Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules

Genomic insights into the alphaproteobacterium Georhizobium sp. MAB10 revealed a pathway of Mn(II) oxidation-coupled anoxygenic photoautotrophy: a novel understanding of the biotic process in deep-sea ferromanganese nodule formation

Under light conditions, Mn(II) facilitates the photoautotrophic growth of Georhizobium sp. MAB10, a strain derived from deep-sea ferromanganese nodules, along with the generation of dark Mn oxides (β-MnO2). This study investigated the genetic basis of Mn(II) oxidation-coupled anoxygenic photoautotrophy using genome sequencing and biochemical assays of strain MAB10. Preliminary results indicated the presence of genes encoding a functional pheophytin-quinone-type photosynthetic reaction center and a putative key enzyme for Mn(II) oxidation, namely FtsP/CotA-like multicopper oxidase GE001273. Under light conditions, Mn(II) significantly reduced the respiration rate and elevated the intracellular NADH/NADtotal ratio. This suggested that Mn(II)-derived electrons entered the cyclic photophosphorylation, partially replacing the oxidative phosphorylation for ATP production and enhancing the electron flow to complex I for NADH generation. In vitro enzymatic studies confirmed that GE001273 was a catalyst for Mn(II) oxidation in the outer membrane. Comprehensive genomic analyses of respiration and carbon and nitrogen metabolism revealed the high ecophysiological flexibility of strain MAB10 during Mn(II) oxidation-coupled anoxygenic photoautotrophy in deep-sea habitats. These analyses provided insights into bacterial Mn(II) oxidation-coupled anoxygenic photoautotrophy during microorganism-mediated deep-sea ferromanganese nodule formation.

IMPORTANCE

Microorganisms are believed to participate in the biotic process of deep-sea ferromanganese nodule formation [Mn(II) oxidation]. Despite the multitude of studies and reviews focusing on the details of Mn(II) oxidation catalyzed by diverse heterotrophs, the mechanistic roles of manganese chemolithotrophs from ferromanganese nodules remain unclear. We demonstrate that strain Georhizobium sp. MAB10 can utilize Mn(II)-derived electrons for photoautotrophic growth, with concomitant generation of dark β-MnO2 type Mn oxides under near-infrared light condition. This study uses genomic and biochemical assays to explore the genetic basis of Mn(II) oxidation-coupled anoxygenic photoautotrophy. The comprehensive analyses of respiration and carbon and nitrogen metabolism further elucidated the high ecophysiological flexibility of strain MAB10 in deep-sea habits. These findings expand our understanding of the role of chemolithotrophs in deep-sea ferromanganese nodule formation and justify further investigations into the molecular basis for Mn(II) oxidation-coupled anoxygenic photoautotrophy.

Microbes as marine habitat formers and ecosystem engineers

Despite their small individual size, marine prokaryotic and eukaryotic microbes can form large 3D structures and complex habitats. These habitats contribute to seafloor heterogeneity, facilitating colonization by animals and protists. They also provide food and refuge for a variety of species and promote novel ecological interactions. Here we illustrate the role of microbes as ecosystem engineers and propose a classification based on five types of habitat: microbial mats, microbial forests, microbial-mineralized habitats, microbial outcrops and microbial nodules. We also describe the metabolic processes of microbial habitat formers and their ecological roles, highlighting current gaps in knowledge. Their biogeography indicates that these habitats are widespread in all oceans and are continuously being discovered across latitudes and depths. These habitats are also expected to expand under future global change owing to their ability to exploit extreme environmental conditions. Given their high ecological relevance and their role in supporting endemic species and high biodiversity levels, microbial habitats should be included in future spatial planning, conservation and management measures.

Metal Release from Manganese Nodules in Anoxic Seawater and Implications for Deep-Sea Mining Dewatering Operations

The potential mining of deep-sea polymetallic nodules has been gaining increasing attention due to their enrichment in metals essential for a low-carbon future. To date, there have been few scientific studies concerning the geochemical consequences of dewatered mining waste discharge into the pelagic water column, which can inform best practices in future mining operations. Here, we report the results of laboratory incubation experiments that simulate mining discharge into anoxic waters such as those that overlie potential mining sites in the North Pacific Ocean. We find that manganese nodules are reductively dissolved, with an apparent activation energy of 42.8 kJ mol-1, leading to the release of associated metals in the order manganese > nickel > copper > cobalt > cadmium > lead. The composition of trace metals released during the incubation allows us to estimate a likely trace metal budget from the simulated dewatering waste plume. These estimates suggest that released cobalt and copper are the most enriched trace metals within the plume, up to ∼15 times more elevated than the background seawater. High copper concentrations can be toxic to marine organisms. Future work on metal toxicity to mesopelagic communities could help us better understand the ecological effects of these fluxes of trace metals.

Removal of thallium by MnOx coated limestone sand filter through regeneration of KMnO4: Combination of physiochemical and biochemical actions

Treatment of industrial thallium(Tl)-containing wastewater is crucial for mitigating environmental risks and health threats associated with this toxic metal. The incorporation of Mn oxides (MnOx) into the filtration system is a promising solution for efficient Tl(I) removal. However, further research is needed to elucidate the underlying mechanism behind MnOx-enhanced filtration and the rules of its stable operation. In this study, limestone, a cost-effective material, was selected as the filter media. Raw water with Mn(II), Tl(I), and other pollutants was prepared after a thorough investigation of actual industrial wastewater conditions. KMnO4 was added to induce the formation of MnO2 on limestone surfaces, while long-term operation led to enrichment of manganese oxidizing microorganisms (MnOM). Results revealed a dual mechanism. Firstly, most Mn(II) were oxidized by KMnO4 to form MnO2 attaching to limestone sands, and both Tl(I) and residual Mn(II) were adsorbed onto the newly formed MnO2. Subsequently, enzymes secreted by MnOM facilitated oxidation of remaining Mn(II), resulting in the generation of biogenic manganese oxides (BioMnOx) with numerous vacancies during long-term operation. The generated BioMnOx not only adsorbed Mn(II) and Tl(I) but also promoted their oxidation process. This approach offers an effective and sustainable method for removing both Mn(II) and Tl(I) from industrial wastewater, thereby addressing the challenges posed by thallium-contaminated effluents.

Population-level prokaryotic community structures associated with ferromanganese nodules in the Clarion-Clipperton Zone (Pacific Ocean) revealed by 16S rRNA gene amplicon sequencing

Although deep-sea ferromanganese nodules are a potential resource for exploitation, their formation mechanisms remain unclear. Several nodule-associated prokaryotic species have been identified by amplicon sequencing of 16S rRNA genes and are assumed to contribute to nodule formation. However, the recent development of amplicon sequence variant (ASV)-level monitoring revealed that closely related prokaryotic populations within an operational taxonomic unit often exhibit distinct ecological properties. Thus, conventional species-level monitoring might have overlooked nodule-specific populations when distinct populations of the same species were present in surrounding environments. Herein, we examined the prokaryotic community diversity of nodules and surrounding environments at the Clarion-Clipperton Zone in Japanese licensed areas by 16S rRNA gene amplicon sequencing with ASV-level resolution for three cruises from 2017 to 2019. Prokaryotic community composition and diversity were distinct by habitat type: nodule, nodule-surface mud, sediment, bottom water and water column. Most ASVs (~80%) were habitat-specific. We identified 178 nodule-associated ASVs and 41 ASVs associated with nodule-surface mud via linear discriminant effect size analysis. Moreover, several ASVs, such as members of SAR324 and Woeseia, were highly specific to nodules. These nodule-specific ASVs are promising targets for future investigation of the nodule formation process.

