Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site

Application of Biofloc-Down flow hanging sponge system to remove nitrogen components in recirculating zero water exchange aquaculture system

This study presents a novel approach to sustainable aquaculture by integrating biofloc technology (BFT) with a compact down-flow hanging sponge (DHS) reactor. The integrated BFT-DHS system effectively removed nitrogen compounds while maintaining ammonia-nitrogen (NH4+-N) concentrations below 1 mg-N L-1 without water exchange. Application of this system in a tank bred with juvenile Oreochromis niloticus showed a high NH4+-N removal rate of up to 97 % and nitrite (NO2- -N) concentrations were maintained at 0.1 ± 0.1 mg-N L-1. Microbial analysis revealed Gordonia as the predominant genus in the biofloc contributing to heterotrophic nitrification, while the Peptostreptococcaceae family dominated the DHS reactor. Heterotrophic nitrification seemed to be the primary process for enhanced nitrogen removal. Pathogenic bacteria, Vibrio sp. was absent throughout the study. This study highlights the potential integration of BFT and DHS system for sustainable aquaculture practice with effective nitrogen removal.

Electrode-based floating treatment wetlands: Insights into design operation factors influencing bioenergy generation and treatment performance

Exponential increases in energy consumption and wastewater have often irreversible environmental impacts. As a result, bio-electrochemical devices like microbial fuel cells (MFCs), which convert chemical energy in organic matter to electricity using exoelectrogenic bacteria, have gained interest. However, operational factors affecting efficiency and energy output need further study. This research investigated bioenergy production and COD, TN, and TP removal in mesoscale floating treatment wetlands (FTW-MFC) using Phragmites australis, Iris pseudacorus, and a mix of both. The Iris FTW-MFC achieved a high voltage peak of 2100 mV. The maximum power densities of 484 mW/m2, 1196 mW/m2, and 441 mW/m2 were observed for Phragmites, Iris, and mixed FTW-MFCs, respectively. Despite promising bioenergy yields, pollutant removal was unsatisfactory. A low area/height ratio (0.38 m2/0.8 m) and high loading rate (18.1 g/m2·d COD) boosted bioenergy output but hindered treatment performance and stressed plants, causing root decay. No significant pollutant removal differences were found between FTW-MFC and FTW. Higher relative plant growth rates occurred in the FTW-MFC. Microbial analysis shown that representatives of Pseudomonas and Clostridium species were consistently found across all samples, involved in both organic compound transformation and electricity generation, contributed to successful microscale results. A supporting microscale MFC experiment showed wastewater composition's impact on bioenergy yield and pollutant removal. Pre-inoculated reactors improved organic matter transformation and electricity generation, while aeration increased voltage and treatment performance. The role of plants requires further verification in future experiments.

Study on the enhancement of low carbon-to-nitrogen ratio urban wastewater pollutant removal efficiency by adding sulfur electron acceptors

The effective elimination of nitrogen and phosphorus in urban sewage treatment was always hindered by the deficiency of organic carbon in the low C/N ratio wastewater. To overcome this organic-dependent barrier and investigate community changes after sulfur electron addition. In this study, we conducted a simulated urban wastewater treatment plant (WWTP) bioreactor by using sodium sulfate as an electron acceptor to explore the removal efficiency of characteristic pollutants before and after the addition of sulfur electron acceptor. In the actual operation of 90 days, the removal rate of sulfur electrons' chemical oxygen demand (COD), ammonia nitrogen, and total phosphorus (TP) with sulfur electrons increased to 94.0%, 92.1% and 74%, respectively, compared with before the addition of sulfur electron acceptor. Compared with no added sulfur(phase I), the reactor after adding sulfur electron acceptor(phase II) was demonstrated more robust in nitrogen removal in the case of low C/N influent. the effluent ammonia nitrogen concentration of the aerobic reactor in Pahse II was kept lower than 1.844 mg N / L after day 40 and the overall concentration of total phosphorus in phase II (0.35 mg P/L) was lower than that of phase I(0.76 mg P/L). The microbial community analysis indicates that Rhodanobacter, Bacteroidetes, and Thiobacillus, which were the predominant bacteria in the reactor, may play a crucial role in inorganic nitrogen removal, complex organic degradation, and autotrophic denitrification under the stress of low carbon and nitrogen ratios. This leads to the formation of a distinctive microbial community structure influenced by the sulfur electron receptor and its composition. This study contributes to further development of urban low-carbon-nitrogen ratio wastewater efficient and low-cost wastewater treatment technology.

Optimization of operating parameters and microbiological mechanism of a low C/N wastewater treatment system dominated by iron-dependent autotrophic denitrification

Ferrous iron (Fe2+) reduces the amount of external carbon source used for the denitrification of low-C/N wastewater. The effects of key operating parameters on the efficiency of ferrous-dependent autotrophic denitrification (FDAD) and the functioning mechanism of the microbiome can provide a regulatory strategy for improving the denitrification efficiency of low C/N wastewater. In this study, the response surface method (RSM) was used to explore the influence of four important parameters-the molar ratio of Fe2+ to NO3--N (Fe/N), total organic carbon (TOC), the molar ratio of inorganic carbon to NO3--N (IC/N) and sludge volume (SV, %)-on the FDAD efficiency. Functional prediction and molecular ecological networks based on high-throughputs sequencing techniques were used to explore changes in the structure, function, and biomarkers of the sludge microbial community. The results showed that Fe/N and TOC were the main parameters affecting FDAD efficiency. Higher concentrations of TOC and high Fe/N ratios provided more electron donors and improved denitrification efficiency, but weakened the importance of biomarkers (Rhodanobacter, Thermomonas, Comamonas, Thauera, Geothrix and unclassified genus of family Gallionellaceae) in the sludge ecological network. When Fe/N > 4, the denitrification efficiency fluctuated significantly. Functional prediction results indicated that genes that dominated N2O and NO reduction and the genes that dominated Fe2+ transport showed a slight decrease in abundance at high Fe/N levels. In light of these findings, we recommend the following optimization ranges of parameters: Fe/N (3.5-4); TOC/N (0.36-0.42); IC/N (3.5-4); and SV (approximately 35%).

Bioreduction of chromate in a syngas-based membrane biofilm reactor

This study leveraged synthesis gas (syngas), a renewable resource attainable through the gasification of biowaste, to achieve efficient chromate removal from water. To enhance syngas transfer efficiency, a membrane biofilm reactor (MBfR) was employed. Long-term reactor operation showed a stable and high-level chromate removal efficiency > 95%, yielding harmless Cr(III) precipitates, as visualised by scanning electron microscopy and energy dispersive X-ray analysis. Corresponding to the short hydraulic retention time of 0.25 days, a high chromate removal rate of 80 µmol/L/d was attained. In addition to chromate reduction, in situ production of volatile fatty acids (VFAs) by gas fermentation was observed. Three sets of in situ batch tests and two groups of ex situ batch tests jointly unravelled the mechanisms, showing that biological chromate reduction was primarily driven by VFAs produced from in situ syngas fermentation, whereas hydrogen originally present in the syngas played a minor role. 16 S rRNA gene amplicon sequencing has confirmed the enrichment of syngas-fermenting bacteria (such as Sporomusa), who performed in situ gas fermentation leading to the synthesis of VFAs, and organics-utilising bacteria (such as Aquitalea), who utilised VFAs to drive chromate reduction. These findings, combined with batch assays, elucidate the pathways orchestrating synergistic interactions between fermentative microbial cohorts and chromate-reducing microorganisms. The findings facilitate the development of cost-effective strategies for groundwater and drinking water remediation and present an alternative application scenario for syngas.

Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide

The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.

