Microbe-microbe interactions trigger Mn(II)-oxidizing gene expression

Enhancing microbial superoxide generation and conversion to hydroxyl radicals for enhanced bioremediation using iron-binding ligands

Harnessing bacteria for superoxide production in bioremediation holds immense promise, yet its practical application is hindered by slow production rates and the relatively weak redox potential of superoxide. This study delves into a cost-effective approach to amplify superoxide production using an Arthrobacter strain, a prevalent soil bacterial genus. Our research reveals that introducing a carbon source along with specific iron-binding ligands, including deferoxamine (DFO), diethylenetriamine pentaacetate (DTPA), citrate, and oxalate, robustly augments microbial superoxide generation. Moreover, our findings suggest that these iron-binding ligands play a pivotal role in converting superoxide into hydroxyl radicals by modulating the electron transfer rate between Fe(III)/Fe(II) and superoxide. Remarkably, among the tested ligands, only DTPA emerges as a potent promoter of this conversion process when complexed with Fe(III). We identify an optimal Fe(III) to DTPA ratio of approximately 1:1 for enhancing hydroxyl radical production within the Arthrobacter culture. This research underscores the efficacy of simultaneously introducing carbon sources and DTPA in facilitating superoxide production and its subsequent conversion to hydroxyl radicals, significantly elevating bioremediation performance. Furthermore, our study reveals that DTPA augments superoxide production in cultures of diverse soils, with various soil microorganisms beyond Arthrobacter identified as contributors to superoxide generation. This emphasizes the universal applicability of DTPA across multiple bacterial genera. In conclusion, our study introduces a promising methodology for enhancing microbial superoxide production and its conversion into hydroxyl radicals. These findings hold substantial implications for the deployment of microbial reactive oxygen species in bioremediation, offering innovative solutions for addressing environmental contamination challenges.

Algae promotes the biogenic oxidation of Mn(II) by accelerated extracellular superoxide production

Microbial manganese (Mn) oxidation, predominantly occurs within the anaerobic-aerobic interfaces, plays an important role in environmental pollution remediation. The anaerobic-aerobic transition zones, notably riparian and lakeside zones, are hotspots for algae-bacteria interactions. Here, we adopted a Mn(II)-oxidizing bacterium Pseudomonas sp. QJX-1 to investigate the impact of algae on microbial Mn(II) oxidation and verify the underlying mechanisms. Interestingly, we achieved a remarkable enhancement in bacterial Mn(II)-oxidizing activity within the algae-bacteria co-culture, despite the inability to oxidize Mn(II) for the algae used in this study. In addition, the bacterial density almost remains constant in the presence of algal cells. Therefore, the increased Mn(II) oxidation by QJX-1 in the presence of algae cannot be due to the increased biomass. Within this co-culture system, the Mn(II) oxidation rate surged to an impressive 0.23 mg/L/h, in stark contrast to 0.02 mg/L/h recorded within pure QJX-1 system. The presence of algae could inhibit the Fe-S cluster activity of QJX-1 by the produced active substance in co-culture, and result in the acceleration of extracellular superoxide production due to the impairment of electron transfer functions located in QJX-1 cell membranes. Moreover, elevated peroxidase gene expression and heightened extracellular catalase activity not only expedited Mn(II) ions oxidation but also facilitated conversion of intermediate Mn(III) ions into microbial Mn oxides, achieved through the degradation of hydrogen peroxide. Therefore, the acceleration of extracellular superoxide production and the decomposition of hydrogen peroxide are identified as the principal mechanisms behind the observed enhancement in Mn(II) oxidation within algae-bacteria co-cultures. Our findings highlight the need to consider the effect of algae on microbial Mn(II) oxidation, which plays an important role in the environmental pollution remediation.

