Two new Beggiatoa species inhabiting marine mangrove sediments in the Caribbean.

Beggiatoaceae, giant sulphur-oxidizing bacteria, are well known to occur in cold and temperate waters, as well as hydrothermal vents, where they form dense mats on the floor. However, they have never been described in tropical marine mangroves. Here, we describe two new species of benthic Beggiatoaceae colonizing a marine mangrove adjacent to mangrove roots. We combined phylogenetic and lipid analysis with electron microscopy in order to describe these organisms. Furthermore, oxygen and sulphide measurements in and ex situ were performed in a mesocosm to characterize their environment. Based on this, two new species, Candidatus Maribeggiatoa sp. and Candidatus Isobeggiatoa sp. inhabiting tropical marine mangroves in Guadeloupe were identified. The species identified as Candidatus Maribeggiatoa group suggests that this genus could harbour a third cluster with organisms ranging from 60 to 120 μm in diameter. This is also the first description of an Isobeggiatoa species outside of Arctic and temperate waters. The multiphasic approach also gives information about the environment and indications for the metabolism of these bacteria. Our study shows the widespread occurrence of members of Beggiatoaceae family and provides new insight in their potential role in shallow-water marine sulphide-rich environments such as mangroves

Macromolecular composition and substrate range of three marine fungi across major cell types

Abstract Marine fungi exist as three major cell types: unicellular yeasts, filamentous hyphae and zoosporic early-diverging forms, such as the Chytridiomycota (chytrids). To begin to understand the ecological and biogeochemical influence of these cell types within the wider context of other plankton groups, cell size and macromolecular composition must be assessed across all three cell types. Using a mass–balance approach to culture, we describe quantitative differences in substrate uptake and subsequent macromolecular distribution in three model marine fungi: the yeast Metschnikowia zobellii, the filamentous Epicoccum nigrum and chytrid Rhizophydium littoreum. We compared these model cell types with select oleaginous phytoplankton of specific biotechnological interest through metanalysis. We hypothesise that fungal cell types will maintain a significantly different macromolecular composition to one another and further represent an alternative grazing material to bacterioplankton and phytoplankton for higher trophic levels. Assessment of carbon substrate range and utilisation using phenotype arrays suggests that marine fungi have a wide substrate range. Fungi also process organic matter to an elevated-lipid macromolecular composition with reduced-protein content. Because of their size and increased lipid composition compared to other plankton groups, we propose that fungi represent a compositionally distinct, energy-rich grazing resource in marine ecosystems. We propose that marine fungi could act as vectors of organic matter transfer across trophic boundaries, and supplement our existing understanding of the microbial loop and carbon transfer in marine ecosystems.</jats:p

A unique bacteriohopanetetrol stereoisomer of marine anammox

Anaerobic ammonium oxidation (anammox) is a major process of bioavailable nitrogen removal from marine systems. Previously, a bacteriohopanetetrol (BHT) isomer, with unknown stereochemistry, eluting later than BHT using high performance liquid chromatography (HPLC), was detected in ‘Ca. Scalindua profunda’ and proposed as a biomarker for anammox in marine paleo-environments. However, the utility of this BHT isomer as an anammox biomarker is hindered by the fact that four other, non-anammox bacteria are also known to produce a late-eluting BHT stereoisomer. The stereochemistry in Acetobacter pasteurianus, Komagataeibacter xylinus and Frankia sp. was known to be 17β, 21β(H), 22R, 32R, 33R, 34R (BHT-34R). The stereochemistry of the late-eluting BHT in Methylocella palustris was unknown. To determine if marine anammox bacteria produce a unique BHT isomer, we studied the BHT distributions and stereochemistry of known BHT isomer producers and of previously unscreened marine (‘Ca. Scalindua brodeae’) and freshwater (‘Ca. Brocadia sp.’) anammox bacteria using HPLC and gas chromatographic (GC) analysis of acetylated BHTs and ultra high performance liquid chromatography (UHPLC)-high resolution mass spectrometry (HRMS) analysis of non-acetylated BHTs. The 34R stereochemistry was confirmed for the BHT isomers in Ca. Brocadia sp. and Methylocella palustris. However, ‘Ca. Scalindua sp.’ synthesise a stereochemically distinct BHT isomer, with still unconfirmed stereochemistry (BHT-x). Only GC analysis of acetylated BHT and UHPLC analysis of non-acetylated BHT distinguished between late-eluting BHT isomers. Acetylated BHT-x and BHT-34R co-elute by HPLC. As BHT-x is currently only known to be produced by ‘Ca. Scalindua spp.’, it may be a biomarker for marine anammox

