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It has recently been shown that in anaerobic microorganisms the tricarboxylic acid (TCA) cycle, including the seemingly irreversible citrate synthase reaction, can be reversed and used for autotrophic fixation of carbon 1 , 2 . This reversed oxidative TCA cycle requires ferredoxin-dependent 2-oxoglutarate synthase instead of the NAD-dependent dehydrogenase as well as extremely high levels of citrate synthase (more than 7% of the proteins in the cell). In this pathway, citrate synthase replaces ATP-citrate lyase of the reductive TCA cycle, which leads to the spending of one ATP-equivalent less per one turn of the cycle. Here we show, using the thermophilic sulfur-reducing deltaproteobacterium Hippea maritima , that this route is driven by high partial pressures of CO 2 . These high partial pressures are especially important for the removal of the product acetyl coenzyme A (acetyl-CoA) through reductive carboxylation to pyruvate, which is catalysed by pyruvate synthase. The reversed oxidative TCA cycle may have been functioning in autotrophic CO 2 fixation in a primordial atmosphere that is assumed to have been rich in CO 2 . In the deltaproteobacterium Hippea maritima , the tricarboxylic acid (TCA) cycle can be reversed by high partial pressures of CO 2 for the autotrophic fixation of carbon.

Microalgae are a group of autotrophic microorganisms that live in marine, freshwater and soil ecosystems and produce organic substances in the process of photosynthesis. Due to their high metabolic flexibility, adaptation to various cultivation conditions as well as the possibility of rapid growth, the number of studies on their use as a source of biologically valuable products is growing rapidly. Currently, integrated technologies for the cultivation of microalgae aiming to isolate various biologically active substances from biomass to increase the profitability of algae production are being sought. To implement this kind of development, the high productivity of industrial cultivation systems must be accompanied by the ability to control the biosynthesis of biologically valuable compounds in conditions of intensive culture growth. The review considers the main factors (temperature, pH, component composition, etc.) that affect the biomass growth process and the biologically active substance synthesis in microalgae. The advantages and disadvantages of existing cultivation methods are outlined. An analysis of various methods for the isolation and overproduction of the main biologically active substances of microalgae (proteins, lipids, polysaccharides, pigments and vitamins) is presented and new technologies and approaches aimed at using microalgae as promising ingredients in value-added products are considered.

Background and aimsSoil autotrophic microorganisms and plant primary production play crucial roles in soil carbon (C) cycling. However, the information remains limited to whether and how nitrogen (N) application influences the contribution of soil microbial C fixation to the soil organic C (SOC) pool.MethodsWe investigated the effects of soil autotrophic bacterial communities on SOC storage and maize yield. A field experiment was conducted with four application rates of urea on the semiarid Loess Plateau, N application at 0 kg ha− 1 (N0), 100 kg ha− 1 (N1), 200 kg ha− 1 (N2), and 300 kg ha− 1 (N3), respectively.ResultsOur results showed that SOC storage and maize yield were significantly increased by N application, but no significant SOC storage difference between N2 and N3 treatments, no further yield increase beyond 200 N kg ha− 1 application was observed. N application significantly impacted soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial communities via changing soil pH, nitrate N, and soil water content. The diversity of soil autotrophic bacterial communities decreased with increasing rate of N application. We detected a high abundance of the autotrophic bacterial dominant genera Xanthobacter, Bradyrhizobium, Aminobacter, and Nitrosospira. The co-occurrence network of autotrophic bacteria contained four distinct modules. Structural equation modeling further indicated that the autotrophic bacterial communities had positive relationships with SOC storage and maize yield.ConclusionsTaken together, our results highlighted that N application stimulated the activity of soil autotrophic bacterial communities, contributing to an increase in SOC. The increase of SOC under N fertilization can stabilize soil fertility for maize production.

Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15–30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.

