Elioraea tepida, sp. nov., a Moderately Thermophilic Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Mat Community of an Alkaline Siliceous Hot Spring in Yellowstone National Park, WY, USA

Strain MS-P2T was isolated from microbial mats associated with Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, WY, USA. The isolate grows chemoheterotrophically by oxygen-dependent respiration, and light stimulates photoheterotrophic growth under strictly oxic conditions. Strain MS-P2T synthesizes bacteriochlorophyll a and the carotenoid spirilloxanthin. However, photoautotrophic growth did not occur under oxic or anoxic conditions, suggesting that this strain should be classified as an aerobic anoxygenic phototrophic bacterium. Strain MS-P2T cells are motile, curved rods about 0.5 to 1.0 μm wide and 1.0 to 1.5 μm long. The optimum growth temperature is 45–50 °C, and the optimum pH for growth is circum-neutral (pH 7.0–7.5). Sequence analysis of the 16S rRNA gene revealed that strain MS-P2T is closely related to Elioraea species, members of the class Alphaproteobacteria, with a sequence identity of 96.58 to 98%. The genome of strain MS-P2T is a single circular DNA molecule of 3,367,643 bp with a mol% guanine-plus-cytosine content of 70.6%. Based on phylogenetic, physiological, biochemical, and genomic characteristics, we propose this bacteriochlorophyll a-containing isolate is a new species belonging to the genus Elioraea, with the suggested name Elioraeatepida. The type-strain is strain MS-P2T (= JCM33060T = ATCC TSD-174T).

Differentiation of communities of macroinvertebrates and cottoid fish associated with methane seeps of different bottom landscapes of Lake Baikal

The paper presents the results of the study of communities of macroinvertebrates and cottoid fish inhabiting methane seeps of Lake Baikal. For the analysis, we used video surveillance and collection of animals carried out with the help of "Mir" deep-water submersible, as well as NIOZ-type box-corer samplers from the board of a research vessel. Posolskaya Bank and Saint Petersburg methane seeps are located in different basins (southern and middle) and at different depths (300–500 m and ~ 1400 m), characterized by the different underwater landscapes (slope of underwater upland and hills formed by gas hydrates), by the structure of gas hydrates and their depth location in sediments, as well as the composition of microbial mats and communities of microorganisms of bottom sediments. Both seeps are characterized by bubble discharge of methane gas and the formation of highly productive communities of large invertebrates and cottoid fish on seep habitats. Seep animal communities consisted of species-depleted invertebrates and fish of the surrounding deep-water benthal of the Lake. We showed the similarities and differences in the composition of the faunas of two seeps, as well as the quantitative characteristics of taxonomic groups of macroinvertebrates and cottoid fishes. Obligate species have not been revealed on the methane seep Posolskaya Bank. For the methane seep Saint Petersburg, the gastropod species Kobeltocochlea tamarae Sitnikova, Teterina et Maximova, 2021 (Caenogastropoda: Benedictiidae) was designated as an obligate species; among bottom cottoid fishes, Neocottus werestschagini (Taliev, 1953) (Cottoidei: Abyssocottidae) had possible a transitional state to obligate. We presented the data on the assimilation by seep animals of mixed photo- and chemosynthetic food with different proportions of methane-derived carbon. A hypothesis has been substantiated that deep-water seep areas could serve as refugium for the preservation of endemic fauna during the Pliocene-Pleistocene glaciations of Lake Baikal.

New Ediacaran fossils from the Ukraine, some with a putative tunicate relationship

Sack-like body fossils Finkoella ukrainica gen. et sp. nov. and F. oblonga sp. nov., and reticulate fossil Pharyngomorpha reticulata gen. et sp. nov. are described from the upper Ediacaran shallow-marine deposits of Ukraine, which are no younger than 557 Ma. The first two resemble the flattened bodies of tunicates showing mainly the outline of tunica, while the third is considered as a fragment of the pharyngeal basket of a tunicate. F. ukrainica is represented by smaller individuals interpreted as juveniles, which may occur in clusters together with less numerous larger individuals. The larger forms are interpreted as adults, some of which show the preserved oral/atrial syphons and possible traces of internal organs bulging through the tunica. Moreover, Burykhia sp. from the uppermost Ediacaran of the same region is presented. This is the second and younger occurrence of the genus Burykhia, which is preserved as a possible fragment of the pharyngeal basket. All the fossils are preserved as the “death masks” between microbial mats, and their appearance depends partly on the relation to the parting surface on which they are observed. The presented new taxa along with the literature data reinforce the possibility that tunicates originated already in late Ediacaran.

