Present-day thermal and water activity environment of the Mars Sample Return collection

The Mars Sample Return mission intends to retrieve a sealed collection of rocks, regolith, and atmosphere sampled from Jezero Crater, Mars, by the NASA Perseverance rover mission. For all life-related research, it is necessary to evaluate water availability in the samples and on Mars. Within the first Martian year, Perseverance has acquired an estimated total mass of 355 g of rocks and regolith, and 38 μmoles of Martian atmospheric gas. Using in-situ observations acquired by the Perseverance rover, we show that the present-day environmental conditions at Jezero allow for the hydration of sulfates, chlorides, and perchlorates and the occasional formation of frost as well as a diurnal atmospheric-surface water exchange of 0.5-10 g water per m2 (assuming a well-mixed atmosphere). At night, when the temperature drops below 190 K, the surface water activity can exceed 0.5, the lowest limit for cell reproduction. During the day, when the temperature is above the cell replication limit of 245 K, water activity is less than 0.02. The environmental conditions at the surface of Jezero Crater, where these samples were acquired, are incompatible with the cell replication limits currently known on Earth.

Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments

Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.

Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia

Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.

Organic-rich bimineralic ooids record biological processes in Shark Bay, Western Australia

Marine ooids have formed in microbially colonized environments for billions of years, but the microbial contributions to mineral formation in ooids continue to be debated. Here we provide evidence of these contributions in ooids from Carbla Beach, Shark Bay, Western Australia. Dark 100-240 μm diameter ooids from Carbla Beach contain two different carbonate minerals. These ooids have 50-100 μm-diameter dark nuclei that contain aragonite, amorphous iron sulfide, detrital aluminosilicate grains and organic matter, and 10-20 μm-thick layers of high-Mg calcite that separate nuclei from aragonitic outer cortices. Raman spectroscopy indicates organic enrichments in the nuclei and high-Mg calcite layers. Synchrotron-based microfocused X-ray fluorescence mapping reveals high-Mg calcite layers and the presence of iron sulfides and detrital grains in the peloidal nuclei. Iron sulfide grains within the nuclei indicate past sulfate reduction in the presence of iron. The preservation of organic signals in and around high-Mg calcite layers and the absence of iron sulfide suggest that organics stabilized high-Mg calcite under less sulfidic conditions. Aragonitic cortices that surround the nuclei and Mg-calcite layers do not preserve microporosity, iron sulfide minerals nor organic enrichments, indicating growth under more oxidizing conditions. These morphological, compositional, and mineralogical signals of microbial processes in dark ooids from Shark Bay, Western Australia, record the formation of ooid nuclei and the accretion of magnesium-rich cortical layers in benthic, reducing, microbially colonized areas.

A review of microbial-environmental interactions recorded in Proterozoic carbonate-hosted chert

The record of life during the Proterozoic is preserved by several different lithologies, but two in particular are linked both spatially and temporally: chert and carbonate. These lithologies capture a snapshot of dominantly peritidal environments during the Proterozoic. Early diagenetic chert preserves some of the most exceptional Proterozoic biosignatures in the form of microbial body fossils and mat textures. This fossiliferous and kerogenous chert formed in shallow marine environments, where chert nodules, layers, and lenses are often surrounded by and encased within carbonate deposits that themselves often contain kerogen and evidence of former microbial mats. Here, we review the record of biosignatures preserved in peritidal Proterozoic chert and chert-hosting carbonate and discuss this record in the context of experimental and environmental studies that have begun to shed light on the roles that microbes and organic compounds may have played in the formation of these deposits. Insights gained from these studies suggest temporal trends in microbial-environmental interactions and place new constraints on past environmental conditions, such as the concentration of silica in Proterozoic seawater, interactions among organic compounds and cations in seawater, and the influence of microbial physiology and biochemistry on selective preservation by silicification.

Aqueous alteration processes in Jezero crater, Mars-implications for organic geochemistry

The Perseverance rover landed in Jezero crater, Mars, in February 2021. We used the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) instrument to perform deep-ultraviolet Raman and fluorescence spectroscopy of three rocks within the crater. We identify evidence for two distinct ancient aqueous environments at different times. Reactions with liquid water formed carbonates in an olivine-rich igneous rock. A sulfate-perchlorate mixture is present in the rocks, which probably formed by later modifications of the rocks by brine. Fluorescence signatures consistent with aromatic organic compounds occur throughout these rocks and are preserved in minerals related to both aqueous environments.