Phelipanche ramosa is a widespread parasitic weed of significant economic importance, particularly affecting tomatoes and tobacco. Despite its well-documented impact on agriculture, its microbial associations remain poorly understood. For the first time, we used Next-Generation Sequencing (NGS) to determine the composition of microorganisms (bacteria and fungi) on the flower stigma of P. ramosa and its host, Nicotiana tabacum , as well as to explore their potential functions. The stigma is a nutrient-rich environment that fosters a varied microbial community, encompassing both beneficial and pathogenic organisms affecting plant health and reproductive success. Unique bacterial populations were identified in P. ramosa stigmas, which were absent or less abundant in N. tabacum stigmas. We identified 49 bacterial OTUs in P. ramosa stigmas, primarily Proteobacteria (87.5%) with dominant genera like Pantoea and Pseudomonas . In contrast, N. tabacum stigmas (18 OTUs) were also rich in Proteobacteria (69.6%) but showed higher levels of Leuconostoc and Enterobacteriaceae. Phelipanche ramosa stigmas exhibited a higher abundance of Actinobacteria, while N. tabacum stigmas had a greater proportion of Firmicutes. Fungal communities differed significantly: P. ramosa stigmas (109 OTUs) were dominated by Basidiomycota, while N. tabacum (69 OTUs) was primarily colonised by Ascomycota, with the genus Candida common in the host but absent in the parasite. Specific genera such as Chalastospora , Ustilaginaceae, and Bensingtonia were more abundant or exclusive to P. ramosa stigmas. Nicotiana tabacum stigmas hosted a potentially functionally rich bacterial microbiome, while P. ramosa harbored a more limited one. In contrast, both the structural diversity and functional (metabolic) potential of the fungal communities were higher in P. ramosa compared to N. tabacum . Microbiome network analysis highlighted distinct physiological functions associated with autotrophic and heterotrophic lifestyles. Some identified microorganisms may play key roles in nutrient availability and pathogenicity, including potentially beneficial ones that could provide new opportunities for biological control. This study highlights the significant relationships between microbial diversity and functional traits, underscoring the importance of these dynamics in the structure and functioning of the stigma microbiome.

Serpentinization of ultramafic rocks provides molecular hydrogen (H 2 ) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H 2 -/CO 2 -dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO 2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, “ Ca . Lithacetigenota”, that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H 2 -utilizing lithotrophy. Rather than CO 2 , these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein—the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. “ Ca . Lithacetigenota” glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H 2 even under hyperalkaline, CO 2 -poor conditions. Unique non-CO 2 -reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.

Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N -(3-oxotetradecanoyl)- l -homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B 2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter.

Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsr B and mcr A genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha -, Beta -, Gammaproteobacteria , Actinobacteria and Firmicutes , whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.

Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts. Sponges live in symbiosis with diverse microorganisms. This study uses metabolic modelling to show that the microbial symbionts rely on sponge-derived metabolites to maintain community stability and facilitate elemental cycling, and identifies a key microbial clade that drives cross-feeding processes.

Microbes can provide a more sustainable and energy-efficient method of food and nutrient production compared to plant and animal sources, but energy-intensive carbon (e.g., sugars) and nitrogen (e.g., ammonia) inputs are required. Gas-fixing microorganisms that can grow on H₂ from renewable water splitting and gaseous CO₂ and N₂ offer a renewable path to overcoming these limitations but confront challenges owing to the scarcity of genetic engineering in such organisms. Here, we demonstrate that the hydrogen-oxidizing carbon- and nitrogen-fixing microorganism Xanthobacter autotrophicus grown on a CO₂/N₂/H₂ gas mixture can overproduce the vitamin riboflavin (vitamin B₂).We identify plasmids and promoters for use in this bacterium and employ a constitutive promoter to overexpress riboflavin pathway enzymes. Riboflavin production is quantified at 15 times that of the wild-type organism. We demonstrate that riboflavin overproduction is maintained when the bacterium is grown under hybrid inorganic-biological conditions, in which H₂ from water splitting, along with CO₂ and N₂, is fed to the bacterium, establishing the viability of the approach to sustainably produce food and nutrients.