Biomineralized manganese oxide mediated nitrogen-contained wastewater treatment

In recent years, manganese (Mn) has emerged as an accelerator for nitrogen metabolism. However, the bioactivity of manganese is limited by the restricted contact between microbes and manganese minerals in the solid phase and by the toxicity of manganese to microbes. To enhance the bioactivity of solid-phase manganese, biomineralized manganese oxide (MnOx) modified by Lactobacillus was introduced. Nitrogen removal performance have confirmed the effective role of biomineralized MnOx in accelerating the removal of total inorganic nitrogen (TIN). Metagenomic analysis has confirmed the enhancement of the nitrogen metabolic pathway and microbial extracellular electron transfer (MEET) in biomineralized MnOx treatment group (BIOA group). Additionally, the enrichment of manganese oxidation and denitrification genus indicates a coupling between nitrogen metabolism and manganese metabolism. One point of views is that biomineralized MnOx-mediated nitrogen transformation processes could serve as a substitute for traditional nitrogen removal processes.

Microbiologically influenced corrosion of AISI 202 and 316L stainless steels under manganese-oxidizing biofilms

In this work, we study the microbiologically influenced corrosion (MIC) of AISI 316L (1-2% Mn) and AISI 202 (8-12% Mn) in the presence of manganese-oxidizing biofilms. Microbiological and 16S rRNA amplicon sequencing analysis on biofilms formed on the surfaces of both the SS materials after exposure to seawater for two months showed the presence of predominant Mn-oxidizing bacteria (MnOB) groups. The Mn contents in the biofilms formed on AISI 202 and 316L were 0.577 and 0.193 ppm, respectively. Mixed biofilms of 11 pure axenic cultures of MnOB isolated and identified from both the SS biofilms were used for MIC studies on SS. Electrochemical studies showed four orders of magnitude high icorr values (1.271 × 10-4 A.cm-2) and the onset of crevice corrosion potentials (502 mV) confirming the localized corrosion of AISI 202 and 316L, respectively, under MnOB biofilms. X-ray photoelectron spectroscopic (XPS) analysis on biotic surfaces showed a reduced Mn content from 10.1 to 7.9 atom.% confirming the Mn oxidation in AISI 202. This study confirms that MnOB biofilms on the SS surfaces can lead to MIC due to biogenic Mn oxidation, depletion of Fe and Mn content, and enrichment of Cr content.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03845-z.

Association between blood heavy metal concentrations and skin cancer in the National Health and Nutrition Examination Survey, 2011-2018

We aimed to evaluate the associations between blood cadmium (Cd), mercury (Hg), lead (Pb), manganese (Mn), and selenium (Se) concentrations and skin cancer. This cross-sectional study was based on National Health and Nutritional Examination Survey (NHANES) data. A binomial logistic regression model was used to analyze the associations between exposure to the metal elements and the risk of skin cancer, and further stratified analyses were conducted by gender, age, body mass index, ethnicity, education, smoking, alcohol drinking, and hypertension. A total of 16,034 participants were included. After fully adjusting for multivariate, the odd ratio (OR)[95% confidence interval (95% CI)] values for skin cancer in those with blood Mn concentrations in the second, third, and fourth quartiles were 0.52 (0.33-0.82), 0.57 (0.36-0.9), and 0.56 (0.35-0.89), respectively, compared with those in the lowest quartile. The ORs (95% CI) for each 1-SD increment in log-transformed values for blood Mn concentrations were 0.79 (0.66-0.94), 0.8 (0.66-0.97), and 0.79 (0.66-0.96), respectively. A significant association between blood Hg and skin cancer was also observed in participants who drank alcohol, with a corresponding OR (95% CI) of 2.61 (1.37-5.00) (p interaction = 0.006). Our study indicated that a higher blood Mn concentration was negatively associated with skin cancer, and blood Hg was positively associated with skin cancer in participants who drank alcohol.

