The extensive use of 3-nitro-4-hydroxybenzene arsonic acid (roxarsone) in the production of broiler chickens can lead to increased soil arsenic concentration and arsenic contaminated dust. While roxarsone is the dominant arsenic species in fresh litter, inorganic As (V) predominates in composted litter. Microbial activity has been implicated as the cause, but neither the specific processes nor the organisms have been identified. Here we demonstrate the rapid biotransformation of roxarsone under anaerobic conditions by Clostridium species in chicken litter enrichments and a pure culture of a fresh water arsenate respiring species (Clostridium sp. strain OhILAs). The main products were 3-amino-4-hydroxybenzene arsonic acid and inorganic arsenic. Growth experiments and genomic analysis indicate strain OhILAs may use roxarsone as a terminal electron acceptor for anaerobic respiration. Electronic structure analysis suggests that the reducing equivalents should go to the nitro group, while liberation of inorganic arsenic from the intact benzene ring by cleaving the C-As bond is unlikely. Clostridium and Lactobacillus species are common in the chicken cecum and litter. Thus, the organic-rich manure and anaerobic conditions typically associated with composting provide the conditions necessary for the native microbial populations to transform the roxarsone in the litter releasing the more toxic inorganic arsenic.

SignificanceIt has remained an unresolved question whether microorganisms recovered from the most arid environments on Earth are thriving under such extreme conditions or are just dead or dying vestiges of viable cells fortuitously deposited by atmospheric processes. Based on multiple lines of evidence, we show that indigenous microbial communities are present and temporally active even in the hyperarid soils of the Atacama Desert (Chile). Following extremely rare precipitation events in the driest parts of this desert, where rainfall often occurs only once per decade, we were able to detect episodic incidences of biological activity. Our findings expand the range of hyperarid environments temporarily habitable for terrestrial life, which by extension also applies to other planetary bodies like Mars.

Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ∼47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 103 to 6.10 × 105 and 3.28 × 104 to 2.46 × 106 amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.

Glycerol ether lipids have been developed as proxies to reconstruct past environmental changes or in their intact polar form to fingerprint the viable microbial community composition. However, due to the structural complexity, the full characterization of glycerol ether lipids requires separate protocols for the analysis of the polar head groups and the alkyl chain moieties in core ether lipids. As a consequence, the valuable relationship between core ether lipid composition and specific polar head groups is often lost; this limits our understanding of the diversity of ether lipids and their utilities as biogeochemical proxies. Here, we report a novel reverse-phase liquid chromatography-electrospray ionization-mass spectrometry (RP-ESI-MS) protocol that enables the simultaneous analysis of polar head groups (e.g., phosphocholine, phosphoglycerol, phosphoinositol, hexose, and dihexose) and alkyl moieties (e.g., alkyl moieties modified with different numbers of cycloalkyl moieties, hydroxyl and alkyl groups, and double bonds) in crude lipid extracts without further preparation. This protocol greatly enhances the detection of archaeal intact polar lipids (IPLs) and core lipids (CLs) with double-bond-and hydroxyl-group-bearing alkyl moieties. With these improvements, widely used ratios that describe relative distribution of the core lipid, such as the TEX 86 and ring index, can now be directly determined in specific intact polar lipids (IPL-specific TEX 86 and ring index). Since IPLs are the putative precursors of the environmentally persistent core lipids, their detailed examination by this protocol can potentially provide new insights into diagenetic and biological mechanisms inherent to these proxies. In a series of 12 samples from diverse settings, core and IPL-specific TEX 86 values follow the order: 2G-GDGTs > core GDGTs > 1G-GDGTs > 1G-GDGT-PI; and the ring indices follow: 1G-GDGTs ≈ core GDGTs > 2G-GDGTs > 1G-GDGT

Intact polar lipid distributions have become a valuable tool for the study of microbial ecosystems. In order to expand the detection and interpretation of the presence of these lipids, improved analytical methods are needed. Therefore, two high pressure liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS 2 Keywords: intact polar lipid, reversed phase, HILIC, biomarker, complex matrix ) methods, based on hydrophilic interaction chromatography (HILIC) and reversed phase (RP) chromatography were developed, taking advantage of new chromatographic possibilities such as smaller particle size and recently developed column fillings. Both were optimized to cover the broad range of compounds found in environmental samples and to cope with the associated complex sample matrices. The capabilities of the resulting methods were tested on pure standards and an environmental sample. Both methods offer improved peak resolution and detection limit, and reduced chromatographic background at twofold shorter run time compared with the previous method based on a diol column. The HILIC method offers separation according to lipid class similar to a diol column, and can thus be recommended for lipid fingerprinting. The method based on RP separation offers the unique possibility of analyzing intact polar lipids and core lipids in the same chromatographic run and an alternative mode of lipid separation based mainly on side chain structure. This method is especially suitable for separation of compounds based on side chain length, degree of saturation and/or presence of acyl/ether bonds. The combination of both newly developed chromatographic methods provides a powerful tool for the analysis of lipid distributions in environmental samples at ultra-low concentration.

Microorganisms in marine subsurface sediments substantially contribute to global biomass. Sediments warmer than 40°C account for roughly half the marine sediment volume, but the processes mediated by microbial populations in these hard-to-access environments are poorly understood. We investigated microbial life in up to 1.2-kilometer-deep and up to 120°C hot sediments in the Nankai Trough subduction zone. Above 45°C, concentrations of vegetative cells drop two orders of magnitude and endospores become more than 6000 times more abundant than vegetative cells. Methane is biologically produced and oxidized until sediments reach 80° to 85°C. In 100° to 120°C sediments, isotopic evidence and increased cell concentrations demonstrate the activity of acetate-degrading hyperthermophiles. Above 45°C, populated zones alternate with zones up to 192 meters thick where microbes were undetectable.

Bacterial endospores are dominant members of the marine deep biosphere.

Recent advances in lipidomic analysis in combination with various physiological experiments set the stage for deciphering the structure-function of haloarchaeal membrane lipids. Here we focused primarily on changes in lipid composition of Haloferax volcanii, but also performed a comparative analysis with four other haloarchaeal species (Halobacterium salinarum, Halorubrum lacusprofundi, Halorubrum sodomense and Haloplanus natans) all representing distinctive cell morphologies and behaviors (i.e., rod shape vs. pleomorphic behavior). Common to all five haloarchaea, our data reveal an extraordinary high level of menaquinone, reaching up to 72% of the total lipids. This ubiquity suggests that menaquinones may function beyond their ordinary role as electron and proton transporter, acting simultaneously as ion permeability barriers and as powerful shield against oxidative stress. In addition, we aimed at understanding the role of cations interacting with the characteristic negatively charged surface of haloarchaeal membranes. We propose for instance that by bridging the negative charges of adjacent anionic phospholipids, Mg acts as surrogate for cardiolipin, a molecule that is known to control curvature stress of membranes. This study further provides a bioenergetic perspective as to how haloarchaea evolved following oxygenation of Earth's atmosphere. The success of the aerobic lifestyle of haloarchaea includes multiple membrane-based strategies that successfully balance the need for a robust bilayer structure with the need for high rates of electron transport - collectively representing the molecular basis to inhabit hypersaline water bodies around the planet.