Geological, multispectral, and meteorological imaging results from the Mars 2020 Perseverance rover in Jezero crater

Perseverance's Mastcam-Z instrument provides high-resolution stereo and multispectral images with a unique combination of spatial resolution, spatial coverage, and wavelength coverage along the rover's traverse in Jezero crater, Mars. Images reveal rocks consistent with an igneous (including volcanic and/or volcaniclastic) and/or impactite origin and limited aqueous alteration, including polygonally fractured rocks with weathered coatings; massive boulder-forming bedrock consisting of mafic silicates, ferric oxides, and/or iron-bearing alteration minerals; and coarsely layered outcrops dominated by olivine. Pyroxene dominates the iron-bearing mineralogy in the fine-grained regolith, while olivine dominates the coarse-grained regolith. Solar and atmospheric imaging observations show significant intra- and intersol variations in dust optical depth and water ice clouds, as well as unique examples of boundary layer vortex action from both natural (dust devil) and Ingenuity helicopter-induced dust lifting. High-resolution stereo imaging also provides geologic context for rover operations, other instrument observations, and sample selection, characterization, and confirmation.

Compositionally and density stratified igneous terrain in Jezero crater, Mars

Before Perseverance, Jezero crater's floor was variably hypothesized to have a lacustrine, lava, volcanic airfall, or aeolian origin. SuperCam observations in the first 286 Mars days on Mars revealed a volcanic and intrusive terrain with compositional and density stratification. The dominant lithology along the traverse is basaltic, with plagioclase enrichment in stratigraphically higher locations. Stratigraphically lower, layered rocks are richer in normative pyroxene. The lowest observed unit has the highest inferred density and is olivine-rich with coarse (1.5 millimeters) euhedral, relatively unweathered grains, suggesting a cumulate origin. This is the first martian cumulate and shows similarities to martian meteorites, which also express olivine disequilibrium. Alteration materials including carbonates, sulfates, perchlorates, hydrated silicates, and iron oxides are pervasive but low in abundance, suggesting relatively brief lacustrine conditions. Orbital observations link the Jezero floor lithology to the broader Nili-Syrtis region, suggesting that density-driven compositional stratification is a regional characteristic.

Aqueously altered igneous rocks sampled on the floor of Jezero crater, Mars

The Perseverance rover landed in Jezero crater, Mars, to investigate ancient lake and river deposits. We report observations of the crater floor, below the crater's sedimentary delta, finding the floor consists of igneous rocks altered by water. The lowest exposed unit, informally named Séítah, is a coarsely crystalline olivine-rich rock, which accumulated at the base of a magma body. Fe-Mg carbonates along grain boundaries indicate reactions with CO₂-rich water, under water-poor conditions. Overlying Séítah is a unit informally named Máaz, which we interpret as lava flows or the chemical complement to Séítah in a layered igneous body. Voids in these rocks contain sulfates and perchlorates, likely introduced by later near-surface brine evaporation. Core samples of these rocks were stored aboard Perseverance for potential return to Earth.

An olivine cumulate outcrop on the floor of Jezero crater, Mars

The geological units on the floor of Jezero crater, Mars, are part of a wider regional stratigraphy of olivine-rich rocks, which extends well beyond the crater. We investigate the petrology of olivine and carbonate-bearing rocks of the Séítah formation in the floor of Jezero. Using multispectral images and x-ray fluorescence data, acquired by the Perseverance rover, we performed a petrographic analysis of the Bastide and Brac outcrops within this unit. We find that these outcrops are composed of igneous rock, moderately altered by aqueous fluid. The igneous rocks are mainly made of coarse-grained olivine, similar to some Martian meteorites. We interpret them as an olivine cumulate, formed by settling and enrichment of olivine through multi-stage cooling of a thick magma body.

Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats

Cyanobacteria and extracellular polymeric substances (EPS) in peritidal pustular microbial mats have a two-billion-year-old fossil record. To understand the composition, production, degradation, and potential role of EPS in modern analogous communities, we sampled pustular mats from Shark Bay, Australia and analyzed their EPS matrix. Biochemical and microscopic analyses identified sulfated organic compounds as major components of mat EPS. Sulfur was more abundant in the unmineralized regions with cyanobacteria and less prevalent in areas that contained fewer cyanobacteria and more carbonate precipitates. Sequencing and assembly of the pustular mat sample resulted in 83 high-quality metagenome-assembled genomes (MAGs). Metagenomic analyses confirmed cyanobacteria as the primary sources of these sulfated polysaccharides. Genes encoding for sulfatases, glycosyl hydrolases, and other enzymes with predicted roles in the degradation of sulfated polysaccharides were detected in the MAGs of numerous clades including Bacteroidetes, Chloroflexi, Hydrogenedentes, Myxococcota, Verrucomicrobia, and Planctomycetes. Measurable sulfatase activity in pustular mats and fresh cyanobacterial EPS confirmed the role of sulfatases in the degradation of sulfated EPS. These findings suggest that the synthesis, modification, and degradation of sulfated polysaccharides influence microbial interactions, carbon cycling, and biomineralization processes within peritidal pustular microbial mats.

Perseverance rover reveals an ancient delta-lake system and flood deposits at Jezero crater, Mars

[Figure: see text].

The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages

The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.

A new model for silicification of cyanobacteria in Proterozoic tidal flats

Microbial fossils preserved by early diagenetic chert provide a window into the Proterozoic biosphere, but seawater chemistry, microbial processes, and the interactions between microbes and the environment that contributed to this preservation are not well constrained. Here, we use fossilization experiments to explore the processes that preserve marine cyanobacterial biofilms by the precipitation of amorphous silica in a seawater medium that is analogous to Proterozoic seawater. These experiments demonstrate that the exceptional silicification of benthic marine cyanobacteria analogous to the oldest diagnostic cyanobacterial fossils requires interactions among extracellular polymeric substances (EPS), photosynthetically induced pH changes, magnesium cations (Mg²⁺ ), and >70 ppm silica.

Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.

Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada

Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two fossil morphologies with similar shapes and sizes: one exhibits mm-scale ridges and a distinct lower boundary and the other is devoid of these diagnostic features. We interpret these as taphomorphs of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. We explore the cast-and-mould preservation of both taphomorphs by petrography, Raman spectroscopy, X-ray fluorescence microprobe and X-ray diffraction. All fossils and the surrounding sedimentary matrix contain quartz grains, iron-rich chlorite and muscovite. The ridged fossils contain about 70% larger quartz grains compared to the ridgeless taphomorph, indicating a lower abundance of clay minerals in the ridged fossil. Chlorite and muscovite likely originated from smectite and kaolinite precursors that underwent lower greenschist facies metamorphism. Kaolinite and smectite are inferred to have been abundant in sediments around the ridged fossil, which enabled the preservation of a continuous, distinct, clay- and kerogen-rich bottom boundary. The prevalence of quartz in the ridged fossils of the WCF and in erniettomorphs from other localities also suggests a role for this mineral in three-dimensional preservation of erniettomorphs in sandstone and siltstone deposits.

Formation of Zerovalent Iron in Iron-Reducing Cultures of Methanosarcina barkeri

Methanogenic archaea have been shown to reduce iron from ferric [Fe(III)] to ferrous [Fe(II)] state, but minerals that form during iron reduction by different methanogens remain to be characterized. Here, we show that zerovalent iron (ZVI) minerals, ferrite [α-Fe(0)] and austenite [γ-Fe(0)], appear in the X-ray diffraction spectra minutes after the addition of ferrihydrite to the cultures of a methanogenic archaeon, Methanosarcina barkeri (M. barkeri). M. barkeri cells and redox-active, nonenzymatic soluble organic compounds in organic-rich spent culture supernatants can promote the formation of ZVI; the latter compounds also likely stabilize ZVI. Methanogenic microbes that inhabit organic- and Fe(III)-rich anaerobic environments may similarly reduce Fe(III) to Fe(II) and ZVI, with implications for the preservation of paleomagnetic signals during sediment diagenesis and potential applications in the protection of iron metals against corrosion and in the green synthesis of ZVI.

Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs

The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.

An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids

The phylum Cyanobacteria includes free-living bacteria and plastids, the descendants of cyanobacteria that were engulfed by the ancestral lineage of the major photosynthetic eukaryotic group Archaeplastida. Endosymbiotic events that followed this primary endosymbiosis spread plastids across diverse eukaryotic groups. The remnants of the ancestral cyanobacterial genome present in all modern plastids, enable the placement of plastids within Cyanobacteria using sequence-based phylogenetic analyses. To date, such phylogenetic studies have produced conflicting results and two competing hypotheses: (1) plastids diverge relatively recently in cyanobacterial evolution and are most closely related to nitrogen-fixing cyanobacteria, or (2) plastids diverge early in the evolutionary history of cyanobacteria, before the divergence of most cyanobacterial lineages. Here, we use phylogenetic analysis of ribosomal proteins from an expanded data set of cyanobacterial and representative plastid genomes to infer a deep placement for the divergence of the plastid ancestor lineage. We recover plastids as sister to Gloeomargarita and show that the group diverges from other cyanobacterial groups before Pseudanabaena, a previously unreported placement. The tree topologies and phylogenetic distances in our study have implications for future molecular clock studies that aim to model accurate divergence times, especially with respect to groups containing fossil calibrations. The newly sequenced cyanobacterial groups included here will also enable the use of novel cyanobacterial microfossil calibrations.

Open-source sensor for measuring oxygen partial pressures below 100 microbars

The ability to measure partial pressures of oxygen below 100 microbars and nanomolar dissolved oxygen concentrations in in situ laboratory systems benefits many fields including microbiology, geobiology, oceanography, chemistry, and materials science. Here, we present an easily constructible open-source design for a networked luminescence lifetime measurement system for in situ measurements in arbitrary laboratory containers. The system is well suited for measuring oxygen partial pressures in the 0–100 μbar range, with the maximum potentially usable upper range limit at around 10 mbar, depending on experimental conditions. The sensor has a limited drift and its detectability limit for oxygen is at 0.02 μbar for short timescale measurements. Each sensor can connect to a Wi-Fi network and send the logged data either over the Internet or to a local server, enabling a large number of parallel unattended experiments. Designs are also provided for attaching the sensor to various commercially available containers used in laboratories. The design files are released under an open source license, which enables other laboratories to build, customize, and use these sensors.

A Field Guide to Finding Fossils on Mars

The Martian surface is cold, dry, exposed to biologically harmful radiation and apparently barren today. Nevertheless, there is clear geological evidence for warmer, wetter intervals in the past that could have supported life at or near the surface. This evidence has motivated National Aeronautics and Space Administration and European Space Agency to prioritize the search for any remains or traces of organisms from early Mars in forthcoming missions. Informed by (1) stratigraphic, mineralogical and geochemical data collected by previous and current missions, (2) Earth's fossil record, and (3) experimental studies of organic decay and preservation, we here consider whether, how, and where fossils and isotopic biosignatures could have been preserved in the depositional environments and mineralizing media thought to have been present in habitable settings on early Mars. We conclude that Noachian-Hesperian Fe-bearing clay-rich fluvio-lacustrine siliciclastic deposits, especially where enriched in silica, currently represent the most promising and best understood astropaleontological targets. Siliceous sinters would also be an excellent target, but their presence on Mars awaits confirmation. More work is needed to improve our understanding of fossil preservation in the context of other environments specific to Mars, particularly within evaporative salts and pore/fracture-filling subsurface minerals.