Sequestration and oxidation of heavy metals mediated by Mn(II) oxidizing microorganisms in the aquatic environment

Microorganisms can oxidize Mn(II) to biogenic Mn oxides (BioMnOx), through enzyme-mediated processes and non-enzyme-mediated processes, which are generally considered as the source and sink of heavy metals due to highly reactive to sequestrate and oxidize heavy metals. Hence, the summary of interactions between Mn(II) oxidizing microorganisms (MnOM) and heavy metals is benefit for further work on microbial-mediated self-purification of water bodies. This review comprehensively summarizes the interactions between MnOM and heavy metals. The processes of BioMnOx production by MnOM has been firstly discussed. Moreover, the interactions between BioMnOx and various heavy metals are critically discussed. On the one hand, modes for heavy metals adsorbed on BioMnOx are summarized, such as electrostatic attraction, oxidative precipitation, ion exchange, surface complexation, and autocatalytic oxidation. On the other hand, adsorption and oxidation of representative heavy metals based on BioMnOx/Mn(II) are also discussed. Thirdly, the interactions between MnOM and heavy metals are also focused on. Finally, several perspectives which will contribute to future research are proposed. This review provides insight into the sequestration and oxidation of heavy metals mediated by Mn(II) oxidizing microorganisms. It might be helpful to understand the geochemical fate of heavy metals in the aquatic environment and the process of microbial-mediated water self-purification.

Application of manganese oxides in wastewater treatment: Biogeochemical Mn cycling driven by bacteria

Manganese oxides (MnOx) are recognized as a strongest oxidant and adsorbent, of which composites have been proved to be effective in the removal of contaminants from wastewater. This review provides a comprehensive analysis of Mn biochemistry in water environment including Mn oxidation and Mn reduction. The recent research on the application of MnOx in the wastewater treatment was summarized, including the involvement of organic micropollutant degradation, the transformation of nitrogen and phosphorus, the fate of sulfur and the methane mitigation. In addition to the adsorption capacity, the Mn cycling mediated by Mn(II) oxidizing bacteria and Mn(IV) reducing bacteria is the driving force for the MnOx utilization. The common category, characteristics and functions of Mn microorganisms in recent studies were also reviewed. Finally, the discussion on the influence factors, microbial response, reaction mechanism and potential risk of MnOx application in pollutants' transformation were proposed, which might be the promising opportunities for the future investigation of MnOx application in wastewater treatment.

Light-independent anaerobic microbial oxidation of manganese driven by an electrosyntrophic coculture

Anaerobic microbial manganese oxidation (AMMO) has been considered an ancient biological metabolism for Mn element cycling on Archaean Earth before the presence of oxygen. A light-dependent AMMO was recently observed under strictly anoxic conditions, providing a new proxy for the interpretation of the evolution of oxygenic photosynthesis. However, the feasibility of biotic Mn(II) oxidation in dark geological habitats that must have been abundant remains unknown. Therefore, we discovered that it would be possible to achieve AMMO in a light-independent electrosyntrophic coculture between Rhodopseudomonas palustris and Geobacter metallireducens. Transmission electron microscopy analysis revealed insoluble particle formation in the coculture with Mn(II) addition. X-ray diffraction and X-ray photoelectron spectroscopy analysis verified that these particles were a mixture of MnO2 and Mn3O4. The absence of Mn oxides in either of the monocultures indicated that the Mn(II)-oxidizing activity was induced via electrosyntrophic interactions. Radical quenching and isotopic experiments demonstrated that hydroxyl radicals (•OH) produced from H2O dissociation by R. palustris in the coculture contributed to Mn(II) oxidation. All these findings suggest a new, symbiosis-dependent and light-independent AMMO route, with potential importance to the evolution of oxygenic photosynthesis and the biogeochemical cycling of manganese on Archaean and modern Earth.

A manganese-oxidizing bacterium-Enterobacter hormaechei strain DS02Eh01: Capabilities of Mn(II) immobilization, plant growth promotion and biofilm formation

