Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents

Aerobic denitrifying bacterial community with low C/N ratio remove nitrate from micro-polluted water: Metagenomics unravels denitrification pathways

The efficient nitrogen removal from micro-polluted source water is an international challenge to be solved urgently. However, the inner denitrification mechanism of native aerobic denitrifying bacterial communities in response to carbon scarcity remains relatively unclear. Here, the bacterial community XT6, screened from an oligotrophic reservoir, exhibited aerobic denitrifying capacity under low-carbon environments. Up to 76.79-81.64 % of total organic carbon (TOC) and 51.48-67.60 % of NO3--N were removed by XT6 within 48 h at C/N ratios of 2.0-3.0. Additionally, the nitrogen balance experiments further manifested that 26.27-38.13 % of NO3--N was lost in gaseous form. As the C/N ratio decreased, XT6 tended to generate more extracellular polymeric substances (EPS), with the tightly bound EPS showing the largest increase. Pseudomonas and Variovorax were quite abundant in XT6, constituting 59.69 % and 28.65 % of the total sequences, respectively. Furthermore, metagenomics analysis evidenced that XT6 removed TOC and nitrate mainly through the tricarboxylic acid cycle and aerobic denitrification. Overall, the abovementioned results provide a deeper understanding of the nitrogen metabolic pathways of indigenous aerobic denitrifying bacterial communities with low C/N ratios and offer useful guidance for controlling nitrogen pollution in oligotrophic ecosystems.

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.

Diversity and dynamics of bacteria from iron-rich microbial mats and colonizers in the Mediterranean Sea (EMSO-Western Ligurian Sea Observatory): Focus on Zetaproteobacteria

Autotrophic microaerophilic iron-oxidizing Zetaproteobacteria seem to play an important role in mineral weathering and metal corrosion in different environments. Here, we compare the bacterial and zetaproteobacterial communities of a mature iron-rich mat together with in situ incubations of different Fe-bearing materials at the EMSO-Ligure West seafloor observatory, which is located on the abyssal plain in the NW Mediterranean Sea. Our results on bacterial communities enable us to make a clear distinction between those growing on mild steel anthropic substrata and those developing on basaltic substrata. Moreover, on anthropic substrata we highlight an influence of mat age on the bacterial communities. Regarding zetaproteobacterial communities, our results point to an increase in ZetaOTUs abundance and diversification with the age of the mat. We corroborate the key role of the ZetaOTU 2 in mat construction, whatever the environment, the substrata on which they develop or the age of the mat. We also show that ZetaOTU 28 is specific to anthropogenic substrata. Finally, we demonstrate the advantage of using dPCR to precisely quantify very low abundant targets, as Zetaproteobacteria on our colonizers. Our study, also, allows to enrich our knowledge on the biogeography of Zetaproteobacteria, by adding new information on this class and their role in the Mediterranean Sea.

Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study

Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface.

Boosting the denitrification efficiency of iron-based constructed wetlands in-situ via plant biomass-derived biochar: Intensified iron redox cycle and microbial responses

Considering the unsatisfied denitrification performance of carbon-limited wastewater in iron-based constructed wetlands (ICWs) caused by low electron transfer efficiency of iron substrates, utilization of plant-based conductive materials in-situ for improving the long-term reactivity of iron substrates was proposed to boost the Fe (III)/Fe (II) redox cycle thus enhance the nitrogen elimination. Here, we investigated the effects of withered Iris Pseudacorus biomass and its derived biochar on nitrogen removal for 165 days in ICWs. Results revealed that accumulate TN removal capacity in biochar-added ICW (BC-ICW) increased by 14.7 % compared to biomass-added ICW (BM-ICW), which was mainly attributed to the synergistic strengthening of iron scraps and biochar. The denitrification efficiency of BM-ICW improved by 11.6 % compared to ICWs, while its removal capacity declined with biomass consumption. Autotrophic and heterotrophic denitrifiers were enriched in BM-ICW and BC-ICW, especially biochar increased the abundance of electroactive species (Geobacter and Shewanella, etc.). An active iron cycle exhibited in BC-ICW, which can be confirmed by the presence of more liable iron minerals on iron scraps surface, the lowest Fe (III)/Fe (II) ratio (0.51), and the improved proportions of iron cycling genes (feoABC, korB, fhuF, TC.FEV.OM, etc.). The nitrate removal efficiency was positively correlated with the nitrogen, iron metabolism functional genes and the electron transfer capacity (ETC) of carbon materials (P < 0.05), indicating that redox-active carbon materials addition improved the iron scraps bioavailability by promoting electron transfer, thus enhancing the autotrophic nitrogen removal. Our findings provided a green perspective to better understand the redox properties of plant-based carbon materials in ICWs for deep bioremediation in-situ.