Microbial features with uranium pollution in artificial reservoir sediments at different depths under drought stress

The uranium (U) containing leachate from uranium tailings dam into the natural settings, may greatly affect the downstream environment. To reveal such relationship between uranium contamination and microbial communities in the most affected downstream environment under drought stress, a 180 cm downstream artificial reservoir depth sediment profile was collected, and the microbial communities and related genes were analyzed by 16S rDNA and metagenomics. Besides, the sequential extraction scheme was employed to shed light on the distinct role of U geochemical speciations in shaping microbial community structures. The results showed that U content ranged from 28.1 to 70.1 mg/kg, with an average content of 44.9 mg/kg, significantly exceeding the value of background sediments. Further, U in all the studied sediments was related to remarkably high portions of mobile fractions, and U was likely deposited layer by layer depending on the discharge/leachate inputs from uranium-involving anthoropogenic facilities/activities upstream. The nexus between U speciation, physico-chemical indicators and microbial composition showed that Fe, S, and N metabolism played a vital role in microbial adaptation to U-enriched environment; meanwhile, the fraction of Ureducible and the Fe and S contents had the most significant effects on microbial community composition in the sediments under drought stress.

Iron coatings on carbonate rocks shape the attached bacterial aquifer community

Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 105 cells/mm2 after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 106: 1 and 103: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.

Deep groundwater irrigation altered microbial community and increased anammox and methane oxidation in paddy wetlands of Sanjiang Plain, China

The over-utilizing of nitrogen fertilizers in paddy wetlands potentially threatens to the surrounding waterbody, and a deep understanding of the community and function of microorganisms is crucial for paddy non-point source pollution control. In this study, top soil samples (0-15 cm) of paddy wetlands under groundwater's irrigation at different depths (H1: 6.8 m, H2: 13.7 m, H3: 14.8 m, H4: 15.6 m, H5: 17.0 m, and H6: 17.8 m) were collected to investigate microbial community and function differences and their interrelation with soil properties. Results suggested some soil factor differences for groundwater's irrigation at different depths. Deep-groundwater's irrigation (H2-H6) was beneficial to the accumulation of various electron acceptors. Nitrifying-bacteria Ellin6067 had high abundance under deep groundwater irrigation, which was consistent with its diverse metabolic capacity. Meanwhile, denitrifying bacteria had diverse distribution patterns. Iron-reducing bacteria Geobacter was abundant in H1, and Anaeromyxobacter was abundant under deep groundwater irrigation; both species could participate in Fe-anammox. Furthermore, Geobacter could perform dissimilatory nitrate reduction to ammonia using divalent iron and provide substrate supply for anammox. Intrasporangium and norank_f_Gemmatimonadacea had good chromium- and vanadium-reducting potentials and could promote the occurrence of anammox. Low abundances of methanotrophs Methylocystis and norank_f_Methyloligellaceae were associated with the relatively anoxic environment of paddy wetlands, and the presence of aerobic methane oxidation was favorable for in-situ methane abatement. Moisture, pH, and TP had crucial effects on microbial community under phylum- and genus-levels. Microorganisms under shallow groundwater irrigation were highly sensitive to environmental changes, and Fe-anammox, nitrification, and methane oxidation were favorable under deep groundwater irrigation. This study highlights the importance of comprehensively revealing the microbial community and function of paddy wetlands under groundwater's irrigation and reveals the underlying function of indigenous microorganisms in agricultural non-point pollution control and greenhouse gas abatement.

Growth of microalgae and cyanobacteria consortium in a photobioreactor treating liquid anaerobic digestate from vegetable waste

This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing 3N-BBM medium was inoculated with Microglena sp., Tetradesmus obliquus, and Desmodesmus subspicatus mixture with a density of 1.0 × 104 cells/mL and the consortium was cultivated for 30 days. Then, the bioreactor was semi-continuously fed with liquid digestate with hydraulic retention time (HRT) of 30 days, and the treatment process was continued for the next 15 weeks. The change in the microalgal and cyanobacterial species domination was measured in regular intervals using cell counting with droplet method on a microscope slide. At the end of the experiment, Desmonostoc sp. cyanobacteria (identified with 16S ribosomal RNA genetical analysis) as well as Tetradesmus obliquus green algae along with Rhodanobacteraceae and Planococcaceae bacteria (determined with V3-V4 16sRNA metagenomic studies) dominated the microbial community in the photobioreactor. The experiment demonstrated high treatment efficiency, since nitrogen and soluble COD were removed by 89.3 ± 0.5% and 91.2 ± 1.6%, respectively, whereas for phosphates, 72.8 ± 2.1% removal rate was achieved.

Effect of solar and artificial lighting on microalgae cultivation and treatment of liquid digestate

A comparative study was carried out to assess the effect of two light sources on microalgae cultivation and the treatment of liquid digestate. The R1 photobioreactor operated with LED lightning allowed to achieve moderate nutrient removal rates whereas soluble COD (Chemical Oxygen Demand) was reduced in 90%. After switching this reactor into sunlight, the removal rate of phosphates increased to 66%. However, the greatest removal rate of both nutrients and sCOD of up to 93% was observed in the R2 photobioreactor operated only under sunlight. Microglena sp. was the dominant algae growing in the R1 reactor, and the main bacteria families detected were Chitinophagaceae, Sphingomonadaceae and Xanthobacteraceae. In contrast, Tetradesmus obliquus dominated in the R2 reactor and Rhodanobacteraceae, Chitinophagaceae and A4b were predominant bacteria in this run. Furthermore, much greater biomass productivity as well as overall biomass density was observed in the R2 photobioreactor cultivated exclusively with solar lightning.

Effects of tea oil camellia (Camellia oleifera Abel.) shell-based organic fertilizers on the physicochemical property and microbial community structure of the rhizosphere soil

Soil microorganisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the soil physicochemical property and microbial community structure. In this study, four organic fertilizers were first prepared based on tea oil camellia shell (TOCS). Our findings indicate that the application of BOFvo increased both total pore volume and BET surface area of the rhizosphere soils, as well there was a remarkable enhancement in total organic matter (TOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), total potassium (TK), and available potassium (AK) contents of the rhizosphere soils. Meanwhile, in comparison to the CK and CF groups, the utilization of BOFvo led to a substantial increase in both average yield and fruiting rate per plant at maturity, as well resulted in a significant increase in TN and TP contents of tea oil camellia leaves. Furthermore, our findings suggest that the application of TOCS-based organic fertilizers significantly enhances the microbial diversity in the rhizosphere soils with Proteobacteria and Ascomycota being the dominant bacterial and fungal phyla, respectively, and Rhodanobacter and Fusarium being the dominant bacterial and fungal genus, respectively. Redundancy analysis (RDA) indicates that the physicochemical characteristics of TOCS-based organic fertilizers had a significant impact on the composition and distribution of microbial communities in the rhizosphere soils. This study will facilitate the promotion and application of TOCS-based organic fertilizers, thereby establishing a foundation for the reuse of tea oil camellia waste resources.

