Carbon Fixation Genes Research Articles

Isolation and Whole-genome analysis of Desmodesmus sp. SZ-1: Novel acid-tolerant carbon-fixing microalga

Utilizing microalgae to capture flue gas pollutants is an effective strategy for mitigating greenhouse gas emissions. However, existing carbon-fixing microalgae exhibit poor tolerance towards acidic flue gas. In this study, the Desmodesmus sp. SZ-1, which can thrive in acidic environments and efficiently sequester CO2, was isolated. Desmodesmus sp. SZ-1 exhibited strong acid tolerance ability, with an average carbon fixation rate of 497.6 mg/L/d under 10 % CO2 and pH 3.5. Physiological analysis revealed that SZ-1 responded to high CO2 by increasing chlorophyll levels while coping with acidic stress by activating antioxidant enzymes. Genome analysis revealed a large number of carbon fixation and acid adaptation genes, involved in membrane lipid biosynthesis, H+ pumps, molecular chaperones, peroxidase system, amino acid synthesis, and carbonic anhydrase. This study provides a novel algal resource for mitigating acid gas emissions and a comprehensive genetic database for genetically modifying microalgae.

Effects of manure and nitrogen fertilization on soil microbial carbon fixation genes and associated communities in the Loess Plateau of China

The effects of long-term fertilization on soil carbon (C) cycling have been a key focus of agricultural sustainable development research. However, the influences of different fertilization treatments on soil microbial C fixation profiles are still unclear. Metagenomics technology and multivariate analysis were employed to inquire changes in soil properties, soil microbial C fixation genes and associated bacterial communities, and the influence of dominant soil properties on C fixation genes. The contents of soil C and nitrogen fractions were signicficantly higher in manure or combined with nitrogen fertilization (NM) than other treatments. The composition of soil microbial C fixation genes and associated bacterial communities varied among different fertilization treatments. Compared with other treatments, the total abundance of microbial C fixation genes and the abundance of Proteobacteria were significantly higher in NM than in other treatments, as well as the abundances of C fixation genes involved in dicarboxylate/4-hydroxybutyrate cycle and reductive citrate cycle. Key functional genes and main bacterial communities presented in the middle of the co-occurrence network. Soil organic carbon, total nitrogen, and microbial biomass nitrogen were the dominant soil properties influencing microbial C fixation genes and associated bacterial communitis. Fertilization increased the abundance of C fixation genes by affecting the changes in bacterial communities abundance mediated by soil properties. Overall, elucidating the responses of soil microbial C fixation genes and associated communities to different fertilization will enhance our understanding of the processes of soil C fixation in farmland.

Biotransformations of arsenic in marine sediments across marginal slope to hadal zone

Arsenic compounds are accumulating in deep ocean, but their ecological impacts on deep-sea ecosystem remain elusive. We studied 32 sediment cores (101 layers for metagenomes, along with 41 global reference sediment metagenomes) collected from the South China Sea and the Mariana Trench (MT), characterized with high arsenic accumulation in MT. In these metagenomes we revealed a significantly positive correlation between relative abundance of arsenite methyltransferase gene (arsM) and sampling depth, which suggests that arsenic methylation is the most prevalent arsenic biotransformation process in the deep sea. Lower relative abundance of arsenic efflux gene, compared with arsM, indicates that microbes in deep-sea sediments were prone to methylate arsenite and retain it rather than efflux it. Phylogenetic analysis identified seven clades of ArsM proteins, including two new clades derived primarily from deep-sea microorganisms. Five metagenome-assembled genomes containing aioA for arsenite oxidation also harbor carbon fixation genes in the deep-sea sediment layers, suggesting previously unnoticed contribution of arsenite-oxidizing autotrophic bacteria to the carbon cycle. Therefore, deep-sea microorganisms adopt different detoxification and transformation strategies in response to arsenic compounds, which renews our understanding of arsenic in their ecological impacts and potential contribution in deep ocean.

Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer

Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ13C of dissolved inorganic carbon (δ13C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.