Biologically agglutinated eukaryotic microfossil from Cryogenian cap carbonates

Cryogenian cap carbonates that overlie Sturtian glacial deposits were formed during a post-glacial transgression. Here, we describe microfossils from the Kakontwe Formation of Zambia and the Taishir Formation of Mongolia-both Cryogenian age, post-Sturtian cap carbonates-and investigate processes involved in their formation and preservation. We compare microfossils from these two localities to an assemblage of well-documented microfossils previously described in the post-Sturtian Rasthof Formation of Namibia. Microfossils from both new localities have 10 ± 1 μm-thick walls composed of carbonaceous matter and aluminosilicate minerals. Those found in the Kakontwe Formation are spherical or ovoid and 90 ± 5 μm to 200 ± 5 μm wide. Structures found in the Taishir Formation are mostly spherical, 50 ± 5 μm to 140 ± 5 μm wide, with distinct features such as blunt or concave edges. Chemical and mineralogical analyses show that the walled structures and the clay fraction extracted from the surrounding sediments are composed of clay minerals, especially muscovite and illite, as well as quartz, iron and titanium oxides, and some dolomite and feldspar. At each locality, the mineralogy of the microfossil walls matched that of the clay fractions of the surrounding sediment. The abundance of these minerals in the walled microfossils relative to the surrounding carbonate matrix and microbial laminae, and the presence of minerals that cannot precipitate from solution (titanium oxide and feldspar), suggests that the composition represents the original mineralogy of the structures. Furthermore, the consistency in mineralogy of both microfossils and sediments across the three basins, and the uniformity of size and shape among mineral grains in the fossil walls indicate that these organisms incorporated these minerals by primary biological agglutination. The discovery of new, mineral-rich microfossil assemblages in microbially laminated and other fine-grained facies of Cryogenian cap carbonates from multiple localities on different palaeocontinents demonstrates that agglutinating eukaryotes were widespread in carbonate-dominated marine environments in the aftermath of the Sturtian glaciation.

Experimental fossilization of mat-forming cyanobacteria in coarse-grained siliciclastic sediments

Microbial fossils and textures are commonly preserved in Ediacaran and early Cambrian coarse-grained siliciclastic sediments that were deposited in tidal and intertidal marine settings. In contrast, the fossilization of micro-organisms in similar marine environments of post-Cambrian age is less frequently reported. Thus, temporal discrepancies in microbial preservation may have resulted from the opening and closing of a unique taphonomic window during the terminal Proterozoic and early Phanerozoic, respectively. Here, we expand upon previous work to identify environmental factors which may have facilitated the preservation of cyanobacteria growing on siliciclastic sand, by experimentally determining the ability of microbial mats to trap small, suspended mineral grains, and precipitate minerals from ions in solution. We show that (i) fine grains coat the sheaths of filamentous cyanobacteria (e.g., Nodosilinea sp.) residing within the mat, after less than 1 week of cell growth under aerobic conditions, (ii) clay minerals do not coat sterile cellulose fibers and rarely coat unsheathed cyanobacterial cells (e.g., Nostoc sp.), (iii) stronger disturbances (where culture jars were agitated at 170 rpm; 3 mm orbital diameter) produce the smoothest and most extensive mineral veneers around cells, compared with those agitated at slower rotational speeds (150 and 0 rpm), and (iv) mineral veneers coating cyanobacterial cells are ~1 μm in width. These new findings suggest that sheathed filamentous cyanobacteria may be preferentially preserved under conditions of high fluid energy. We integrate these results into a mechanistic model that explains the preservation of microbial fossils and textures in Ediacaran sandstones and siltstones, and in fine-grained siliciclastic deposits that contain exceptionally preserved microbial mats.

Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction

We investigated the influence of organic substrates and phosphate concentration on the rates of dissimilatory microbial sulfate reduction and the ³⁴S/³²S isotopic fractionation produced by several Desulfovibrio species. Our experiments corroborate the previously reported species-specific correlation between sulfur isotope fractionation and cell-specific sulfate reduction rates. We also identify cell size as a key factor that contributes to the species-effect of this correlation. Phosphate limitation results in larger cells and contributes to a small decrease in sulfur isotope fractionation concomitant with an apparent increase in cell-specific sulfate reduction rates. Sulfur isotope fractionation in phosphate-limited cultures asymptotically approaches a lower limit of approximately 5‰ as cell-specific sulfate reduction rates increase to >100 fmol cell⁻¹ day⁻¹. These experimental results test models that link the reversibilities of enzymatic steps in dissimilatory sulfate reduction to sulfur isotope fractionation and show that these models can provide consistent predictions across large variations in physiological states experienced by sulfate reducing bacteria.

Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas

Ooids are sedimentary grains that are distributed widely in the geologic record. Their formation is still actively debated, which limits our understanding of the significance and meaning of these grains in Earth's history. Central questions include the role played by microbes in the formation of ooids and the sources of ubiquitous organic matter within ooid cortices. To address these issues, we investigated the microbial community composition and associated lipids in modern oolitic sands at Pigeon Cay on Cat Island, The Bahamas. Surface samples were taken along a transect from the shallow, turbulent surf zone to calmer, deeper water. Grains transitioned from shiny and abraded ooids in the surf zone, to biofilm-coated ooids at about 3 m water depth. Further offshore, grapestones (cemented aggregates of ooids) dominated. Benthic diatoms and Proteobacteria dominated biofilms. Taxa that may promote carbonate precipitation were abundant, particularly those associated with sulfur cycling. Compared to the lipids associated with surface biofilms, relict lipids bound within carbonate exhibited remarkably similar profiles in all grain types. The enhanced abundance of methyl-branched fatty acids and β-hydroxy fatty acids, 1-O-monoalkyl glycerol ethers and hopanoids bound within ooid and grapestone carbonate confirms a clear association of benthic sedimentary bacteria with these grains. Lipids bound within ooid cortices also contain molecular indicators of microbial heterotrophic degradation of organic matter, possibly in locally reducing conditions. These included the loss of labile unsaturated fatty acids, enhanced long-chain fatty acids/short-chain fatty acids, enriched stable carbon isotopes ratios of fatty acids, and very high stanol/stenol ratios. To what extent some of these molecular signals are derived from later heterotrophic endolithic activity remains to be fully resolved. We speculate that some ooid carbonate forms in microbial biofilms and that early diagenetic degradation of biofilms may also play a role in early stage carbonate precipitation around ooids.

System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions

The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.

Novel archaeal tetraether lipids with a cyclohexyl ring identified in Fayetteville Green Lake, NY, and other sulfidic lacustrine settings

RATIONALE

The meromictic Fayetteville Green Lake (FGL) is of significant geobiological interest because of microbial cycling of sulfur within and below the permanent chemocline and in the euxinic deep waters. Studies of glycerol dibiphytanyl glycerol tetraethers (GDGTs) may help shed light on understanding the activity of archaeal communities in these habitats.

METHODS

Normal-phase and reversed-phase liquid chromatography/mass spectrometry (LC/MS) analysis on total lipid extracts of environmental samples revealed series of GDGTs with different biphytane structures. Comparison of the mass spectrum of biphytane obtained from separated novel GDGTs with that of a synthetic C₄₀ biphytane confirms our structural assignments.

RESULTS

A unique cyclohexyl ring configured in the middle of a C₄₀ biphytane chain was identified in these novel GDGTs. We suggest the trivial name S-GDGTs for these compounds, where 'S' stands for 'sulfidic' and 'six-membered ring'. S-GDGT derivatives composed of biphytanes modified with double bonds and cyclopentane rings were also detected in the samples we analyzed. Intact polar lipid precursors of S-GDGT include compounds with mono- and diglycosyl head groups.

CONCLUSIONS

The carbon isotopic composition of S-GDGTs and their occurrence in FGL, Messel Shale as well as Salt Pond and salt marshes on Cape Cod suggest that S-GDGTs may be produced by chemoautotrophic archaea that prefer sulfidic conditions. Copyright © 2016 John Wiley & Sons, Ltd.

The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems

The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids. We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (∼370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.

Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria

Microbe-mediated soil uptake is the largest and most uncertain variable in the budget of atmospheric hydrogen (H2 ). The diversity and ecophysiological role of soil microorganisms that can consume low atmospheric abundances of H2 with high-affinity [NiFe]-hydrogenases is unknown. We expanded the library of atmospheric H2 -consuming strains to include four soil Harvard Forest Isolate (HFI) Streptomyces spp., Streptomyces cattleya and Rhodococcus equi by assaying for high-affinity hydrogenase (hhyL) genes and quantifying H2 uptake rates. We find that aerial structures (hyphae and spores) are important for Streptomyces H2 consumption; uptake was not observed in S. griseoflavus Tu4000 (deficient in aerial structures) and was reduced by physical disruption of Streptomyces sp. HFI8 aerial structures. H2 consumption depended on the life cycle stage in developmentally distinct actinobacteria: Streptomyces sp. HFI8 (sporulating) and R. equi (non-sporulating, non-filamentous). Strain HFI8 took up H2 only after forming aerial hyphae and sporulating, while R. equi only consumed H2 in the late exponential and stationary phase. These observations suggest that conditions favouring H2 uptake by actinobacteria are associated with energy and nutrient limitation. Thus, H2 may be an important energy source for soil microorganisms inhabiting systems in which nutrients are frequently limited.