While biogenic Mn oxides (BioMnO_x) generated by Mn(II)-oxidizing bacteria (MOB) have attracted increasing attention, a MOB strain isolated from Mn-polluted sediments was identified and assigned as Enterobacter hormaechei DS02Eh01. Its Mn(II) immobilization activity, plant growth-promoting traits, and biofilm formation capability were investigated. The results showed that strain DS02Eh01 was found to be able to tolerate Mn(II) up to 122 mM. The strain immobilized Mn(II) in aquatic media mainly through extracellular adsorption, bio-oxidation and pH-induced precipitation as well as manganese oxidation. DS02Eh01-derived BioMnO_x are negatively charged and have a larger specific surface area (86.70 m²/g) compared to the previously reported BioMnO_x. The strain can immobilize Mn(II) at extreme levels, for instance, when it was exposed to 20 mM Mn(II), about 59% of Mn(II) were found immobilized and 17% of Mn(II) were converted to MnO_x. The SEM and TEM observation revealed that the DS02Eh01-derived BioMnO_x were aggregates doped with granules and microbial pellets. The precipitated Mn(II) and the Mn(III)/Mn(IV) oxides co-existed in BioMnO_x, in which Mn(II) and Mn(IV) were found dominant with Mn(II) accounting for 49.6% and Mn(IV) accounting for 41.3%. DS02Eh01 possesses plant growth-promoting traits and biofilm formation capacity even under Mn(II) exposure. Mn(II) exposure at 5 mM was found to stimulate strain DS02Eh01 to form biofilms, from which, the extracted EPS was mainly composed of aromatic proteins. This study reveals that E. hormaechei strain DS02Eh01 possesses the potential in environmental ecoremediation via coupling processes of macrophytes extraction, biochemical immobilization and biosorption.

Soil Amoebae Affect Iron and Chromium Reduction through Preferential Predation between Two Metal-Reducing Bacteria

Soil protists are essential but often overlooked in soil and could impact microbially driven element cycling in natural ecosystems. However, how protists influence heavy metal cycling in soil remains poorly understood. In this study, we used a model protist, Dictyostelium discoideum, to explore the effect of interactions between soil amoeba and metal-reducing bacteria on the reduction of soil Fe(III) and Cr(VI). We found that D. discoideum could preferentially prey on the Fe(III)-reducing bacterium Shewanella decolorationis S12 and significantly decrease its biomass. Surprisingly, this predation pressure also stimulated the activity of a single S. decolorationis S12 bacterium to reduce Fe(III) by enhancing the content of electron-transfer protein cyt c, intracellular ATP synthesis, and reactive oxygen species (e.g., H₂O₂). We also found that D. discoideum could not prey on the Cr(VI)-reducing bacterium Brevibacillus laterosporus. In contrast, B. laterosporus became edible to amoebae in the presence of S. decolorationis S12, and their Cr(VI) reduction ability decreased under amoeba predation pressure. This study provides direct evidence that protists can affect the Cr and Fe cycling via the elective predation pressure on the metal-reducing bacteria, broadening our horizons of predation of protists on soil metal cycling.

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.

Initial Formation and Accumulation of Manganese Deposits in Drinking Water Pipes: Investigating the Role of Microbial-Mediated Processes

Microbial Mn(II) oxidation occurs in areas with insufficient disinfectants in drinking water distribution systems. However, the overall processes of microbial-mediated Mn deposit formation are unclear. This research investigated the initial Mn(II) oxidation, deposit accumulation, and biofilm development in pipe loops fed with nondisinfected finished water for 300 days. The results show that it took 20 days for microbial Mn(II) oxidation and deposition to be initiated visibly in new pipes continuously receiving 100 μg/L Mn(II). Once started, the deposit accumulation accelerated. A pseudo-first-order kinetic model could simulate the disappearance of Mn(II) in well-mixed pipe loop water. The observed rate constant reached 2.81 h^-1 [corresponding to a Mn(II) half-life of 0.25 h] after 136 days of operation. Without oxygen, Mn(II) in the water also decreased rapidly to 1.0 μg/L through adsorption to deposits, indicating that after the initial microbial formation of MnO_x, subsequent MnO_x accumulation was attributable to a combination of microbial and physicochemical processes. Compared to the no-Mn condition, Mn(II) input resulted in 1 order of magnitude increase in biofilm formation. This study sheds light on the increasingly rapid processes of Mn accumulation on the inner surfaces of water pipes resulting from the biological activity of Mn(II)-oxidizing biofilms and the build-up of MnO_x with strong adsorption capacity.

Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination

The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.

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.