Alpha radiation from polymetallic nodules and potential health risks from deep-sea mining

In search for critical elements, polymetallic nodules at the deep abyssal seafloor are targeted for mining operations. Nodules efficiently scavenge and retain several naturally occurring uranium-series radioisotopes, which predominantly emit alpha radiation during decay. Here, we present new data on the activity concentrations of thorium-230, radium-226, and protactinium-231, as well as on the release of radon-222 in and from nodules from the NE Pacific Ocean. In line with abundantly published data from historic studies, we demonstrate that the activity concentrations for several alpha emitters are often higher than 5 Bq g^-1 at the surface of the nodules. These observed values can exceed current exemption levels by up to a factor of 1000, and even entire nodules commonly exceed these limits. Exemption levels are in place for naturally occurring radioactive materials (NORM) such as ores and slags, to protect the public and to ensure occupational health and radiation safety. In this context, we discuss three ways of radiation exposure from nodules, including the inhalation or ingestion of nodule fines, the inhalation of radon gas in enclosed spaces and the potential concentration of some radioisotopes during nodule processing. Seen in this light, inappropriate handling of polymetallic nodules poses serious health risks.

A review: Manganese-driven bioprocess for simultaneous removal of nitrogen and organic contaminants from polluted waters

Water pollutants, such as nitrate and organics have received much attention for their harms to ecological environment and human health. The redox transformation between Mn(Ⅱ) and Mn(Ⅳ) for nitrogen and organics removal have been recognized for a long time. Mn(Ⅱ) can act as inorganic electron donor to drive autotrophic denitrification so as to realize simultaneous removal of Mn(Ⅱ), nitrate and organic pollutants. Mn oxides (MnOx) also play an important role in the adsorption and degradation of some organic contaminants and they can change or create new oxidation pathways in the nitrogen cycle. Herein, this paper provides a comprehensive review of nitrogen and organic contaminants removal pathways through applying Mn(Ⅱ) or MnOx as forerunners. The main current knowledge, developments and applications, pollutants removal efficiency, as well as microbiology and biochemistry mechanisms are summarized. Also reviewed the effects of factors such as the carbon source, the environmental factors and operation conditions have on the process. Research gaps and application potential are further proposed and discussed. Overall, Mn-based biotechnology towards advanced wastewater treatment has a promising prospect, which can achieve simultaneous removal of nitrogen and organic contaminants, and minimize sludge production.

Cyclic di-GMP Signaling Links Biofilm Formation and Mn(II) Oxidation in Pseudomonas resinovorans

Bioaugmentation of biological sand filters with Mn(II)-oxidizing bacteria (MOB) is used to increase the efficiency of Mn removal from groundwater. While the biofilm-forming ability of MOB is important to achieve optimal Mn filtration, the regulatory link between biofilm formation and Mn(II) oxidation remains unclear. Here, an environmental isolate of Pseudomonas resinovorans strain MOB-513 was used as a model to investigate the role of c-di-GMP, a second messenger crucially involved in the regulation of biofilm formation by Pseudomonas, in the oxidation of Mn(II). A novel role for c-di-GMP in the upregulation of Mn(II) oxidation through induction of the expression of manganese-oxidizing peroxidase enzymes was revealed. MOB-513 macrocolony biofilms showed a strikingly stratified pattern of biogenic Mn oxide (BMnOx) accumulation in a localized top layer. Remarkably, elevated cellular levels of c-di-GMP correlated not only with increased accumulation of BMnOx in the same top layer but also with the appearance of a second BMnOx stratum in the bottom region of macrocolony biofilms, and the expression of mop genes correlated with this pattern. Proteomic analysis under Mn(II) conditions revealed changes in the abundance of a PilZ domain protein. Subsequent analyses supported a model in which this protein sensed c-di-GMP and affected a regulatory cascade that ultimately inhibited mop gene expression, providing a molecular link between c-di-GMP signaling and Mn(II) oxidation. Finally, we observed that high c-di-GMP levels were correlated with higher lyophilization efficiencies and higher groundwater Mn(II) oxidation capacities of freeze-dried bacterial cells, named lyophiles, showing the biotechnological relevance of understanding the role of c-di-GMP in MOB-513. IMPORTANCE The presence of Mn(II) in groundwater, a common source of drinking water, is a cause of water quality impairment, interfering with its disinfection, causing operation problems, and affecting human health. Purification of groundwater containing Mn(II) plays an important role in environmental and social safety. The typical method for Mn(II) removal is based on bacterial oxidation of metals to form insoluble oxides that can be filtered out of the water. Evidence of reducing the start-up periods and enhancing Mn removal efficiencies through bioaugmentation with appropriate biofilm-forming and MOB has emerged. As preliminary data suggest a link between these two phenotypes in Pseudomonas strains, the need to investigate the underlying regulatory mechanisms is apparent. The significance of our research lies in determining the role of c-di-GMP for increased biofilm formation and Mn(II)-oxidizing capabilities in MOB, which will allow the generation of super-biofilm-elaborating and Mn-oxidizing strains, enabling their implementation in biotechnological applications.

Fast-growing Arctic Fe-Mn deposits from the Kara Sea as the refuges for cosmopolitan marine microorganisms

The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions, and organic matter inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Thermodesulfobacteriota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.

Using deep-sea images to examine ecosystem services associated with methane seeps

Deep-sea images are routinely collected during at-sea expeditions and represent a repository of under-utilized knowledge. We leveraged dive videos collected by the remotely-operated vehicle Hercules (deployed from E/V Nautilus, operated by the Ocean Exploration Trust), and adapted biological trait analysis, to develop an approach that characterizes ecosystem services. Specifically, fisheries and climate-regulating services related to carbon are assessed for three southern California methane seeps: Point Dume (∼725 m), Palos Verdes (∼506 m), and Del Mar (∼1023 m). Our results enable qualitative intra-site comparisons that suggest seep activity influences ecosystem services differentially among sites, and site-to-site comparisons that suggest the Del Mar site provides the highest relative contributions to fisheries and carbon services. This study represents a first step towards ecosystem services characterization and quantification using deep-sea images. The results presented herein are foundational, and continued development should help guide research and management priorities by identifying potential sources of ecosystem services.

Manganese oxidation counteracts the deleterious effect of low temperatures on biofilm formation in Pseudomonas sp. MOB-449

Mn removal from groundwater by biological sand filter technology is negatively impacted by low temperatures in winter periods. Therefore, the need to study Mn(II)-oxidizing bacteria (MOB) having the potential to oxidize Mn(II) and form biofilms at low temperatures is imperative. These MOB can have potential as inocula for sand filter bioaugmentation strategies to optimize Mn removal during winter periods. We previously showed that a Pseudomonas sp. MOB-449 (MOB-449), isolated from a Mn biofilter, oxidizes Mn(II) in a biofilm-dependent way at low temperatures. In this work, MOB-449 Mn(II) oxidation and growth capacities were evaluated under planktonic and biofilm conditions at different temperatures. At 18°C, MOB-449 showed enhanced biofilm formation due to the addition of Mn(II) to the medium correlating with Mn(II) oxidation, compared to biofilms grown in control medium. Moreover, this enhancement on biofilm formation due to the addition of Mn(II) was only observed at 18°C. At this temperature, Mn(II) oxidation in membrane fractions collected from biofilms was induced by uncoupling oxidative phosphorylation from the electron transport chain with 2,4-Dinitrophenol. In Pseudomonas, a role for c-type cytochrome in Mn(II) oxidation has been demonstrated. Accordingly, transcriptional profiles of all terminal oxidases genes found in MOB-449 showed an induction of cytochrome c terminal oxidases expression mediated by Mn(II) oxidation at 18°C. Finally, heme peroxidase activity assays and MS analysis revealed that PetC, a cytochrome c5, and also CcmE, involved in the cytochrome c biogenesis machinery, are induced at 18°C only in the presence of Mn(II). These results present evidence supporting that cytochromes c and also the cytochrome c terminal oxidases are activated at low temperatures in the presence of Mn(II). Overall, this work demonstrate that in MOB-449 Mn(II) oxidation is activated at low temperatures to gain energy, suggesting that this process is important for survival under adverse environmental conditions and contributing to the understanding of the physiological role of bacterial Mn(II) oxidation.