The Impact of LED Lighting Spectra in a Plant Factory on the Growth, Physiological Traits and Essential Oil Content of Lemon Balm (Melissa officinalis)

With the recent development of LED lighting systems for plant cultivation, the use of vertical farming under controlled conditions is attracting increased attention. This study investigated the impact of a number of LED light spectra (red, blue, green and white) on the growth, development and essential oil content of lemon balm (Melissa officinalis), a herb and pharmaceutical plant species used across the world. White light and red-rich light spectra gave the best outputs in terms of impact on the growth and yield. For blue-rich spectra, the development and yield was lower despite having a significant impact on the photosynthesis activity, including Fv/Fm and NDVI values. For the blue-rich spectra, a peak wavelength of 450 mn was better than that of 435 nm. The results have practical value in terms of increased yield and the reduction of electricity consumption under controlled environmental conditions for the commercial production of lemon balm.</jats:p

The paleolimnologist's guide to compound-specific stable isotope analysis - An introduction to principles and applications of CSIA for quaternary lake sediments

The stable isotope composition of key chemical elements for life on Earth (e.g., carbon, hydrogen, nitrogen, oxygen, sulfur) tracks changes in fluxes and turnover of these elements in the biogeosphere. Over the past 15-20 years, the potential to measure these isotopic compositions for individual, source-specific organic molecules (biomarkers) and to link them to a range of environmental conditions and processes has been unlocked and amplified by increasingly sensitive, affordable and wide-spread analytical technology. Paleoenvironmental research has seen enormous step-changes in our understanding of past ecosystem dynamics. Vital to these paradigm shifts is the need for well-constrained modern and recent analogues. Through increased understanding of these environments and their biological pathways we can successfully unravel past climatic changes and associated ecosystem adaption. With this review, we aim to introduce scientists working in the field of Quaternary paleolimnology to the tools that compound-specific isotope analysis (CSIA) provides for the gain of information on biogeochemical conditions in ancient environments. We provide information on fundamental principles and applications of novel and established CSIA applications based on the carbon, hydrogen, nitrogen, oxygen and sulfur isotopic composition of biomarkers. While biosynthesis, sources and associated isotope fractionation patterns of compounds such as n-alkanes are relatively well-constrained, new applications emerge from the increasing use of functionalized alkyl lipids, steroids, hopanoids, isoprenoids, GDGTs, pigments or cellulose. Biosynthesis and fractionation are not always fully understood

Archaeal and bacterial glycerol dialkyl glycerol tetraether (GDGT) lipids in environmental samples by high temperature-gas chromatography with flame ionisation and time-of-flight mass spectrometry detection

Archaeal isoprenoidal glycerol dibiphytanyl glycerol tetraether lipids (iGDGTs) and their non-isoprenoidal branched bacterial analogues (brGDGTs) have widespread applications in biogeochemistry and paleothermometry. Analysis of GDGTs usually involves separation using high performance liquid chromatography, typically coupled via atmospheric pressure chemical ionisation to mass spectrometric detection in selected ion-monitoring mode (HPLC–APCI-MS). However, reliable determination of ratios and, in particular, quantification by this technique, can be challenging due to differences in ionisation efficiencies of the various compounds. Quantification of GDGTs also relies on external calibration of the relative response to an internal standard with authenticated GDGTs, which are often not readily accessible. Here, we tested the suitability of high temperature gas chromatography with flame ionisation detection (HTGC-FID) for the determination of concentrations and tetraether lipid-based ratios in marine and terrestrial samples. For this, we identified GDGTs in environmental samples using HTGC coupled to time-of-flight mass spectrometry (HTGC–MS). Using a purified GDGT standard, we show we can quantify GDGT-0 in environmental samples by GC-FID. Some GDGT-based ratios measured by HTGC-FID exhibited a linear correlation (1:1) with ratios derived from HPLC–MS and weight-based ratios of mixtures of purified standards. However, ratios relying on minor isomers, such as TEX86 and MBT/CBT have many unresolved challenges for determination by HTGC. Detection limits were higher than for HPLC–MS. However, the advantages of employing HTGC-based methods include: (1) the independence from MS tuning-related differences in ionisation energies; (2) the potential for direct comparison with other, non-GDGT based biomarkers; and (3) a more complete insight into biomarker distributions in environmental samples by the extension of the temperature range. Quantitative elution of GDGTs from a HTGC column as demonstrated herein, will also enable their analysis by compound-specific isotope ratio mass spectrometry