Organic management improved the multifunctionality in recolonization soil by increasing microbial diversity and function

Abstract Organic management enhances the formation of distinct and stable soil microbial communities, however, its influence on the temporal recovery of microbiome and multifunctionality of sterilized soil remains poorly understood. We used amplicon sequencing and metagenomic sequencing to investigate the effects of microbial communities in long‐term organic and conventional managed soils on restoring soil microbiome and functionality. We calculated multifunctionality of soils at days 30 and 90 of recolonization using the averaging approach. Results showed that organic management (O) significantly increased alpha diversity, niche width and network complexity of microbial community compared to conventional management (C). The alpha diversity, niche width and network complexity of microbial community in soils with organic soil suspension were significantly increased compared to conventional management at days 30 and 90 of recolonization. Soil multifunctionality of sterilized organic managed soil inoculated with organic soil suspension (OO) was 14.6% to 70.6% higher than that of the rest treatments. Macrogenomic analysis revealed that O significantly enriched functional pathways of ABC transporters, carbon metabolism, biosynthesis of amino acids, two‐component and nitrogen metabolism as well as most of the functional genes for carbon degradation, carbon fixation, nitrogen cycling and phosphorus cycles compared to C. These functional pathways and genes were also significantly enriched in soils with organic soil suspension at day 30 and 90 of recolonization. Furthermore, alpha diversity, niche width, network complexity, functional pathways and functional genes of microbiome correlated positively with soil multifunctionality. Synthesis and applications. Our results emphasize the importance of organic management induced changes in diversity, network complexity, and functionality of microbial communities for promoting recovery to soil microbial and functional losses, providing the theoretical basis for sustainable impact of organic management in agronomic production on soil microbiome and function. Read the free Plain Language Summary for this article on the Journal blog.

Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire.

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.

Identification of carbon fixation microorganisms and pathways in an aquifer contaminated with long-chain petroleum hydrocarbons.

Petroleum hydrocarbons (PHCs) can be biodegraded into CO2, and PHC-contaminated aquifers are always deemed as carbon sources. Fortunately, some carbon fixation microorganisms have been found in PHC-contaminated sites. However, most of the studies are related to volatile short-chain PHC, and few studies focus on long-chain PHC-contaminated sites. To reveal the carbon fixation microorganisms in these sites, in the study, a long-chain PHC polluted site in North China was selected. Through hydrochemical and metagenomics analysis, the structure and capacity of carbon fixing microorganisms in the site were revealed. Results showed that there were many kinds of carbon fixed microorganisms that were identified such as Flavobacterium, Pseudomonas. HP/4HB, rTCA, and DC/4HB cycles were dominated carbon fixation pathways. The long-chain PHC were weakly correlated with carbon fixation microorganisms, but it may stimulate the growth of some carbon fixation microorganisms, such as microorganisms involved in rTCA cycle. PRACTITIONER POINTS: The microorganisms with carbon fixation gene exist in the aquifer contaminated by long-chain petroleum hydrocarbon. Microorganisms that have the ability to degrade petroleum also have the ability to carbon fixation. Long-chain petroleum hydrocarbon may promote the growth of carbon fixation microorganisms.

Metagenomic insights into microbial variation and carbon cycling function in crop rotation systems

The decomposition and utilization of plant-derived carbon by microorganisms and carbon fixation are crucial pathways for enhancing soil organic carbon (SOC) storage. However, a gap remains in our understanding of the impact of microorganisms on the decomposition of plant-derived carbon and their capacity for carbon fixation in crop rotation systems. Based on a 12-year experiment with wheat–maize (WM), wheat–cotton (WC), and wheat–soybean (WS) rotations, the microbial communities and carbon cycle function were investigated. The results indicated that WS rotation significantly increased SOC content compared to WM and WC. In addition, a significant increase was observed in microbially available carbon and microbial biomass carbon in the WS soil compared with those in the others. Further analysis of the microbial community factors that influenced SOC content revealed that WS rotation, in contrast to WM rotation, enhanced the diversity and richness of bacteria and fungi. Analysis of microbial carbon decomposition functions revealed an increase in starch, lignin, and hemicellulose decomposition genes in the WS soil compared to the others. The changes in carbon decomposition genes were primarily attributed to six bacterial genera, namely Nocardioides, Agromyces, Microvirga, Skermanella, Anaeromyxobacter, and Arthrobacter, as well as four fungal genera, namely Dendryphion, Staphylotrichum, Apiotrichum, and Abortiporus, which were significantly influenced by the crop rotation systems. In addition, microbial carbon fixation-related genes such as ACAT, IDH1, GAPDH, rpiA, and rbcS were significantly enriched in WS. Species annotation of differential carbon fixation genes identified 18 genera that play a role in soil carbon fixation variation within the crop rotation systems. This study highlights the impact of crop rotation systems on SOC content and alterations in specific microbial communities on carbon cycle function.

Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina

BackgroundDeciphering the genetic architecture of drought tolerance could allow the candidate genes identification responding to water stress. In the Andean Patagonian forest, the genus Nothofagus represents an ecologically relevant species to be included in different genomic studies. These studies are scarce in South American ecosystems however represent an important source of genomic data in order to interpret future climate-change environment scenarios of these emblematic forests. Here, we achieved the assemblage of the transcriptome of N. alpina while searching for key genes of activated or suppressed metabolic pathways in response to drought stress.ResultsDe novo transcriptome assembly resulted in 104,030 transcripts. Following confirmation of drought conditions, based on reduction of leaf water potential and stomatal conductance, a differential gene expression analysis resulted in 2720 significantly expressed genes (1601 up-regulated and 1119 down-regulated). Enrichment analysis (over-representation analysis and gene set enrichment analysis) resulted in more than one hundred stress-responsive term ontologies (i.e. biological processes) and pathways. Terms such as response to abscisic acid and pathways such as plant hormone signal transduction or starch and sucrose metabolism were over-represented. Protein–protein interaction assessment resulted in networks with significantly expressed top common hub gene clusters (e.g. plant-type cell wall biogenesis among down-regulated or ABA-signalling among up-regulated). These networks evidenced important regulators at gene expression such as transcriptional factors.ConclusionsResponses of N. alpina seedlings to drought stress were evidenced by the activation of several genes linked to GO biological processes and KEGG pathways, which were mainly based on over-expression of specific protein kinases, phosphatases, synthases and transcription factors. This suggests an up-regulation of signalling pathways, triggered through plant hormones such as abscisic acid or auxin, which could counteract the osmotic stress created as a probable immediate response to drought. On the other hand, groups of carbon fixation genes related to the galactose metabolism, photosynthesis, secondary wall biogenesis, and fatty acid biosynthesis degradation were down-regulated under drought. Overall, our results provide new genomic data for understanding how non-model long-lived trees of Patagonian forests would acclimate to environmental changes.

Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora

Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.

Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis.

Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.

Preserved particulate organic carbon is likely derived from the subsurface sulfidic photic zone of the Proterozoic Ocean: evidence from a modern, oxygen-deficient lake.

Biological processes in the Proterozoic Ocean are often inferred from modern oxygen-deficient environments (MODEs) or from stable isotopes in preserved sediment. To date, few MODE studies have simultaneously quantified carbon fixation genes and attendant stable isotopic signatures. Consequently, how carbon isotope patterns reflect these pathways has not been thoroughly vetted. Addressing this, we profiled planktonic productivity and quantified carbon fixation pathway genes and associated organic carbon isotope values (δ13 CPOC ) of size-fractionated (0.2-2.7 and >2.7 μm) particulate matter from meromictic Fayetteville Green Lake, NY, USA. The high-O2 Calvin-Benson-Bassham (CBB) gene (cbbL) was most abundant in the <2.7 μm size fraction in shallow oxic and deep hypoxic waters, corresponding with cyanobacterial and eukaryote algal populations. The low-O2 CBB gene (cbbM) was most abundant near the lower oxycline boundary in the larger size fraction, coincident with purple sulfur bacteria populations. The reverse citric acid cycle gene (aclB) was equally abundant in both size fractions in the deepest photic zone, coinciding with green sulfur bacteria populations. Methane coenzyme reductase A (mcrA), of anaerobic methane cyclers, was most abundant at the lower oxycline boundary in both size fractions, coinciding with Methanoregula populations. δ13 CPOC values overlapped with the high-O2 CBB fixation range except for two negative excursions near the lower oxycline boundary, likely reflecting assimilation of isotopically-depleted groundwater-derived carbon by autotrophs and sulfate-reducers. Throughout aphotic waters, δ13 CPOC values of the large size fraction became 13 C-enriched, likely reflecting abundant purple sulfur bacterial aggregates. Eukaryote algae- or cyanobacteria-like isotopic signatures corresponded with increases in cbbL, cbbM, and aclB, and enrichment of exopolymer-rich prokaryotic photoautotrophs aggregates. Results suggest that δ13 CPOC values of preserved sediments from areas of the Proterozoic Ocean with sulfidic photic zones may reflect a mixture of alternate carbon-fixing populations exported from the deep photic zone, challenging the paradigm that sedimentary stable carbon isotope values predominantly reflect oxygenic photosynthesis from surface waters.

Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.

Inhibition of high sulfur on functional microorganisms and genes in slightly contaminated soil by cadmium and chromium

It is generally accepted that sulfur can passivate the bioavailability of heavy metals in soil, but it is not clear whether high sulfur in cadmium (Cd) and chromium (Cr) contaminated soil has negative effect on soil microbial community and ecological function. In this study, total sulfur (TS) inhibited the Chao 1, Shannon, Phylogenetic diversity (Pd) of bacterial and Pd of fungi in slightly contaminated soil by Cd and Cr around pyrite. TS, total potassium, pH, total chromium, total cadmium, total nitrogen, soil organic matter were the predominant factors for soil microbial community; the contribution of TS in shaping bacterial and fungal communities ranked at first and fifth, respectively. Compared with the low sulfur group, the abundance of sulfur sensitive microorganisms Gemmatimonas, Pseudolabrys, MND1, and Schizothecium were decreased by 68.79–97.22% (p < 0.01) at high sulfur one; the carbon fixation, nitrogen cycling, phosphorus cycling and resistance genes abundance were significantly lower (p < 0.01) at the latter. Such variations were strongly and closely correlated to the suppression of energy metabolism (M00009, M00011, M00086) and carbon fixation (M00173, M00376) functional module genes abundance in the high sulfur group. Collectively, high sulfur significantly suppressed the abundances of functional microorganisms and functional genes in slightly contaminated soil with Cd and Cr, possibly through inhibition of energy metabolism and carbon fixation of functional microorganisms. This study provided new insights into the environmental behavior of sulfur in slightly contaminated soil with Cd and Cr.

Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen.

Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.

Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms.

Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.

Microbe interactions drive the formation of floating iron films in circumneutral wetlands

Floating iron (Fe) films are widely found in wetlands that can form oxic-anoxic boundaries under circumneutral conditions. These films play a crucial role in the redox transformations and bioavailability of nutrients and trace metals. Current studies mainly focus on chemical oxidation during Fe film formation under circumneutral conditions. The functional microorganisms and associated microbial processes involved in Fe film formation have yet to be investigated in detail. Here, we investigated the microbial communities and involved microbial processes for the formation of floating Fe films in wetlands. Ferrihydrite was the dominant Fe(III) phase in films, accompanied by moderate levels of carbon and silicon. The Fe species and microbial analysis indicated that Fe films contain mixed-valent Fe and can form biotically. Microbial community analysis showed that the dominant genera in these Fe films were Fe-oxidizing and reducing bacteria and methanotrophs, including Leptothrix, Ferriphasclus, Gallionella, Geobacter and Methylococcales. Leptothrix, Ferriphasclus and Gallionella, as classical Fe(II)-oxidizing bacteria (FeOB), can oxidize Fe(II) with limited oxygen and form special structures that are consistent with Fe film morphology. Geobacter can provide a source of Fe(II) for FeOB growth, and Methylococcales can perform methane oxidation to provide energy for Fe cycling. The high ratios of Gallionella- and Geobacter-related microorganisms and carbon fixation genes proved the contribution of potential of Fe cycling and autotrophic microbial communities to the formation of Fe films. The diversity of microbial community suggested that Fe(II) oxidation could trigger carbon fixation, while Fe(III) reduction accelerated Fe and carbon cycling through anaerobic respiration and autotrophic chemosynthesis. These results highlight the contribution of these multiple microbial processes to Fe and carbon cycling during the formation of floating Fe films in wetlands. However, further studies are required to fully elucidate the interaction of functional microorganisms involved in floating film formation and their biogeochemical role in wetlands.