Linking Zetaproteobacterial diversity and substratum type in iron-rich microbial mats from the Lucky Strike hydrothermal field (EMSO-Azores observatory)

Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named "corals." Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity.IMPORTANCEUp until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin

The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.

"Candidatus Siderophilus nitratireducens": a putative nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales

Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-dependent iron-oxidizing (NDFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with the NDFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, "Candidatus Siderophilus nitratireducens," carries genes central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). Using thermodynamics, we demonstrate that iron oxidation coupled to nap based dissimilatory reduction of nitrate to nitrite is energetically favorable under realistic Fe3+/Fe2+ and NO3-/NO2- concentration ratios. Ultimately, by bridging the gap between laboratory investigations and nitrate real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NDFOs taxonomic diversity and ecological role.

Zeolite enhanced iron-modified biocarrier drives Fe(II)/Fe(III) cycle to achieve nitrogen removal from eutrophic water

The problem of nitrogen removal in eutrophic water needs to be solved. Two new autotrophic nitrogen removal technologies, ammonia oxidation coupled with Fe(III) reduction (Feammox) and Nitrate-dependent Fe(II) oxidation (NDFO), have been shown to have the potential to treat eutrophic water. However, the continuous addition of iron sources not only costs more, but also leads to sludge mineralization. In this study, nano-sized iron powder was loaded on the surface of K3 filler as a solid iron source for the extracellular metabolism of iron-trophic bacteria. At the same time, due to the high selective adsorption of zeolite for ammonia can improve the low nitrogen metabolism rate caused by low nitrogen concentrations in eutrophic water, three kinds of modified functional biological carriers were prepared by mixing zeolite powder and iron powder in different proportions (Z1, Zeolite:iron = 1; Z2, Zeolite:iron = 2; Z3, Zeolite:iron = 3). Z3 exhibited the best performance, with removal efficiencies of 54.8% for total nitrogen during 70 days of cultivation. The chemical structure and state of iron compounds changed under microorganism activity. The ex-situ test detected high NDFO and Feammox activities, with values of 1.02 ± 0.23 and 0.16 ± 0.04 mgN/gVSS/h. The enrichment of NDFO bacteria (Gallionellaceae, 0.73%-1.43%-0.74%) and Feammox bacteria (Alicycliphilus, 1.51%-0.88%-2.30%) indicated that collaboration between various functional microorganisms led to autotrophic nitrogen removal. Hence, zeolite/iron-modified biocarrier could drive the Fe(II)/Fe(III) cycle to remove nitrogen autotrophically from eutrophic water without carbon and Fe resource addition.

Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

IMPORTANCE

Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.

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

IMPORTANCE

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.

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

IMPORTANCE

In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.

Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem

BACKGROUND

Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms.

RESULTS

We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions.

CONCLUSIONS

Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.

Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole

The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.

Performances and mechanisms of simultaneous removal of nitrate and phosphate by biofilter assembled with sponge iron/copper and corn cobs

Sponge iron (SI) is a potential material for removing nitrate and phosphate from water. We decorated the SI with copper (Cu) to enhance its removal performance. To gain insight into the nitrate and phosphate removal utilizing SI/Cu and microbial coupling systems, three biofilters filled with corn cob (CC), corn cob + sponge iron (CS) and corn cob + sponge iron/copper (CSCu) were constructed. The results showed that the effluent NO3--N and PO43--P concentrations of CSCu remained consistently below 1 and 0.1 mg/L. The introduction of SI/Cu led to the enrichment of the Dechloromonas genus, making it the dominant microbial group, occupying 42.65% of the effective sequences. Modification of SI with Cu increased nitrogen cycle-related functional genes abundance in CSCu, with a 634% increase in nirS compared to CS. These findings proved that SI/Cu was a promising material, providing an approach to concomitantly removing nitrate and phosphate.

Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field

Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.

The biochar/Fe-modified biocarrier driven simultaneous NDFO and Feammox to remove nitrogen from eutrophic water

Novelty techniques of Fe(III) reduction coupled to anaerobic ammonium oxidation (i.e. Feammox) and nitrate-dependent Fe(II) oxidation (i.e. NDFO) provide new insights into autotrophic nitrogen removal from eutrophic waters. Given that Feammox and NDFO can theoretically complete the simultaneous NH+ 4-N and NO- 3-N removal via Fe(III)/Fe(II) cycle, this study introduces iron powder to the surface of the biocarrier as a solid-phase source of Fe, and biochar was used as an electron shuttle to mix with the iron powder to improve the bioavailability of iron. Batch experiments was carried out for 70 days using simulated eutrophic water as the medium to investigate the effects of the modified biocarrier for enhanced nitrogen removal. The results showed that BC1 (Fe:BC=1:1) with the highest relative Fe content exhibited the highest nitrogen removal efficiency of 66.74%. XPS and XRD results showed both Fe(III) and Fe(II) compounds on the biocarrier surface, confirming the occurrence of Fe(III)/Fe(II) cycle. The ex-situ activity test indicated that functional activity was positively correlated with the iron content of the biocarrier. The in-situ experiments with different substrates showed the occurrence of Feammox and NDFO. NDFO bacteria (Gallionellaceae), Feammox bacteria (Alicycliphilus), denitrifying and digesting bacteria were enriched, suggesting that the coupled nitrogen removal of NDFO and Feammox is the result of cooperation between different functional microorganisms. Thus, the Fe-modified biocarrier showed superior performance and application potential in catalyzing autotrophic nitrogen removal from eutrophic water by functional microorganisms.

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

BACKGROUND

Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.

RESULTS

We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.

CONCLUSIONS

BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.

Nanoplastics impacts on Thiobacillus denitrificans: Effects of size and dissolved organic matter

The widespread distribution of nanoplastics and dissolved organic matter (DOM) in sewage raises concerns about the potential impact of DOM on the bioavailability of nanoplastics. In this study, the effects of different sizes (100 nm and 350 nm) of polystyrene nanoplastics (PS-NPs, 50 mg/L) and combined with 10 mg/L or 50 mg/L DOMs (fulvic acid, humic acid and sodium alginate) on the growth and denitrification ability of Thiobacillus denitrificans were investigated. Results showed that 100 nm PS-NPs (50 mg/L) cause a longer delay in the nitrate reduction (3 days) of T. denitrificans than 350 nm PS-NPs (2 days). Furthermore, the presence of DOM exacerbated the adverse effect of 100 nm PS-NPs on denitrification, resulting in a delay of 1-4 days to complete denitrification. Fulvic acid (50 mg/L) and humic acid (50 mg/L) had the most significant adverse effect on increasing 100 nm PS-NPs (50 mg/L), causing a reduction of 20 mmol/L nitrate by T. denitrificans in nearly 7 days. It is noteworthy that the presence of DOM did not modify the adverse effect of 350 nm PS-NPs on denitrification. Further analysis of toxicity mechanism of PS-NPs revealed that they could induce reactive oxygen species (ROS) and suppressed denitrification gene expression. The results suggested that DOM may assist in the cellular internalization of PS-NPs by inhibiting PS-NPs aggregation, leading to the increased ROS levels and accelerated T. denitrificans death. This study highlights the potential risk of nanoplastics to autotrophic denitrifying bacteria in the presence of DOM and provides new insights for the treatment of nitrogen-containing wastewater by T. denitrificans.

