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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.

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.

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.

The Qinghai-Tibetan lakes are experiencing water increase and salinity decrease due to climate warming. However, little is known about how the salinity decrease will affect the composition of autotrophic microbial populations and their carbon fixation pathways. The compositional and physiological responses of autotrophic microbiotas to salinity in lakes remain unclear. In this study, the community composition and carbon fixation pathways of autotrophic microorganisms in lacustrine sediments with a salinity gradient (82.6 g/L to 0.54 g/L) were investigated by using metagenomic analysis. A total of 117 metagenome-assembled genomes (MAGs) with carbon fixation potentially belonging to 20 phyla were obtained. The abundance of these potential autotrophs increased significantly with decreasing salinity, and the variation of sediment autotrophic microbial communities was mainly affected by salinity, pH, and total organic carbon. Notably, along the decreasing salinity gradient, the dominant lineage shifted from Desulfobacterota to Proteobacteria . Meanwhile, the dominant carbon fixation pathway shifted from the Wood-Lungdahl pathway to the less-energy-efficient Calvin-Benson-Bassham cycle, with glycolysis shifting from the Embden-Meyerhof-Parnas pathway to the less-exergonic Entner-Doudoroff pathway. These results suggest that the physiological efficiency of autotrophic microorganisms decreased when the environmental salinity became lower. Metabolic inference of these MAGs revealed that carbon fixation may be coupled to the oxidation of reduced sulfur compounds and ferrous iron, dissimilatory nitrate reduction at low salinity, and dissimilatory sulfate reduction in hypersaline sediments. These results extend our understanding of metabolic versatility and niche diversity of autotrophic microorganisms in saline environments and shed light on the response of autotrophic microbiomes to salinity. These findings are of great significance for understanding the impact of desalination caused by climate warming on the carbon cycle of saline lake ecosystems. IMPORTANCE The Qinghai-Tibetan lakes are experiencing water increase and salinity decrease due to climate warming. However, little is known about how the salinity decrease will affect the composition of autotrophic microbial populations and their carbon fixation pathways. In this study, we used genome-resolved metagenomics to interpret the dynamic changes in the autotrophic microbial community and metabolic pathways along a salinity gradient. The results showed that desalination drove the shift of the dominant microbial lineage from Desulfobacterota to Proteobacteria , enriched autotrophs with lower physiological efficiency pathways, and enhanced coupling between the carbon cycle and other element cycles. These results can predict the future response of microbial communities to lake desalination and improve our understanding of the effect of climate warming on the carbon cycle in saline aquatic ecosystems.

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.

Global warming has resulted in substantial glacier retreats in high-elevation areas, exposing deglaciated soils to harsh environmental conditions. Autotrophic microbes are pioneering colonizers in the deglaciated soils and provide nutrients to the extreme ecosystem devoid of vegetation. However, autotrophic communities remain less studied in deglaciated soils. We explored the diversity and succession of the cbbL gene encoding the large subunit of form I RubisCO, a key CO2-fixing enzyme, using molecular methods in deglaciated soils along a 10-year deglaciation chronosequence on the Tibetan Plateau. Our results demonstrated that the abundance of all types of form I cbbL (IA/B, IC and ID) rapidly increased in young soils (0–2.5 years old) and kept stable in old soils. Soil total organic carbon (TOC) and total nitrogen (TN) gradually increased along the chronosequence and both demonstrated positive correlations with the abundance of bacteria and autotrophs, indicating that soil TOC and TN originated from autotrophs. Form IA/B autotrophs, affiliated with cyanobacteria, exhibited a substantially higher abundance than IC and ID. Cyanobacterial diversity and evenness increased in young soils (<6 years old) and then remained stable. Our findings suggest that cyabobacteria play an important role in accumulating TOC and TN in the deglaciated soils. Autotrophic microorganisms rapidly colonized young deglaciated soils and their abundance positively correlated with total organic carbon and total nitrogen, suggesting that soil TOC and TN originated from autotrophs.