Spatial patterns of microbial diversity in Fe-Mn deposits and associated sediments in the Atlantic and Pacific oceans

Mining of deep-sea Fe-Mn deposits will remove crusts and nodules from the seafloor. The growth of these minerals takes millions of years, yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea, microbes have been identified to affect manganese oxide formation. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two areas in the Atlantic Ocean, the Tropic Seamount and the Rio Grande Rise. Samples were collected using ROV and dredge in 2016 and 2018 oceanographic campaigns, and the 16S rRNA gene was sequenced using Illumina platform. Additionally, we compared our results with microbiome data of Fe-Mn crusts, nodules, and sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean. We found that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to Pacific areas. Crusts and nodules from Atlantic seamounts have unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher abundance of potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to sediments, crusts, nodules, and geochemistry. Despite the time scale of million years for these deposits to grow, a combination of environmental settings played a significant role in shaping the microbiome of crusts and nodules. Our results suggest that microbes of Fe-Mn deposits are key in biogeochemical reactions in deep-sea ecosystems. These findings demonstrate the importance of microbial community analysis in environmental baseline studies for areas within the potential of deep-sea mining.

Heat Treatment of Aluminum Alloys with the Natural Combination of Dopants

Aluminothermic reduction without the separation of individual metals is currently considered as a possible method for processing ferromanganese sea nodules and creating new alloys. In this study, the product of their reduction-a manganese-based polymetallic mixture-was added to pure aluminum, as a mixture of alloying elements in their natural ratios. After extrusion, two new aluminum alloys with a total percentage of metallic additives ranging from 1 to 6 percent were prepared. The possibilities of the precipitation strengthening of these aluminum alloys, especially those containing Mn, Fe, Si, Ni, and Cu, were investigated under a wide range of heat treatment conditions. After each tested combination of annealing and artificial aging temperatures, the phase composition and the microstructure changes were recorded by X-ray diffraction, optical, and scanning electron microscopy with EDS analysis. Under none of the tested heat treatment conditions is a significant hardening effect observed, even though the precipitate phases are observed by TEM. However, the changes in the morphology of the present intermetallic phases caused by the heat treatment are revealed, which highlights the further possible development of these multicomponent alloys.

Enhanced removal of antibiotics and antibiotic resistance genes in a soil microbial fuel cell via in situ remediation of agricultural soils with multiple antibiotics

Soil microbial fuel cells (MFCs) have been applied for the in situ remediation of soils polluted by single antibiotics. However, the investigation of only single antibiotic pollution has hindered MFC application in real-world soil remediation, where the effects of multiple antibiotics with similar chemical structures on the fate of antibiotics and their corresponding antibiotic resistance genes (ARGs) remain unknown. In this study, antibiotic removal rates, microbial community compositions, metabolite compositions, and ARG abundances were investigated in soil MFCs by adding two commonly used antibiotics (sulfadiazine, SDZ, and sulfamethoxazole, SMX), and comparing them with the addition of only a single antibiotic (SDZ). The antibiotic removal rate was higher in the soil MFC with addition of mixed antibiotics compared to the single antibiotic due to enhanced biodegradation efficiency in both the upper (57.24% of the initial antibiotic concentration) and lower layers (57.07% of the initial concentration) of the antibiotic-polluted soils. Bacterial community diversity in the mixed antibiotic conditions increased, and this likely resulted from the decreased toxicity of intermediates produced during antibiotic biodegradation. Moreover, the addition of mixed antibiotics led to lower risks of ARG release into soil environments, as reflected by higher abundances of host bacteria in the single antibiotic treatment. These results encourage the further development of soil MFC technology for in situ remediation of antibiotic-polluted soils.

Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring

Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.

Enhanced performance and mechanisms of sulfamethoxazole removal in vertical subsurface flow constructed wetland by filling manganese ore as the substrate

Sulfamethoxazole (SMX), a typical sulfonamide antibiotic, is ubiquitous in secondary effluent and may pose undesirable effects on the aquatic ecosystem and human health. Constructed wetland (CW) is more and more applied in advanced sewage treatment, and the substrate plays an important role in removing pollutants. Manganese (Mn) ore has been widely concerned as a new type of substrate to remove pollutants in CW due to its high adsorption and redox properties. However, the removal mechanism of antibiotics by Mn ore CW is still unclear. In this study, Mn ore was selected as the substrate of a vertical flow constructed wetland (VFCW) while gravel substrate was selected as a control group, and the removal efficiencies of SMX in two VFCWs were investigated and compared. Experimental devices were layered as different regions, including anaerobic (0-32 cm), anoxic (32-64 cm) and aerobic (64-80 cm) zones, to examine the removal characteristics of SMX in different regions. And the removal mechanism of SMX was also explored by examining the adsorption and oxidation of Mn ore and the microbial degradation performance. The results showed that the final removal efficiency of SMX in CW filled with Mn ore substrate (M-CW) (48.4%) increased by 39.6%, compared with CW filled with gravel substrate (G-CW) (8.8%). According to the calculation of mass balance, the total loss of SMX caused by the oxidation of Mn ore and biodegradation accounted for 33.0% of the total SMX input in M-CW, the SMX loss caused by the biodegradation in G-CW accounted for 13.0%, and the substrate adsorption in M-CW and G-CW occupied 15.0% and 7.0% of the total SMX input, respectively. Mn(II) was formed during the oxidation of SMX by Mn(III, IV) and dissimilated Mn(III, IV) reduction by microorganisms in anaerobic environment (0-32 cm). Whereafter, the produced Mn(II) entered into the aerobic zone (64-80 cm) with the water flow and was re-oxidized into biogenic Mn oxides (BioMnOx) which had high adsorption and oxidation performance for SMX. Therefore, Mn ore could enhance SMX removal efficiency in anaerobic and aerobic zones by Mn redox process.

Ligand-Assisted Formation of Soluble Mn(III) and Bixbyite-like Mn2O3 by Shewanella putrefaciens CN32

Functional material synthesis through biomineralization is effective and environmentally friendly. Biomineralized manganese (Mn) oxides are important for remediation and energy storage. Manganese(II) biomineralization is achieved by a diverse group of bacteria. We show that in the presence of oxygen the dissimilatory manganese-reducing bacterium Shewanella putrefaciens CN32 can oxidize Mn(II). The Mn(II) oxidation was accelerated with the increase in the initial Mn(II) concentration from 0.5 to 3 mM. The reaction was mainly associated with a cell-free filtrate, rather than the direct enzymatic oxidation or indirect oxidation by reactive oxygen species or macrocyclic siderophores. Instead, indirect oxidization of Mn(II) into soluble Mn(III) and bixbyite-like Mn₂O₃ via microbially produced extracellular ligands (molecular weights of 1-3 kDa) was identified. This work broadens our view about microbial Mn(II) oxidation and unveils the important roles of Shewanella species in the geochemical cycling of manganese.