A gravity-driven membrane bioreactor in treating the real decentralized domestic wastewater: Flux stability and membrane fouling

Domestic wastewater in decentralized sites is capturing increasing attention. However, conventional treatment technology is not sufficiently cost-effective. In this study, real domestic wastewater was treated directly using a gravity-driven membrane bioreactor (GDMBR) at 45 mbar without backwashing or chemical cleaning, and the effects of different membrane pore sizes (0.22 μm, 0.45 μm, and 150 kDa) on flux development and contaminants removal were examined. The results showed that the flux initially decreased and then stabilized throughout long-term filtration and that the stabilized flux level of the GDMBR equipped the membranes with the pore size of 150 kDa and 0.22 μm was higher than that of 0.45 μm membrane and was in the range of 3.25-4.25 L m^-2h^-1. The flux stability was related to spongelike and permeable biofilm generation on the membrane surface in the GDMBR system. The presence of aeration shear on the membrane surface would cause the slough off of biofilm from the membrane surface, especially in the scenarios of GDMBR with the membrane pore size of 150 kDa and 0.22 μm, contributing to lower accumulation of extracellular polymeric substance (EPS) and smaller biofilm thickness compared to that of 0.45 μm membrane. Furthermore, the GDMBR system achieved efficient removals of chemical oxygen demand (COD), and ammonia, with average removal efficiencies of 60-80% and 70%. The high biological activity and microbial community diversity within the biofilm would improve its biodegradation and should be responsible for the efficient removal performance of contaminants. Interestingly, the membrane effluent could effectively retain total nitrogen (TN) and total phosphorus (TP). Therefore, it's feasible to adopt the GDMBR process to treat the actual domestic wastewater in the decentralized locations, and these findings could be expected to develop some simple and environmentally friendly strategies for decentralized wastewater treatment with fewer inputs.

Characteristics of groundwater microbial communities and the correlation with the environmental factors in a decommissioned acid in-situ uranium mine

Microorganisms play an important role in the bioremediation process for the decommissioned acid in-situ leaching uranium mine. It is crucial to understand the original microbial community characteristics before the in-situ bioremediation. However, there are limited studies on the groundwater microbial characteristics in the decommissioned acid in-situ uranium mine. To this end, we collected groundwater samples, including the groundwater that originally residual in the borehole (RW) and the aquifer water (AW), from a decommissioned acid in-situ uranium mine in the southern margin of Ili Basin in Xinjiang, China. The occurrence characteristics of the groundwater microbial communities and their correlation with environmental factors were systematically studied based on the high throughput 16S rRNA gene sequencing data and geochemical data. Results found that the AW samples had higher alpha- and beta- diversity than the RW samples. The relative abundance of Sporosarcina, Sulfobacillus, Pedobacter and Pseudomonas were significantly different in the AW and RW samples, which had significant correlation with pH, metals, and sulfate, etc. A series of reducing microorganisms were discovered, such as sulfate reduction (e.g., Desulfosporosinus) and metal reduction (e.g., Arthrobacter, Bacillus, Clostridium, Pseudomonas, and Rhodanobacter), which have the potential to attenuate sulfate and uranium in groundwater. In addition, we found that pH and redox potential (Eh) were the dominant environmental factors affecting the microbial composition. This study extends our knowledge of microbial community structure changes in the decommissioned acid in-situ uranium mine and has positive implications for assessing the potential of natural attenuation and bioremediation strategies.

Characterization of Enrichment Cultures of Anammox, Nitrifying and Denitrifying Bacteria Obtained from a Cold, Heavily Nitrogen-Polluted Aquifer

Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 g/L, respectively) and a very low content of organic carbon (2.5 mg/L). To assess the potential for bioremediation of polluted groundwater in situ, enrichment cultures of anammox, nitrifying, and denitrifying bacteria were obtained and analyzed. Fed-batch enrichment of anammox bacteria was not successful. Stable removal of ammonium and nitrite (up to 100%) was achieved in a continuous-flow reactor packed with a nonwoven fabric at 15 °C, and enrichment in anammox bacteria was confirmed by FISH and qPCR assays. The relatively low total N removal efficiency (up to 55%) was due to nonstoichiometric nitrate buildup. This phenomenon can be explained by a shift in the metabolism of anammox bacteria towards the production of more nitrates and less N₂ at low temperatures compared to the canonical stoichiometry. In addition, the too high an estimate of specific anammox activity suggests that N cycle microbial groups other than anammox bacteria may have contributed significantly to N removal. Stable nitrite production was observed in the denitrifying enrichment culture, while no "conventional" nitrifiers were found in the corresponding enrichment cultures. Xanthomonadaceae was a common taxon for all microbial communities, indicating its exclusive role in this ecosystem. This study opens up new knowledge about the metabolic capabilities of N cycle bacteria and potential approaches for sustainable bioremediation of heavily N-polluted cold ecosystems.

Long-term fertilization has different impacts on bacterial communities and phosphorus forms in sugarcane rhizosphere and bulk soils under low-P stress

The application of phosphorus (P) fertilizer effectively improves soil P availability, but it also affects soil microbial communities. However, the responses of soil bacterial communities and P forms to long-term P fertilization, and the relationships of bacterial communities with soil P forms remain unclear in P-deficient field. In this study, the impacts of different P fertilization treatments (chemical nitrogen and potassium (NK); chemical N, P and K (NPK); and NPK plus straw (NPKS)) on the bacterial communities and P forms in sugarcane rhizosphere (RS) and bulk soils (BS) were evaluated. Compared with the NK, the NPK and NPKS treatments significantly (P<0.05) increased the yield and quality characters of sugarcane, especially under NPKS. Additionally, P fertilization significantly increased the available P (AP), soluble inorganic P (Pi) and retained Pi in both the RS and BS, but they significantly increased the Chao1 and Shannon index only in the BS; and almost all these indices were significantly higher in the RS than in the BS. The bacterial community compositions were also significantly altered by P fertilization, with major changes in the RS and minor changes in the BS. The bacterial genera that were enriched in the sugarcane rhizosphere mainly included Bradyrhizobium, Rhodanobacter, Pseudolabrys, Conexibacter, and Burkholderia-Caballeronia-Paraburkholderia, some of which potentially promote the plant growth. Compared to NK, functional groups involved in the cycling of carbon, N, and sulfur significantly increased or decreased with fertilizer P application. Moreover, the relative abundances of many bacterial species were significantly correlated with the soil P forms. In conclusion, long-term P fertilization altered bacterial structure and functions in P-deficient sugarcane soil, which could help the soil P cycling and suppling. The results provide useful information to stimulate the power of the microbes by fertilization measures to improve soil nutrients and crop production.

Glycerol amendment enhances biosulfidogenesis in acid mine drainage-affected areas: An incubation column experiment

Microbial sulfate (SO₄²⁻) reduction in Acid Mine Drainage (AMD) environments can ameliorate the acidity and extreme metal concentrations by consumption of protons via the reduction of SO₄²⁻ to hydrogen sulfide (H₂S) and the concomitant precipitation of metals as metal sulfides. The activity of sulfate-reducing bacteria can be stimulated by the amendment of suitable organic carbon sources in these generally oligotrophic environments. Here, we used incubation columns (IC) as model systems to investigate the effect of glycerol amendment on the microbial community composition and its effect on the geochemistry of sediment and waters in AMD environments. The ICs were built with natural water and sediments from four distinct AMD-affected sites with different nutrient regimes: the oligotrophic Filón Centro and Guadiana acidic pit lakes, the Tintillo river (Huelva, Spain) and the eutrophic Brunita pit lake (Murcia, Spain). Physicochemical parameters were monitored during 18 months, and the microbial community composition was determined at the end of incubation through 16S rRNA gene amplicon sequencing. SEM-EDX analysis of sediments and suspended particulate matter was performed to investigate the microbially-induced mineral (neo)formation. Glycerol amendment strongly triggered biosulfidogenesis in all ICs, with pH increase and metal sulfide formation, but the effect was much more pronounced in the ICs from oligotrophic systems. Analysis of the microbial community composition at the end of the incubations showed that the SRB Desulfosporosinus was among the dominant taxa observed in all sulfidogenic columns, whereas the SRB Desulfurispora, Desulfovibrio and Acididesulfobacillus appeared to be more site-specific. Formation of Fe³⁺ and Al³⁺ (oxy)hydroxysulfates was observed during the initial phase of incubation together with increasing pH while formation of metal sulfides (predominantly, Zn, Fe and Cu sulfides) was observed after 1–5 months of incubation. Chemical analysis of the aqueous phase at the end of incubation showed almost complete removal of dissolved metals (Cu, Zn, Cd) in the amended ICs, while Fe and SO₄²⁻ increased towards the water-sediment interface, likely as a result of the reductive dissolution of Fe(III) minerals enhanced by Fe-reducing bacteria. The combined geochemical and microbiological analyses further establish the link between biosulfidogenesis and natural attenuation through metal sulfide formation and proton consumption.

Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages

Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.

Autotoxin affects the rhizosphere microbial community structure by influencing the secretory characteristics of grapevine roots

Autotoxins secreted by roots into the soil can trigger rhizosphere microecological imbalances and affect root secretory properties resulting in conditions such as replanting disease. However, information on the effect of autotoxins on root secretion characteristics and regulation of the composition of rhizosphere microorganisms by altered root exudates is limited. In this study, autotoxin ρ-hydroxybenzoic acid (4-HBA) was added to the soil of potted grapevine seedlings, CO₂ pulse-labeling, and DNA stable isotope probing were used to track the rhizosphere microbiome that assimilates root exudates. Bacterial and fungal microbiomes that assimilated plant-derived carbon were identified by high-throughput sequencing. Results showed that 4-HBA treatment altered bacterial and fungal communities in ¹³C-labeled organisms, with a lower abundance of beneficial bacteria (e.g., Gemmatimonas, Streptomyces, and Bacillus) and a higher abundance of potential pathogen fungi (e.g., Fusarium, Neocosmospora, Gibberella, and Fusicolla) by changing the composition of root exudates. The exogenous addition of upregulated compound mixtures of root exudates reduced the abundance of beneficial bacterial Bacillus and increased the abundance of potential pathogen fungi Gibberella. These results suggest that 4-HBA can alter root secretion properties and altered root exudates may enrich certain potential pathogens and reduce certain beneficial bacteria, thereby unbalancing the structure of the rhizosphere microbial community.

Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans

Rhodanobacter has been found as the dominant genus in aquifers contaminated with high concentrations of nitrate and uranium in Oak Ridge, TN, USA. The in situ stimulation of denitrification has been proposed as a potential method to remediate nitrate and uranium contamination. Among the Rhodanobacter species, Rhodanobacter denitrificans strains have been reported to be capable of denitrification and contain abundant metal resistance genes. However, due to the lack of a mutagenesis system in these strains, our understanding of the mechanisms underlying low-pH resistance and the ability to dominate in the contaminated environment remains limited. Here, we developed an in-frame markerless deletion system in two R. denitrificans strains. First, we optimized the growth conditions, tested antibiotic resistance, and determined appropriate transformation parameters in 10 Rhodanobacter strains. We then deleted the upp gene, which encodes uracil phosphoribosyltransferase, in R. denitrificans strains FW104-R3 and FW104-R5. The resulting strains were designated R3_Δupp and R5_Δupp and used as host strains for mutagenesis with 5-fluorouracil (5-FU) resistance as the counterselection marker to generate markerless deletion mutants. To test the developed protocol, the narG gene encoding nitrate reductase was knocked out in the R3_Δupp and R5_Δupp host strains. As expected, the narG mutants could not grow in anoxic medium with nitrate as the electron acceptor. Overall, these results show that the in-frame markerless deletion system is effective in two R. denitrificans strains, which will allow for future functional genomic studies in these strains furthering our understanding of the metabolic and resistance mechanisms present in Rhodanobacter species. IMPORTANCE Rhodanobacter denitrificans is capable of denitrification and is also resistant to toxic heavy metals and low pH. Accordingly, the presence of Rhodanobacter species at a particular environmental site is considered an indicator of nitrate and uranium contamination. These characteristics suggest its future potential application in bioremediation of nitrate or concurrent nitrate and uranium contamination in groundwater ecosystems. Due to the lack of genetic tools in this organism, the mechanisms of low-pH and heavy metal resistance in R. denitrificans strains remain elusive, which impedes its use in bioremediation strategies. Here, we developed a genome editing method in two R. denitrificans strains. This work marks a crucial step in developing Rhodanobacter as a model for studying the diverse mechanisms of low-pH and heavy metal resistance associated with denitrification.

The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification

Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H⁺)-, aluminium (Al³⁺)-, and nitrate nitrogen (NO₃^--N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H⁺ loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.

Ecological management model for the improvement of soil fertility through the regulation of rare microbial taxa in tea (Camellia sinensis L.) plantation soils

Agricultural management is essential to enhance soil ecosystem service function through optimizing soil physical conditions and improving nutrient supply, which is predominantly regulated by soil microorganisms. Several studies have focused on soil biodiversity and function in tea plantation systems. However, the effects of different agriculture managements on soil fertility and microbes remain poorly characterized, especially for what concerns perennial agroecosystems. In this study, 40 soil samples were collected from 10 tea plantation sites in China to explore the effects of ecological and conventional managements on soil fertility, as well as on microbial diversity, community composition, and co-occurrence network. Compared with conventional management, ecological management was found to significantly enhance soil fertility, microbial diversity, and microbial network complexity. Additionally, a significant difference in community composition was clearly observed under the two agriculture managements, especially for rare microbial taxa, whose relative abundance significantly increased under ecological management. Random forest modeling revealed that rare taxa (e.g., Rokubacteria and Mortierellomycota), rather than dominant microbial taxa (e.g., Proteobacteria and Ascomycota), were key variables for predicting soil fertility. This indicates that rare taxa might play a fundamental role in biological processes. Overall, our results suggest that ecological management is more efficient than conventional management in regulating rare microbial taxa and maintaining a good soil fertility in tea plantation systems.

Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa

Excessive production and application of rare-earth metal oxide nanoparticles warrants assessment of their environmental risks. Little is known about the impact of these nanoparticles on soil bacterial communities. We quantified the effects of nano-Gd₂O₃ and nano-La₂O₃, at the different concentrations and exposure regimes, on soil bacterial community structure and function as well as the structure-function relationship. Further, we constructed and analyzed a co-occurrence network to identify and characterize potential keystone taxa that were related to the enzyme activities and responded to the increasing concentrations of nanoparticles. Both nano-Gd₂O₃ and nano-La₂O₃ significantly altered the bacterial community structure and function in a concentration-dependent manner; however, these negative effects were observed on day 1 or day 7 but not on day 60, indicating that these effects were transient and the bacterial communities can mitigate the effect of these nanoparticles over time. Interestingly, the nanoparticle exposure decoupled the relationship between the structure and function of the soil bacterial communities. The decoupling was due to changes in the composition and relative abundances of potential keystone taxa related to bacterial community functions. Altogether, we provide insights into the interactions between the rare-earth metal oxide nanoparticles and soil bacterial communities. Our results facilitate the environmental risk assessment and safe usage of rare-earth metal oxide nanoparticles.

Differential Vaginal Microbiota Profiling in Lactic-Acid-Producing Bacteria between Infertile Women with and without Chronic Endometritis

Purpose: Chronic endometritis (CE) is an infectious and inflammatory disorder associated with infertility of unknown etiology, repeated implantation failure, and recurrent pregnancy loss. In the current clinical practice, intrauterine interventions such as endometrial biopsy/histopathologic examinations and/or hysteroscopy are required for the diagnosis of CE. In this study, we analyzed the microbiota in vaginal secretions (VS) as a potential prediction tool for CE in infertile women. Methods: Using next-generation sequencing analysis, we compared the VS and endometrial fluid (EF) microbiota in infertile women with (n = 20) or without CE (n = 103). Results: The detection rate of Streptococcus and Enterococcus as well as the bacterial abundance of Atopobium and Bifidobacterium in the VS microbiota was significantly lower in the CE group than in the non-CE group. Meanwhile, the detection rate and bacterial abundance of Lactobacillus in the EF and VS microbiota were at similar levels between the two groups. Conclusion: These findings suggest that VS microbiota in infertile women with CE is characterized by the reduction in Bifidobacterium and lactic-acid-producing bacteria other than Lactobacillus. Our results hold promise for the prediction of CE, not by somewhat interventional intrauterine procedures, but by less invasive VS sampling. TRIAL REGISTRATION NUMBER: UMIN000029449 (registration date 6 October 2017).

Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality

Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.

Water recycle system in an artificial closed ecosystem - Lunar Palace 1: Treatment performance and microbial evolution

Water recycle systems have important implications to realize material circulation in biological regeneration life support systems, which is of significance for long-term space missions and future planetary base. Based on membrane biological activated carbon reactor (MBAR) technologies, the 'Lunar Palace 365' experiment established various treatment processes for condensate wastewater, domestic wastewater, urine, and used nutrient solutions. The 370-day operation data showed the COD_Mn index of purified condensate wastewater decreased to 0.74 ± 0.15 mg/L, which met the standards for drinking water quality. The average removal rate of organic contaminants in domestic wastewater by the MBAR was 85.7% ± 10.2%, and this MBAR also had a stable nitrification performance with effluent NO₃^--N concentrations fluctuating from 145.57 mg/L to 328.59 mg/L. Moreover, the purification of urine achieved the conversion of urea-N to NH₄⁺-N and thus the partial recovery of nitrogen. 16S rDNA sequencing results revealed the evolution of microbial diversity and composition during the long-term operation. Meiothermus, Rhodanobacter, and Ochrobactrum were the dominant microorganisms in various MBARs.

How does partial substitution of chemical fertiliser with organic forms increase sustainability of agricultural production?

To ensure global food security, agriculture must increase productivity while reducing environmental impacts associated with chemical nitrogen (N) fertilisation. This necessitates towards more sustainable practices such as recycling organic waste to substitute chemical fertiliser N inputs. However, hitherto how such strategy controls the succession of microbial communities and their relationship with crop yields and environmental impacts have not been comprehensively investigated. We conducted a field experiment with vegetable production in China examining partial substitution (25-50%) of chemical fertiliser with organic forms (pig manure or municipal sludge compost) considering key sustainability metrics: productivity, soil health, environmental impacts and microbial communities. We demonstrate that partial organic substitution improved crop yields, prevented soil acidification and improved soil fertility. Treatments also reduced detrimental environmental impacts with lower N₂O emission, N leaching and runoff, likely due to reduced inorganic nitrogen surplus. Microbial communities, including key genes involved in the N cycle, were dynamic and time-dependent in response to partial organic substitution, and were also important in regulating crop yields and environmental impacts. Partial organic substitution increased bacterial diversity and the relative abundance of several specific microbial groups (e.g. Sphingomonadales, Myxococcales, Planctomycetes, and Rhizobiales) involved in N cycling. Additionally, partial organic substitution reduced the number of bacterial ammonia oxidizers and increased the number of denitrifiers, with the proportion of N₂O-reducers being more pronounced, suggesting a mechanism for reducing N₂O emissions. Comprehensive economic cost-benefit evaluation showed that partial organic substitution increased economic benefit per unit area by 37-46%, and reduced agricultural inputs and environmental impacts per unit product by 22-44%. Among them, 50% substitution of pig manure was the most profitable strategy. The study is crucial to policy-making as it highlights the potential advantages of shifting towards systems balancing chemical and organic fertilisers with economic benefits for farmers, reduced environmental damage and an efficient way for organic waste disposal.

The anaerobic oxidation of methane in paddy soil by ferric iron and nitrate, and the microbial communities involved

The anaerobic oxidation of methane (AOM) mediated by microorganisms is a key process in the reduction of methane emissions, and AOM-coupled electron acceptors have been shown to regulate methane emissions into the atmosphere in marine systems. Paddy fields are a significant source of methane and account for 20% of global methane emissions, but the effect of electron acceptors on the methane emission process in flooded paddy fields has been poorly characterized. This study aimed to determine whether the electron acceptors ferric iron and nitrate, and biochar, acting as an electron shuttle, can regulate the AOM process in paddy soil, with or without interaction between biochar and these two electron acceptors. We also aimed to characterize which microorganisms are actively involved. Here, we added ¹³C-labeled CH₄ (¹³CH₄) into anaerobic microcosms to evaluate the role of electron acceptors by measuring the methane oxidation rate and the enrichment of ¹³C-labeled CO₂ (¹³CO₂). We then combined DNA-stable isotope probing with amplicon sequencing to study the active microorganisms. We found for the first time that, in addition to nitrate, ferric iron can also effectively promote AOM in paddy soil. However, there was no significant effect of biochar. Ferric iron-dependent AOM was mainly carried out by iron-reducing bacteria (Geobacter, Ammoniphilus and Clostridium), and nitrate-dependent AOM was mainly by nitrate-reducing bacteria (Rhodanobacter, Paenibacillus and Planococcus). Our results demonstrate that the AOM process, regulated by the electron acceptors ferric iron and nitrate, can alleviate methane emission from paddy soil. The potentially active microorganisms related to electron acceptor reduction may be crucial for this methane sink and deserve further research.

Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes

Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.

The Impacts of Field Management on Soil and Tea Root Microbiomes

Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures.

Pepper root rot resistance and pepper yield are enhanced through biological agent G15 soil amelioration

Pepper root rot is a serious soil-borne disease that hinders pepper production, and efforts are being made to identify biological agents that can prevent and control pepper root rot. Our group recently discovered and produced a biological agent, named G15, which reduces the diversity and richness of fungi and bacteria when applied to pepper fields. In the soil of the G15-treatment condition, the pathogenic fungus Fusarium was inhibited, while the richness of beneficial bacteria Rhodanobacter was increased. Also, the ammonia nitrogen level was decreased in the G15-treatment soil, and the pH, total carbon, and total potassium levels were increased. Compared to the control condition, pepper yield was increased in the treatment group (by 16,680 kg acre^-1). We found that G15 could alter the microbial community structure of the pepper rhizosphere. These changes alter the physical and chemical properties of the soil and, ultimately, improve resistance to pepper root rot and increase pepper yield.

Shift of Dominant Species in Plant Community and Soil Chemical Properties Shape Soil Bacterial Community Characteristics and Putative Functions: A Case Study on Topographic Variation in a Mountain Pasture

Reducing management intensity according to the topography of pastures can change the dominant plant species from sown forages to weeds. It is unclear how changes in species dominance in plant community drive spatial variation in soil bacterial community characteristics and functions in association with edaphic condition. Analysing separately the effects of both plant communities and soil chemical properties on bacterial community is crucial for understanding the biogeographic process at a small scale. In this paper, we investigated soil bacterial responses in five plant communities (two forage and three weed), where >65% of the coverage was by one or two species. The structure and composition of the bacterial communities in the different microbiome were analysed using sequencing and their characteristics were assessed using the Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Firmicutes and Planctomycetes responded only to one specific plant community, and each plant community harboured unique operational taxonomic units (OTUs) at the species level. There were a large percentage of uniquely absent OTUs for specific plant communities, suggesting that a negative effect is critical in the relationship between plants and bacteria. Bacterial diversity indices were influenced more by soil chemical properties than by plant communities. Some putative functions related to C and N recycling including nitrogen fixation were correlated with pH, electrical conductivity (EC) and nutrient levels, and this also implied that some biological functions, such as ureolysis and carbon metabolism, may decline when fertilisation intensity is reduced. Taken together, these results suggest that a shift of dominant species in plant community exerts individual effects on the bacterial community composition, which is different from the effect of soil chemical properties.