The heterogeneity of microbial diversity and its drivers in two types of sediments from tidal flats in Beibu Gulf, China

Mudflats and sandflats are two common types of coastal tidal flats, the structure and function differences of microbial communities between them are still underappreciated. Beibu Gulf is a diurnal tidal regime located in China, the differences between the two type of tidal flats could be more distinct. In this study, we collected a total of 6 samples from Beibu Gulf, consisting of 3 sandflats samples and 3 mudflats samples, classified based on clay and silt content. Generally, the mudflats samples exhibited higher levels of NH4+_N and TOC, but lower in ORP and pH. The microbial diversity of the two types of tidal flats was investigated, revealing great differences existed and sandflats had higher microbial richness and diversity than mudflats. Furthermore, we analyzed the association between microbial communities and environmental factors, finding NH4+_N to have the highest contribution to the total variation in microbial community structure, and microbial groups such as Desulfobacterota, Campilobacterota, Chloroflexota, Calditrichota, Spirochaetota, Zixibacteria, Latescibacterota and Sva0485 group in mudflats were positively associated with NH4+_N. The functions of microbial community were predicted using metagenomic sequences and metagenome assembled genome (MAG). Mudflats contained more genes for carbon fixation. Nitrate and nitrite reduction were widely existed in mudflats and sandflats, but nitrogen fixation was only existed in mudflats, and Campilobacterota, Desulfobacterota and Gammaproteobacteria MAGs were mainly responsible for it. Sandflats composed more genes for ammonium oxidation, but no MAG was found whether in sandflats or mudflats. Microbes in mudflats exhibited a greater abundance of genes related to sulfur cycling, especially in reduction process, unique MAGs in mudflats such as Calditrichota, Chloroflexota, Desulfobacterota and Zixibacteria MAGs are responsible for sulfate and sulfite reduction. Finally, we predicted functions of ammonium related microbes in mudflats based on MAGs and found Campilobacterota and Desulfobacterota MAGs were important for high accumulation of ammonium in mudflats. This study illuminated the structural and functional differences of microbial communities in mudflats and sandflats, providing new insights into the relationship of microbial communities and environment in the tidal flat.

Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral.

Recent deep-ocean exploration has uncovered a variety of cold-water coral (CWC) ecosystems around the world ocean, but it remains unclear how microbiome is associated with these corals at a molecular levels. This study utilized metabarcoding, tissue section observation, and metatranscriptomes to investigate the microbiome (Symbiodiniaceae and bacteria) of CWC species (Narella versluysi, Heterogorgia uatumani, and Muriceides sp.) from depths ranging from 260 m to 370 m. Warm-water coral (WWC) species (Acropora pruinosa, Pocillopora damicornis, and Galaxea fascicularis) were used as control groups. Results revealed that CWC host diverse bacteria and Symbiodiniaceae cells were observed in endoderm of CWC tissues. Several new candidate bacterial phyla were found in both CWC and WWC, including Coralsanbacteria, Coralqiangbacteria, Coralgsqaceae, Coralgongineae, etc. Both the 16S rRNA gene sequencing and metatranscriptomes revealed that Actinobacteria and Proteobacteria were abundant bacterial phyla in CWC. At the gene transcription level, the CWC-associated Symbiodiniaceae community showed a low-level transcription of genes involved in photosynthesis, CO2 fixation, glycolysis, citric acid cycle, while bacteria associated with CWC exhibited a high-level transcription of genes for carbon fixation via the Wood-Lijungdahl pathway, short chain fatty acids production, nitrogen, and sulfur cycles. IMPORTANCE This study shed new light on the functions of both Symbiodiniaceae and bacteria in cold-water coral (CWC). The results demonstrated that Symbiodiniaceae can survive and actively transcribe genes in CWC, suggesting a possible symbiotic or parasitic relationship with the host. This study also revealed complete non-photosynthetic CO2 fixation pathway of bacteria in CWC, as well as their roles in short chain fatty acids production and assimilation of host-derived organic nitrogen and sulfur. These findings highlight the important role of bacteria in the carbon, nitrogen sulfur cycles in CWC, which were possibly crucial for CWC survival in in deep-water environments.

Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean.

Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.