Reproducible Spectrum and Hyperspectrum Data Analysis Using NeXL

NeXL is a collection of Julia language packages (libraries) for X-ray microanalysis data processing. NeXLCore provides basic atomic and X-ray physics data and models including support for microanalysis-related data types for materials and k-ratios. NeXLMatrixCorrection provides algorithms for matrix correction and iteration. NeXLSpectrum provides utilities and tools for energy-dispersive X-ray spectrum and hyperspectrum analysis including display, manipulation, and fitting. NeXL is integrated with the Julia language infrastructure. NeXL builds on the Gadfly plotting library and the DataFrames tabular data library. When combined with the DrWatson package, NeXL can provide a highly reproducible environment in which to process microanalysis data. Data availability and reproducible data analysis are two keys to scientific reproducibility. Not only should readers of journal articles have access to the data, they should also be able to reproduce the analysis steps that take the data to final results. This paper will both discuss the NeXL framework and provide examples of how it can used for reproducible data analysis.

Can we use mine waste as substrate in constructed wetlands to intensify nutrient removal? A critical assessment of key removal mechanisms and long-term environmental risks

The utilization of natural ores and/or mine waste as substrate in constructed wetlands (CWs) to enhance nutrient removal performance has been gaining high popularity recently. However, the knowledge regarding the long-term feasibility and key removal mechanisms, particularly the potential negative environmental effects of contaminants leached from mine waste is far insufficient. This study, for the first time, performed a critical assessment by using different CWs with three mine waste (coal gangue, iron ore and manganese ore) as substrates in a 385-day experiment treating wastewater with varying nutrient loadings. The results showed that the addition of mine waste in CWs increased removal of total phosphorus (TP) by 17-34%, and total nitrogen (TN) by 11-51%. The higher removal of TP is mainly attributed to the strong binding mechanism of phosphate with the oxides and hydroxides of Mn, Fe and/or Al, which are leached out of mine waste. Moreover, integration of mine waste in CWs also significantly stimulated biofilm establishment and enriched the relative abundance of key functional genes related to the nitrogen cycle, supporting the observed high-rate nitrogen removal. However, leaching of heavy metals (Fe, Mn, Cu and Cr) from the beded mine waste in the experimented CWs was monitored, which further influenced cytoplasmic enzymes and created oxidative stress damage to plants, resulting in a decline of nutrient uptake by plants.

Potential impacts of polymetallic nodule removal on deep-sea meiofauna

Deep seabed mining is potentially imminent in the Clarion Clipperton Fracture Zone (CCFZ; northeast Pacific). Seabed collectors will remove polymetallic nodules and the surrounding surface sediments, both inhabited by meiofauna, along their path. To determine potential impacts of polymetallic nodule removal, we investigated the importance of nodule presence for the abundance, composition and diversity of sediment meiofauna, and evaluated the existence and composition of nodule crevice meiofauna in the Global Sea Mineral Resources (GSR) exploration contract area. Nodule-free and nodule-rich sediments displayed high biodiversity with many singletons and doubletons, potentially representing rare taxa. Nodule presence negatively influenced sediment meiofaunal abundances but did not markedly affect taxonomic composition or diversity. This is the first report on CCFZ nodule crevice meiofauna, whose abundance related positively to nodule dimensions. Though dominated by the same taxa, nodules and sediments differed regarding the taxonomic and trophic composition of the meio- and nematofauna. Nevertheless, there were no taxa endemic to the nodule crevices and nodule crevice meiofauna added only little to total small-scale (~ cm) meiofaunal abundance and diversity. We formulated environmental management recommendations at the contract area and regional (CCFZ) scale related to sampling effort, set-aside preservation and monitoring areas, and potential rehabilitation measures.

The role and related microbial processes of Mn-dependent anaerobic methane oxidation in reducing methane emissions from constructed wetland-microbial fuel cell

Anaerobic oxidation of methane (AOM) plays an important role in global carbon cycle and greenhouse gas emission reduction. In this study, an effective green technology to reduce methane emissions was proposed by introducing Mn-dependent anaerobic oxidation of methane (Mn-AOM) and microbial fuel cell (MFC) technology into constructed wetland (CW). The results indicate that the combination of biological methods and bioelectrochemical methods can more effectively control the methane emission from CW than the reported methods. The role of dissimilated metal reduction in methane control in CW and the biochemical process associated with Mn-AOM were also investigated. The results demonstrated that using Mn ore as the matrix and operating MFC effectively reduced methane emissions from CW, and higher COD removal rate was obtained in CW-MFC (Mn) during the 200 days of operation. Methane emission from CW-MFC (Mn) (53.76 mg/m²/h) was 55.61% lower than that of CW (121.12 mg/m²/h). The highest COD removal rate (99.85%) in CW-MFC (Mn) was obtained. As the dissimilative metal-reducing microorganisms, Geobacter (5.10%) was found enriched in CW-MFC (Mn). The results also showed that the presence of Mn ore was beneficial to the biodiversity of CW-MFCs and the growth of electrochemically active bacteria (EAB) including Proteobacteria (35.32%), Actinobacteria (2.38%) and Acidobacteria (2.06%), while the growth of hydrogenotrophic methanogens Methanobacterium was effectively inhibited. This study proposed an effective way to reduce methane from CW. It also provided reference for low carbon technology of wastewater treatment.

Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

Antimonate Controls Manganese(II)-Induced Transformation of Birnessite at a Circumneutral pH

Manganese (Mn) oxides, such as birnessite (δ-MnO₂), are ubiquitous mineral phases in soils and sediments that can interact strongly with antimony (Sb). The reaction between birnessite and aqueous Mn(II) can induce the formation of secondary Mn oxides. Here, we studied to what extent different loadings of antimonate (herein termed Sb(V)) sorbed to birnessite determine the products formed during Mn(II)-induced transformation (at pH 7.5) and corresponding changes in Sb behavior. In the presence of 10 mM Mn(II)_aq, low Sb(V)_aq (10 μmol L^-1) triggered the transformation of birnessite to a feitknechtite (β-Mn(III)OOH) intermediary phase within 1 day, which further transformed into manganite (γ-Mn(III)OOH) over 30 days. Medium and high concentrations of Sb(V)_aq (200 and 600 μmol L^-1, respectively) led to the formation of manganite, hausmannite (Mn(II)Mn(III)₂O₄), and groutite (αMn(III)OOH). The reaction of Mn(II) with birnessite enhanced Sb(V)_aq removal compared to Mn(II)-free treatments. Antimony K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy revealed that heterovalent substitution of Sb(V) for Mn(III) occurred within the secondary Mn oxides, which formed via the Mn(II)-induced transformation of Sb(V)-sorbed birnessite. Overall, Sb(V) strongly influenced the products of the Mn(II)-induced transformation of birnessite, which in turn attenuated Sb mobility via incorporation of Sb(V) within the secondary Mn oxide phases.

Forced Biomineralization: A Review

Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.

The Energetic Potential for Undiscovered Manganese Metabolisms in Nature

Microorganisms are found in nearly every surface and near-surface environment, where they gain energy by catalyzing reactions among a wide variety of chemical compounds. The discovery of new catabolic strategies and microbial habitats can therefore be guided by determining which redox reactions can supply energy under environmentally-relevant conditions. In this study, we have explored the thermodynamic potential of redox reactions involving manganese, one of the most abundant transition metals in the Earth's crust. In particular, we have assessed the Gibbs energies of comproportionation and disproportionation reactions involving Mn²⁺ and several Mn-bearing oxide and oxyhydroxide minerals containing Mn in the +II, +III, and +IV oxidation states as a function of temperature (0-100°C) and pH (1-13). In addition, we also calculated the energetic potential of Mn²⁺ oxidation coupled to O₂, NO₂ ^-, NO₃ ^-, and FeOOH. Results show that these reactions-none of which, except O₂ + Mn²⁺, are known catabolisms-can provide energy to microorganisms, particularly at higher pH values and temperatures. Comproportionation between Mn²⁺ and pyrolusite, for example, can yield 10 s of kJ (mol Mn)^-1. Disproportionation of Mn³⁺ can yield more than 100 kJ (mol Mn)^-1 at conditions relevant to natural settings such as sediments, ferromanganese nodules and crusts, bioreactors and suboxic portions of the water column. Of the Mn²⁺ oxidation reactions, the one with nitrite as the electron acceptor is most energy yielding under most combinations of pH and temperature. We posit that several Mn redox reactions represent heretofore unknown microbial metabolisms.