Long-Term Fertilization Shapes the Putative Electrotrophic Microbial Community in Paddy Soils Revealed by Microbial Electrosynthesis Systems

Electrotrophs play an important role in biogeochemical cycles, but the effects of long-term fertilization on electrotrophic communities in paddy soils remain unclear. Here, we explored the responses of electrotrophic communities in paddy soil-based microcosms to different long-term fertilization practices using microbial electrosynthesis systems (MESs), high-throughput quantitative PCR, and 16s rRNA gene-based Illumina sequencing techniques. Compared to the case in the unfertilized soil (CK), applications of only manure (M); only chemical nitrogen, phosphorous, and potassium fertilizers (NPK); and M plus NPK (MNPK) clearly changed the electrotrophic bacterial community structure. The Streptomyces genus of the Actinobacteria phylum was the dominant electrotroph in the CK, M, and MNPK soils. The latter two soils also favored Truepera of Deinococcus-Thermus or Arenimonas and Thioalkalispira of Proteobacteria. Furthermore, Pseudomonas of Proteobacteria and Bacillus of Firmicutes were major electrotrophs in the NPK soil. These electrotrophs consumed biocathodic currents coupled with nitrate reduction and recovered 18-38% of electrons via dissimilatory nitrate reduction to ammonium (DNRA). The increased abundances of the nrfA gene for DNRA induced by electrical potential further supported that the electrotrophs enhanced DNRA for all soils. These expand our knowledge about the diversity of electrotrophs and their roles in N cycle in paddy soils and highlight the importance of fertilization in shaping electrotrophic communities.

Assessment of diversity and composition of bacterial community in sludge treatment reed bed systems

Due to their low emission of odours and lack of the need to apply additional chemical agents, sludge treatment reed beds (STRBs) constitute an economically feasible and eco-friendly approach to sewage sludge management. Correctly designed and operated STRBs ensure effective reduction of the dry matter content coupled with the mineralisation of organic compounds. Successful operation of STRBs relies on complex interactions between the plants and microorganisms responsible for the decomposition of organic matter and nutrient cycling. While the biocenoses of wetland systems dedicated to wastewater treatment have been intensively investigated, in the case of sludge treatment applications, there is a deficit of available microbial data. The aim of this study was to explore the diversity and spatial distribution of the bacteria in three distinct STRBs which differ in maturation and feeding patterns. Analyses of the dry mass and organic matter content showed the general trend of the sludge stabilisation processes advancing through the bed depth, with the best performance in the Matured Continuous Feed (MCF) bed being noted. Samples from the MCF bed showed the statistically greatest biodiversity in relation to the other beds. Moreover, increased biodiversity of microorganisms was observed on the surface of the STRBs and the bottom zone of the MCF equipped with a passive aeration system, which proves the application of such solutions in order to enhance the performance of the process. The results of 16S rRNA gene sequencing revealed that Bacteroidetes, Proteobacteria and Firmicutes contributed approximately 80% of all identified sequences read. Network analysis revealed dominant role of Bacteroidetes in the formation of interspecies co-existence patterns. Nitrospira was the most abundant organism responsible for nitrogen metabolism in the STRBs.

Effects of hydraulic loading rate and substrate on ammonium removal in tidal flow constructed wetlands treating black and odorous water bodies

The efficient removal of ammonium nitrogen (NH₄⁺-N) is vital to eliminating black and odorous water bodies. In this work, tidal flow constructed wetlands with gravel (TFCW-G) and with a mixture of zeolite and gravel (TFCW-Z) were set up to treat black and odorous water bodies at different hydraulic loading rates (HLRs). Results showed that zeolite significantly enhanced nitrogen removal, and the maximum NH₄⁺-N removal efficiency of 96.69% was achieved in TFCW-Z at HLR of 3 m·d^-1 with a flooding and drying cycle of 2 h. Zeolite addition changed the microbial community structure and the abundance of nitrification genes. Comammox Nitrospira was the only enriched strain accounting for NH₄⁺-N removal in TFCW-G, while the co-occurrence of comammox Nitrospira and the canonical and potential ammonia-oxidizing bacteria were identified in TFCW-Z. Summarily, high performance, together with low footprint and low maintenance cost, are characteristics that make the TFCW-Z a promising and competitive alternative.

Both artificial root exudates and natural Koelreuteria paniculata exudates modify bacterial community structure and enhance phenanthrene biodegradation in contaminated soils

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants that represent a serious threat to the health of humans and ecosystems. The effects of plant root and artificial root exudates (ARE) on the biodegradation of phenanthrene (PHE) and their impact on soil bacterial community structure was the focus of this work using four treatments for 180 days. Treatments included; control treatment (CK), low concentration of ARE (AREL), high concentration of ARE (AREH), and planting Koelreuteria paniculata saplings (KOE). The diversity and composition of soil bacterial community were analyzed using high-throughput sequencing. The results showed that KOE treatments had the most significant effect on the biodegradation of PHE compared to controls. ARE treatments had the similar effects on the biodegradation of PHE in soil with high efficiency in AREH than AREL. Both KOE and ARE treatments reduced diversity of bacterial community but increased the abundance of PAHs degrading bacterial populations within representative phyla, including Proteobacteria and Firmicutes. During the study, the total bacterial OTUs showed the number of unique genus types initially increased, then lowered in the later stages of the incubation process. Specific bacterial populations enriched by the treatments and supported by the exudates seemed to determine the biodegradation of PHE and not the overall bacterial diversity.

Pathways regulating nitrogen removal in constructed ditch wetlands: effects of different inflow ratios and artificial aeration

Constructed ditch wetland (CDW) is a combination of idle ditch and constructed wetland, which is typically used in rural areas to remove pollutants from domestic wastewater. However, its low total nitrogen (TN) removal remains a pressing issue. To enhance total nitrogen removal, an approach of supplying water at two locations in the CDW at different influent flow ratios, combined with artificial aeration, was proposed to adjust carbon and oxygen distribution in the system. The highest average TN removal was achieved at low influent concentration (CDW4; influent flow ratio 1:2). The removal of TN in winter and spring were 58.93 and 83.26%, respectively. The distribution of carbon sources in the back zone enhanced denitrification. Of the high influent concentration treatments, CDW2 (2:1) achieved 16.97% more TN removal on average compared with CDW1 (3:0), after extra artificial aeration was applied in the front zone. However, nitrification was a limiting step in the system, which became the primary problem preventing pollutant purification. Moreover, nitrifying bacteria abundance was negatively correlated to the influent flow ratio and autotrophic denitrifying bacterial abundance was positively correlated to the influent flow ratios. Graphical abstract.