Profiling microbial removal of micropollutants in sand filters: Biotransformation pathways and associated bacteria

Although there is growing evidence that micropollutants can be microbially converted in rapid sand filters of drinking water treatment plants (DWTPs), little is known about the biotransformation pathways and associated microbial strains in this process. Here, we constructed sand filter columns filled with manganese or quartz sand obtained from full-scale DWTPs to explore the biotransformation of eight micropollutants. Under seven different empty bed contact times (EBCTs), the column experiments showed that caffeine and atenolol were easily removed (up to 92.1% and 97.6%, respectively) with adsorption and microbial biotransformation of the filters. In contrast, the removal of other six micropollutants (i.e., naproxen, carbamazepine, atrazine, trimethoprim, sulfamethoxazole, and sulfadiazine) in the filters were less than 27.1% at shorter EBCTs, but significantly increased at EBCT = 4 h, indicating the dominant role of microbial biotransformation in these micropollutants removal. Integrated analysis of metagenomic reads and transformation products of micropollutants showed a shift in caffeine oxidation and demethylation pathways at different EBCTs, simultaneous occurrence of atrazine hydrolysis and oxidation pathways, and sulfadiazine and sulfamethoxazole oxidation in the filters. Furthermore, using genome-centric analysis, we observed previously unidentified degrading strains, e.g., Piscinibacter, Hydrogenophaga, and Rubrivivax for caffeine transformation, and Methylophilus and Methyloversatilis for atenolol transformation.

Transient surface hydration impacts biogeography and intercellular interactions of non-motile bacteria

There are many hydrated surface niches that are neither static nor continuously flowing that are colonized by microbes such as bacteria. Such periodic hydrodynamic regimes are distinct from aquatic systems where microbial dissemination is reasonably predicted by assuming continuous flow or static systems where motile microbes largely control their own fate. Here we show how non-motile bacteria exhibit rapid, dispersive bursts of movement over surfaces using transient confluent hydration from the environment, which we term "surface hydrodispersion" where cells traverse thousands of cell lengths within minutes. The fraction of the population disseminated by surface hydrodispersion is small-on order of 1 cell per million. Thus, surface hydrodispersion can promote isolated distribution of single cells, which is unlike other characterized active and passive surface motilities. We describe this translocation using a continuous time random walk modeling approach and find in computational simulations that transient fluid accumulation, dilution, and gravitational pull are the contributing factors. Surface hydrodispersion, consistent with advection, is unlike simple colony expansion as it dramatically alters spatial relationships, shown here with Staphylococcus aureus, which becomes increasingly virulent when isolated from Corynebacterium striatum Surface hydrodispersion of non-motile bacteria exploiting transient fluid availability and gravity is a mechanism that can result in sporadic and sudden shifts in microbial community behavior. To better understand how this movement can impact biogeography on the millimeter scale, this work describes a system for study of primary factors behind this movement as well as a stochastic model describing this dispersal.Importance: Understanding the dynamics within microbiome communities is a challenge. Knowledge of phylogeny and spatial arrangement has led to increased understanding of numerous polymicrobial communities yet, these snapshots do not convey the dynamics of populations over time. The actual biogeography of any microbiome controls the potential interactions, governing any possible antagonistic or synergistic behavior. Accordingly, a shift in biogeography can enable new behavior. Little is known about the movement mechanisms of "non-motile" microbes. Here we characterize a universal means of movement we term hydrodispersion where non-motile bacteria are transported thousands of cell lengths in minutes. We show that only a small fraction of the population is translocated by hydrodispersion and describe this movement further using a random-walk mathematical model approach in silico We demonstrate the importance of hydrodispersion by showing that Staphylococcus aureus can separate from a coculture inoculation with Corynebacterium striatum thus permitting transition to a more virulent state.

The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review

The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.

The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity

Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.

