New keratose sponges after the end-Permian extinction provide insights into biotic recoveries.

We challenge the prevailing view that the end-Permian extinction impeded the Triassic evolution of sponges. Here, we report a deep-water community dominated by abundant keratose sponges in the lowest Triassic strata from Southwest China. The sponge fossils occur as dark elliptical imprints in mudstone with distinct oscula on their tops. The structure of preserved fibers suggests closest affinity with the extant Dictyoceratida, an aspiculate demosponge. The exceptional preservation plays a crucial role in retaining their exquisite structures. Sedimentary, taphonomic, pyrite framboid, and trace elemental analyses indicate that the sponges proliferated in an oxygen-poor habitat, demonstrating the high tolerance of sponges to severe conditions. Sponge proliferation is a signal of environmental upheaval but they also stabilized the ecosystem, driving the first phase of biotic recovery after the end-Permian extinction.

Identification and Current Palaeobiological Understanding of "Keratosa"-Type Nonspicular Demosponge Fossils in Carbonates: With a New Example from the Lowermost Triassic, Armenia.

Structures similar to fossilized nonspicular demosponges have been reported in carbonates throughout the Phanerozoic and recently in rocks dating back to 890 Ma ago. Interpretation of these records is increasingly influential to our understanding of metazoans in multiple aspects, including their early evolution, the ecology in fossil reefs, and recovery after mass extinction events. Here, we propose six identification criteria of "Keratosa"-type nonspicular demosponge fossils based on the well-established taphonomical models and their biological characteristics. Besides, sponge fossils of this kind from the lowermost Triassic of Chanakhchi (Armenia) are described with a 3-D reconstruction to exemplify the application of these criteria in recognition of such organisms. Subsequently, the state-of-the-art understanding of the taxonomy and evolution of these fossil sponges, a previously poorly addressed topic, is summarized. The morphology of the Triassic Chanakhchi fossils indicates an affinity with verongimorphs, a group that may have evolved by Cambrian Age 3. Other than that, further efforts are encouraged to forge quantitative criteria based on the here proposed descriptive version and to explore the taxonomic diversity and evolutionary details of these fossil nonspicular demosponges.

Adaptive specialization of a unique sponge body from the Cambrian Qingjiang biota.

Sponge fossils from the Cambrian black shales have attracted attention from both palaeontologists and geochemists for many years in terms of their high diversity, beautiful preservation and perplexing adaptation to inhospitable living environments. However, the body shape of these sponges, which contributes to deciphering adaptive evolution, has not been scrutinized. New complete specimens of the hexactinellid sponge Sanshapentella tentoriformis sp. nov. from the Qingjiang biota (black shale of the Cambrian Stage 3 Shuijingtuo Formation, ca 518 Ma) allow recognition of a unique dendriform body characterized by a columnar trunk with multiple conical high peaks and distinctive quadripod-shaped dermal spicules that frame each high peak. The body shape of this new sponge along with other early Cambrian hexactinellids, is classified into three morpho-groups that reflect different levels of adaptivity to the environment. The cylindrical and ovoid bodies generally adapted to a large spectrum of environments; however, the dendriform body of S. tentoriformis was restricted to the relatively deep-water, oxygen-deficient environment. From a hindsight view, the unique body shape represents a consequence of adaptation that helps maintain an effective use of oxygen and a low energy cost in hypoxic conditions.

Ingredients for microbial life preserved in 3.5 billion-year-old fluid inclusions.

It is widely hypothesised that primeval life utilised small organic molecules as sources of carbon and energy. However, the presence of such primordial ingredients in early Earth habitats has not yet been demonstrated. Here we report the existence of indigenous organic molecules and gases in primary fluid inclusions in c. 3.5-billion-year-old barites (Dresser Formation, Pilbara Craton, Western Australia). The compounds identified (e.g., H2S, COS, CS2, CH4, acetic acid, organic (poly-)sulfanes, thiols) may have formed important substrates for purported ancestral sulfur and methanogenic metabolisms. They also include stable building blocks of methyl thioacetate (methanethiol, acetic acid) - a putative key agent in primordial energy metabolism and thus the emergence of life. Delivered by hydrothermal fluids, some of these compounds may have fuelled microbial communities associated with the barite deposits. Our findings demonstrate that early Archaean hydrothermal fluids contained essential primordial ingredients that provided fertile substrates for earliest life on our planet.