The Mechanism of Microbial-Ferromanganese Nodule Interaction and the Contribution of Biomineralization to the Formation of Oceanic Ferromanganese Nodules

Ferromanganese nodules are an important mineral resource in the seafloor; however, the genetic mechanism is still unknown. The biomineralization of microorganisms appears to promote ferromanganese nodule formation. To investigate the possible mechanism of microbial–ferromanganese nodule interaction, to test the possibility of marine microorganisms as deposition template for ferromanganese nodules minerals, the interactions between Jeotgalibacillus campisalis strain CW126-A03 and ferromanganese nodules were studied. The results showed that strain CW126-A03 increased ion concentrations of Fe, Mn, and other metal elements in solutions at first. Then, metal ions were accumulated on the cells’ surface and formed ultra-micro sized mineral particles, even crystalline minerals. Strain CW126-A03 appeared to release major elements in ferromanganese nodules, and the cell surface may be a nucleation site for mineral precipitation. This finding highlights the potentially important role of biologically induced mineralization (BIM) in ferromanganese nodule formation. This BIM hypothesis provides another perspective for understanding ferromanganese nodules’ genetic mechanism, indicating the potential of microorganisms in nodule formation.

Mn oxides changed nitrogen removal process in constructed wetlands with a microbial electrolysis cell

Intensified Mn redox cycling could enhance nutrient removal in constructed wetlands (CWs). In this study, Mn oxides (birnessite-coated sand) were used as the matrix in horizontal flow CWs (HFCWs) with a microbial electrolysis cell (MEC) (E-B-CW) or without an MEC (B-CW). The model CWs were developed to investigate the capacities and mechanisms of nitrogen removal with increased Mn redox cycling. The results showed that E-B-CW had the highest average removal efficiencies for NH₄-N, NO₃-N and TN, followed by B-CW and control HFCW (C-CW). The Mn(III) oxides (MnOOH or Mn₂O₃) and the Mn(IV) oxide (MnO₂) were all detected in E-B-CW and B-CW, while the matrix in E-B-CW had much more Mn(IV) oxides than B-CW. Interestingly, clustering heat map showed that ammonification and nitrate reduction were related to Mn-oxidizing bacteria and the relative abundance of Mn-oxidizing bacteria in E-B-CW was highest due to the re-oxidation of Mn(II) by the MEC.

Reductive transformation of birnessite and the mobility of co-associated antimony

Manganese (Mn) oxide minerals, such as birnessite, are thought to play an important role in affecting the mobility and fate of antimony (Sb) in the environment. In this study, we investigate Sb partitioning and speciation during anoxic incubation of Sb(V)-coprecipitated birnessite in the presence and absence of Mn(II)_aq at pH 5.5 and 7.5. Antimony K-edge XANES spectroscopy revealed that Sb(V) persisted as the only solid-phase Sb species for all experimental treatments. Manganese K-edge EXAFS and XRD results showed that, in the absence of Mn(II), the Sb(V)-bearing birnessite underwent no detectable mineralogical transformation during 7 days. In contrast, the addition of 10 mM Mn(II) at pH 7.5 induced relatively rapid (within 24 h) transformation of birnessite to manganite (~93%) and hausmannite (~7%). Importantly, no detectable Sb was measured in the aqueous phase for this treatment (compared with up to ∼90 μmol L^-1 Sb in the corresponding Mn(II)-free treatment). At pH 5.5 , birnessite reacted with 10 mM Mn(II)_aq displayed no detectable mineralogical transformation, yet had substantially increased Sb retention in the solid phase, relative to the corresponding Mn(II)-free treatment. These findings suggest that the Mn(II)-induced transformation and recrystallization of birnessite can exert an important control on the mobility of co-associated Sb.

Characterization of Fines Produced by Degradation of Polymetallic Nodules from the Clarion–Clipperton Zone

The discharge of fluid–particle mixture tailings can cause serious disturbance to the marine environment in deep-sea mining of polymetallic nodules. Unrecovered nodule fines are one of the key components of the tailings, but little information has been gained on their properties. Here, we report major, trace, and rare earth element compositions of <63 μm particles produced by the experimental degradation of two types of polymetallic nodules from the Clarion–Clipperton Zone. Compared to the bulk nodules, the fines produced are enriched in Al, K, and Fe and depleted in Mn, Co, Ni, As, Mo, and Cd. The deviation from the bulk composition of original nodules is particularly pronounced in the finer fraction of particles. With X-ray diffraction patterns showing a general increase in silicate and aluminosilicates in the fines, the observed trends indicate a significant contribution of sediment particles released from the pores and cracks of nodules. Not only the amount but also the composition of nodule fines is expected to significantly differ depending on the minimum recovery size of particles at the mining vessel.

Aspects of Estimation and Reporting of Mineral Resources of Seabed Polymetallic Nodules: A Contemporaneous Case Study

Exploration of seabed polymetallic nodules identifies the Clarion Clipperton Zone and the Indian Ocean Nodule Field to be of economic interest. Mineral resource estimation is important to the owner of the resource (all of mankind; and managed by the International Seabed Authority; ISA) and to developers (commercial and government groups holding contracts with the ISA). The Committee for Mineral Reserves International Reporting Standards was developed for the land-based minerals industry and adapted in 2015 for ISA-managed nodules. Nodules can be sampled in a meaningful manner using mechanical devices, albeit with minor issues of bias. Grade and moisture content are measured using the established methodology for land-based minerals. Tonnage of resource is determined via the abundance of nodules in kilograms per square metre of seabed. This can be estimated from physical samples and, in some cases, from photographs. Contemporary resource reporting for nodules classify the level of confidence in the estimate, by considering deposit geology, sample geostatistics, etc. The reporting of estimates also addresses reasonable prospects for eventual economic extraction, including factors such as mining technology, the marine environment, metallurgical processing, and metals markets. Other requirements are qualified persons responsible for estimation and reporting, site inspection, and sample chain of custody.

Interactions between Escherichia coli survival and manganese and iron oxides in water under freeze-thaw

Pathogenic survivals were dramatically affected by Fe³⁺ and Mn²⁺ under freeze-thaw (FT), and the dissolutions of manganese and iron oxides (MIOs) were also accelerated under FT. But the mutual influences of pathogenic bacterial survival and MIOs under FT have not been profoundly explored yet. In this work, aqueous systems containing Escherichia coli as well as synthetic ferrihydrite (Fh) and manganese dioxide (MnO₂) were experimented under simulated FT cycles to study the mutual influences of metal oxides and bacteria survival while oxide dissolutions and appearances, bacterial morphology and activities (survival number, cell surface hydrophobicity (CSH) and superoxide dismutase (SOD)) were obtained. The results showed that broken E. coli cells by ice growth were observed, but both oxides promoted E. coli survival under FT stress and prolonged bacterial survival time by 1.2-2.9 times, which were mainly attributed to the release of Fe³⁺ and Mn²⁺ caused by FT. The dissolutions of Fh and MnO₂ under FT, which took place at a low level in absence of E. coli cells, were markedly enhanced with bacterial interferences by 2-8 times and higher dissolved manganese concentrations were detected than iron. This was probably because that concentrated organic matters which were released from broken cells, rejected into unfrozen liquid layer and acted as electron donors and ligands to oxide dissolution. Compared with Fh system, more significant promotion of E. coli survival under FT in MnO₂ systems were found because of more SOD generations associated with high dissolved manganese concentrations and the stronger cellular protection by MnO₂ aggregations. The results suggested that FT significantly influenced the interactions between metal oxides and bacterial in water, resulting to changes in pathogen activity and metal element cycling.