Autotrophic Fixed-Film Systems Treating High Strength Ammonia Wastewater

The aim of the study was enrichment of nitrifying bacteria and to investigate the potential of autotrophic fixed-film and hybrid bioreactors to treat high strength ammonia wastewater (up to 1,000 mg N/L). Two types of fixed-film systems [moving bed biofilm reactor (MBBR) and BioCord^TM] in two different configurations [sequencing batch reactor (SBR) and a continuous stirred tank reactor (CSTR)] were operated for 306 days. The laboratory-scale bioreactors were seeded with activated sludge from a municipal wastewater treatment plant and fed synthetic wastewater with no organics. Strategies for acclimation included biomass reseeding (during bioreactor start-up), and gradual increase in the influent ammonia concentration [from 130 to 1,000 mg N/L (10% every 5 days)]. Stable ammonia removal was observed up to 750 mg N/L from 45 to 145 days in the MBBR SBR (94-100%) and CSTR (72-100%), and BioCord^TM SBR (96-100%) and CSTR (92-100%). Ammonia removal declined to 87% ± 6, in all bioreactors treating 1,000 mg N/L (on day 185). Following long-term operation at 1,000 mg N/L (on day 306), ammonia removal was 93-94% in both the MBBR SBR and BioCord^TM CSTR; whereas, ammonia removal was relatively lower in MBBR CSTR (20-35%) and BioCord^TM SBR (45-54%). Acclimation to increasing concentrations of ammonia led to the enrichment of nitrifying (Nitrosomonas, Nitrospira, and Nitrobacter) and denitrifying (Comamonas, OLB8, and Rhodanobacter) bacteria [16S rRNA gene sequencing (Illumina)] in all bioreactors. In the hybrid bioreactor, the nitrifying and denitrifying bacteria were relatively more abundant in flocs and biofilms, respectively. The presence of dead cells (in biofilms) suggests that in the absence of an organic substrate, endogenous decay is a likely contributor of nutrients for denitrifying bacteria. The nitrite accumulation and abundance of denitrifying bacteria indicate partial denitrification in fixed-film bioreactors operated under limited carbon conditions. Further studies are required to assess the contribution of organic material produced in autotrophic biofilms (by endogenous decay and soluble microbial products) to the overall treatment process. Furthermore, the possibility of sustaining autotrophic nitrogen in high strength waste-streams in the presence of organic substrates warrants further investigation.

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO₃ for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

Seasonal Variation in the Rhizosphere and Non-Rhizosphere Microbial Community Structures and Functions of Camellia yuhsienensis Hu

Camellia yuhsienensis Hu, endemic to China, is a predominant oilseed crop, due to its high yield and pathogen resistance. Past studies have focused on the aboveground parts of C. yuhsienensis, whereas the microbial community of the rhizosphere has not been reported yet. This study is the first time to explore the influence of seasonal variation on the microbial community in the rhizosphere of C. yuhsienensis using high-throughput sequencing. The results showed that the dominant bacteria in the rhizosphere of C. yuhsienensis were Chloroflexi, Proteobacteria, Acidobacteria, Actinobacteria, and Planctomycetes, and the dominant fungi were Ascomycota, Basidiomycota, and Mucoromycota. Seasonal variation has significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. A significant increase in bacterial abundance and diversity in the rhizosphere reflected the root activity of C. yuhsienensis in winter. Over the entire year, there were weak correlations between microorganisms and soil physiochemical properties in the rhizosphere. In this study, we found that the bacterial biomarkers in the rhizosphere were chemoorganotrophic Gram-negative bacteria that grow under aerobic conditions, and fungal biomarkers, such as Trichoderma, Mortierella, and Lecanicillium, exhibited protection against pathogens in the rhizosphere. In the rhizosphere of C. yuhsienensis, the dominant functions of the bacteria included nitrogen metabolism, oxidative phosphorylation, glycine, serine and threonine metabolism, glutathione metabolism, and sulfur metabolism. The dominant fungal functional groups were endophytes and ectomycorrhizal fungi of a symbiotroph trophic type. In conclusion, seasonal variation had a remarkable influence on the microbial communities and functions, which were also significantly different in the rhizosphere and non-rhizosphere of C. yuhsienensis. The rhizosphere of C. yuhsienensis provides suitable conditions with good air permeability that allows beneficial bacteria and fungi to dominate the soil microbial community, which can improve the growth and pathogen resistance of C. yuhsienensis.

Iron scraps enhance simultaneous nitrogen and phosphorus removal in subsurface flow constructed wetlands

In rural domestic wastewater treatment using subsurface constructed wetland system (SFCWs), the lack of a carbon source for denitrification and limited phosphorus uptake are responsible for low removal of nitrogen and phosphorus, and a suitable substrate is therefore, necessary. Iron is an important component in nitrogen and phosphorus biogeochemical cycles. Few studies have addressed the application of iron in SFCWs. Therefore, we constructed SFCWs that used iron scraps as a substrate. Enhanced nitrification, denitrification and removal of phosphorus were observed. The large proportion of nitrite-oxidising bacteria present in CWs with iron scraps (CW-T) compared to gravel beds indicated that iron may enhance ammonium (NH₄⁺) oxidation. More nitrate-reducing bacteria related to Fe and autotrophic denitrifying bacteria were discovered in the back zone of CW-T and these enhanced denitrification process. Phosphate (PO₄^3-) reacted with ferrous ion (Fe²⁺) and ferric ion (Fe³⁺) to generate the precipitant. Moreover, Fe³⁺ reacted with water to generate iron oxide (FeOOH) that had a large adsorption capacity for phosphorus. After six months of operation, average NH₄⁺-N, total nitrogen and total phosphorus removal rates were 66.98 ± 13.37 %, 71.26 ± 13.57 % and 93.54 ± 6.64 %, respectively. Iron scraps can potentially be utilised in SFCWs in rural domestic wastewater treatment.

Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest

Nitrous oxide (N₂O) is an important greenhouse gas contributing to global climate change. Emissions of N₂O from acidic forests are increasing rapidly; however, little is known about the mechanisms driving these emissions. We analyzed soil samples from a high N₂O emission area (HEA, 224-601 μg N m^-2 h^-1) and an adjacent low emission area (LEA, 20-30 μg N m^-2 h^-1) of a highly acidified forest. HEA showed similar carbon and nitrogen (N) pools and microbial biomass to LEA, but significantly higher moisture and extractable nutrients than LEA did. GeoChip 4 detected 298 gene families (unadjusted P < 0.05; 94, adjusted P < 0.05) showing significantly different structures between HEA and LEA. Both areas had highly diverse N cycling functional genes. However, HEA had higher relative abundances of nor, P450nor, and archaeal nitrifier nirK, which provided evidence for the importance of denitrifiers in N₂O emission. HEA also showed significantly higher relative abundances of lignin- and cellulose-degrading genes, oxygen-limitation-response genes and denitrifier ppk, but lower abundances of N- and phosphorus (P) -limitation-response genes especially denitrifier pstS, corresponding to the higher moisture and extractable nutrients conducive to denitrification. The moisture, extractable nutrients and pH explained over 50% variation in microbial communities, and extractable P appeared as the key factor driving community variation and consequently regulated N₂O production. CAPSULE ABSTRACT: N₂O emission in highly acidified forest soils was related to the diverse N functional genes, especially denitrification genes, and was affected by soil properties.

Microbiota in Waterlogged Archaeological Wood: Use of Next-Generation Sequencing to Evaluate the Risk of Biodegradation

Waterlogged archaeological wood (WAW) is considered a precious material, first-hand account of past civilizations. Like any organic material, it is subjected to biodegradative action of microorganisms whose activity could be particularly fast and dangerous during the phases of excavation, storage and restoration. The present work aimed to characterize the microorganisms present in WAW during these tricky periods to evaluate the biological risk it is exposed to. The bacterial and fungal communities inhabiting woods coming from two archaeological sites (Pisa and Naples) were investigated through Next-Generation Sequencing (NGS). High-throughput sequencing of extracted DNA fragments was performed using the reversible terminator-based sequencing chemistry with the Illumina MiSeq platform. The analyses revealed that the two archaeological sites showed distinct richness and biodiversity, as expected. In all the WAWs, the bacterial community harbored mainly Proteobacteria, whereas Bacteroidetes was well represented only in Naples communities and taxa belonging to the phyla Chloroflexi only in the Pisa site. Concerning the fungal community, the two sites were dominated by different phyla: Ascomycota for Naples samples and Basidiomycota for Pisa. Interestingly, most of the identified bacterial and fungal taxa have cellulolytic or ligninolytic ability. These results provide new and useful background information concerning the composition of WAW microbiota and the threat it represents for this precious material.

Influence of Resistance-Inducing Chemical Elicitors against Pine Wilt Disease on the Rhizosphere Microbiome

Pine wilt disease (PWD) caused by Bursaphelenchus xylophilus is a major threat to pine forests worldwide. Induction of resistance is a promising and safe management option that should be investigated in relation to its possible influence on the pine tree ecosystem, including the surrounding microbial communities. In this study, two main resistance-inducing chemical elicitors, methyl salicylic acid (MeSA) and acibenzolar-s-methyl (ASM), were tested for their control efficiency against PWD and their influence on the rhizosphere microbial composition. Foliar treatment of pine seedlings with the chemical elicitors resulted in a reduction in PWD severity, with ASM showing better control efficacy, reaching up to 73% compared to the untreated control. Moreover, bacterial community analysis of the rhizosphere revealed significant changes in several microbial taxa that were present at low relative abundance. In particular, ASM treatment resulted in a significant increase in specific microbial taxa, including members of the Rhodanobacter, Devosia, Bradyrhizobium, Acidibacter, Mesorhizobium, and Hyphomicrobium genera, which are known to play ecological and plant growth-promoting roles. Furthermore, chitinolytic bacteria were shown to be reduced in response to treatment with both MeSA and ASM. Altogether, the present findings demonstrate the occurrence of significant alterations in several ecologically important microbial taxa after treatment with resistance-inducing chemicals. As compared to MeSA treatment, ASM treatment was more effective at suppressing PWD and resulted in more beneficial changes in rhizosphere microbial composition.

Spatiotemporal distribution and interaction of denitrifying functional genes in a novel DAS-NUA biofilter used for groundwater nitrate treatment

A newly combined dewatered alum sludge (DAS) and neutralized used acid (NUA) biofilter has been constructed and investigated recently, aiming for improving nitrate (NO₃^--N) removal in simulated groundwater and exploring the spatiotemporal distribution of nirS and nosZ. The biofilter achieved 81.54% and 13.6 g N/ (m³ d) removal efficiency of NO₃^--N during the stabilization period. Spatiotemporal distributions of diversity and composition of nirS and nosZ varied approximately in two media with depths and time. Both DAS and NUA played important roles in attenuating nitrate because of predominant denitrifying genera functions, and the core differences were Rhodanobacter and Rhodobacter in DAS while Halomonas, Pseudogulbenkiania, and Cupriavidus in NUA. Acting as the strongly correlated genera, Magnetospirillum and Halomonas had a significantly positive or negative correlation with other dominant genera. Positive correlations existed among COD, TN, NO₃^--N, NO₂^--N, and both nirS and nosZ in the DAS filter, whereas the correlations were negative in the NUA filter. Particularly, the effluent concentration of NO₃^--N had a significantly negative correlation with the relative abundance of Rubrivivax and Pseudomonas. These results could be useful in adjusting the denitrification of nitrogen contaminants at the genetic level, especially in mitigating the influence of discharge of NO₃^--N on the process of groundwater restoration.

Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater

The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and to determine their taxonomy and the physiological characteristics responsible for their adaptation to this environment. Groundwater samples contained high concentrations of acetate, oxalate, nitrate, and sulfate, as well as radionuclides. High-throughput sequencing and analysis of the clone libraries revealed lower microbial diversity in the most strongly contaminated groundwater and a predominance of bacteria of the genera Polynucleobacter, Pusillimonas, Candidatus Pelagibacter, and of the candidate phylum Parcubacteria; these groups include species with an ultra small cell size. Archaeal sequences in the libraries belonged to ammonium oxidizers of the phylum Thaumarchaeota and methanogens of the phylum Euryarchaeota. Pure cultures of obligate and facultative ultramicrobacteria belonging to the genera Chryseobacterium, Microbacterium, Salinibacterium, Pusillimonas, Roseomonas, and Janibacter were isolated from water samples. In genomes of Pusillimonas and Roseomonas strains the genes associated with nitrate reduction, resistance to heavy metals and metalloids were revealed. Several isolates are able to participate in the geochemical process of nitrate conversion to N2 using acetate; this results in decreasing redox potential, which in turn may stimulate radionuclide reduction and decrease radionuclide migration in groundwater.

Soil Microbiota of Dystric Cambisol in the High Tatra Mountains (Slovakia) after Windthrow

There has been much more damage to forests in the Slovak Republic in the second half of the 20th century than to other European countries. Forested mountain massifs have become a filter of industrial and transportation emissions from abroad, as well as from domestic origins. There are not only acidic deposits of sulphur and heavy metals present in forest soils, but other additional environmental problems, such as climate change, storms, fires, floods, droughts, are worsening the situation. Therefore, forest terrestrial ecosystems are becoming more vulnerable due to changes in natural and environmental conditions. In the High Tatra Mountains in Slovakia, which are protected as a national park, four internationally monitored localities were established after the windthrow disaster in 2004 and fire in 2005: REF, with intact forest; EXT, with extracted wood mass; NEX, with non-extracted wood mass; and FIR, the burnt locality. Soils from these localities were microbiologically analysed with special attention to fungi. Bacterial microbiota detected by high-throughput sequencing showed the prevalence of the genera Acidothermus, Mycobacterium, and Nocardia, and a very low presence of the genera Acidibacter, Burkholderia-Paraburkholderia, Optitus and the uncultured genus Desulfurellaceae H16 in the soil sample from the burnt locality when compared with the unburned sites. Additionally, soil mycocoenoses showed a low similarity between the locality with an intact forest ecosystem and the localities with extracted (REF–EXT) and non-extracted (REF–NEX) wood mass. There was no similarity with the burnt locality (FIR), where heat-resistant fungi dominated. It was shown that the windthrow disaster and subsequent extraction or non-extraction of wood mass did not affect the soil microbial communities or their development. On the other hand, the influence of fire was significant.

The effects of Rhodopseudomonas palustris PSB06 and CGA009 with different agricultural applications on rice growth and rhizosphere bacterial communities

In recent years, the photosynthetic bacteria have been used widely in agriculture, but the effects of different agricultural applications on crop rhizosphere microorganism and crops are lack. In this study, we provide new insights into the structure and composition of the rice root-associated microbiomes as well as the effect on crop of the Rhodopseudomonas palustris(R. palustris) PSB06 and CGA009 at the rice seedling stage with seed immersion and root irrigation. Compare with CK group, the length of stem, the peroxidase (POD), and superoxide dismutase (SOD) activities in PSB06 treatment group was significantly higher, while the length of stem in CGA009 treatment group was significantly higher. The POD and SOD activities in CGA009 treatment groups only were higher slightly than the CK group. In the study, the dominant phyla were Proteobacteria (51.95–61.66%), Bacteroidetes (5.40–9.39%), Acidobacteria (4.50–10.52%), Actinobacteria (5.06–8.14%), Planctomycetes (2.90–4.48%), Chloroflexi (2.23–5.06%) and Firmicutes (2.38–7.30%), accounted for 87% bacterial sequences. The principal coordinate analysis (pCoA) and mantel results showed the two application actions of R. palustris CGA009 and PSB06 had significant effects on rice rhizosphere bacterial communities (p < 0.05). The PSB06 can significantly promote the rice growth and enhance stress resistance of rice at the seedling stage, while the R. palustris CGA009 has no significant effect on rice. Dissimilarity test and canonical correspondence analysis (CCA) results showed that the TN and pH were the key factors affecting rice rhizosphere bacterial community in the seedling stage. This study will provide some guidance advices for the study of the microecological regulation of photosynthetic bacteria on crops.