at 24 m depth in the northern Adriatic Sea for periods varying from 9 days to 10 months. During the 10-month period, species richness significantly decreased. Although no significant change in Shannon diversity and evenness was observed, the composition of the foraminiferal assemblages changed with time. This change is due to interspecific differences in tolerance to anoxia. Reophax nanus, Textularia agglutinans and Quinqueloculina stelligera all showed a significant decrease with time, strongly suggesting they are sensitive to anoxia. Conversely, Eggerella scabra, Bulimina marginata, Lagenammina atlantica, Hopkinsina pacifica and Bolivina pseudoplicata appeared to be resistant to the experimental conditions. Quinqueloculina seminula was apparently sensitive to anoxia but showed a clear standing stock increase during the first month of the experiment, which we interpret as an opportunistic response to increasing organic matter availability due to the degradation of the dead macrofaunal organisms. None of the anoxia-sensitive species is able to accumulate intracellular nitrates. Nitrate accumulation could be shown for some tested specimens of the dominant anoxia-tolerant species E. scabra and B. marginata. However, tests on the denitrification capacity of these taxa yielded negative results, suggesting that their resistance to long-term anoxia is not due to their ability to denitrify

Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria

Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future

Enhanced hyporheic exchange flow around woody debris does not increase nitrate reduction in a sandy streambed

Anthropogenic nitrogen pollution is a critical problem in freshwaters. Although riverbeds are known to attenuate nitrate, it is not known if large woody debris (LWD) can increase this ecosystem service through enhanced hyporheic exchange and streambed residence time. Over a year, we monitored the surface water and pore water chemistry at 200 points along a ~50m reach of a lowland sandy stream with three natural LWD structures. We directly injected 15N-nitrate at 108 locations within the top 1.5m of the streambed to quantify in situ denitrification, anammox and dissimilatory nitrate reduction to ammonia, which, on average, contributed 85%, 10% and 5% of total nitrate reduction, respectively. Total nitrate reducing activity ranged from 0-16µM h-1 and was highest in the top 30cm of the stream bed. Depth, ambient nitrate and water residence time explained 44% of the observed variation in nitrate reduction; fastest rates were associated with slow flow and shallow depths. In autumn, when the river was in spate, nitrate reduction (in situ and laboratory measures) was enhanced around the LWD compared with non-woody areas, but this was not seen in the spring and summer. Overall, there was no significant effect of LWD on nitrate reduction rates in surrounding streambed sediments, but higher pore water nitrate concentrations and shorter residence times, close to LWD, indicated enhanced delivery of surface water into the streambed under high flow. When hyporheic exchange is too strong, overall nitrate reduction is inhibited due to short flow-paths and associated high oxygen concentrations

Anaerobic animals from an ancient, anoxic ecological niche

Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats

Mangrove trees affect the community structure and distribution of anammox bacteria at an anthropogenic-polluted mangrove in the Pearl River Delta reflected by 16S rRNA and hydrazine oxidoreductase (HZO) encoding gene analyses

Anaerobic ammonium oxidizing (anammox) bacterial community structures were investigated in surface (1–2 cm) and lower (20–21 cm) layers of mangrove sediments at sites located immediately to the mangrove trees (S0), 10 m (S1) and 1000 m (S2) away from mangrove trees in a polluted area of the Pearl River Delta. At S0, both 16S rRNA and hydrazine oxidoreductase (HZO) encoding genes of anammox bacteria showed high diversity in lower layer sediments, but they were not detectable in lower layer sediments in mangrove forest. S1 and S2 shared similar anammox bacteria communities in both surface and lower layers, which were quite different from that of S0. At all three locations, higher richness of anammox bacteria was detected in the surface layer than the lower layer; 16S rRNA genes revealed anammox bacteria were composed by four phylogenetic clusters affiliated with the “Scalindua” genus, and one group related to the potential anammox bacteria; while the hzo genes showed that in addition to sequences related to the “Scalindua”, sequences affiliated with genera of “Kuenenia”, “Brocadia”, and “Jettenia” were also detected in mangrove sediments. Furthermore, hzo gene abundances decreased from 36.5 × 104 to 11.0 × 104 copies/gram dry sediment in lower layer sediments while increased from below detection limit to 31.5 × 104 copies/gram dry sediment in lower layer sediments from S0 to S2. The results indicated that anammox bacteria communities might be strongly influenced by mangrove trees. In addition, the correlation analysis showed the redox potential and the molar ratio of ammonium to nitrite in sediments might be important factors affecting the diversity and distribution of anammox bacteria in mangrove sediments

Складові компоненти мовної особистості в контексті міжкультурної комунікації

Стаття присвячена аналізу складових компонентів мовної особистості в контексті міжкультурної комунікації, їх взаємодії та функціонуванню з точки зору прагматичної спрямованості мовленнєвого впливу. Детально розглядаються три рівні структури мовної особистості (структурно-мовний, лінгвокогнітивний ті мотиваційний) із визначенням специфіки їхніх складових компонентів.Статья посвящена анализу составляющих компонентов языковой личности в контексте межкультурной коммуникаций, их взаимодействию и функционированию с точки зрения прагматической направленности речевого воздействия. Детально рассматриваются три уровня структуры языковой личности (структурно-языковой, лингвокогнитивный и мотивационный) с последующим определением специфики их составляющих компонентов.The article is dedicated to the linguistic personality constituent components' analysis in terms of cross-cultural communication, their interaction and functioning with the speech influence pragmatic orientation taken into consideration. The three levels of the linguistic personality (that is, structural linguistic, lingo cognitive and motivation ones) are under analysis with the following their constituent components specificity determinatio

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases

Denitrification likely catalyzed by endobionts in an allogromiid foraminifer

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 6 (2012): 951–960, doi:10.1038/ismej.2011.171.Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N2) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear and it is possible that the ability to perform complete denitrification is due to symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. These associations may have been a driving force for early foraminiferal diversification, which is thought to have occurred in the Neoproterozoic when anoxia was widespread.This research was supported by NSF grant EF-0702491 to JMB, KLC and VPE; some ship support was provided by NSF MCB-0604084 to VPE and JMB.2012-06-0

Molecular analysis of enrichment cultures of ammonia oxidizers from the Salar de Huasco, a high altitude saline wetland in northern Chile

We analyzed enrichment cultures of ammonia-oxidizing bacteria (AOB) collected from different areas of Salar de Huasco, a high altitude, saline, pH-neutral water body in the Chilean Altiplano. Samples were inoculated into mineral media with 10 mM NH4+ at five different salt concentrations (10, 200, 400, 800 and 1,400 mM NaCl). Low diversity (up to three phylotypes per enrichment) of beta-AOB was detected using 16S rDNA and amoA clone libraries. Growth of beta-AOB was only recorded in a few enrichment cultures and varied according to site or media salinity. In total, five 16S rDNA and amoA phylotypes were found which were related to Nitrosomonas europaea/Nitrosococcus mobilis, N. marina and N. communis clusters. Phylotype 1-16S was 97% similar with N. halophila, previously isolated from Mongolian soda lakes, and phylotypes from amoA sequences were similar with yet uncultured beta-AOB from different biofilms. Sequences related to N. halophila were frequently found at all salinities. Neither gamma-AOB nor ammonia-oxidizing Archaea were recorded in these enrichment cultures