Global diversity of microbial communities in marine sediment

Marine sediment covers 70% of Earth’s surface and harbors as much biomass as seawater. However, the global taxonomic diversity of marine sedimentary communities, and the spatial distribution of that diversity remain unclear. We investigated microbial composition from 40 globally distributed sampling locations, spanning sediment depths of 0.1 to 678 m. Statistical analysis reveals that oxygen presence or absence and organic carbon concentration are key environmental factors for defining taxonomic composition and diversity of marine sedimentary communities. Global marine sedimentary taxonomic richness predicted by species–area relationship models is 7.85 × 10³ to 6.10 × 10⁵ for Archaea and 3.28 × 10⁴ to 2.46 × 10⁶ for Bacteria as amplicon sequence variants, which is comparable to the richness in seawater and that in topsoil.

Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ∼47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 10³ to 6.10 × 10⁵ and 3.28 × 10⁴ to 2.46 × 10⁶ amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.

Cathodic polarization enables SEM illustration of manganese biomineralization in natural biofilms

Manganese biomineralization occurred readily on metal surfaces in a natural freshwater environment. SEM demonstration of actual bacterial participation was challenging due to the rapidity of biofilm growth and typical microbe-mineral agglomeration. By optimizing cathodic polarization, we slowed down the process so effectually as to document biomineralization by rod-shaped rather than by filamentous bacteria which occurred more frequently at open circuit.

Multiple organic substrates support Mn(II) removal with enrichment of Mn(II)-oxidizing bacteria

Three different organic substrates, K-medium, sterilized activated sludge (SAS), and methanol, were examined for utility as substrates for enriching manganese-oxidizing bacteria (MnOB) in an open bioreactor. The differences in Mn(II) oxidation performance between the substrates were investigated using three down-flow hanging sponge (DHS) reactors continuously treating artificial Mn(II)-containing water over 131 days. The results revealed that all three substrates were useful for enriching MnOB. Surprisingly, we observed only slight differences in Mn(II) removal between the substrates. The highest Mn(II) removal rate for the SAS-supplied reactor was 0.41 kg Mn⋅m^-3⋅d^-1, which was greater than that of K-medium, although the SAS performance was unstable. In contrast, the methanol-supplied reactor had more stable performance and the highest Mn(II) removal rate. We conclude that multiple genera of Comamonas, Pseudomonas, Mycobacterium, Nocardia and Hyphomicrobium play a role in Mn(II) oxidation and that their relative predominance was dependent on the substrate. Moreover, the initial inclusion of abiotic-MnO₂ in the reactors promoted early MnOB enrichment.

Comparative genomic and metabolic analysis of manganese-oxidizing mechanisms in Celeribacter manganoxidans DY25T: Its adaptation to the environment of polymetallic nodules

Manganese (Mn) nodule is one of the ubiquitous polymetallic concretions and mainly consists of Mn - Fe oxi-hydroxide precipitations. A primary oxidation of Mn(II) to MnO₂, in which microorganisms may play important roles, is followed by agglomeration of MnO₂ into nodules. Celeribater manganoxidans DY25^T, belonging to family Rhodobacteraceae, has ability to catalyze the formation of MnO₂ [1]. The concentration of MnO₂ formed by harvested cells reached 7.08 μM after suspended in 10 mM HEPES (pH 7.5). Genomic and physiological characteristics of strain DY25^T provided a better understanding of its Mn-oxidizing mechanism. Fifteen genes (including four multicopper oxidases) may be involved in Mn(II)-oxidation, whereas only three of them can promote this process. Sulfur-oxidizing activity was detected, which may be associated with manganese oxidation. Genes involved in import and export of primary elemental ingredients (C, N, P and S) and metallic elements (e.g. Mn) were discovered, demonstrating its potential roles in the biogeochemical cycle.

Effects of graphite and Mn ore media on electro-active bacteria enrichment and fate of antibiotic and corresponding resistance gene in up flow microbial fuel cell constructed wetland

This study assessed the influence of substrate type on pollutants removal, antibiotic resistance gene (ARG) fate and bacterial community evolution in up-flow microbial fuel cell constructed wetlands (UCW-MFC) with graphite and Mn ore electrode substrates. Better COD removal and higher bacterial community diversity and electricity generation performance were achieved in Mn ore constructed UCW-MFC (Mn). However, the lower concentration of sulfadiazine (SDZ) and the total abundances of ARGs were obtained in the effluent in the graphite constructed UCW-MFC (s), which may be related to higher graphite adsorption and filter capacity. Notably, both reactors can remove more than 97.8% of ciprofloxacin. In addition, significant negative correlations were observed between SDZ, COD concentration, ARG abundances and bacterial a-diversity indices. The LEfse analysis revealed significantly different bacterial communities due to the substrate differences in the two reactors, and Geobacter, a typical model electro-active bacteria (EAB), was greatly enriched on the anode of UCW-MFC (Mn). In contrast, the relative abundance of methanogens (Methanosaeta) was inhibited. PICRUSt analysis results further demonstrated that the abundance of extracellular electron transfer related functional genes was increased, but the methanogen function genes and multiple antibiotic resistance genes in UCW-MFC (Mn) anode were reduced. Redundancy analyses indicated that substrate type, antibiotic accumulation and bacterial community were the main factors affecting ARGs. Moreover, the potential ARG hosts and the co-occurrence of ARGs and intI1 were revealed by network analysis.

Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics

Rocky outcrops covered with thick Fe and Mn oxide coatings, which are known as ferromanganese (Fe-Mn) crusts, are commonly found on slopes of aged seamounts in bathyal and abyssal zones. Although the presence of diverse microorganisms on these Fe-Mn crusts has been reported, little is known about their metabolism. Here, we report the metabolic potential of the microbial community in an abyssal crust collected in the Takuyo-Daigo Seamount, in the north-western Pacific. We performed shotgun metagenomic sequencing of the Fe-Mn crust, and detected putative genes involved in dissolution and precipitation of Fe and Mn, nitrification, sulfur oxidation, carbon fixation, and decomposition of organics in the metagenome. In addition, four metagenome-assembled genomes (MAGs) of abundant members in the microbial community were recovered from the metagenome. The MAGs were affiliated with Thaumarchaeota, Alphaproteobacteria, and Gammaproteobacteria, and were distantly related to previously reported genomes/MAGs of cultured and uncultured species. Putative genes involved in the above reactions were also found in the crust MAGs. Our results suggest that crust microbial communities play a role in biogeochemical cycling of C, N, S, Fe, and Mn, and imply that they contribute to the growth of Fe-Mn crusts.