Metagenome-Assembled Genome Sequences from an Anoxygenic Photosynthetic Consortium Involved in Sulfur Cycling.

We sequenced the metagenome of an anoxygenic photosynthetic consortium originating from pond water and reconstructed four metagenome-assembled genomes. These genomes include Desulfocapsa, Paludibacter, Lamprocystis, and Rhodocyclaceae representatives and indicate the presence of genes for dissimilatory sulfate reduction and oxidation of reduced sulfur compounds.

Siboglinidae Tubes as an Additional Niche for Microbial Communities in the Gulf of Cádiz-A Microscopical Appraisal.

Siboglinids were sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV, and Anastasya MV). These invertebrates are characteristic to cold seeps and are known to host chemosynthetic endosymbionts in a dedicated trophosome organ. However, little is known about their tube as a potential niche for other microorganisms. Analyses by scanning and transmission electron microscopy showed dense biofilms on the tube in Al Gacel MV and Anastasya MV specimens by prokaryotic cells. Methanotrophic bacteria were the most abundant forming these biofilms as further supported by 16S rRNA sequence analysis. Furthermore, elemental analyses with electron microscopy and energy-dispersive X-ray spectroscopy point to the mineralization and silicification of the tube, most likely induced by the microbial metabolisms. Bacterial and archaeal 16S rRNA sequence libraries revealed abundant microorganisms related to these siboglinid specimens and certain variations in microbial communities among samples. Thus, the tube remarkably increases the microbial biomass related to the worms and provides an additional microbial niche in deep-sea ecosystems.

Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy.

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10-12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3-4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

Composition, Diversity and Functional Analysis of the Modern Microbiome of the Middle Triassic Cava Superiore Beds (Monte San Giorgio, Switzerland).

Organic-rich laminated shales and limestones from the Monte San Giorgio (Lugano Prealps, Switzerland) are known as famous fossil lagerstätten for excellently preserved fossils from the Middle Triassic Period. The various bituminous shales from Monte San Giorgio are thermally immature and rich in diverse organic compounds, which provide unique substrates for active soil microbial communities. We selected the Cava superior beds of the Acqua del Ghiffo site for this study. To investigate its microbial structure and diversity, contig assembly, Operational Taxonomic Units (OTUs) clustering, and rarefaction analysis were performed for bacterial 16S rDNA preparations from bituminous and non-bituminous limestone strata with the MetaAmp pipeline. Principal coordinates analysis shows that the microbial communities from the bituminous strata differ significantly from limestone samples (P < 0.05 Unifrac weighted). Moreover, metagenomic tools could also be used effectively to analyze the microbial communities shift during enrichment in specific growth media. In the nutrient-rich media, one or few taxa, mainly Proteobacteria and Firmicutes, were enriched which led to the drastic diversity loss while oligotrophic media could enrich many taxa simultaneously and sustain the richness and diversity of the inoculum. Piphillin, METAGENassist and MicrobiomeAnalyst pipeline also predicted that the Monte San Giorgio bituminous shales and oligotrophic enriched microbiomes degrade complex polycyclic aromatic hydrocarbons.

Frutexites-like structures formed by iron oxidizing biofilms in the continental subsurface (Äspö Hard Rock Laboratory, Sweden).

Stromatolitic iron-rich structures have been reported from many ancient environments and are often described as Frutexites, a cryptic microfossil. Although microbial formation of such structures is likely, a clear relation to a microbial precursor is lacking so far. Here we report recent iron oxidizing biofilms which resemble the ancient Frutexites structures. The living Frutexites-like biofilms were sampled at 160 m depth in the Äspö Hard Rock Laboratory in Sweden. Investigations using microscopy, 454 pyrosequencing, FISH, Raman spectroscopy, biomarker and trace element analysis allowed a detailed view of the structural components of the mineralized biofilm. The most abundant bacterial groups were involved in nitrogen and iron cycling. Furthermore, Archaea are widely distributed in the Frutexites-like biofilm, even though their functional role remains unclear. Biomarker analysis revealed abundant sterols in the biofilm most likely from algal and fungal origins. Our results indicate that the Frutexites-like biofilm was built up by a complex microbial community. The functional role of each community member in the formation of the dendritic structures, as well as their potential relation to fossil Frutexites remains under investigation.