Removal of tetracycline by denitrifying Mn(II)-oxidizing bacterium Pseudomonas sp. H117 and biomaterials (BMO and MBMO): Efficiency and mechanisms

Coexistence of multiple pollutants such as antibiotic, nitrate and heavy metal has received increasing attention resently. In this study, the functions of Pseudomonas sp.H117 on the removal of tetracycline(TC), nitrate and Mn(II), and biological materials (BMO(biogenic manganese oxides), MBMO(magnetic BMO)) on the removal of TC were investigated. Strain H117 showed higher TC removal efficiency of 68.86% (0.071 mg·L^-1·h^-1) within 96 h. Meanwhile, NO₃-N and Mn(II) achieved high removal efficiency of 100% (0.211 mg·L^-1·h^-1) and 64.64% (0.265 mg·L^-1·h^-1), respectively. Furthermore, trapping experiments testified that Mn(III) intermediate formed during the biological manganese oxidation process, which contribute to the TC degradation. 91.29% and 96.63% of TC removal efficiency within 12 h were achieved by BMO and MBMO. Moreover, XPS, FTIR spectra, kinetics analysis and adsorption isotherms elucidated Mn(III) oxidation, chemical adsorption and ligand exchange reactions contribute to the removal of TC by biomaterials.

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems

Rapid sand biofiltration (RSBF) is widely used for the removal of contaminants from drinking water treatment systems. Biofilm microbiomes in the biofilter media play essential roles in biotransformation of contaminants, but is not comprehensively understood. This study reports on Mn(II) oxidation and the core microbiomes in magnetite sand RSBF (MagS-RSBF) and manganese sand RSBF (MnS-RSBF). MnS-RSBF showed a relatively higher Mn(II) removal rate (40-91.2%) than MagS-RSBF during the start-up. MagS-RSBF and MnS-RSBF had similar Mn(II) removal rates (94.13% and 99.16%) over stable operation for 80 days. Mn(II) removal rates at different depths in the MnS-RSBF reactor significantly changed with operation time, and the filter in the upper layer of MnS-RSBF made the largest contribution to Mn(II) oxidation once operation had stabilized. PacBio single molecule sequencing of full-length 16S rRNA gene indicated that biofilter medium had a significant impact on the core microbiomes of the biofilms from the two biofilters. The magnetite sand biofilter facilitated the enrichment of Mn(II)-oxidizing biofilms. The dominant populations consisted of Pedomicrobium, Pseudomonas, and Hyphomicrobium in the RSBF, which have been affiliated with putative manganese-oxidizing bacteria (MnOB). The relative abundance of Pedomicrobium manganicum increased with operation time in both RSBF reactors. In addition, Nordella oligomobilis and Derxia gummosa were statistically correlated with Mn(II) oxidation. Species-species co-occurrence networks indicated that the microbiome of MnS-RSBF had more complex correlations than that of MagS-RSBF, implying that biofilter medium substantially shaped the microbial community in the RSBF. Hyphomicrobium and nitrite-oxidizing Nitrospira moscoviensis were positively correlated. The core microbiomes' composition of both RSBF reactors converged over operation time. A hybrid biofilter medium with magnetite sand and manganese sand may therefore be best in rapid sand filtration for Mn(II) oxidation.

Light-driven anaerobic microbial oxidation of manganese

Oxygenic photosynthesis supplies organic carbon to the modern biosphere, but it is uncertain when this metabolism originated. It has previously been proposed^1,2 that photosynthetic reaction centres capable of splitting water arose by about 3 billion years ago on the basis of the inferred presence of manganese oxides in Archaean sedimentary rocks. However, this assumes that manganese oxides can be produced only in the presence of molecular oxygen³, reactive oxygen species^4,5 or by high-potential photosynthetic reaction centres^6,7. Here we show that communities of anoxygenic photosynthetic microorganisms biomineralize manganese oxides in the absence of molecular oxygen and high-potential photosynthetic reaction centres. Microbial oxidation of Mn(II) under strictly anaerobic conditions during the Archaean eon would have produced geochemical signals identical to those used to date the evolution of oxygenic photosynthesis before the Great Oxidation Event^1,2. This light-dependent process may also produce manganese oxides in the photic zones of modern anoxic water bodies and sediments.