Simultaneous partial nitrification, Anammox and nitrate-dependent Fe(II) oxidation (NDFO) for total nitrogen removal under limited dissolved oxygen and completely autotrophic conditions

Sustainable nitrogen removal from wastewater at reduced energy and/or chemical consumptions is challenging. This paper investigated, for the first time, the feasibility of coupled partial nitrification, Anammox and nitrate-dependent Fe(II) oxidation (NDFO) for sustainable autotrophic nitrogen removal. With NH₄⁺-N as the only nitrogen-containing compound in the influent, near-complete nitrogen removal (a total of 97.5 % with a maximal total nitrogen removal rate of 6.64 ± 2.68 mgN/L/d) was achieved in a sequencing batch reactor for a 203-d operation without organic carbon source addition and forced aeration. Anammox (predominated by Candidatus Brocadia) and NDFO bacteria (such as Denitratisoma) were successfully enriched, with total relative abundances up to 11.54 % and 10.19 %, respectively. Dissolved oxygen (DO) concentration was a key factor affecting the coupling of multi (ammonia oxidization, Anammox, NDFO, iron-reduction, etc.) bacterial communities, resulting in different total nitrogen removal efficiencies and rates. In batch tests, the optimal DO concentration was 0.50-0.68 mg/L with a maximal total nitrogen removal efficiency of 98.7 %. Fe(II) in the sludge not only competed with nitrite oxidizing bacteria for DO to prevent complete nitrification, but promoted the transcription of NarG and NirK genes (10.5 and 3.5 times higher than the group without Fe(II) addition) as indicated by the reverse transcription quantitative polymerase chain reaction (RT-qPCR), resulting in increased NDFO rate (by 2.7 times) and promoted NO₂^--N generated from NO₃^--N, which back fed the Anammox process, achieving near-complete nitrogen removal. The reduction of Fe(III) by iron-reducing bacteria (IRB) and hydrolytic and fermentative anaerobes enabled a sustainable Fe(II)/Fe(III) recycling, avoiding the need in continuous Fe(II) or Fe (III) dosage. The coupled system is expected to benefit the development of novel autotrophic nitrogen removal processes with neglectable energy and material consumptions for the treatment of wastewater with low organic carbon and NH₄⁺-N contents in underdeveloped regions, such as decentralized rural wastewaters.

Nitrate leaching and its implication for Fe and As mobility in a Southeast Asian aquifer

The drinking water quality in Southeast Asia is at risk due to arsenic (As) groundwater contamination. Intensive use of fertilizers may lead to nitrate (NO3-) leaching into aquifers, yet very little is known about its effect on iron (Fe) and As mobility in water. We ran a set of microcosm experiments using aquifer sediment from Vietnam supplemented with 15NO3- and 13CH4. To assess the effect of nitrate-dependent anaerobic methane oxidation (N-DAMO) we also inoculated the sediment with two different N-DAMO enrichment cultures. We found that native microorganisms and both N-DAMO enrichments could efficiently consume all NO3- in 5 days. However, CH4 oxidation was observed only in the inoculated microcosms, suggesting that the native microbial community did not perform N-DAMO. In uninoculated microcosms, NO3- was preferentially used over Fe(III) as an electron acceptor and consequently inhibited Fe(III) reduction and As mobilization. The addition of N-DAMO enrichment cultures led to Fe(III) reduction and stimulated As and Mn release into the water. The archaeal community in all treatments was dominated by Ca. Methanoperedens while the bacterial community consisted of various denitrifiers. Our results suggest that input of N fertilizers to the aquifer decreases As mobility and that CH4 cannot serve as an electron donor for NO3- reduction.

Nitrogen transformation promotes the anaerobic degradation of PAHs in water level fluctuation zone of the Three Gorges Reservoir in Yangtze River, China: Evidences derived from in-situ experiment