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia.

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight-secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of µm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation.

Unusual Deep Water sponge assemblage in South China-Witness of the end-Ordovician mass extinction.

There are few sponges known from the end-Ordovician to early-Silurian strata all over the world, and no records of sponge fossils have been found yet in China during this interval. Here we report a unique sponge assemblage spanning the interval of the end-Ordovician mass extinction from the Kaochiapien Formation (Upper Ordovician-Lower Silurian) in South China. This assemblage contains a variety of well-preserved siliceous sponges, including both Burgess Shale-type and modern type taxa. It is clear that this assemblage developed in deep water, low energy ecosystem with less competitors and more vacant niches. Its explosion may be related to the euxinic and anoxic condition as well as the noticeable transgression during the end-Ordovician mass extinction. The excellent preservation of this assemblage is probably due to the rapid burial by mud turbidites. This unusual sponge assemblage provides a link between the Burgess Shale-type deep water sponges and the modern forms. It gives an excellent insight into the deep sea palaeoecology and the macroevolution of Phanerozoic sponges, and opens a new window to investigate the marine ecosystem before and after the end-Ordovician mass extinction. It also offers potential to search for exceptional fossil biota across the Ordovician-Silurian boundary interval in China.

Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin--A New Type of Cryptoendolithic Fungi.

Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basanites) from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stages in zygospore formation are documented in the studied samples, representing a reproduction cycle. Spore structures of both Zygomycetes and Ascomycetes are mineralized by romanechite-like Mn oxide phases, indicating an involvement in Mn(II) oxidation to form Mn(III,VI) oxides. Zygospores still exhibit a core of carbonaceous matter due to their resistance to degradation. The fungi are closely associated with fossiliferous marine sediments that have been introduced into the vesicles. At the contact to sediment infillings, fungi produced haustoria that penetrated and scavenged on the remains of fragmented marine organisms. It is most likely that such marine debris is the main carbon source for fungi in shallow volcanic rocks, which favored the establishment of vital colonies.

Anthropogenic and solar forcing in δ13C time pattern of coralline sponges.

We present the results of a re-analysis of a previously published carbon isotope data-set related to coralline sponges in the Caribbean Sea. The original interpretation led to the discrimination between a pre-industrial period, with a signal controlled by solar-induced climatic variations, followed by the industrial era, characterized by a progressive δ(13)C negative shift due to the massive anthropogenic carbon emissions. Our re-analysis allowed to extract from the raw isotopic data evidence of a solar forcing still visible during the industrial era, with a particular reference to the 88-year Gleissberg periods. These signals are related to slope changes in both the δ(13)C versus time and the δ(13)C versus carbon emission curves.

Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data.

The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered.

First report of fossil "keratose" demosponges in Phanerozoic carbonates: preservation and 3-D reconstruction.

Fossil record of Phanerozoic non-spicular sponges, beside of being important with respect to the lineage evolution per se, could provide valuable references for the investigation of Precambrian ancestral animal fossils. However, although modern phylogenomic studies resolve non-spicular demosponges as the sister group of the remaining spiculate demosponges, the fossil record of the former is extremely sparse or unexplored compared to that of the latter; the Middle Cambrian Vauxiidae Walcott 1920, is the only confirmed fossil taxon of non-spicular demosponges. Here, we describe carbonate materials from Devonian (Upper Givetian to Lower Frasnian) bioherms of northern France and Triassic (Anisian) microbialites of Poland that most likely represent fossil remnants of keratose demosponges. These putative fossils of keratose demosponges are preserved as automicritic clumps. They are morphologically distinguishable from microbial fabrics but similar to other spiculate sponge fossils, except that the skeletal elements consist of fibrous networks instead of assembled spicules. Consistent with the immunological behavior of sponges, these fibrous skeletons often form a rim at the edge of the automicritic aggregate, separating the inner part of the aggregate from foreign objects. To confirm the architecture of these fibrous networks, two fossil specimens and a modern thorectid sponge for comparison were processed for three-dimensional (3-D) reconstruction using serial grinding tomography. The resulting fossil reconstructions are three-dimensionally anastomosing, like modern keratose demosponges, but their irregular and nonhierarchical meshes indicate a likely verongid affinity, although a precise taxonomic conclusion cannot be made based on the skeletal architecture alone. This study is a preliminary effort, but an important start to identify fossil non-spicular demosponges in carbonates and to re-evaluate their fossilization potential.