Mn oxide formation by phototrophs: Spatial and temporal patterns, with evidence of an enzymatic superoxide-mediated pathway

Manganese (Mn) oxide minerals influence the availability of organic carbon, nutrients and metals in the environment. Oxidation of Mn(II) to Mn(III/IV) oxides is largely promoted by the direct and indirect activity of microorganisms. Studies of biogenic Mn(II) oxidation have focused on bacteria and fungi, with phototrophic organisms (phototrophs) being generally overlooked. Here, we isolated phototrophs from Mn removal beds in Pennsylvania, USA, including fourteen Chlorophyta (green algae), three Bacillariophyta (diatoms) and one cyanobacterium, all of which consistently formed Mn(III/IV) oxides. Isolates produced cell-specific oxides (coating some cells but not others), diffuse biofilm oxides, and internal diatom-specific Mn-rich nodules. Phototrophic Mn(II) oxidation had been previously attributed to abiotic oxidation mediated by photosynthesis-driven pH increases, but we found a decoupling of Mn oxide formation and pH alteration in several cases. Furthermore, cell-free filtrates of some isolates produced Mn oxides at specific time points, but this activity was not induced by Mn(II). Manganese oxide formation in cell-free filtrates occurred via reaction with the oxygen radical superoxide produced by soluble extracellular proteins. Given the known widespread ability of phototrophs to produce superoxide, the contribution of phototrophs to Mn(II) oxidation in the environment may be greater and more nuanced than previously thought.

Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges

Functional differentiation and metabolite exchange enable microbial consortia to perform complex metabolic tasks and efficiently cycle the nutrients. Inspired by the cooperative relationships in environmental microbial consortia, synthetic microbial consortia have great promise for studying the microbial interactions in nature and more importantly for various engineering applications. However, challenges coexist with promises, and the potential of consortium-based technologies is far from being fully harnessed. Thorough understanding of the underlying molecular mechanisms of microbial interactions is greatly needed for the rational design and optimization of defined consortia. These knowledge gaps could be potentially filled with the assistance of the ongoing revolution in systems biology and synthetic biology tools. As current fundamental and technical obstacles down the road being removed, we would expect new avenues with synthetic microbial consortia playing important roles in biological and environmental engineering processes such as bioproduction of desired chemicals and fuels, as well as biodegradation of persistent contaminants.

Removal of micropollutants and cyanobacteria from drinking water using KMnO4 pre-oxidation coupled with bioaugmentation

Increasing micropollutant and cyanobacterial contamination of drinking water threatens human health worldwide. However, these contaminates are not efficiently removed by common drinking water treatment processes, and thus additional treatments are frequently required. Recent investigations have demonstrated that KMnO₄ pre-oxidation can efficiently remove some micropollutants and cyanobacteria but the release of cyanobacterial toxins and Mn²⁺ limit its use. To overcome these problems, we proposed a KMnO₄ pre-oxidation coupled with bioaugmentation (e.g., sand filtration) method to treat micropollutant- and cyanobacteria-laden water. We used 2-hydroxy-4-methoxybenzophenone-5-sulfonic acid (BP-4, a common micropollutant in drinking water sources) and Microcystis aeruginosa (a widely distributed cyanobacterial species) as model pollutants to verify the feasibility of the proposed method. Results revealed that KMnO₄ pre-oxidation efficiently removed existing natural organic matter and Microcystis aeruginosa but failed to remove BP-4 and released Mn²⁺ and microcystin-LR (MC-LR) during treatment. Following the addition of a manganese-oxidizing bacterial strain (Pseudomonas sp. QJX-1) to the KMnO₄-treated solution, we found that the bacteria could transform Mn²⁺ to Mn(III&IV) oxides, with the formed Mn oxides then able to remove BP-4 and MC-LR. Overall, the proposed method exhibited advantages in the removal of natural organic matter (i.e., decreasing disinfection byproduct formation), micropollutants, and cyanobacteria as well as preventing the release of Mn²⁺, and thus may be considered a good alternative for treating polluted drinking water.

Comparative metabolomics reveals defence-related modification of citrinin by Penicillium citrinum within a synthetic Penicillium-Pseudomonas community

Co-occurring microorganisms have been proved to influence the performance of each other by metabolic means in nature. Here we generated a synthetic fungal-bacterial community comprising Penicillium citrinum and Pseudomonas aeruginosa employing the previously described membrane-separated co-culture device. By applying a newly designed molecular networking routine, new citrinin-related metabolites induced by the fungal-bacterial cross-talk were unveiled in trace amounts. A mechanically cycled co-culture setup with external pumping forces accelerating the chemically interspecies communication was then developed to boost the production of cross-talk-induced metabolites. Multivariate data analysis combined with molecular networking revealed the accumulation of a pair of co-culture-induced molecules whose productions were positively correlated to the exchange rate in the new co-cultures, facilitating the discovery of the previously undescribed antibiotic citrinolide with a novel skeleton. This highly oxidized citrinin adduct showed significantly enhanced antibiotic property against the partner strain P. aeruginosa than its precursor citrinin, suggesting a role in the microbial competition. Thus, we propose competitive-advantage-oriented structural modification driven by microbial defence response mechanism in the interspecies cross-talk might be a promising approach in the search for novel antibiotics. Besides, this study highlights the utility of MS-based metabolomics as an effective tool in the direct biochemical analysis of the community metabolism.

Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater

Biogenic manganese oxide (BioMnO_x) can efficiently adsorb various minor metals. The production of BioMnO_x in reactors to remove metals during wastewater treatment processes is a promising biotechnological method. However, it is difficult to preferentially enrich manganese-oxidizing bacteria (MnOB) to produce BioMnO_x during wastewater treatment processes. A unique method of cultivating MnOB using methane-oxidizing bacteria (MOB) to produce soluble microbial products is proposed here. MnOB were successfully enriched in a methane-fed reactor containing MOB. BioMnO_x production during the wastewater treatment process was confirmed. Long-term continual operation of the reactor allowed simultaneous removal of Mn(II), Co(II), and Ni(II). The Co(II)/Mn(II) and Ni(II)/Mn(II) removal ratios were 53% and 19%, respectively. The degree to which Mn(II) was removed indicated that the enriched MnOB used utilization-associated products and/or biomass-associated products. Microbial community analysis revealed that methanol-oxidizing bacteria belonging to the Hyphomicrobiaceae family played important roles in the oxidation of Mn(II) by using utilization-associated products. Methane-oxidizing bacteria were found to be inhibited by MnO₂, but the maximum Mn(II) removal rate was 0.49 kg m^-3 d^-1.

Benzophenone-4 Promotes the Growth of a Pseudomonas sp. and Biogenic Oxidation of Mn(II)

Interactions between microbes and micropollutants (MPs) play a crucial role in water purification or treatment. Current studies have generally focused on the direct degradation or cometabolism of MPs. Considering the increasing interest in and importance of the roles of MPs in microbial metabolism, we adopted an Mn(II)-oxidizing Pseudomonas sp. QJX-1 using tyrosine (Tyr) as the sole carbon and nitrogen source to investigate the effects of seven MPs on its growth and function. Six MPs exhibited an inhibition effect on bacterial growth and Mn(II) oxidation. Only benzophenone-4 (BP-4) promoted the growth of QJX-1 and biogenic oxidation Mn(II), but its concentration was not directly coupled to growth, which was unexpected. RNA-seq data suggested that the addition of BP-4 did not significantly change the basic metabolic function of QJX-1, but stimulated the upregulation of the pyruvate and gluconeogenesis metabolic pathways of Tyr for QJX-1 growth. Furthermore, protein identification and extracellular superoxide detection indicated that Mn(II) oxidation was largely driven by the formation of superoxide in response to Tyr starvation; the acceleration of superoxide production, due to BP-4 accelerating Tyr consumption, was responsible for the promotion effect of BP-4 on QJX-1 Mn(II) oxidation. Our findings highlight the dual effects that MPs can have on the growth and function of a single strain in aquatic ecosystem, i.e., the coexistence of inhibition and promotion.

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.