Sic Parvis Magna: Manganese-Substituted Tricalcium Phosphate and Its Biophysical Properties

Succeeding in the substitution of pharmaceutical compounds with ions deliverable with the use of resorbable biomaterials could have far-reaching benefits for medicine and economy. Calcium phosphates are known as excellent accommodators of foreign ions. Manganese, the fifth most abundant metal on Earth was studied here as an ionic dopant in β-tricalcium phosphate (β-TCP) ceramics. β-TCP containing different amounts of Mn²⁺ ions per Mn_xCa_3-x(PO₄)₂ formula (x = 0, 0.001, 0.01, and 0.1) was investigated for a range of physicochemical and biological properties. The results suggested the role of Mn²⁺ as a structure booster, not breaker. Mn²⁺ ions increased the size of coherent X-ray scattering regions averaged across all crystallographic directions and also lowered the temperature of transformation of the hydroxyapatite precursor to β-TCP. The particle size increased fivefold, from 20 to 100 nm, in the 650-750 °C region, indicating that the reaction of formation of β-TCP was accompanied by a considerable degree of grain growth. The splitting of the antisymmetric stretching mode of the phosphate tetrahedron occurred proportionally to the Mn²⁺ content in the material, while electron paramagnetic resonance spectra suggested that Mn²⁺ might substitute for three out of five possible calcium ion positions in the unit cell of β-TCP. The biological effects of Mn-free β-TCP and Mn-doped β-TCP were selective: moderately proliferative to mammalian cells, moderately inhibitory to bacteria, and insignificant to fungi. Unlike pure β-TCP, β-TCP doped with the highest concentration of Mn²⁺ ions significantly inhibited the growth of all bacterial species tested: Staphylococcus aureus, Salmonella typhi, Escherichia coli, Pseudomonas aeruginosa, and Enterococcus faecalis. The overall effect against the Gram-positive bacteria was more intense than against the Gram-negative microorganisms. Meanwhile, β-TCP alone had an augmentative effect of the viability of adipose-derived mesenchymal stem cells (ADMSCs) and the addition of Mn²⁺ tended to reduce the extent of this augmentative effect, but without imparting any toxicity. For all Mn-doped β-TCP concentrations except the highest, the cell viability after 72 h incubation was significantly higher than that of the negative control. Assays evaluating the effect of Mn²⁺-containing β-TCP formulations on the differentiation of ADMSCs into three different lineages-osteogenic, adipogenic, and chondrogenic-demonstrated no inhibitory or adverse effects compared to pure β-TCP and powder-free positive controls. Still, β-TCP delivering the lowest amount of Mn²⁺ seemed most effective in sustaining the differentiation process toward all three phenotypes, indicating that the dose of Mn²⁺ in β-TCP need not be excessive to be effective.

Influence of application of manganese ore in constructed wetlands on the mechanisms and improvement of nitrogen and phosphorus removal

Vertical up-flow constructed wetlands (CWs) with manganese ore (Mn ore) as media (M-CWs) were developed to treat simulated polluted river water. The results showed that the average removal efficiencies for NH₄-N, NO₃-N, TN and TP were 91.74%, 83.29%, 87.47% and 65.12% in M-CWs, respectively, which were only 79.12%, 72.90%, 75.85% and 43.23% in the CWs without Mn ore (C-CWs). Nutrient mass balance showed that nitrogen (N) removal was improved by enhanced microbial processes, media storage and plant uptake in M-CWs. Moreover, almost 50% of phosphorus (P) was retained by media storage because of the adsorption processes on Mn ore. It was found that addition of Mn ore enhanced denitrification as the relative abundance of denitrifying bacteria increased. The produced Mn(II) and more abundant Gammaproteobacteria confirmed alternative N removal pathways including anoxic nitrification coupled to Mn ore reduction and denitrification using Mn(II) as electron donor. Mn(II) concentration in the effluent of M-CWs was below the drinking water limit of 0.1 mg/L, which makes them environmentally-friendly.

Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner

Manganese biomineralization is a widespread process among bacteria and fungi. To date, there is no conclusive experimental evidence for how and if this process impacts microbial fitness in the environment. Here, we show how a model organism for manganese oxidation is growth inhibited by nitrite, and that this inhibition is mitigated in the presence of manganese. We show that such manganese-mediated mitigation of nitrite inhibition is dependent on the culture inoculum size, and that manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. We provide evidence that MnOX protection involves both its ability to catalyze nitrite oxidation into (nontoxic) nitrate under physiological conditions and its potential role in influencing processes involving reactive oxygen species (ROS). Taken together, these results demonstrate improved microbial fitness through MnOX deposition in an ecological setting, i.e., mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS.IMPORTANCE We present here a direct fitness benefit (i.e., growth advantage) for manganese oxide biomineralization activity in Roseobacter sp. strain AzwK-3b, a model organism used to study this process. We find that strain AzwK-3b in a laboratory culture experiment is growth inhibited by nitrite in manganese-free cultures, while the inhibition is considerably relieved by manganese supplementation and manganese oxide (MnOX) formation. We show that biogenic MnOX interacts directly with nitrite and possibly with reactive oxygen species and find that its beneficial effects are established through formation of dispersed MnOX granules in a manner dependent on the population size. These experiments raise the possibility that manganese biomineralization could confer protection against nitrite toxicity to a population of cells. They open up new avenues of interrogating this process in other species and provide possible routes to their biotechnological applications, including in metal recovery, biomaterials production, and synthetic community engineering.

How does manganese dioxide affect humus formation during bio-composting of chicken manure and corn straw?

The aim of this study is to reveal the roles of MnO₂ in Maillard reaction of biotic composting, and to identify its effectiveness in promoting humus formation. Corn straw (CS) and chicken manure (CM) have been chosen to be composted. During CS composting, addition of MnO₂ rapidly reduced reducing sugars concentration (decreased by 84.0%) in 5 days and significantly improved humus production by 38.7% compared with treatment without MnO₂. Whereas in CM composting, the promoting effect of MnO₂ on humus formation was relatively weak by comparing with the treatment group of CS. Additionally, the presence of MnO₂ has reshaped bacteria community, which might be the reason of MnO₂ stimulated bacteria to utilize organic matter during CM composting. Therefore, the structural equation modeling has confirmed that MnO₂ mainly performed as chemical catalyst to promote humus formation during CS composting. Besides catalyst, MnO₂ also played as a bioactive activator in CM composting.

Thermal Pre-Treatment of Polymetallic Nodules to Create Metal (Ni, Cu, Co)-Rich Individual Particles for Further Processing

Polymetallic nodules are a potential source of industrially demanded metals such as Ni, Co, Cu, and Mo (up to 3 wt %). Even if there is no deep-sea mining of manganese nodules today, a forecasted gap between metal demand and supply as well as continuously high metal prices may make seabed mining economically viable in the future. Up to now, a well-established industrial-scale extraction method for manganese nodules has been missing. Therefore, the aim of this study is to explore how economically interesting metals can be extracted from the nodules in a cost- and energy-efficient way. Polymetallic nodules have a heterogeneous chemical and structural composition without individual metal-rich particles. The economically interesting metals are distributed between different mineral phases (Mn-Fe-(oxy)hydroxides) as well as different growth structures that are intergrown with each other on a nm‒µm scale. Because of that a typical ore processing with the beneficiation of valuable particles is not feasible. The process presented here starts with a pyro-metallurgical pre-treatment of the polymetallic nodules, with the aim of creating artificial metal-rich (Ni, Cu, Co, Mo) particles with enrichment factors up to 10 compared to the original average metal contents. Afterwards, these particles should be beneficiated by conventional mineral processing steps to create a concentrate while reducing the mass stream in the process. The resulting metal particles can be further treated in conventional hydrometallurgical and/or pyro-metallurgical processes.

Heterogeneity of Microbial Communities on Deep-Sea Ferromanganese Crusts in the Takuyo-Daigo Seamount

Rock outcrops of aged deep-sea seamounts are generally covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Although the presence of microorganisms in Fe-Mn crusts has been reported, limited information is currently available on intra- and inter-variations in crust microbial communities. Therefore, we collected several Fe-Mn crusts in bathyal and abyssal zones (water depths of 1,150-5,520 m) in the Takuyo-Daigo Seamount in the northwestern Pacific, and examined microbial communities on the crusts using culture-independent molecular and microscopic analyses. Quantitative PCR showed that microbial cells were abundant (10⁶-10⁸ cells g^-1) on Fe-Mn crust surfaces through the water depths. A comparative 16S rRNA gene analysis revealed community differences among Fe-Mn crusts through the water depths, which may have been caused by changes in dissolved oxygen concentrations. Moreover, community differences were observed among positions within each Fe-Mn crust, and potentially depended on the availability of sinking particulate organic matter. Microscopic and elemental analyses of thin Fe-Mn crust sections revealed the accumulation of microbial cells accompanied by the depletion of Mn in valleys of bumpy crust surfaces. Our results suggest that heterogeneous and abundant microbial communities play a role in the biogeochemical cycling of Mn, in addition to C and N, on crusts and contribute to the extremely slow growth of Fe-Mn crusts.