Molecular phylogeny of the leafy liverwort Lejeunea (Porellales): evidence for a neotropical origin, uneven distribution of sexual systems and insufficient taxonomy.

BACKGROUND: Lejeunea is a largely epiphytic, subcosmopolitan liverwort genus with a complex taxonomic history. Species circumscriptions and their relationships are subject to controversy; biogeographic history and diversification through time are largely unknown. METHODOLOGY AND RESULTS: We employed sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region of 332 accessions to explore the phylogeny of the Harpalejeunea-Lejeunea-Microlejeunea complex. Lejeunea forms a well-supported clade that splits into two main lineages corresponding to L. subg. Lejeunea and L. subg. Crossotolejeunea. Neotropical accessions dominate early diverging lineages of both main clades of Lejeunea. This pattern suggests an origin in the Neotropics followed by several colonizations from the Neotropics into the Paleotropics and vice versa. Most Afro-Madagascan clades are related to Asian clades. Several temperate Lejeunea radiations were detected. Eighty two of the 91 investigated Lejeunea species could be identified to species level. Of these 82 species, 54 were represented by multiple accessions (25 para- or polyphyletic, 29 monophyletic). Twenty nine of the 36 investigated species of L. subg. Lejeunea were monoicous and 7 dioicous. Within L. subg. Crossotolejeunea, 15 of the 46 investigated species were monoicous and 31 dioicous. Some dioicous as well as some monoicous species have disjunct ranges. CONCLUSIONS/SIGNIFICANCE: We present the first global phylogeny of Lejeunea and the first example of a Neotropical origin of a Pantropical liverwort genus. Furthermore, we provide evidence for the Neotropics as a cradle of Lejeunea lineages and detect post-colonization radiations in Asia, Australasia, Afro-Madagascar and Europe. Dioicy/monoicy shifts are likely non-randomly distributed. The presented phylogeny points to the need of integrative taxonomical studies to clarify many Lejeunea binomials. Most importantly, it provides a framework for future studies on the diversification of this lineage in space and time, especially in the context of sexual systems in Lejeuneaceae.

Deposition of biogenic iron minerals in a methane oxidizing microbial mat.

The syntrophic community between anaerobic methanotrophic archaea and sulfate reducing bacteria forms thick, black layers within multi-layered microbial mats in chimney-like carbonate concretions of methane seeps located in the Black Sea Crimean shelf. The microbial consortium conducts anaerobic oxidation of methane, which leads to the formation of mainly two biomineral by-products, calcium carbonates and iron sulfides, building up these chimneys. Iron sulfides are generated by the microbial reduction of oxidized sulfur compounds in the microbial mats. Here we show that sulfate reducing bacteria deposit biogenic iron sulfides extra- and intracellularly, the latter in magnetosome-like chains. These chains appear to be stable after cell lysis and tend to attach to cell debris within the microbial mat. The particles may be important nuclei for larger iron sulfide mineral aggregates.

Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific.

On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth.

The anamorphic genus Monotosporella (Ascomycota) from Eocene amber and from modern Agathis resin.

The anamorphic fungal genus Monotosporella (Ascomycota, Sordariomycetes) has been reco-vered from a piece of Early Eocene Indian amber, as well as from the surface of extant resin flows in New Caledonia. The fossil fungus was obtained from the Tarkeshwar Lignite Mine of Gujarat State, western India, and was part of the biota of an early tropical angiosperm rainforest. The amber inclusion represents the second fossil record of Sordariomycetes, as well as the first fossil of its particular order (either Savoryellales or Chaetosphaeriales). The fossil fungus is distinguished from extant representatives by possessing both short conidiophores and small two-septate pyriform conidia, and is described as Monotosporella doerfeltii sp. nov. Inside the amber, the anamorph is attached to its substrate, which is likely the degraded thallus of a cladoniform lichen. The extant New Caledonian species is assigned to Monotosporella setosa. It was found growing on semi-solidified resin flows of Agathis ovata (Araucariaceae), and is the first record of Monotosporella from modern resin substrates.