Cyanophycin mediates the accumulation and storage of fixed carbon in non-heterocystous filamentous cyanobacteria from coniform mats

Thin, filamentous, non-heterocystous, benthic cyanobacteria (Subsection III) from some marine, lacustrine and thermal environments aggregate into macroscopic cones and conical stromatolites. We investigate the uptake and storage of inorganic carbon by cone-forming cyanobacteria from Yellowstone National Park using high-resolution stable isotope mapping of labeled carbon (H(13)CO3 (-)) and immunoassays. Observations and incubation experiments in actively photosynthesizing enrichment cultures and field samples reveal the presence of abundant cyanophycin granules in the active growth layer of cones. These ultrastructurally heterogeneous granules rapidly accumulate newly fixed carbon and store 18% of the total particulate labeled carbon after 120 mins of incubation. The intracellular distribution of labeled carbon during the incubation experiment demonstrates an unexpectedly large contribution of PEP carboxylase to carbon fixation, and a large flow of carbon and nitrogen toward cyanophycin in thin filamentous, non-heterocystous cyanobacteria. This pattern does not occur in obvious response to a changing N or C status. Instead, it may suggest an unusual interplay between the regulation of carbon concentration mechanisms and accumulation of photorespiratory products that facilitates uptake of inorganic C and reduces photorespiration in the dense, surface-attached communities of cyanobacteria from Subsection III.

Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3

The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling between carbon and sulfur metabolisms to the overall magnitude of the sulfur isotope effect, this study compared sulfur isotope fractionations by mutants of Desulfovibrio vulgaris Hildenborough. We tested mutant strains lacking one or two periplasmic (Hyd, Hyn-1, Hyn-2, and Hys) or cytoplasmic hydrogenases (Ech and CooL), and a mutant lacking type I tetraheme cytochrome (TpI-c 3). In batch culture, wild-type D. vulgaris and its hydrogenase mutants had comparable growth kinetics and produced the same sulfur isotope effects. This is consistent with the reported redundancy of hydrogenases in D. vulgaris. However, the TpI-c 3 mutant (ΔcycA) exhibited slower growth and sulfate reduction rates in batch culture, and produced more H2 and an approximately 50% larger sulfur isotope effect, compared to the wild type. The magnitude of sulfur isotope fractionation in the CycA deletion strain, thus, increased due to the disrupted coupling of the carbon oxidation and sulfate reduction pathways. In continuous culture, wild-type D. vulgaris and the CycA mutant produced similar sulfur isotope effects, underscoring the influence of environmental conditions on the relative contribution of hydrogen cycling to the electron transport. The large sulfur isotope effects associated with the non-ideal stoichiometry of sulfate reduction in this study imply that simultaneous fermentation and sulfate reduction may be responsible for some of the large naturally-occurring sulfur isotope effects. Overall, mutant strains provide a powerful tool to test the effect of specific redox proteins and pathways on sulfur isotope fractionation.