Evolution of Holdfast Diversity and Attachment Strategies of Ediacaran Benthic Macroalgae

Holdfast morphologies and attachment strategies of benthic macroalgae are somewhat flexible and controlled by both the substrate condition and species. Six forms (tapered base, globose holdfast, composite globose holdfast, discoidal holdfast, rhizoids and horizontal rhizomes) of attachment structures of Ediacaran benthic macroalgae are recognized from the early Ediacaran Lantian biota and late Ediacaran Miaohe biota in South China based on functional morphology. Each form is considered either adapted to firm substrates that dominate the Precambrian seafloor, or soft substrates that are more common in the Phanerozoic. The results show a diversification in both holdfast morphology and attachment strategies of macroalgae during the Ediacaran Period. In the early Ediacaran Lantian biota, none of the benthic macroalgae is adapted to soft substrates, while in the late Ediacaran Miaohe biota, a considerable number (41%) of species are adapted to relatively soft substrates. This shift might be an adaptive response to the diversification of macroalgae and a changing substrate condition during the Ediacaran Period: the decline of microbial mats and increase of water content in the sediments in the Ediacaran.

Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins

Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. BLAST analysis of some transcribed proteins indicated that they likely functioned as a nitrate reductase. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.

Composition of microorganisms in carbonated mineral waters of the Mukhen deposit (Khabarovsk territory)

The chemical composition, distribution, structure, number of physiological groups of cultivated bacteria and their biodiversity in the cold carbonic mineral waters of Mukhen and in microbial mats were studied. It is shown that the mineral waters are cold, hydrocarbonate-calcium-magnesium, enriched with iron, manganese, barium. Carbon dioxide predominates in the gaseous composition of waters. Microbiological studies have shown that no sanitary-indicative microflora was found in mineral waters, which indicates the purity of underground waters. Carbonic waters were characterized by a low number of physiological groups of autochthonous bacteria. Among the studied microorganisms, chemolithotrophic thionic bacteria predominated, which indicates the predominance of oxidation processes of reduced sulfur compounds with the participation of bacteria in groundwater. In the microbial mats, various chemolithotrophic and heterotrophic microorganisms were identified, participating in the geochemical cycles of carbon, nitrogen, sulfur, iron, manganese, and silicon. The number of physiological groups of bacteria was higher than in mineral waters, along with this saprophytic bacteria predominated significantly. A sufficiently high rate of protein and cellulose decomposition by microorganisms of microbial mats was shown. A low diversity of cultured heterotrophic bacteria with the dominance of microorganisms of the genus Bacillus was found in mineral waters and in microbial mats. By using the methods of X-ray phase analysis, the important role of microorganisms of microbial mats in the precipitation of silicate minerals and the formation of calcium carbonates was shown.

Ooids forming in situ within microbial mats (Kiritimati atoll, central Pacific)

Ooids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here, we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but these particles grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of the term ‘ooid’ and are in fact very similar to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which leads to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Ciénegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent a modern analog of ancient, hypersaline coastal microbial mats, where functions were preserved over time, whereas taxonomic composition was subject to diversification in the face of local and planetary perturbations.

Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats

Methylmercury, biomagnifying through food chains, is highly toxic for aquatic life. Its production and degradation are largely driven by microbial transformations; however, diversity and metabolic activity of mercury transformers, resulting in methylmercury concentrations in environments, remain poorly understood. Microbial mats are thick biofilms where oxic and anoxic metabolisms cooccur, providing opportunities to investigate the complexity of the microbial mercury transformations over contrasted redox conditions. Here, we conducted a genome-resolved metagenomic and metatranscriptomic analysis to identify putative activity of mercury reducers, methylators and demethylators in microbial mats strongly contaminated by mercury. Our transcriptomic results revealed the major role of rare microorganisms in mercury cycling. Mercury methylators, mainly related to Desulfobacterota, expressed a large panel of metabolic activities in sulfur, iron, nitrogen, and halogen compound transformations, extending known activities of mercury methylators under suboxic to anoxic conditions. Methylmercury detoxification processes were dissociated in the microbial mats with methylmercury cleavage being carried out by sulfide-oxidizing Thiotrichaceae and Rhodobacteraceae populations, whereas mercury reducers included members of the Verrucomicrobia, Bacteroidetes, Gammaproteobacteria, and different populations of Rhodobacteraceae. However most of the mercury reduction was potentially carried out anaerobically by sulfur- and iron-reducing Desulfuromonadaceae, revising our understanding of mercury transformers ecophysiology.