Enhanced triclosan and nutrient removal performance in vertical up-flow constructed wetlands with manganese oxides

Limited concentrations of oxygen in constructed wetlands (CWs) have inhibited their ability to remove emerging organic contaminants (EOCs) at μg/L or ng/L levels. Manganese (Mn) oxides were proposed as a solution, as they are powerful oxidants with strong adsorptive capabilities. In the present study, triclosan (TCS) was selected as a typical EOC, and CW microcosms with Mn oxides (birnessite) coated sand (B-CWs) and without (C-CWs) were developed to test the removal capacities of TCS and common nutrients. We found that the addition of Mn oxides coated sand significantly improved removal efficiencies of TCS, NH₄-N, COD, NO₃-N and TP (P < 0.05). The average concentration of Mn(II) effluent was 0.036 mg L^-1, mostly lower than the drinking water limit. To gain insight into the mechanisms of pollution removal, Mn transformation, dissolved oxygen (DO) distribution, bacterial abundance, and microbial community composition were also investigated. Maximum Mn(II) was detected at 20 cm height of the B-CWs in anoxic zone. Although Mn-oxidizing bacteria existed in the layer of 30-50 cm with 10³-10⁴ CFU g^-1 dry substate, Mn oxides were only detected at height from 40 to 50 cm with rich oxygen in B-CW. The quantities of bacterial 16S rRNA, amoA, narG and nosZ were not significantly different between two systems (P > 0.05), while Illumina high-throughput sequencing analysis revealed that the abundance of denitrifying bacteria was significant higher in B-CWs, and the abundance of Gammaproteobacteria that have a recognized role in Mn transformation were significantly increased. The results indicated that Mn oxides could enhance TCS and common pollutants removal in both anoxic and aerobic areas through the recycling of Mn between Mn(II) and biogenic Mn oxides.

Assessing the impacts of seabed mineral extraction in the deep sea and coastal marine environments: Current methods and recommendations for environmental risk assessment

Mineral extraction from the seabed has experienced a recent surge of interest from both the mining industry and marine scientists. While improved methods of geological investigation have enabled the mapping of new seafloor mineral reserves, the ecological impacts of mining in both the deep sea and the shallow seabed are poorly known. This paper presents a synthesis of the empirical evidence from experimental seabed mining and parallel industries to infer the effects of seabed mineral extraction on marine ecosystems, focusing on polymetallic nodules and ferromanganese concretions. We use a problem-structuring framework to evaluate causal relationships between pressures caused by nodule extraction and the associated changes in marine ecosystems. To ensure that the rationale behind impact assessments is clear, we propose that future impact assessments use pressure-specific expert elicitation. We further discuss integrating ecosystem services in the impact assessments and the implications of current methods for environmental risk assessments.

Experimental Microbial Alteration and Fe Mobilization From Basaltic Rocks of the ICDP HSDP2 Drill Core, Hilo, Hawaii

The interaction of a single bacterial species (Burkholderia fungorum) with basaltic rocks from the ICDP HSDP2 drill core and synthetic basaltic glasses was investigated in batch laboratory experiments to better understand the role of microbial activity on rock alteration and Fe mobilization. Incubation experiments were performed with drill core basaltic rock samples to investigate differences in the solution chemistry during biotic and abiotic alteration. Additionally, colonization experiments with synthetic basaltic glasses of different Fe redox states and residual stresses were performed to evaluate their influence on microbial activity and surface attachment of cells. In biotic incubation experiments bacterial growth was observed and the release of Fe and other major elements from drill core basaltic rocks to solution exceeded that of abiotic controls only when the rock sample assay was nutrient depleted. The concentration of dissolved major elements in solution in biotic colonization experiments with synthetic basaltic glasses increased with increasing residual stress and Fe(II) content. Furthermore, the concentration of dissolved Fe and Al increased similarly in biotic colonization experiments indicating that their dissolution might be triggered by microbial activity. Surface morphology imaging by SEM revealed that cells on basaltic rocks in incubation experiments were most abundant on the glass and surfaces with high roughness and almost absent on minerals. In colonization experiments, basaltic glasses with residual stress and high Fe(II) content were intensely covered with a cellular biofilm. In contrast, glasses with high Fe(III) content and no residual stress were sparsely colonized. We therefore conclude that structurally bound Fe is most probably used by B. fungorum as a nutrient. Furthermore, we assume that microbial activity overall increased rock dissolution as soon as the environment becomes nutrient depleted. Our results show that besides compositional effects, other factors such as redox state and residual stress can control microbial alteration of basaltic glasses.

From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean

Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.

Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific

Deep-sea ferromanganese crusts are found ubiquitously on the surface of seamounts of the world’s oceans. Considering the wide distribution of the crusts, archaeal and bacterial communities on these crusts potentially play a significant role in biogeochemical cycling between oceans and seamounts; however little is known about phylogenetic diversity, abundance and function of the crust communities. To this end, we collected the crusts from the northwest Pacific basin and the Philippine Sea. We performed comprehensive analysis of the archaeal and bacterial communities of the collected crust samples by culture-independent molecular techniques. The distance between the sampling points was up to approximately 2,000 km. Surrounding sediments and bottom seawater were also collected as references near the sampling points of the crusts, and analyzed together. 16S rRNA gene analyses showed that the community structure of the crusts was significantly different from that of the seawater. Several members related to ammonia-oxidizers of Thaumarchaeota and Betaproteobacteria were detected in the crusts at most of all regions and depths by analyses of 16S rRNA and amoA genes, suggesting that the ammonia-oxidizing members are commonly present in the crusts. Although members related to the ammonia-oxidizers were also detected in the seawater, they differed from those in the crusts phylogenetically. In addition, members of uncultured groups of Alpha-, Delta- and Gammaproteobacteria were commonly detected in the crusts but not in the seawater. Comparison with previous studies of ferromanganese crusts and nodules suggests that the common members determined in the present study are widely distributed in the crusts and nodules on the vast seafloor. They may be key microbes for sustaining microbial ecosystems there.

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities

Concentrated seabed deposits of polymetallic nodules, which are rich in economically valuable metals (e.g., copper, nickel, cobalt, manganese), occur over vast areas of the abyssal Pacific Ocean floor. Little is currently known about the diversity of microorganisms inhabiting abyssal habitats. In this study, sediment, nodule, and water column samples were collected from the Clarion-Clipperton Zone of the Eastern North Pacific. The diversities of prokaryote and microeukaryote communities associated with these habitats were examined. Microbial community composition and diversity varied with habitat type, water column depth, and sediment horizon. Thaumarchaeota were relatively enriched in the sediments and nodules compared to the water column, whereas Gammaproteobacteria were the most abundant sequences associated with nodules. Among the Eukaryota, rRNA genes belonging to the Cryptomonadales were relatively most abundant among organisms associated with nodules, whereas rRNA gene sequences deriving from members of the Alveolata were relatively enriched in sediments and the water column. Nine operational taxonomic unit (OTU)s were identified that occur in all nodules in this dataset, as well as all nodules found in a study 3000-9000 km from our site. Microbial communities in the sediments had the highest diversity, followed by nodules, and then by the water column with <1/3 the number of OTUs as in the sediments.