Cyanobacterial diversity and activity in modern conical microbialites

Modern conical microbialites are similar to some ancient conical stromatolites, but growth, behavior and diversity of cyanobacteria in modern conical microbialites remain poorly characterized. Here, we analyze the diversity of cyanobacterial 16S rRNA gene sequences in conical microbialites from 14 ponds fed by four thermal sources in Yellowstone National Park and compare cyanobacterial activity in the tips of cones and in the surrounding topographic lows (mats), respectively, by high-resolution mapping of labeled carbon. Cones and adjacent mats contain similar 16S rRNA gene sequences from genetically distinct clusters of filamentous, non-heterocystous cyanobacteria from Subsection III and unicellular cyanobacteria from Subsection I. These sequences vary among different ponds and between two sampling years, suggesting that coniform mats through time and space contain a number of cyanobacteria capable of vertical aggregation, filamentous cyanobacteria incapable of initiating cone formation and unicellular cyanobacteria. Unicellular cyanobacteria are more diverse in topographic lows, where some of these organisms respond to nutrient pulses more rapidly than thin filamentous cyanobacteria. The densest active cyanobacteria are found below the upper 50 μm of the cone tip, whereas cyanobacterial cells in mats are less dense, and are more commonly degraded or encrusted by silica. These spatial differences in cellular activity and density within macroscopic coniform mats imply a strong role for diffusion limitation in the development and the persistence of the conical shape. Similar mechanisms may have controlled the growth, morphology and persistence of small coniform stromatolites in shallow, quiet environments throughout geologic history.

Formation and stability of oxygen-rich bubbles that shape photosynthetic mats

Gas release in photic-zone microbialites can lead to preservable morphological biosignatures. Here, we investigate the formation and stability of oxygen-rich bubbles enmeshed by filamentous cyanobacteria. Sub-millimetric and millimetric bubbles can be stable for weeks and even months. During this time, lithifying organic-rich laminae surrounding the bubbles can preserve the shape of bubbles. Cm-scale unstable bubbles support the growth of centimetric tubular towers with distinctly laminated mineralized walls. In environments that enable high photosynthetic rates, only small stable bubbles will be enclosed by a dense microbial mesh, while in deep waters extensive microbial mesh will cover even larger photosynthetic bubbles, increasing their preservation potential. Stable photosynthetic bubbles may be preserved as sub-millimeter and millimeter-diameter features with nearly circular cross-sections in the crests of some Proterozoic conical stromatolites, while centrimetric tubes formed around unstable bubbles provide a model for the formation of tubular carbonate microbialites that are not markedly depleted in (13)C.

Sporulenes, heptaprenyl metabolites from Bacillus subtilis spores

Sporulene, a C₃₅-terpenoid hydrocarbon with an unusual pentacyclic structure, is produced by Bacillus subtilis during sporulation.

A polycyclic terpenoid that alleviates oxidative stress

Polycyclic terpenoid lipids such as hopanes and steranes have been widely used to understand ancient biology, Earth history, and the oxygenation of the ocean-atmosphere system. Some of these lipids are believed to be produced only by aerobic organisms, whereas others actually require molecular oxygen for their biosynthesis. A persistent question remains: Did some polycyclic lipids initially evolve in response to certain environmental or metabolic stresses, including the presence of oxygen? Here, we identify tetracyclic isoprenoids in spores of the bacterium Bacillus subtilis. We call them sporulenes. They are produced by cyclization of regular polyprenes, a reaction that is more favorable chemically than the formation of terpenoids such as hopanoids and steroids from squalene. The simplicity of the reaction suggests that the B. subtilis cyclase may be analogous to evolutionarily ancient cyclases. We show that these molecules increase the resistance of spores to a reactive oxygen species, demonstrating a specific physiological role for a nonpigment bacterial lipid biomarker. Geostable derivatives of these compounds in sediments could thus be used as direct indicators of oxidative stress and aerobic environments.

A likely role for anoxygenic photosynthetic microbes in the formation of ancient stromatolites

Although cyanobacteria are the dominant primary producers in modern stromatolites and other microbialites, the oldest stromatolites pre-date geochemical evidence for oxygenic photosynthesis and cyanobacteria in the rock record. As a step towards the development of laboratory models of stromatolite growth, we tested the potential of a metabolically ancient anoxygenic photosynthetic bacterium to build stromatolites. This organism, Rhodopseudomonas palustris, stimulates the precipitation of calcite in solutions already highly saturated with respect to calcium carbonate, and greatly facilitates the incorporation of carbonate grains into proto-lamina (i.e. crusts). The appreciable stimulation of the growth of proto-lamina by a nonfilamentous anoxygenic microbe suggests that similar microbes may have played a greater role in the formation of Archean stromatolites than previously assumed.