Polycyclic aromatic hydrocarbons (PAHs) pose a great threat to human health and ecological system safety. The interception of nitrogen is common found in the riparian zone. However, there is no evidence on how nitrogen addition affects the anaerobic degradation of PAHs in soil of the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) in Yangtze River, China. Here, we investigated the PAHs degradation rate, the variation of key functional genes and microbial communities after nitrogen addition in soil that experienced a flooding period of water-level-fluctuation. The results revealed that the ∑16PAHs were decreased 16.19 %-36.65 % and more 3-5-rings PAHs were biodegraded with nitrogen addition in WLFZ. The most genes involved in PAHs-anaerobic degradation and denitrification were up-regulated by nitrate addition, and phyla Firmicutes, Actinobacteria and Proteobacteria were more advantages in nitrogen addition groups. The Tax4Fun based genome function analysis revealed that the microbial activity of PAHs-degradation increased with nitrate addition. The co-occurrence network analysis indicated that nitrogen addition accelerated the metabolism of nitrogen and PAHs. It is the first time to provide the direct experimental evidences that nitrogen transformation in the WLFZ soil promotes anaerobic PAHs degradation. This work is of importance to understand the effect of nitrogen intercepted in the WLFZ soil of TGR in Yangtze River, China.

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.

Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge

The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter

Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.

Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments

Microbial nitrate reduction can be driven by organic carbon oxidation, as well as by inorganic electron donors, such as reduced forms of sulfur and iron. An apparent inverse oxygen isotope fractionation effect was observed during nitrate reduction in sediment incubations from five sampling sites of a freshwater lake, Hongze Lake, China. Incubations with organic and inorganic electron donor additions were performed. Especially, the inverse oxygen isotope effect was intensified after glucose addition, whereas the incubations with sulfide and Fe²⁺ showed normal fractionation factors. Nitrate reductase encoding genes, napA and narG, were analysed with metagenomics. Higher napA/narG ratios were associated with higher oxygen fractionation factors. The most abundant clade (59%) of NapA in the incubation with glucose was affiliated with Rhodocyclales. In contrast, it only accounted for 8%-9% of NapA in the incubations with sulfide and Fe²⁺ . Differences in nitrate reductases might explain different oxygen isotope effects. Our findings also suggested that large variance of O-nitrate isotope fractionations might have to be considered in the interpretation of natural isotope records.

Use of sponge iron as an indirect electron donor to provide ferrous iron for nitrate-dependent ferrous oxidation processes: Denitrification performance and mechanism

Sponge iron (SI) can serve as an indirect electron donor to provide Fe(II) for the nitrate-dependent ferrous oxidation (NDFO) process, producing OH^- and magnetite. The SI-NDFO system mainly uses Fe(OH)₂ as an electron donor, achieving a TN reduction rate of 0.42 mg-TN/(gVSS·h) for a period of at least 90 days. The enrichment of iron-oxidizing bacteria and the competition of iron-carbon micro-electrolysis for reaction sites on the surface of SI are the main reasons for the improvement of total nitrogen removal efficiency (TNRE). With an influent NO₃^--N concentration of 50 mg/L and a SI concentration of 50 g/L (at pH 5.0 and 30 °C), the TNRE reached a maximum level of 38.28%. In addition, reducing the pH environment was found to improve the denitrification efficiency of the SI-NDFO system, although denitrification stability was also reduced as a result. Overall, the SI-mediated NDFO process is a promising technique.

Cooperation triggers nitrogen removal and algal inhibition by actinomycetes during landscape water treatment: Performance and metabolic activity

The actinomycetes strain Streptomyces sp. XD-11-9-3 and Streptomyces sp. 5 were isolated and presented poor denitrification performance. Co-culture of actinomycetes triggers nitrogen removal capacity under aerobic conditions (reduced 96% of total nitrogen). Nitrogen balance analysis presented that 71% of initial nitrogen converted as gaseous nitrogen. Moreover, co-culture increased the concentrations of adenosine triphosphate (>2.1 folds) and electron-transmission system activity (>1.5 folds) significantly. The co-culture presented excellent carbon source metabolism activity (especially amines and carboxylic acids) compared with monoculture. The removal efficiency of total nitrogen in the micro-polluted landscape water water reached 61% in the co-culture system, and the algal survival could be inhibited significantly. However, the dominant niche of the co-culture system restrained the diversity of the indigenous nirS-type denitrifying bacterial community. This study provided a novel pathway to the research of co-culture inefficiency aerobic denitrifier and further application in the restoration of polluted water.