Dark carbon fixation in the Arabian Sea oxygen minimum zone contributes to sedimentary organic carbon (SOM)

In response to rising CO2concentrations and increasing global sea surface temperatures,oxygen minimum zones (OMZ), or“dead zones”, are expected to expand. OMZs are fueled by highprimary productivity, resulting in enhanced biological oxygen demand at depth, subsequent oxygen depletion, and attenuation of remineralization. This results in the deposition of organic carbon‐rich sediments. Carbon drawdown is estimated by biogeochemical models; however, a major process is ignored: carbon fixation in the mid‐and lower water column. Here, we show that chemoautotrophic carbon fixation is important in the Arabian Sea OMZ; and manifests in a13C‐depleted signature of sedimentary organic carbon. We determined theδ13C values of Corg deposited in close spatial proximity but over a steepbottom‐water oxygen gradient, and theδ13C composition of biomarkers of chemoautotrophic bacteriacapable of anaerobic ammonia oxidation (anammox). Isotope mixing models show that detritus fromanammox bacteria or other chemoautotrophs likely forms a substantial part of the organic matter depositedwithin the Arabian Sea OMZ (~17%), implying that the contribution of chemoautotrophs to settling organicmatter is exported to the sediment. This has implications for the evaluation of past, and future, OMZs:biogeochemical models that operate on the assumption that all sinking organic matter is photosynthetically derived, without new addition of carbon, could significantly underestimate the extent of remineralization. Oxygen demand in oxygen minimum zones could thus be higher than projections suggest, leading to a more intense expansion of OMZs than expected

From ether to acid: a plausible degradation pathway of glycerol dialkyl glycerol tetraethers

Glycerol dialkyl glycerol tetraethers (GDGTs) are ubiquitous microbial lipids with extensive demonstrated and potential roles as paleoenvironmental proxies. Despite the great attention they receive, comparatively little is known regarding their diagenetic fate. Putative degradation products of GDGTs, identified as hydroxyl and carboxyl derivatives, were detected in lipid extracts of marine sediment, seep carbonate, hot spring sediment and cells of the marine thaumarchaeon Nitrosopumilus maritimus. The distribution of GDGT degradation products in environmental samples suggests that both biotic and abiotic processes act as sinks for GDGTs. More than a hundred newly recognized degradation products afford a view of the stepwise degradation of GDGT via (1) ether bond hydrolysis yielding hydroxyl isoprenoids, namely, GDGTol (glycerol dialkyl glycerol triether alcohol), GMGD (glycerol monobiphytanyl glycerol diether), GDD (glycerol dibiphytanol diether), GMM (glycerol monobiphytanol monoether) and bpdiol (biphytanic diol); (2) oxidation of isoprenoidal alcohols into corresponding carboxyl derivatives and (3) chain shortening to yield C39and smaller isoprenoids. This plausible GDGT degradation pathway from glycerol ethers to isoprenoidal fatty acids provides the link to commonly detected head-to-head linked long chain isoprenoidal hydrocarbons in petroleum and sediment samples. The problematic C80to C82tetraacids that cause naphthenate deposits in some oil production facilities can be generated from H-shaped glycerol monoalkyl glycerol tetraethers (GMGTs) following the same process, as indicated by the distribution of related derivatives in hydrothermally influenced sediments.Seventh Framework Programme (European Commission) (ERC Grant 247153

Human and mouse essentiality screens as a resource for disease gene discovery.

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery