Microbially-mediated Processes Research Articles

Response processes to water quality changes driven by the dynamic regeneration of the surface microlayer film in slow-flowing freshwater bodies

The freshwater surface microlayer film (SMF) is a dynamically evolving micro-ecosystem closely related to water quality and microbial growth in water. However, the mechanisms of dynamic regeneration of SMF after their destruction and their impacts on the aquatic environment are still largely unknown. Herein, we modeled the dynamic processes of SMF destruction and recovery in the natural environment by constructing a water-SMF ecosystem. Chemical and biological changes in the dynamic regeneration of SMF were investigated. The results showed that the dynamic regeneration of SMF was very fast, with a regeneration thickness of up to 300 ± 50 μm in two days, and at the same time, it would rapidly enrich organic matter and Fe ions. In addition, the cyclic dynamic regeneration process of SMF is significantly correlated with the surge metabolic growth of microorganisms associated with organic matter metabolism (e.g., Methylophilus, Nevskia) and iron-redox-associated (e.g., Curvibacter). The experimental results suggest that the microbial-mediated process of iron-organic matter coupled oxidation-reduction in SMF may be another important mechanism driving water quality changes. Overall, our study provides valuable theoretical guidance for predicting changes in water quality in slow-flowing water bodies.

Potential applications of microbial genomics in nuclear non-proliferation.

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

A self-sustaining effect induced by iron sulfide generation and reuse in pyrite-woodchip mixotrophic bioretention systems: An experimental and modeling study

Dual electron donor bioretention systems have emerged as a popular strategy to enhance dissolved nitrogen removal from stormwater runoff. Pyrite-woodchip mixotrophic bioretention systems showed a promoted and stabilized removal of dissolved nutrients under complex rainfall conditions, but the sulfate reduction process that can induce iron sulfide generation and reuse was overlooked. In this study, experiments and models were applied to investigate the effects of filler configuration and dissolved organic carbon (DOC) dissolution rate on treatment performance and iron sulfide generation in pyrite-woodchip bioretention systems. Key parameters govern that DOC dissolution and microbe-mediated processes were obtained by experiments. The water quality models that integrate one-dimensional constant flow, sorption and microbial transformation kinetics were used to predict the performance of bioretention systems. Results showed that the mixotrophic bioretention system with woodchip mixed in the vadose zone and pyrite in the saturated zone achieves a better performance in both nitrogen removal efficiency and by-product control. Comparably, woodchip and pyrite mixed in the saturated zone could encounter a high secondary pollution risk. The sensitivity coefficients of oxic/anoxic DOC dissolution rates to total nitrogen removal are 0.36 and -2.43 respectively. Iron sulfide generation was affected by DOC distribution and the competition between heterotrophic denitrifiers, autotrophic denitrifiers, and sulfate-reducing bacteria (SRB). DOC accumulation has an antagonistic effect on iron production and sulfate reduction. Extra DOC accumulation favors sulfate reduction while high DOC concentration inhibits pyrite-based denitrification and reduces Fe(III) production. The recycling of iron sulfide can improve the robustness and sustainability of bioretention systems.

Microbial-mediated metal(loid) immobilization in mulch-covered tailings

Mulch coverage of mining tailings can create anaerobic conditions and consequently establish an anoxic environment that promotes the metabolic processes of anaerobic microorganisms. This anoxic environment has the potential to decrease heavy metal mobility and bioavailability. While tailings exposed to sunlight have been extensively studied, research on the effects of microbial-mediated geochemical cycling of heavy metals in mulch-covered tailings is scarce. This study aimed to examine the effects of mulch coverage-induced alterations in the structures of tailing microbial communities on the biogeochemical processes associated with heavy metals. Mulch coverage significantly reduced the pH of the tailings and the tailings exhibited heavy metal bioavailability. Random forest analysis demonstrated that mulch coverage-induced changes in the As/Cd-contaminated fractions and nutrients (total organic carbon and total nitrogen) were the most crucial predictors of microbial diversity and ecological clusters in the tailings. Notably, different from direct metal(loid) immobilization, mulch coverage can facilitate heavy metal immobilization in tailings by promoting microbial-mediated Fe, S, and As reduction. Overall, this study demonstrated that mulch coverage of tailings contributed to a reduction in heavy metal mobilization, which can be attributed to shifts in microbial-mediated Fe, S, and As reduction processes.The study provides valuable insights into the potential of mulch coverage as a remediation strategy and underscores the importance of microbial-mediated processes in managing heavy metal pollution in tailing systems.

Microbial stratification and DOM removal in drinking water biofilters: Implications for enhanced performance

Biofiltration is a low-cost, low-energy technology that employs a biologically activated bed of porous medium to reduce the biodegradable fraction of the dissolved organic matter (DOM) pool in source water, resulting in the production of drinking water. Microbial communities at different bed depths within the biofilter play crucial roles in the degradation and removal of dissolved organic carbon (DOC), ultimately impacting its performance. However, the relationships between the composition of microbial communities inhabiting different biofilter depths and their utilisation of various DOC fractions remain poorly understood. To address this knowledge gap, we conducted an experimental study where microbial communities from the upper (i.e., top 10 cm) and lower (i.e., bottom 10 cm) sections of a 30-cm long laboratory-scale biofilter were recovered. These communities were then individually incubated for 10 days using the same source water as the biofilter influent. Our study revealed that the bottom microbial community exhibited lower diversity yet had a co-occurrence network with a higher degree of interconnections among its members compared to the top microbial community. Moreover, we established a direct correlation between the composition and network structure of the microbial communities and their ability to utilise various DOM compounds within a DOM pool. Interestingly, although the bottom microbial community had only 20 % of the total cell abundance compared to the top community at the beginning of the incubation, it utilised and hence removed approximately 60 % more total DOC from the DOM pool than the top community. While both communities rapidly utilised labile carbon fractions, such as low-molecular-weight neutrals, the utilisation of more refractory carbon fractions, like high-molecular-weight humic substances with an average molecular weight of more than ca. 1451 g/mol, was exclusive to the bottom microbial community. By employing techniques that capture microbial diversity (i.e., flow cytometry and 16S rRNA amplicon sequencing) and considering the complexities of DOM (i.e., LCOCD), our study provides novel insights into how microbial community structure could influence the microbial-mediated processes of engineering significance in drinking water production. Finally, our findings could offer the opportunity to improve biofilter performances via engineering interventions that shape the compositions of biofilter microbial communities and enhance their utilisation and removal of DOM, most notably the more classically humified and refractory DOM compound groups.

Treatment of pharmaceutical industry wastewater for water reuse in Jordan using hybrid constructed wetlands

Developing cost-efficient wastewater treatment technologies for safe reuse is essential, especially in developing countries simultaneously facing water scarcity. This study developed and evaluated a hybrid constructed wetlands (CWs) approach, incorporating tidal flow (TF) operation and utilising local Jordanian zeolite as a wetland substrate for real pharmaceutical industry wastewater treatment. Over 273 days of continuous monitoring, the results revealed that the first-stage TFCWs filled with either raw or modified zeolite performed significantly higher reductions in Chemical Oxygen Demand (COD, 58 %–60 %), Total Nitrogen (TN, 32 %–37 %), and Phosphate (PO4, 46 %–64 %) compared to TFCWs filled with normal sand. Water quality further improved after the second stage of horizontal subsurface flow CWs treatment, achieving log removals of 1.09–2.47 for total coliform and 1.89–2.09 for E. coli. With influent pharmaceutical concentrations ranging from 275 to 2000 μg/L, the zeolite-filled hybrid CWs achieved complete removal (>98 %) for ciprofloxacin, ofloxacin, erythromycin, and enrofloxacin, moderate removal (43 %–81 %) for flumequine and lincomycin, and limited removal (<8 %) for carbamazepine and diclofenac. The overall accumulation of pharmaceuticals in plant tissue and substrate adsorption accounted for only 2.3 % and 4.3 %, respectively, of the total mass removal. Biodegradation of these pharmaceuticals (up to 61 %) through microbial-mediated processes or within plant tissues was identified as the key removal pathway. For both conventional pollutants and pharmaceuticals, modified zeolite wetland media could only slightly enhance treatment without a significant difference between the two treatment groups. The final effluent from all hybrid CWs complied with Jordanian treated industry wastewater reuse standards (category III), and systems filled with raw or modified zeolite achieved over 95 % of samples meeting the highest water reuse category I. This study provides evidence of using hybrid CWs technology as a nature-based solution to address water safety and scarcity challenges.

Formation of dolomites from the newly discovered ancient cold seep in the Middle Dongsha area of the South China Sea

Remotely operated vehicle (ROV) observations have recently revealed seep dolomite deposits covering the seafloor on Middle Dongsha of the South China Sea (SCS). Spurred by these findings, we studied the mineralogical and geochemical properties to examine the seep dolomite’s origin, precipitation mechanism, and formation environment. These carbonates mainly comprise dolomite (from 64 to 84 wt%), followed by small amounts of calcite (from 1 to 3 wt%), locally containing magnesite (∼4 wt%), and goethite (∼14 wt%). Extensively developed mineralized cells containing high Mg and Ca contents found in chimneys imply that microbially-mediated processes probably participated in the reactivation of dolomite precipitation. The moderate and concentrated δ13C values (from −36.64 to −39.16‰, V-PDB) indicated that the carbon in carbonates was mainly derived from thermogenic methane. The methane fluids most likely ascended beneath the volcaniclastic unit and inherited enriched positive Eu anomalies due to fluid–rock interactions during their seepage along tectonic faults to the seafloor. The δ18O values (4.2–4.8‰, V-PDB) of carbonate suggested that an 18O-depleted fluid was involved in carbonate precipitation. The high total Rare-Earth Element contents (ΣREE) of seep carbonates varied from 61 ppm to 92 ppm, reflecting the chemical composition of surrounding pore waters at the time of carbonate precipitation, exhibiting less mixing with seawater. It may also indicate higher alkalinity and pH of the pore water. Although the sea-like REE patterns (HREE-enriched, negative Ce anomalies) are not caused by seawater, they may be due to the complexation competition between humic acid (HA) and carbonate for REE at high pore-water alkalinity and high CO32− concentrations. This is consistent with the dolomite chimney pointing toward a formation environment in relatively deep sediments, in particular, close to the sulfate-methane interface in sediments, where the bicarbonate concentration reaches its maximum due to AOM. Moderate Mo and no U enrichments appeared in the carbonates, suggesting a relatively lower intensity of methane seepages with relatively reduced AOM rates. The wide range of (Mo/U)EF values and U–Mo covariation indicates the very dynamic AOM rate (slow to moderate) and redox conditions (mostly suboxic–anoxic, occasionally sulfidic conditions) during carbonate formation due to episodically changing seepage activity.

Repeated labile carbon inputs trigger soil microbial necromass decomposition through increasing microbial diversity and hierarchical interactions

Microbial necromass substantially contributes to soil organic carbon (SOC) sequestration. However, the response of soil microbial necromass to fresh labile carbon (C) inputs and the underlying microbial mechanisms are poorly understood. In this study, we investigated the dynamics of soil microbial necromass following single and repeated labile C inputs in two typical agricultural soils, black soil (Mollisol) and red soil (Ultisol). Our results showed that labile C inputs triggered the decomposition of soil native microbial necromass, regardless of soil type and C input frequency. Following repeated glucose pulses, the microbial necromass decreased by 75 % and 41 % in black and red soils, respectively, in a week. While a single glucose pulse triggered a comparable decline in soil microbial necromass, which occurred gradually over an incubation period of 3–4 weeks. In contrast, the priming effect following a single glucose pulse was 2–3 fold higher than repeated pulses. Repeated glucose pulses increased microbial α-diversity and temporal succession of various K-strategists, enhanced the network complexity and the potential hierarchical interactions between bacteria, fungi and protists, but yielded 1.66 fold less microbial biomass compared to a single pulse. These changes explained variations in soil microbial necromass after glucose pulses. Furthermore, repeated glucose pulses enhanced the linkages between microbial attributes and the degradation of soil microbial necromass. MicroResp assay revealed that the capacity of microbial communities to degrade microbially derived residues was 1.29 and 3.60 fold higher in black and red soils with repeated glucose pulses, respectively, compared to a single pulse. Our findings provide comprehensive insights into the microbially-mediated processes that influence soil microbial necromass degradation following labile C inputs, with important implications for understanding the dynamics and stabilisation of soil microbial necromass.

Microbial Formation on Different Biomedia Surface for Wastewater Treatment

Even though commercial plastic media such as Cosmoball successfully treated municipal wastewater without clogging, its inadequate surface area prevents its use for high biofilm growth rates. This study compares microbial formation on the activated carbon (AC)-coated and non-coated Cosmoball media by submerging four activated carbon AC-coated Cosmo balls and non-coated Cosmo balls in five-liter beakers containing municipal wastewater. The researchers then analyzed the surface morphology of the biofilms on the coated and non-coated surfaces and applied the next-generation sequencing (NGS) technology to the ecology of microbial-mediated processes. By Day 11, the AC-coated media showed a biofilm coverage of 95%, whereas the non-coated media had a biofilm coverage of about 70%. The research has demonstrated that the coated media has a four times higher surface area, thus saving as much as 50% of the aeration tank volume.

Effects of polyethylene microplastics with different particle sizes and concentrations on the community structure and function of periphytic biofilms

The widespread use of microplastics (MPs) inevitably lead to their release into aquatic environment, where they are likely to encounter the periphytic biofilms, leading to changes in microbial community structure and function. However studies on the toxicity of MPs with different particle sizes and concentrations to biofilms are still lacking. Here, the effects of polyethylene (PE) MPs with three sizes (10, 40 and 120 µm) and two concentrations (2 and 20 mg/L) on biofilm communities were investigated in microcosms over a 28-day incubation period. High-throughput sequencing showed that the alpha and beta diversity of biofilm community were significantly altered by MPs, depending on their size and concentration. Typically, larger particle sizes and higher concentrations resulted in more significant changes in biofilm community structure, indicating a stronger shading effect of larger particles. Compared to the controls, 120 µm MPs treatments significantly reduced the Chao1 and Shannon index of biofilm community regardless of the concentration, while 40 µm MPs reduced the Shannon index only at high concentrations. Moreover, MPs resulted in the changes in the abundances of bacterial communities, with the abundance of Cyanobacteria increasing significantly while that of Proteobacteria and Bacteroidetes decreasing in all treatments. Interestingly, functional analysis by FAPROTAX suggested that a decrease in the abundance of chemoheterotrophy genes and an increase in photoautotrophic- and nitrification-associated genes were observed after exposure to MPs, leading to potential changes of the carbon and nitrogen metabolism of biofilms. These results highlighted that MPs exposure had negative impacts on microbial community structure and function, which in turn affects microbial-mediated processes.

Sulphate-reducing bacteria-mediated pyrite formation in the Dachang Tongkeng tin polymetallic deposit, Guangxi, China

Mediation by sulphate-reducing bacteria (SRB) is responsible for pyrite (FeS2) formation. The origin of the Dachang tin polymetallic ore field is related to the mineralisation of submarine hydrothermal vent sediments. Here, we investigated SRB in these ores via morphological, chemical, and isotopic analyses. Polarised and scanning electron microscopy indicated that trace SRB fossils in the metal sulphide ore were present in the form of tubular, beaded, and coccoidal bodies comprising FeS2 and were enclosed within a pyrrhotite (FeS) matrix in the vicinity of micro-hydrothermal vents. The carbon (C), nitrogen (N), and oxygen (O) contents in the FeS2 synthesised by SRB were high, and a clear biological Raman signal was detected. No such signals were discerned in the peripheral FeS. This co-occurrence of FeS, FeS2, and the remains of bacteria (probably chemoautotrophic bacteria) was interpreted as the coprecipitation process of SRB-mediated FeS2 formation, which has, to the best of our knowledge, not been reported before. Our study also illustrates that combined energy-dispersive X-ray spectroscopy, Raman spectroscopy, and isotopic analysis can be used as a novel methodology to document microbial-mediated processes of mineral deposition in submarine hydrothermal vent ecology on geological time scales.

Important role of endogenous microbial symbionts of fish gills in the challenging but highly biodiverse Amazonian blackwaters

Amazonian blackwaters are extremely biodiverse systems containing some of Earth’s most naturally acidic, dissolved organic carbon -rich and ion‐poor waters. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16 S rRNA of gill samples. We find that host transcriptional responses to blackwaters are species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish survive poorly when exposed to sterile/inverted blackwater. Overall, our results suggest a critical role for endogenous symbionts in blackwater fish physiology.

Co-existing two distinct formation mechanisms of micro-scale ooid-like manganese carbonates hosted in Cryogenian organic-rich black shales in South China

Manganese-rich deposits in the lower member of the Datangpo Formation (DTP) (ca. 663–654 Ma) in South China formed in the aftermath of the Cryogenian Sturtian glaciation. The Mn in the DTP occurs dominantly as rhodochrosite and Ca-rhodochrosite. A hydrothermal origin of the Mn2+ is shown by the rare earth element distribution and significantly high Mn/Fe ratios (3–19, average = 10.1). Previous studies suggested a microbially-mediated process for controlling the DTP black-shale hosted Mn carbonate deposits. However, detailed reports on the formation mechanisms of micro-scale (<2–5 μm) ooid-like Mn carbonates in the DTP have rarely been published. Systematic petrography and geochemical analyses in this study demonstrate the coexistence of two types of micro-scale ooidal-like Mn carbonates formed through two distinct mechanisms, either dominated by microbially-mediated or physiochemically-forced pathways. The Type I Mn carbonate has relatively larger grain size of 2–5 μm and exhibits a radial-concentric microfabric that shows signs of growth banding in the form of alternating light and dark laminae, which mainly express variation in Ca and Mn concentrations. The initial precipitation phase of the Type I Mn carbonate is interpreted to be Mn oxide/hydroxide, based on positive Ce anomalies and selective enrichments of particular trace elements. Novel evidence indicates that the capture of Mn as a carbonate phase directly from the water column by primarily precipitated calcite, which is referred to as the Type II Mn carbonate, has also contributed to the DTP Mn-rich deposits. Multiple roles of organic matter in Mn carbonate formation have been established: (1) catalysed Mn-redox cycling; (2) trapping and transportation of initial mineral precipitates to sediments; (3) serving as a carbon source; (4) regulating the morphology of the Mn carbonate. As a key link for understanding Cryogenian carbon and Mn cycling, specific formation pathways for the DTP Mn-carbonates are likely to have been controlled by given atmospheric-oceanic compositions (including oxygen level, pCO2, and redox conditions) in response to major geological and biological events during the interglacial period. In turn, massive storage of inorganic carbon and phosphorous in Mn carbonate phases would have had a substantial influence on biogeochemical carbon cycling during the Cryogenian.

Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria.

Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.

Reductive dissolution of iron phosphate modifies rice root morphology in phosphorus-deficient paddy soils

Root morphology reflects plant adaptations to phosphorus (P) deficiency. We hypothesized that changes in rice root morphology reflect P deficiency decrease after ferric iron (Fe(III))-bound phosphate (Fe–P) dissolution in low-redox paddy soils. We developed a novel in-situ32P phosphor-imaging approach under flooding to estimate P uptake by rice roots released from Fe–P dissolution. 32P-labeled ferrihydrite (31 mg P kg−1) was supplied either (1) in polyamide mesh bags (30 μm mesh size) to prevent roots but not microorganisms from direct Fe–P mobilization, or (2) directly mixed with soil to enable roots and microorganisms unrestricted access to the Fe–P. The establishment of low redox conditions (Eh values between −176 and −224 mV) drove the reductive dissolution of Fe–P. Rice root-derived organic acids alone were unable to control Fe–P dissolution, and Fe(III) reduction is predominately a microbially-mediated process. Direct root access to Fe–P raised both the number and mean diameter of crown roots and root tips, and increased P uptake by 149–231%. Crown root elongation rate, 32P activities along roots and root tips were 5–133% higher when roots directly accessed Fe–P compared to Fe–P excluded from roots in mesh bags. Iron accumulation on roots depended on the rice growth stage, but not on their access to Fe–P. Roots’ access to Fe–P increased rice crown roots elongation and branching and increased P accessibility under P deficiency.

Treatment of Integrated Steel Plant Wastewater Using Conventional and Advanced Techniques

AbstractThe integrated steel industry is considered as one of the important industrial sectors, and its outputs are inputs for other sectors including construction, engineering, medical and scientific equipment, and defence. Massive production, consumption, and export of steel signify a country's economic index. This review outlines the World's steel production quantities, the processes involved, and wastewater generation from the industry and its treatment. Wastewater generated from steel plants is highly complex and requires intensive treatment before discharge into natural water bodies. Technologies adopted for treating wastewater generated from steel industries are deliberated, focusing on coking wastewater treatment. Microbial mediated processes provide an effective means of degrading the contaminants, but the toxicity of certain compounds during higher pollutant load inhibits its further treatment. However, these processes can be integrated with either electrochemical technologies or advanced oxidation processes (AOPs), which can reduce the toxicity level. Hence, when a highly concentrated and complex mixture of contaminants is considered, an integrated approach is a resourceful option in terms of cost‐effectiveness and treatment efficiency.

Comparative Study of Formation Conditions of Fe-Mn Ore Microbialites Based on Mineral Assemblages: A Critical Self-Overview

The role of biogenicity in the mineral world is larger than many might assume. Biological processes and physical and chemical processes interact both at the Earth’s surface and far underground, leading to the formation of banded iron and manganese deposits, among others. Microbial mats can form giant sedimentary ore deposits, which include enrichment of further elements. This article reviews the ways in which microbially-mediated processes contribute to mineralization, the importance of mineralized microbial textural features, and the methods that must be used to obtain high-resolution datasets. If the chosen methodology and/or the size dimension of investigation is not appropriate, then it is not possible to recognize that a system is microbially mediated, and the conclusion will be incomplete. We call attention to variable authigenic mineralization as the result of complex mineralization of cells and extracellular polymeric substances in the starving basins, which form giant ore deposits together with ore-forming minerals. Microbial mats and other biosignatures can serve as indicators of environmental reconstruction in ore formations. We suggest tests and analyses that will allow the potential role of biomineralization to be properly investigated for a more comprehensive view of formation processes and their implications.

The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications.

Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently switch their infection modes in nature, potentially causing substantial impacts on the host-phage community and relevant biogeochemical cycling. Understanding the regulating factors and outcomes of temperate phage life cycle transition is thus fundamental for evaluating their ecological impacts. This review thus systematically summarizes the effects of various factors affecting temperate phage life cycle decisions in both culturable phage-host systems and natural environments. The review further elucidates the ecological implications of the life cycle transition of temperate phages with an emphasis on phage/host fitness, host-phage dynamics, microbe diversity and evolution, and biogeochemical cycles.

Propagule limitation affects the response of soil methane oxidizer community to increased salinity

The extent to which propagule limitation can govern the responses of microbially-mediated processes (such as methane oxidation) to sudden environmental changes, is poorly understood. Here, we compared the ability of the methanotroph community in lakeshore soils of two lakes to respond to an experimental increase in salinity. One set of samples was taken from lakeshore soils of a freshwater lake (Yang Lake), the other from a slightly brackish lake (Qinghai Lake), both on the Tibetan Plateau. Samples were incubated in microcosms by adding ∼ 5 % 13CH4 or 12CH4 and different concentrations of NaCl solution. DNA stable-isotope probing (DNA-SIP) followed by high-throughput sequencing was used to determine how the active methanotrophic populations differed in lakeshore soils with different salinity levels. Samples from saline and freshwater lake initially showed much-reduced methane oxidation ability and methanotrophic activity at increased salinity. For the freshwater samples with the salinity of 25 to 50 g/L after NaCl addition, there was no adaptation and increase in methanotrophy after 7 days. By contrast, samples from the brackish lake showed an initial depression of methane oxidation, followed by greatly increased rates after several days. Sequencing revealed that this recovery of methanotrophy in the brackish lake samples was associated with a major switchover in composition of active methanotroph community. In particular, the relative abundance of Type Ⅰa methanotrophs became more abundant at increased salinity. It appears that in this freshwater lake environment, isolation from any nearby high-salinity-tolerant bacterial sources has prevented the possibility of full adaptation to a high salinity change in the environment, and only a moderate salinity adaptation is possible by species-sorting from within the existing community. By contrast, in the higher-salinity environment, the highly salinity-tolerant Methylomicrobium was able to break the establishment limitation in the high salinity environment and become the dominant methanotroph. Our study provides an instance of propagule limitation preventing adaptation to changed conditions.

Bacterial communities in sediments of an urban wetland in Bogota, Colombia

Urban wetlands are biodiversity reservoirs sustained by microbe-mediated processes. In tropical zones, wetland microbial dynamics remain poorly understood. Chemical parameters, heavy metal content, and microbiological community structure were investigated in surface sediments of the Santa Maria del Lago (SML) wetland in Bogota, Colombia. High-throughput sequencing was employed to generate RNAr 16S and nosZ gene sequence data with which bacteria, archaea, and nosZ-type denitrifier community composition and their phylogenetic relationships were investigated. A canonical correspondence analysis was conducted to determine the relationship between assessed environmental variables and microbial community composition. Results showed that the most abundant bacterial phyla were Proteobacteria, Acidobacteria (group GP18), and Aminicenantes; Archaea were represented by the taxa Methanomicrobia and Thermoprotei, and the nosZ community was dominated by Candidatus Competibacter denitrificans. A phylogenetic analysis revealed a high diversity of Operational Taxonomic Units (OTUs), according to 16S rRNA gene sequence data; however, the quantity and diversity of OTUs from the nosZ community were low compared to previous studies. High concentrations of ammonium, phosphorus, organic carbon, Pb, Fe, Zn, Cu, and Cd, were detected in sediments, but they were not strongly related to observed microbial community compositions. In conclusion, in the same polluted SML wetland sediments diverse bacteria and archaea communities were detected, although not nosZ-type denitrifiers.