Insights into the mechanism of Mn(II)-based autotrophic denitrification: Performance, genomic, and metabonomics

The technologies for groundwater nitrate pollution treatment have drawn increasing global attention. As for autotrophic denitrification (AD), most researches aimed to the mixed microbial culture bioreactors, the mechanism of AD by purely cultured bacteria has not been fully investigated yet. Here, denitrification ability, bacterial activity, and dissolved organic matter evolution of Cupriavidus sp. HY129 in both AD and heterotrophic denitrification (HD) were studied. Genomic analysis and microbial metabolomic analysis were applied to explore the mechanism of AD and the difference and intrinsic factors in AD and HD. The results revealed that HD resulted in higher denitrification efficiency and biomass compared to AD and the bacteria preferred to synthesize humic-like proteins to maintain the progress of AD. Bacteria carry out Mn oxidation outside the bacteria cell and transfer electrons into the cell for AD. Cupriavidus sp. HY129 genome has critical metabolic pathways in both autotrophic and heterotrophic conditions, as well as the MCO gene for mediating the Mn oxidation. Energy metabolism pathways were the most significantly differences between AD and HD. Moreover, sphingolipid metabolism and mineral absorption metabolism were the most essential pathways in the autotrophic process to maintain the normal physiological activities and Mn transfer. The results explored the differences between AD and HD pathways in the same bacteria for the first time and provided new insight into understanding the metabolic characteristics of different denitrification, which provide useful information to the global nitrogen cycle and nitrate pollution treatment.

Denitrification and dissimilatory nitrate reduction to ammonia in long-term lake sediment microcosms with iron(II)

Nitrate is an abundant pollutant in aquatic environments. Competition between the nitrate reduction processes, denitrification, which converts nitrate into nitrogen gas, and dissimilatory nitrate reduction to ammonia (DNRA), which converts nitrate into ammonia, decides whether an ecosystem removes or retains nitrogen. The presence of iron was previously reported to stimulate DNRA while sometimes inhibiting denitrification in in-situ studies, but long-term effect of iron(II) inputs on the competition is unknown. Here we inoculated long-term microcosms with sediments from two freshwater lakes. During 540 days of incubations, the microcosms with nitrate and Fe(II) additions of both lakes were able to sustain high nitrate reduction rates. Lepidocrocite was produced as a product of iron oxidation. We found both denitrification and DNRA were stimulated by nitrate and iron in the absence of external organic carbon addition. Phylogenetic analysis of denitrification genes, nirK and nirS, and DNRA genes, nirB and nrfA, was performed with metagenomic sequencing results. Enrichment was shown for reported Fe(II)-dependent nitrate reducers associated with nirS and nirB. Most of these bacteria are affiliated with Betaproteobacteria. From 16S rRNA gene analysis, Betaproteobacteria was enriched as well. In parallel, heterotrophic denitrifiers and methanotrophic DNRA archaea increased in abundance. Our results suggested heterotrophic and Fe(II)-dependent nitrate reducers both contributed to denitrification and DNRA in long-term microcosm incubations provided with iron.

Harnessing electrical-to-biochemical conversion for microbial synthesis

Electrical-to-biochemical conversion (E2BC) drives cell metabolism for biosynthesis and has become a promising way to realize green biomanufacturing. This review discusses the following aspects: 1. the natural E2BC processes and their underlying E2BC mechanism; 2. development of artificial E2BC for tunable microbial electrosynthesis; 3. design of electrobiochemical systems using self-powered, light-assisted, and nano-biohybrid approaches; 4. synthetic biology methods for efficient microbial electrosynthesis. This review also compares E2BC with electrocatalysis-biochemical conversion (EC2BC), as both strategies may lead to future carbon negative green biomanufacturing.

Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume

Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml-1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to 'omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

Iron Oxidation by a Fused Cytochrome-Porin Common to Diverse Iron-Oxidizing Bacteria

Iron (Fe) oxidation is one of Earth’s major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron oxidizers. The genomes of many diverse iron oxidizers encode a homolog to an outer membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron oxidizer Mariprofundus ferrooxydans PV-1. Cyc2_PV-1 is capable of oxidizing iron, and its redox potential is 208 ± 20 mV, consistent with the ability to accept electrons from Fe²⁺ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. The results of sequence analysis and modeling reveal that the entire Cyc2 family shares a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. On the basis of results from structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe²⁺, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism.