Denitrification is a common feature among members of the genus Bacillus

Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Complete genome sequence of Bacillus subtilis NA05 (=NBRC 116153), a phosphate-solubilizing bacterium isolated from crop field soil

We report the complete genome sequence of the phosphate-solubilizing bacterium Bacillus subtilis NA05 (=NBRC 116153), consisting of a circular chromosome of ~3.8 M bp and two circular plasmids. The data presented here provide further insight into the genetic and functional potential of B. subtilis and the mechanism of phosphate solubilization.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone

The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.

Endosymbiotic bacteria within the nematode-trapping fungus Arthrobotrys musiformis and their potential roles in nitrogen cycling

Endosymbiotic bacteria (ESB) have important effects on their hosts, contributing to its growth, reproduction and biological functions. Although the effects of exogenous bacteria on the trap formation of nematode-trapping fungi (NTF) have been revealed, the effects of ESB on NTF remain unknown. In this study, we investigated the species diversity of ESB in the NTF Arthrobotrys musiformis using high-throughput sequencing and culture-dependent approaches, and compared bacterial profiles to assess the effects of strain source and culture media on A. musiformis. PICRUSt2 and FAPROTAX were used to predict bacterial function. Our study revealed that bacterial communities in A. musiformis displayed high diversity and heterogeneity, with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the dominant phyla. The ESB between A. musiformis groups isolated from different habitats and cultured in the same medium were more similar to each other than the other groups isolated from the same habitat but cultured in different media. Function analysis predicted a broad and diverse functional repertoire of ESB in A. musiformis, and unveiled that ESB have the potential to function in five modules of the nitrogen metabolism. We isolated nitrogen-fixing and denitrifying bacteria from the ESB and demonstrated their effects on trap formation of A. musiformis. Among seven bacteria that we tested, three bacterial species Bacillus licheniformis, Achromobacter xylosoxidans and Stenotrophomonas maltophilia were found to be efficient in inducing trap formation. In conclusion, this study revealed extensive ESB diversity within NTF and demonstrated that these bacteria likely play important roles in nitrogen cycling, including nematode trap formation.

Stable isotope probing reveals compositional and functional shifts in active denitrifying communities along the soil profile in an intensive agricultural area

Denitrifying microbial communities in the vadose zone play an essential role in eliminating the nitrate leached from agricultural practices. This nitrate could otherwise contaminate groundwater and threaten public health. Here, we utilized stable isotope probing combined with amplicon sequencing and functional gene quantification to inspect the composition and function of heterotrophic denitrifying microorganisms along a 9-m soil profile in an intensive agricultural area. Dramatic differences in the composition of the active denitrifiers were uncovered between the surface soil and deep layers of the vadose zone. The main denitrifying bacterial taxa identified from 13C-DNA fractions were Pseudomonadaceae (Pseudomonas), Rhodocyclaceae (Azoarcus), and Burkholderiaceae in the surface soil (0-0.2 m), and were Pseudomonadaceae (Pseudomonas), Burkholderiaceae, Bacillaceae (Bacillus), and Paenibacillaceae (Ammoniphilus) in the deep layers (0.5-9.0 m). Analysis of the functional genes (nirS, nirK, and nosZ) in isotope-labeled DNA revealed an upward nos/nir ratio with increasing soil depth, which may account for the higher nitrous oxide emission potential in the surface soil, as compared to the deeper sand-rich, low organic carbon layers. This study improves our understanding of active denitrifying microbes in the vadose zone and helps in developing techniques to reduce nitrate pollution in groundwater.

Responses of soil bacterial and fungal denitrification and associated N2O emissions to organochloride pesticide

The extensive application of organochloride pesticides in agriculture has raised concerns about their potential negative impacts on soil microbial denitrification and associated N2O emissions. However, most studies have primarily focused on bacteria, and the contribution of fungi to N2O emissions and their response to organochloride pesticides have often been overlooked. In this study, 15N tracing combined with the respiration inhibition method was applied to examine the impacts of chlorothalonil on both fungal and bacterial denitrification. The results demonstrated that fungal N2O emissions dominated in the absence of chlorothalonil, accounting for 73 % of total N2O emissions. Chlorothalonil inhibited fungal and bacterial denitrification via different mechanisms and altered the main pathways of soil N2O emissions. Amplicon sequencing analyses indicated that chlorothalonil significantly reduced the abundances of N2O-producing fungi owing to its fungicidal effect and fungal N2O emissions significantly dropped. Molecular biological analyses revealed that chlorothalonil induced lower electron generation, transport, and consumption efficiencies, which led to the inhibition of denitrifying enzymes in bacteria. Bacterial N2O emissions dramatically increased and became the dominant source. These findings provide insights into the mechanisms by which N2O emissions from fungal and bacterial denitrification are influenced by chlorothalonil.

Improvement of water quality with probiotics inclusion during simulated transport of Yellowfin Seabream Acanthopagrus latus larvae

OBJECTIVE

The expansion of marine aquaculture requires the shipment of early life stages from hatcheries to breeding centers. Thus, maintaining water quality parameters during transportation is crucial. This experiment investigated the effects of a commercial probiotic mixture (PM) (consisting of Bacillus licheniformis, Bacillus subtilis, Pediococcus acidilactici, and Lactobacillus acidophilus with a total count of 107  CFU/g) on water quality, bacterial population, and the survival of larvae of Yellowfin Seabream Acanthopagrus latus during a 24-h simulated transportation experiment.

METHODS

To simulate transportation, purified seawater was used as a control and purified seawater supplemented with 3 g of PM was used as the PM48 treatment. For the PM48 treatment, 3 g of PM was added to 1 L of purified seawater and mixed with 200 L of purified seawater 48 h prior to the main experiment.

RESULT

The use of probiotics resulted in an increase in larval survival up to 93.3% compared with 89.85% in the control group. Initial sampling showed a statistically significant difference inNO 2 - levels between the control and PM48 treatments. After transportation, the pH of the control treatment showed a significant decrease. The total number of bacteria and the total number of Vibrio spp. in water and fish larvae showed that within 48 h, the probiotics became the dominant population in the PM48 treatment. After 24 h, water samples and larvae from the control treatment showed a significant increase in bacterial load.

CONCLUSION

The results showed that probiotics can play a significant role in maintaining biotic and abiotic water quality parameters, leading to a better survival rate of larvae during transportation. These findings represent an important step in improving long-distance transport protocols.

The evolution of nitrogen transformation microorganism consortium under continued manganese domestication conditions

Manganese redox-stimulated bioremediation of nitrogen wastewater is receiving increasing attention. However, the nitrogen metabolic capacity and community evolution during manganese-mediated nitrogen transformation process under continued manganese domestication conditions are ambiguous. In this study, nitrogen- metabolizing microbial consortiums were incubated with synthesized Mn-humic acid complex (Mn-HA) for one month (M1), three months (M2) and six months (M3), respectively. During the Mn-HA incubation period, Bio-MnOx accompanying with bacterial consortiums (MnOB consortiums) with high TIN removal capacities were obtained. The TIN removal rates in M1, M2 and M3 were 0.220, 1.246 and 4.237 mg·L-1·h-1, respectively, which were 15.961, 90.006 and 1550.006 times higher than CK (Control Check group, no Mn-HA added group) (0.014 mg·L-1·h-1), respectively. Functional genes (amoA, AMX and narG) were most abundant in M3, which was associated with the highest nitrogen removal rate in M3. MnOB1 (bacterial consortium in M1), including Geobactor, Geothrix, Anaeromyxobacter and Bacillus, may be responsible for the Mnammox-NDMO (MnOx reduction coupled to ammonium oxidation - nitrate/nitrite-dependent low-valent Mn oxidation) process. MnOB3 (bacterial consortium in M2) enriched nitrifying bacteria Ellin6067, and denitrifying bacteria Denitratisoma, which dominated nitrogen transformation. MnOB6 (bacterial consortium in M3) enriched denitrifiers Denitratisoma, nitrifiers Ellin6067 and potential anammox bacteria SM1A02, Candidatus_Brocadia. Combined with the reduced abundance of Nitrospirae, a short-cut partial nitrification and denitrification (PND) or partial nitrification, denitrification and anammox (PNDA) could occurred in M2 and M3. It is suggested that community may have evolved into an energetically efficient short-cut nitrification, denitrification and anammox consortium to replace the full-range nitrification and denitrification community in M1 and CK under the continued manganese domestication conditions. Enhanced metabolic pathways of hydroxylamine oxidation and the nitric oxide reduction may confirm that PND or PNDA occurred in M2 and M3.

Pollutants reduction via artificial mixing in a drinking water reservoir: Insights into bacterial metabolic activity, biodiversity, interactions and co-existence of core genera

Endogenous pollution due to long periods of hypolimnetic anoxia in stratified reservoirs has become a worldwide concern, which can threaten metabolic activity, biodiversity, water quality security, and ultimately human health. In the present study, an artificial mixing system applied in a drinking water reservoir was developed to reduce pollutants, and the biological mechanism involved was explored. After approximately 44 days of system operation, the reservoir content was completely mixed resulting in the disappearance of anoxic layers. Furthermore, the metabolic activity estimated by the Biolog-ECO microplate technique and biodiversity was enhanced. 16S rRNA gene sequencing indicated a great variability on the composition of bacterial communities. Co-occurrence network analysis showed that interactions among bacteria were significantly affected by the proposed mixing system. Bacteria exhibited a more mutualistic state and >10 keystone genera were identified. Pollutants, including nitrogen, phosphorus, organic matter, iron, and manganese decreased by 30.63-80.15 %. Redundancy discriminant analysis revealed that environmental factors, especially the temperature and dissolved oxygen, were crucial drivers of the bacterial community structure. Furthermore, Spearman's correlation analysis between predominant genera and pollutants suggested that core genus played a vital role in pollutant reduction. Overall, our findings highlight the importance and provide insights on the artificial mixing systems' microbial mechanisms of reducing pollutants in drinking water reservoirs.

Influence of C/N ratio and ammonia on nitrogen removal and N2O emissions from one-stage partial denitrification coupled with anammox

The development of low carbon treatment processes is an important issue worldwide. Partial denitrification coupled with anammox (PD/A) is a novel strategy to remove nitrogen and reduce N2O emissions. The influence of C/N ratio and NH4+ concentration on nitrogen removal and N2O emissions was investigated in batch reactors filled with PD/A coupled sludge. A C/N ratio of 2.1 was effective for nitrogen removal and N2O reduction; higher ammonia concentration might make anammox more active and indirectly reduce N2O emissions. Long-term operation further confirmed that a C/N ratio of 2.1 resulted in a minimum effluent N2O concentration (mean value of 0.94 μmol L-1); as the influent NH4+ concentration decreased to 50 mg L-1 (NH4+-N/NO3--N: 1), the nitrogen removal rate increased to 82.41%. Microbial analysis showed that anammox bacteria (Candidatus Jettenia and Ca. Brocadia) were enriched in the PD/A system and Ca. Brocadia gradually dominated the anammox community, with the relative abundance increasing from 1.69% to 18.44% between days 97 and 141. Finally, functional gene analysis indicated that the abundance of nirS/K and hao involved in partial denitrification and anammox, respectively, increased during long-term operation of the reactor; this change benefitted nitrogen metabolism in anammox, which could indirectly reduce N2O emissions.

Enhanced nitrogen removal of micropolluted source waterbodies using an iron activated carbon system with siliceous materials: Insights into metabolic activity, biodiversity, interactions of core genus and co-existence

Aerobic denitrification technology can effectively abate the nitrogen pollution of water source reservoirs. In this study, 40% siliceous material was used as the carrier to replace the activated carbon in Fe/C material to enhance denitrification and purify water. The removal efficiency of new material for target pollutants were nitrate nitrogen (95.68%), total phosphorus (68.23%) and chemical oxygen demand (46.20%). Aerobic denitrification of water samples and anaerobic denitrification of sediments in three systems jointly assisted nitrogen removal. In a reactor with new material, diversity and richness of denitrifying bacterial communities were enhanced, and the symbiotic structure of aerobic denitrifying bacteria was more complex (Bacillus and Mycobacteria as the dominant bacteria); the microbial distribution better matched the Zif and Mandelbrot models. This system significantly increased the abundance of key enzymes in water samples. The new material effectively removed pollutants and represents a promising and innovative in-situ remediation method for reservoirs.

Long-term effective remediation of black-odorous water via regulating calcium nitrate sustained-release

Nitrate addition is reported as a cost-effective method for remediating black-odorous water, which is mainly induced by the deficiency of electron acceptor. However, excessive release of nitrate and lack of long-term effectiveness significantly limited the application of direct nitrate dosing technology. Herein, for remediating black-odorous water, we constructed a nitrate sustained-release ecological concrete (ecoN-concrete), in which calcium nitrate (Ca(NO3)2) was dosed into concrete block to regulate the release of nitrate. The results showed that chemical oxygen demand (COD), turbidity, ammonia, phosphate, and sulfate were significantly removed in an ecoN-concrete-contained reactor fed with black-odorous water, and its removal efficiency was largely dependent on Ca(NO3)2 dosage. Meanwhile, the released nitrate was lower than 25% of its total dosage and nitrite was lower than 1.5 mg/L during 14 days remediation. After three recycles, the removal efficiencies of COD and turbidity by using ecoN-concrete were still more than 85%, indicating an excellent nitrate sustained-release performance of ecoN-concrete, which can be applied for preventing water re-blackening and re-stinking. Further investigation illustrated that the ecoN-concrete (1) decreased the abundance of Desulfovibrio, Desulfomonile, and Desulforhabdus in the phylum of Desulfobacterota to alleviate the odorous gas production and (2) significantly increased the abundance of Bacillus and Thermomonas, which utilized the released-nitrate for consuming organic matters and ammonia. This study provided an artful Ca(NO3)2 dosing strategy and long-term effective method for black-odorous water remediation.

Understanding the risk of using herbicides for tree root removal into wastewater treatment plant performance

Adding herbicides to sewer lines, a common practice for controlling root intrusion in sewer pipes, may adversely impact downstream wastewater treatment by inhibiting nitrification and denitrification performance. This study investigated the effects of herbicides, namely diquat, triclopyr, and 2-methyl-4-chlorophenoxyacetic acid (MCPA)-dicamba, on these processes. Various parameters were monitored, including oxygen uptake rate (OUR), nutrients (NH₃-N, TP, NO₃-N, and NO₂-N), chemical oxygen demand (COD), and herbicide concentrations. It was found that nitrification was not affected by OUR in the presence of each herbicide at various concentrations (1, 10, and 100 mg L^-1). Additionally, MCPA-dicamba at various concentrations demonstrated minimal inhibition in the nitrification process compared to diquat and triclopyr. COD consumption was not affected by the presence of these herbicides. However, triclopyr significantly inhibited NO₃-N formation in the denitrification process at various concentrations. Similar to nitrification process, both COD consumption and herbicide reduction concentration were not affected by the presence of herbicides during the denitrification process. Adenosine triphosphate measurements showed minimal impact on nitrification and denitrification processes when herbicides were present in the solution up to a concentration of 10 mg L^-1. Tree root kill efficiency experiments were performed on Acacia melanoxylon. Considering the performance on nitrification and denitrification process, diquat emerged as the best herbicide option (concentration of 10 mg L^-1), with a 91.24% root kill efficiency.

Manganese-mediated ammonium removal by a bacterial consortium from wastewater: Experimental proof and biochemical mechanisms

Manganese-redox-mediated nitrogen transformation is promising for ammonium wastewater treatment. However, due to the limited contact between insoluble Mn and the microbe, extracellular electron transfer (EET) inefficiencies become a technical bottleneck in the technical practical application. To overcome this obstacle, humic acid (HA) was introduced to synthesize manganese-humic acid complex (Mn-HA) to increase Mn solubility. The TIN (Total Inorganic Nitrogen) removal rate constant k was 3.18, 1.08, 3.56, 1.13 and 1.05 times higher than CK (Control group) at 10, 15, 20, 40 and 60 mg/L influent nitrate in the MH group, respectively. Mn-HA was inferred to stimulated the nitrogen removal by providing more reaction active sites, bridging Mn-O bonds to transfer electrons and playing a redox role in the respiratory chain. A Mnammox-NDMO (manganese oxide reduction-coupled ammonium oxidation - nitrate/nitrite- dependent manganese oxidation) bacteria consortium was enriched in MH group, containing Mnammox bacteria Geothrix, Geobacter and NDMO bacteria Pseudomonas and Bacillus.

Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments

Epilithic biofilms colonising outdoor stone monuments can intensify the deterioration processes of the stone materials and pose great challenges to their protection. In this study, biodiversity and community structures of the epilithic biofilms colonising the surfaces of five outdoor stone dog sculptures were characterised by high-throughput sequencing. Although they are exposed to the same envrionment in a small yard, the analysis of their biofilm populations revealed high biodiversity and species richness as well as great differences in community compostions. Interestingly, populations responsible for pigment production (e.g., Pseudomonas, Deinococcus, Sphingomonas and Leptolyngbya) and for nitrogen (e.g., Pseudomonas, Bacillus, and Beijerinckia) and sulfur cycling (e.g., Acidiphilium) were the core common taxa in the epilithic biofilms, suggesting the potential biodeterioration processes. Furthermore, significant positive corrolections of metal elements rich in stone with biofilm communities showed that epilithic biofilms could take in minerals of stone. Importantly, geochemical properties of soluble ions (higher concentration of SO₄^2- than NO₃^-) and slightly acidic micro-environments on the surfaces suggest corrosion of biogenic sulfuric acids as a main mechanism of biodeterioration of the sculptures. Interestingly, relative abundacne of Acidiphilium showed a positive correlation with acidic micro-environments and SO₄^2- concentrations, implying they could be an indicator of sulfuric acid corrosion. Together, our findings support that micro-environments are inportant to community assembly of epilithic biofilms and the biodeterioration processes involved.

Efficient nitrogen removal through coupling biochar with zero-valent iron by different packing modes in bioretention system

Three kinds of bioretention were designed to explore the effects of zero-valent iron (ZVI) and biochar on the nitrogen removal performance and to seek a more reasonable packing method in this study. The results showed that the effluent removal rates of nitrate, ammonium and total nitrogen were 53.30 ± 12.68%, 98.41 ± 0.38% and 64.03 ± 8.72% respectively in Bioretention-3 during the rainfall events, while the nitrate concentration decreased gradually with the increase of drying time. According to the batch experiment, it was found that zero-valent iron could release continuously and stably in Bioretention-3 and Bioretention-1 due to the interception effect of biochar on dissolved oxygen. In addition, biochar in soil layer could protect zero-valent iron from excessive oxidation while biochar in the substrate layer could release organic matter to promote heterotrophic denitrification. Microbial community analysis showed that the dominant phyla were Proteobacteria (20.92-40.81%) and Actinobacteriota (9.89-24.54%). The dominant nitrifying genera was Nitrospira while there were also aerobic denitrifying bacteria (Sphingomonas, Bradyrhizobium and Chryseolinea, etc.) in soil layer. In the substrate layer, there was more ferrous iron-mediated autotrophic denitrification process (Thiobacillus, Geobacter and Denitratisoma, etc.) in Bioretention-1 and Bioretention-3 while a larger proportion of Dissimilatory Nitrate Reduction to Ammonium process (DNRA) (Bacillus, Desulfovibrio and Pseudomonas, etc.) in Bioretention-2. In general, this study showed that biochar addition in soil coupled with mixing zero-valent iron and biochar as substrate layer was a more stable and efficient design through various aspects of evidence. It provides a new way for how to use zero-valent iron and biochar to improve nitrogen removal capacity in stormwater management.

Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov

The genus Agrobacterium was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the Rhizobiaceae family. Recently we have isolated two closely related strains, LMG 31531^T and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. A. arsenijevicii KFB 330^T and A. fabacearum LMG 31642^T showed the highest 16S rRNA similarity (98.9 %), followed by A. nepotum LMG 26435^T (98.7 %). A clear genomic feature that distinguishes LMG 31531^T and LMG 31532 from other Agrobacterium species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI > 85 %) and 16S rRNA gene sequence similarity (>96 %) when compared to other members of the genus confirm the position of these two strains as part of the Agrobacterium genus. They are therefore described as Agrobacterium divergens sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus.

A strategy for nitrogen conversion in aquaculture water based on poly-γ-glutamic acid synthesis

Ammonia and nitrite are nitrogenous pollutants in aquaculture effluents, which pose a major threat to the health of aquatic animals. In this study, we developed a nitrogen conversion strategy based on synthesis of poly-γ-glutamic acid (γ-PGA) by Bacillus subtilis NX-2. The nitrogen removal efficiency of NX-2 was closely related to synthesizing γ-PGA, and was positively correlated with the inoculum level. The degradation rates of ammonia nitrogen and nitrite at 10⁴ CFU/mL were 84.42 % and 62.56 %, respectively. Through adaptive laboratory evolution (ALE) experiment, we obtained a strain named ALE 5 M with ammonia degradation rate of 98.03 % and nitrite of 93.62 % at the inoculum level of 10⁴ CFU/mL. Transcriptome analysis showed that the strain was more likely to produce γ-PGA after ALE. By enzyme activity and qPCR analysis, we confirmed that ALE 5 M degraded ammonia nitrogen through γ-PGA synthesis, which provided a new way for nitrogen removal in aquaculture water.

Nitrate as an alternative electron acceptor destabilizes the mineral associated organic carbon in moisturized deep soil depths

Numerous studies have investigated the effects of nitrogen (N) addition on soil organic carbon (SOC) decomposition. However, most studies have focused on the shallow top soils <0.2 m (surface soil), with a few studies also examining the deeper soil depths of 0.5-1.0 m (subsoil). Studies investigating the effects of N addition on SOC decomposition in soil >1.0 m deep (deep soil) are rare. Here, we investigated the effects and the underlying mechanisms of nitrate addition on SOC stability in soil depths deeper than 1.0 m. The results showed that nitrate addition promoted deep soil respiration if the stoichiometric mole ratio of nitrate to O₂ exceeded the threshold of 6:1, at which nitrate can be used as an alternative acceptor to O₂ for microbial respiration. In addition, the mole ratio of the produced CO₂ to N₂O was 2.57:1, which is close to the theoretical ratio of 2:1 expected when nitrate is used as an electron acceptor for microbial respiration. These results demonstrated that nitrate, as an alternative acceptor to O₂, promoted microbial carbon decomposition in deep soil. Furthermore, our results showed that nitrate addition increased the abundance of SOC decomposers and the expressions of their functional genes, and concurrently decreased MAOC, and the ratio of MAOC/SOC decreased from 20% before incubation to 4% at the end of incubation. Thus, nitrate can destabilize the MAOC in deep soils by stimulating microbial utilization of MAOC. Our results imply a new mechanism on how above-ground anthropogenic N inputs affect MAOC stability in deep soil. Mitigation of nitrate leaching is expected to benefit the conservation of MAOC in deep soil depths.

Insights into integrated glycerol-driven partial denitrification-anaerobic ammonium oxidation system using bioinformatic analysis: The dominance of Bacillus spp. and the potential of nitrite producing via assimilatory nitrate reduction

Partial denitrification-anaerobic ammonium oxidation (PD/A) was considered a novel technology for biological nitrogen removal. In this study, a glycerol-driven PD/A granular sludge reactor was constructed, and its nitrogen removal efficiency and microbial mechanisms were investigated systematically. After optimization, the PD/A reactor achieved 92.3 % of the nitrogen removal (~90 % by anammox) with the influent COD/NO₃^--N ratio of 2.6, and approximate 1.36 mol NO₃^--N was required for removing 1 mol NH₄⁺-N. Granular sludge with layered structure (anaerobic ammonium oxidizing bacteria (AnAOB) was wrapped by the heterotrophic bacteria) was successfully developed, which resulted in the sludge floating. Bacillus was firstly found to be the dominant genus in PD/A system with an abundance of 46.1 %, whereas the AnAOB only accounted for 0.2-2.8 %. Metatranscriptomic analysis showed that the metabolic characteristics obviously changed during the operation, and the differential expressing genes mainly belonged to ABC transport and quorum sensing pathway. Further analysis about the expressing patterns of nitrogen metabolism related genes indicated that the anammox related genes (mainly from Candidatus Brocadia and Candidatus Jettenia) exhibited a much higher expressing level than other genes. Interestingly, the assimilatory nitrate reduction process in Bacillus showed great NO₂^--N producing potential, so it was considered to be an essential pathway participating in PD/A process. This study provided a comprehensive insight into the glycerol-driven PD/A system.

Effect of hydrothermal pretreatment and compound microbial agents on compost maturity and gaseous emissions during aerobic composting of kitchen waste

Though aerobic composting is commonly used in kitchen waste (KW) disposal, the high-oil and high-salt characteristics of KW could affect composting efficiency and lead to the land using risk of produced fertilizer. The impact of hydrothermal pretreatment (HTP) and addition of compound microbial agent (CMA) on compost maturity, greenhouse gas (GHGs) emissions and bacterial community during the kitchen waste composting were evaluated in the present work. Results indicated that N2O, CH4 and CO2 emissions from treatment by HTP and CMA addition were reduced by 82.72%, 13.77% and 20.78 %, respectively, comparing with the control (without HTP and without CMA addition). The seed germination index (GI) value of the HTP and CMA addition treatment was 1.03 and had the highest maturity in all treatments. Furthermore, the bacterial community analysis indicated that CMA inoculation could increase the relative abundance of genus Bacillus at the thermophilic stage of composting to accelerate organic biodegradation. This work provided important insight into mitigating GHGs emissions and improving compost quality in kitchen waste composting.

Characteristics of sludge-based pyrolysis biochar and its application of enhancing denitrification

A modified biochar for enhanced denitrification was developed through a facile pyrolysis method using sewage sludge as raw material and melamine as nitrogen source. Through electrochemical analysis, sludge-based pyrolysis biochar (SPBC) has superior electrical conductivity and poor redox activity. SPBC can increase the electron transfer through the geoconductor mechanism. The effect and the mechanism of SPBC on denitrification were studied. The nitrate treatment efficiency increased with the increase of SPBC dosage. From the perspective of molecular biology, the activities of NAR and NIR enzymes, the degradation efficiency of glucose and the ETSA of bacteria were all promoted with the increase of SPBC, thereby promoting the removal of NO₃^-. In addition, SPBC had a certain screening effect on microbial communities, and biodiversity decreased with the increase of SPBC dosage. Although the biodiversity decreased, the relative abundance of microorganisms conducive to denitrification increased with the increase of SPBC dosage. The transformation strategy of SPBC proposed in this paper provides a technical solution for sludge recycling and application for strengthening denitrification.

Effects of Reductive Soil Disinfestation Combined with Liquid-Readily Decomposable Compounds and Solid Plant Residues on the Bacterial Community and Functional Composition

Reductive soil disinfestation (RSD) incorporated with sole plant residues or liquid-readily decomposable compounds is an effective management strategy to improve soil health. However, the synthetic effects of RSD incorporated with liquid-readily decomposable compounds and solid plant residues on soil ecosystem services remain unclear. Field experiments were carried out to investigate the effects of untreated soil (CK), RSD incorporated with sawdust (SA), molasses (MO), and their combinations (SA + MO) on the bacterial community and functional composition. The results showed that RSD treatments significantly altered soil bacterial community structure compared to CK treatment. The bacterial community structure and composition in MO and SA + MO treatments were clustered compared to SA treatment. This was mainly attributed to the readily decomposable carbon sources in molasses having a stronger driving force to reshape the soil microbial community during the RSD process. Furthermore, the functional compositions, such as the disinfestation efficiency of F. oxysporum (96.4 - 99.1%), abundances of nitrogen functional genes, soil metabolic activity, and functional diversity, were significantly increased in all of the RSD treatments. The highest disinfestation efficiency and abundances of denitrification (nirS and nrfA) and nitrogen fixation (nifH) genes were observed in SA + MO treatment. Specifically, SA + MO treatment enriched more abundant beneficial genera, e.g., Oxobacter, Paenibacillus, Cohnella, Rummeliibacillus, and Streptomyces, which were significantly and positively linked to disinfestation efficiency, soil metabolic activity, and denitrification processes. Our results indicated that combining RSD practices with liquid-readily decomposable compounds and solid plant residues could effectively improve soil microbial community and functional composition.

Partial nitrification in free nitrous acid-treated sediment planting Myriophyllum aquaticum constructed wetland strengthens the treatment of black-odor water

Black-odor water pollution in rural areas, especially swine wastewater, can lead to the deterioration of water quality and thus seriously affect the daily life of people in the area. However, there is a lack of effective treatment measures with simultaneous attention to carbon, nitrogen and sulfur pollution in rural black-odor water bodies. This study evaluated the feasibility of an in-situ pilot-scale constructed wetland (CW) for the synchronous removal of COD, ammonium, and sulfur compounds in the swine wastewater. In this study, the operation strategy of CW sediment pretreated with free nitrous acid (FNA) and Myriophyllum aquaticum plantation was established. Throughout the 114-day operation, the total removal efficiencies of COD and ammonium nitrogen in experimental groups were 81.2 ± 4.2 % and 72.8 ± 1.8 %, respectively, which were significantly higher than CW without any treatment. Removal efficiencies of Sulfur compounds, i.e. sulfide, sulfate, thiosulfate, and sulfite, were 92.3 ± 1.9 % (61.2 % higher than the no-treatment group), 42.1 ± 3.8 %, 97.9 ± 1.7 %, and 42.7 ± 4.5 % respectively. High-throughput sequencing and qPCR revealed that experimental group significantly increased denitrification genes (nirK, nosZ) and sulfur oxidation genes (soxB, fccAB) and enriched the corresponding microbial taxa (Bacillus, Conexibacter and Clostridium sensu stricto). Moreover, metabolic pathways related to nitrogen and sulfur and the degradation of organic matter were up-regulated. These results indicated that partial nitrification in CW planted with M. aquaticum promoted sulfur oxidation denitrification and heterotrophic denitrification. Overall, the in-situ pilot-scale study revealed that the cultivation of M. aquaticum in FNA-treated CW can be a sustainable approach to treat black-odor water bodies.

Development of a post-treatment system using a downflow hanging sponge reactor - an upflow anaerobic reactor for natural rubber processing wastewater treatment

This study aimed to evaluate the nitrogen removal of a post-treatment system for natural rubber processing wastewater (NRPW) under low chemical oxygen demand to total nitrogen (COD/TN) ratios without any supplemental external carbon source. The system including a downflow hanging sponge (DHS) reactor and an upflow anaerobic reactor (UAR) was operated in two phases. In phase 1 (day 0-102), under a nitrogen loading rate (NLR) of 0.23 ± 0.06 kgN m^-3 d^-1 and COD/TN ratio of 0.63 ± 0.47, the DHS-UAR system removed 82.5 ± 11.8% and 83.9 ± 7.6% of TN and ammonium concentrations, respectively. In phase 2 (day 103-229), higher COD/TN ratio of 1.96 ± 0.28 was applied to remove increasing NLRs. At the highest NLR of 0.51 kgN m^-3 d^-1, the system achieved TN and ammonium removal efficiencies of 93.2% and 93.7%, respectively. Nitrogen profiles and the 16S rRNA high-throughput sequencing data suggested that ammonium, a major nitrogen compound in NRPW, was utilized by nitrifying and ammonium assimilation bacteria in DHS, then removed by heterotrophic denitrifying and anammox bacteria in the UAR. The predominance of Acinetobacter detected in both reactors suggested its essential role for the nitrogen conversion.

Bacterial community structure and metabolic activity of drinking water pipelines in buildings: A new perspective on dual effects of hydrodynamic stagnation and algal organic matter invasion

Eutrophication and algal blooms have become global issues. The drinking water treatment process suffers from pollution by algal organic matter (AOM) through cell lysis during the algal blooms. Nevertheless, it remains unclear how AOM invasion affects water quality and microbial communities in drinking water, particularly in the stagnant settings. In this study, the addition of AOM caused the residual chlorine to rapidly degrade and below the limit of 0.05 mg/L, while the NO₂^--N concentration ranged from 0.11 to 3.71 mg/L. Additionally, total bacterial counts increased and subsequently decreased. The results of Biolog demonstrated that the AOM significantly improved the utilization capacity of carbon sources and changed the preference for carbon sources. Full-length 16S rRNA gene sequencing and network modeling revealed a considerable reduction in the abundance of Proteobacteria, whereas that of Bacteroidetes increased significantly under the influence of AOM. Furthermore, the species abundance distributions of the Microcystis group and Scenedesmus group was most consistent with the Mandelbrot model. According to redundancy analysis and structural equation modeling, the bacterial community structure of the control group was most positively regulated by the free residual chlorine concentrations, whereas the Microcystis group and Scenedesmus group were positively correlated with the total organic carbon (TOC) concentration. Overall, these findings provide a scientific foundation for the evolution of drinking water quality under algae bloom pollution.

Improvement of aquaculture water quality by mixed Bacillus and its effects on microbial community structure

Microbial remediation, especially the application of probiotics, has recently gained popularity in improving water quality and maintaining aquatic animal health. The efficacy and mechanism of mixed Bacillus for improvement of water quality and its effects on aquatic microbial community structure remain unknown. To elucidate these issues, we applied two groups of mixed Bacillus (Bacillus megaterium and Bacillus subtilis (A0 + BS) and Bacillus megaterium and Bacillus coagulans (A0 + BC)) to the aquaculture system of Crucian carp. Our results showed that the improvement effect of mixed Bacillus A0 + BS on water quality was better than that of A0 + BC, and the NH₄⁺-N, NO₂^--N, NO₃^--N, and total phosphorus (TP) concentrations were reduced by 46.3%, 76.3%, 35.6%, and 80.3%, respectively. In addition, both groups of mixed Bacillus increased the diversity of the bacterial community and decreased the diversity of the fungal community. Microbial community analysis showed that mixed Bacillus A0 + BS increased the relative abundance of bacteria related with nitrogen and phosphorus removal, such as Proteobacteria, Actinobacteria, Comamonas, and Stenotrophomonas, but decreased the relative abundance of pathogenic bacteria (Acinetobacter and Pseudomonas) and fungi (Epicoccum and Fusarium). Redundancy analysis showed that NH₄⁺-N, NO₂^--N, and TP were the primary environmental factors affecting the microbial community in aquaculture water. PICRUST analysis indicated that all functional pathways in the A0 + BS group were richer than those in other groups. These results indicated that mixed Bacillus A0 + BS addition produced good results in reducing nitrogenous and phosphorus compounds and shaped a favorable microbial community structure to further improve water quality.

Eco-Friendly Solution Based on Rosmarinus officinalis Hydro-Alcoholic Extract to Prevent Biodeterioration of Cultural Heritage Objects and Buildings

Biodeterioration of cultural heritage is caused by different organisms capable of inducing complex alteration processes. The present study aimed to evaluate the efficiency of Rosmarinus officinalis hydro-alcoholic extract to inhibit the growth of deteriogenic microbial strains. For this, the physico-chemical characterization of the vegetal extract by UHPLC–MS/MS, its antimicrobial and antibiofilm activity on a representative number of biodeteriogenic microbial strains, as well as the antioxidant activity determined by DPPH, CUPRAC, FRAP, TEAC methods, were performed. The extract had a total phenol content of 15.62 ± 0.97 mg GAE/mL of which approximately 8.53% were flavonoids. The polyphenolic profile included carnosic acid, carnosol, rosmarinic acid and hesperidin as major components. The extract exhibited good and wide spectrum antimicrobial activity, with low MIC (minimal inhibitory concentration) values against fungal strains such as Aspergillus clavatus (MIC = 1.2 mg/mL) and bacterial strains such as Arthrobacter globiformis (MIC = 0.78 mg/mL) or Bacillus cereus (MIC = 1.56 mg/mL). The rosemary extract inhibited the adherence capacity to the inert substrate of Penicillium chrysogenum strains isolated from wooden objects or textiles and B. thuringiensis strains. A potential mechanism of R. officinalis antimicrobial activity could be represented by the release of nitric oxide (NO), a universal signalling molecule for stress management. Moreover, the treatment of microbial cultures with subinhibitory concentrations has modulated the production of microbial enzymes and organic acids involved in biodeterioration, with the effect depending on the studied microbial strain, isolation source and the tested soluble factor. This paper reports for the first time the potential of R. officinalis hydro-alcoholic extract for the development of eco-friendly solutions dedicated to the conservation/safeguarding of tangible cultural heritage.

Pyrite-Based Autotrophic Denitrifying Microorganisms Derived from Paddy Soils: Effects of Organic Co-Substrate Addition

The presence of organic co-substrate in groundwater and soils is inevitable, and much remains to be learned about the roles of organic co-substrates during pyrite-based denitrification. Herein, an organic co-substrate (acetate) was added to a pyrite-based denitrification system, and the impact of the organic co-substrate on the performance and bacterial community of pyrite-based denitrification processes was evaluated. The addition of organic co-substrate at concentrations higher than 48 mg L^-1 inhibited pyrite-based autotrophic denitrification, as no sulfate was produced in treatments with high organic co-substrate addition. In contrast, both competition and promotion effects on pyrite-based autotrophic denitrification occurred with organic co-substrate addition at concentrations of 24 and 48 mg L^-1. The subsequent validation experiments suggested that competition had a greater influence than promotion when organic co-substrate was added, even at a low concentration. Thiobacillus, a common chemolithoautotrophic sulfur-oxidizing denitrifier, dominated the system with a relative abundance of 13.04% when pyrite served as the sole electron donor. With the addition of organic co-substrate, Pseudomonas became the dominant genus, with 60.82%, 61.34%, 70.37%, 73.44%, and 35.46% abundance at organic matter concentrations of 24, 48, 120, 240, and 480 mg L^-1, respectively. These findings provide an important theoretical basis for the cultivation of pyrite-based autotrophic denitrifying microorganisms for nitrate removal in soils and groundwater.

The synergetic effect of Bacillus species and Yucca shidigera extract on water quality, histopathology, antioxidant, and innate immunity in response to acute ammonia exposure in Nile tilapia

Acute ammonia toxicity suppresses the immune function and enhances the inflammatory pathways in Nile tilapia. The aim of this study was to compare the effect of Bacillus strains probiotic mixture (BS) or Yucca shidigera liquid extract (YSE) alone or their combination in water treatment and in reliving toxicity of an acute ammonia exposure in Nile tilapia through the assessment of fish immune response, inflammatory pathway, oxidative stress response with respect to the histopathological changes, gene expression, enzymes levels and phagocytosis. Five groups were used; the 1st and 2nd groups fed the basal diet; the 3rd group fed basal diet with BS in water, 4th group fed basal diet and supplemented with YSE in water and 5th group received a combination of BS and YSE. After two weeks of treatments, the 2nd, 3rd, 4th, and the 5th groups were exposed to acute ammonia challenge for 72 h. Fish exposed to ammonia displayed significant decreases in RBCs, Hb, PCV, WBCs, phagocytic activity (PA) and index (PI), lysozyme activities and serum antioxidant enzymes (glutathione peroxidase (GPX) and catalase (CAT)). Also, a significant increase in Malondialdehyde (MDA), degenerative changes in the gills, hepatopancrease and spleen associated with an elevated un-ionized ammonia level. A significant restoration of the hematological parameters was observed with the use of BS, YSE or their combination. Additionally, they improved the innate immunity, antioxidant responses, and histopathological changes. At transcriptomic level, ammonia toxicity significantly lowered the mRNA transcription levels of Nuclear erythroid 2-related factor 2 (Nrf2), quinone oxidoreductase 1 (NQO-1), Heme oxygenase 1 (HO-1) and Heat shock proteins (HSP70). While nuclear factor kappa β (NFкβ), Tumor necrosis factor α (TNF-α), Interleukin 1β (IL-1β), and Interleukin 8 (IL8), transcription levels were increased. Interestingly, BS and YSE and their combination significantly increased the expression of these genes with the highest levels reported with BS and YSE combination. We observed that, the most pronounced restoration of some important inflammatory and immune related genes close to the control level was observed when BS-YSE mix was used. Furthermore, a restored water pH, and a maintained ammonia level to the control level were observed in this group. Otherwise, equal effects for the three treatments were observed on the assessed parameters. We recommend the used of BS-YSE mix for water ammonia treatment and relieving ammonia toxicity in fish.

Effects of microplastics and carbon nanotubes on soil geochemical properties and bacterial communities

A 100-day soil incubation experiment was conducted to explore the effects of conventional (high-density polyethylene, HDPE) and biodegradable (polylactic acid, PLA) microplastics (MPs) and multiwall carbon nanotubes (MWCNTs) on soil geochemical properties and bacterial communities. Generally, soil pH was increased by 10% HDPE and 10% PLA, but decreased by increasing MWCNTs. Soil dissolved organic carbon content was only increased by 10% PLA. NO₃^--N content was significantly decreased by MPs, with a decrement of 99% by 10% PLA. Similarly, available P content was reduced by 10% MPs. The activities of urease and alkaline phosphatase were stimulated by 10% PLA, but generally inhibited by HDPE. Conversely, FDAse activity was stimulated by HDPE, but inhibited by 10% PLA, whereas invertase activity decreased with increasing MWCNTs. Overall, both MPs and MWCNTs changed soil bacterial diversity. Co-exposure to 10% MPs and MWCNTs of 1 and 10 mg/kg caused the lowest species richness and Shannon indexes. MPs especially at the 10% dose changed bacterial community composition and the associated metabolic pathways, causing the enrichment of specific taxa and functional genes. Our findings show that conventional and biodegradable MPs differently change soil geochemical properties and microbial community structure and functions, which can be further modified by co-existing MWCNTs.

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.

Elevated Atmospheric CO2 Modifies Mostly the Metabolic Active Rhizosphere Soil Microbiome in the Giessen FACE Experiment

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.

Characterization of Acinetobacter indicus ZJB20129 for heterotrophic nitrification and aerobic denitrification isolated from an urban sewage treatment plant

The Acinetobacter indicus strain ZJB20129 isolated from an urban sewage treatment plant demonstrated the heterotrophic nitrification-aerobic denitrification (HN-AD) ability. Strain ZJB20129 could remove 98.73% of ammonium-N, 97.26% of nitrite-N and 96.55% of nitrate-N, and the maximum removal rate was 3.66, 4.62 and 5.21 mg/L/h, respectively. Ammonium was preferentially used during simultaneous nitrification and denitrification. Strain ZJB20129 exhibited highest ammonium removal capability when carbon source was sodium succinate, C/N ratio was 15, pH was 8.0, and temperature was 35 ℃. Key enzymes involved in HN-AD including hydroxylamine oxidase, periplasmic nitrate reductase and nitrite reductase as well as their encoding genes were detected, and the metabolic pathway of HN-AD was subsequently predicted. Our results suggested that Acinetobacter indicus ZJB20129 displayed superior nitrogen removal performance on actual wastewater and thus made it have a good application prospect in wastewater biological treatment.

Weak electrical stimulation on biological denitrification: Insights from the denitrifying enzymes

In order to improve the denitrification efficiency of low carbon to nitrogen ratio (C/N) wastewater, we conducted continuous flow experiments of weakly electrically stimulated denitrification using a direct current output voltage. The results showed that the best denitrification was achieved at a voltage of 0.2 V. The removal of nitrate and total nitrogen was increased by 20% and the production of intermediate greenhouse gas (N₂O) was reduced by 62.6%. We explored the specific pathways involved in the weak electrical stimulated denitrification using enzyme activity as a cut-off point. The enzyme activity analysis and 3D fluorescence spectroscopy revealed that nitrate reductase (NAR) and nitrite reductase (NIR) activities were significantly enhanced by weak electrical stimulation, and the aromatic protein content in extracellular polymers substances (EPS) increased, accelerating electron transfer and promoting the conversion of loosely bound EPS (LB) to tightly bound EPS (TB). The accelerated electron transfer further increased enzyme activity and the metabolic rate of microorganisms. This study indicates that weak electrical stimulation could improve activities of biological enzymes to enhance denitrification efficiency.

Food waste composting based on patented compost bins: Carbon dioxide and nitrous oxide emissions and the denitrifying community analysis

Mature compost and rice bran were used as bulking agents to perform Food Waste Rapid Composting (FWRC) in a patented composting bin. The characteristics of CO₂ and N₂O emission and the denitrifying community were investigated. The release of CO₂ and N₂O concentrated in the early composting stage and reduced greatly after 28 h, and the N₂O emission peak of the treatment with mature compost was 8.5 times higher than that of rice bran. The high N₂O generation resulted from massive denitrifying bacteria and NO_x^--N in the composting material. The relative abundances of denitrifiers, correspondingly genes of narG and nirK were much higher in the treatment with mature compost, which contributed to the N₂O emission. Moreover, the correlation matrices revealed that N₂O fluxes correlated well with moisture, pH, temperature, and the abundances of nirK and nosZ genes during FWRC.

Effects of Turning Frequency on Ammonia Emission during the Composting of Chicken Manure and Soybean Straw

Here, we investigated the impact of different turning frequency (TF) on dynamic changes of N fractions, NH3 emission and bacterial/archaeal community during chicken manure composting. Compared to higher TF (i.e., turning every 1 or 3 days in CMS1 or CMS3 treatments, respectively), lower TF (i.e., turning every 5 or 7 days in CMS5 or CMS7 treatments, respectively) decreased NH3 emission by 11.42-18.95%. Compared with CMS1, CMS3 and CMS7 treatments, the total nitrogen loss of CMS5 decreased by 38.03%, 17.06% and 24.76%, respectively. Ammonia oxidizing bacterial/archaeal (AOB/AOA) communities analysis revealed that the relative abundance of Nitrosospira and Nitrososphaera was higher in lower TF treatment during the thermophilic and cooling stages, which could contribute to the reduction of NH3 emission. Thus, different TF had a great influence on NH3 emission and microbial community during composting. It is practically feasible to increase the abundance of AOB/AOA through adjusting TF and reduce NH3 emission the loss of nitrogen during chicken manure composting.

Effect of metal and metal oxide engineered nano particles on nitrogen bio-conversion and its mechanism: A review

Metal and metal oxide engineered nano particles (MMO-ENPs) are widely applied in various industries due to their unique properties. Thus, many researches focused on the influence on nitrogen transformation processes by MMO-ENPs. This review focuses on the effect of MMO-ENPs on nitrogen fixation, nitrification, denitrification and Anammox. Firstly, based on most of the researches, it can be concluded MMO-ENPs have negative effect on nitrogen fixation, nitrification and denitrification while the MMO-ENPs have no promotion effect on Anammox. Then, the influence factors are discussed in detail, including MMO-ENPs dosage, MMO-ENPs kind and exposure time. Both the microbial morphology and population structure were altered by MMO-ENPs. Also, the mechanisms of MMO-ENPs affecting the nitrogen transformation are reviewed. The inhibition of key enzymes and functional genes, the promotion of reactive oxygen species (ROS) production, MMO-ENPs themselves and the suppression of electron transfer all contribute to the negative effect. Finally, the key points for future investigation are proposed that more attention should be attached to the effect on Anammox and the further mechanism in the future studies.

The influence of a static magnetic field on a Chlorella vulgaris - Bacillus licheniformis consortium and its sewage treatment effect

In this study, the influence of a static magnetic field (SMF) on a Chlorella vulgaris-Bacillus licheniformis consortium and the subsequent effect of this algal-bacterial consortium on sewage treatment were explored. Accordingly, the algal density, Fv/Fm, algal aggregation percentage, extracellular polymeric substances (EPS) content, dissolved organic matter distribution, enzymatic activity, metabolites, microbial community diversity and nutrient removal were investigated. For the treatment group exposed to an SMF of 150 mT, the total phosphorus removal rate reached 82.21%, which was 19.10% higher than the control group. On the last day, the algal density of the 150 mT group was the highest, being 56.01% greater than the control group. The high intensity SMF promoted the anti-oxidative stress response in C. vulgaris. It also affected EPS secretion, subsequently influencing the algal aggregation percentage and bacterial growth. Bacillus accounted for the largest proportion of the overall microbial community in the 150 mT group, which was conducive to rapid formation of the C. vulgaris-B. licheniformis consortium. In short, the SMF was conducive to the rapid formation of a C. vulgaris-B. licheniformis consortium. The use of an SMF can promote the efficiency of the algal-bacterial consortium, thereby shortening the processing time.

Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases

Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR is catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases and fractionates the stable isotopes of nitrogen (¹⁴N, ¹⁵N) and oxygen (¹⁶O, ¹⁸O), which is reflected in residual environmental nitrate pools. Data on the relationship between the pattern in oxygen vs nitrogen isotope fractionation (¹⁸ε/¹⁵ε) suggests that systematic differences exist between marine and terrestrial ecosystems that are not fully understood. We examined the ¹⁸ε/¹⁵ε of nitrate-reducing microorganisms that encode Nar, Nap, or both enzymes, as well as gene deletion mutants of Nar and Nap to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of ¹⁸ε/¹⁵ε fractionation ratios of all examined nitrate reductases forms two distinct peaks centered around an ¹⁸ε/¹⁵ε proportionality of 0.55 (Nap) and 0.91 (Nar), with the notable exception of the Bacillus Nar reductases, which cluster isotopically with the Nap reductases. Our findings may explain differences in ¹⁸ε/¹⁵ε fractionation between marine and terrestrial systems and challenge current knowledge about Nar ¹⁸ε/¹⁵ε signatures.

Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic

Nanoscale Zero-Valent Iron (nZVI) is a cost-effective nanomaterial that is widely used to remove a broad range of metal(loid)s and organic contaminants from soil and groundwater. In some cases, this material alters the taxonomic and functional composition of the bacterial communities present in these matrices; however, there is no conclusive data that can be generalized to all scenarios. Here we studied the effect of nZVI application in situ on groundwater from the site of an abandoned fertilizer factory in Asturias, Spain, mainly polluted with arsenic (As). The geochemical characteristics of the water correspond to a microaerophilic and oligotrophic environment. Physico-chemical and microbiological (cultured and total bacterial diversity) parameters were monitored before and after nZVI application over six months. nZVI treatment led to a marked increase in Fe(II) concentration and a notable fall in the oxidation-reduction potential during the first month of treatment. A substantial decrease in the concentration of As during the first days of treatment was observed, although strong fluctuations were subsequently detected in most of the wells throughout the six-month experiment. The possible toxic effects of nZVI on groundwater bacteria could not be clearly determined from direct observation of those bacteria after staining with viability dyes. The number of cultured bacteria increased during the first two weeks of the treatment, although this was followed by a continuous decrease for the following two weeks, reaching levels moderately below the initial number at the end of sampling, and by changes in their taxonomic composition. Most bacteria were tolerant to high As(V) concentrations and showed the presence of diverse As resistance genes. A more complete study of the structure and diversity of the bacterial community in the groundwater using automated ribosomal intergenic spacer analysis (ARISA) and sequencing of the 16S rRNA amplicons by Illumina confirmed significant alterations in its composition, with a reduction in richness and diversity (the latter evidenced by Illumina data) after treatment with nZVI. The anaerobic conditions stimulated by treatment favored the development of sulfate-reducing bacteria, thereby opening up the possibility to achieve more efficient removal of As.

Negative effects of oxytetracycline and copper on nitrogen metabolism in an aerobic fermentation system: Characteristics and mechanisms

Aerobic fermentation is a sustainable option for livestock waste treatment, but little is known about the microbial mechanism that allows oxytetracycline (OTC) and copper (Cu) to affect nitrogen metabolism during aerobic fermentation. In this study, contamination with OTC and Cu alone or in combination reduced the total nitrogen (TN) content of the fermentation products. Metagenomic analysis demonstrated that the contribution of microorganisms to nitrogen metabolism changed significantly in different stages of fermentation. OTC and Cu affected the formation and utilization pattern of NO₂^--N by microorganisms, which were mainly responsible for the reduced N₂O emissions. In the presence of OTC and/or Cu, Myxococcus_stipitatus, Myxococcus_xanthus, and Gimesia_maris were evidently enriched at the end of fermentation, and their increased roles in the dissimilatory reduction of nitrite to ammonium were confirmed by network analysis. Ardenticatena_maritima was the main contributor to denitrification (NO₃^--N to NO). Furthermore, organic matter (OM) was the most important factor responsible for driving the variation in nitrogen-transforming microorganisms and controlling denitrification. OTC affected the formation of OM, which can directly affect TN (λ = -0.37, p < 0.001), and the adverse impact of Cu on nirK- and nifH-dominant microorganisms was validated (p < 0.05).

Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Isolation, expression, and biochemical characterization: nitrite reductase from Bacillus cereus LJ01

Biological remediation of toxic oxygen-containing anions such as nitrate that are common in the environment is of great significance. Therefore, it is necessary to understand the specific role of nitrate and nitrite reductase in the bioremediation process. Bacillus cereus LJ01, which was isolated from traditional Chinese soybean paste, effectively degraded nitrite (such as NaNO₂) at 0–15 mmol L⁻¹ in LB medium. Moreover, the nitrite-degrading active substance (ASDN) was isolated and purified from B. cereus LJ01. The nitrite-degrading activity of nitrite reductase (named LJ01-NiR) was 4004.89 U mg⁻¹. The gene encoding the assimilation of nitrite reductase in B. cereus LJ01 was cloned and overexpressed in E. coli. The purified recombinant LJ01-NiR has a wide range of activities under temperature (20–60 °C), pH (6.5–8.0) and metal ions (Fe³⁺, Fe²⁺, Cu²⁺, Mn²⁺, and Al³⁺). Kinetic parameters of LJ01-NiR, including the values of K_m and V_max were 1.38 mM and 2.00 μmol g⁻¹ min⁻¹, respectively. The results showed that LJ01-NiR could degrade nitrite with or without an electron donor. In addition, sequence analysis revealed that LJ01-NiR was a ferredoxin-dependent nitrite reductase given the presence of conserved [Fe4–S4] cluster and heme-binding domain. The nitrite ion binds to the LJ01-NiR active site by forming three hydrogen bonds with the residues ASN72, ALA133 and ASN140. Due to its high nitrite-degrading activity, LJ01-NiR could potentially be used for environmental pollution treatment.

Biological remediation of toxic oxygen-containing anions such as nitrite in the environment is of great significance. Bacillus cereus LJ01 showed the activity of degradation for nitrite. the enzyme NiR from LJ01 can degrade the nitrite in vitro.

Linking nitrous oxide emissions from starch wastewater digestate amended soil to the abundance and structure of denitrifier communities

Anaerobic digestion is widely used in starch wastewater pre-treatment and can remove the COD effectively, however, the effluents are nutritious and often need supplemental aerobic treatments to remove nutrients prior to discharge. The objective of this study was to investigate the feasibility of using the liquid digestate of starch wastewater (LDSW) as a fertilizer. This pot experiment was conducted with Ipomoea aquatica Forsk in a greenhouse with six treatment groups. The crop growth was significantly promoted, while the accumulation of soil nitrate was not influenced after LDSW addition, compared to the control. In addition, at the same nitrogen input, the yield of high-LDSW treatment was 65.2%, 92.3% and 69.2% higher than those of chemical fertilizer treatment during the three growth periods. Furthermore, average N₂O emission with high-LDSW addition was 15.8 g N/(ha.d), accounting for 15.0% of which under high chemical fertilizer treatment, due to the significantly enhanced denitrification genes (nirK, nirS and nosZ) abundance. Besides, the changes of soil N₂O-reducing bacteria were performed by high-throughput sequencing of nosZ. Our findings suggested that LDSW had many opportunities for sustainable agriculture to guarantee high yields while reducing negative environmental impacts.

Soil Bacterial Community Response and Nitrogen Cycling Variations Associated with Subalpine Meadow Degradation on the Loess Plateau, China

Grassland degradation is an ecological problem worldwide. This study aimed to reveal the patterns of the variations in bacterial diversity and community structure and in nitrogen cycling functional genes along a subalpine meadow degradation gradient on the Loess Plateau, China. Meadow degradation had a significant effect on the beta diversity of soil bacterial communities (P < 0.05) but not on the alpha diversity (P > 0.05). Nonmetric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) indicated that the compositions of bacterial and plant communities changed remarkably with increasing meadow degradation (all P < 0.05). The beta diversities of the plant and soil bacterial communities were significantly correlated (P < 0.05), while their alpha diversities were weakly correlated (P > 0.05) along the meadow degradation gradient. Redundancy analysis (RDA) showed that the structure of the bacterial community was strongly correlated with total nitrogen (TN), nitrate nitrogen (NO₃ ^--N), plant Shannon diversity, plant coverage, and soil bulk density (all P < 0.05). Moreover, the abundances of N fixation and denitrification genes of the bacterial community decreased along the degradation gradient, but the abundance of nitrification genes increased along the gradient. The structure of the set of N cycling genes present at each site was more sensitive to subalpine meadow degradation than the structure of the total bacterial community. Our findings revealed compositional shifts in the plant and bacterial communities and in the abundances of key N cycling genes as well as the potential drivers of these shifts under different degrees of subalpine meadow degradation.IMPORTANCE Soil microbes play a crucial role in the biogeochemical cycles of grassland ecosystems, yet information on how their community structure and functional characteristics change with subalpine meadow degradation is scarce. In this study, we evaluated the changes in bacterial community structure and nitrogen functional genes in degraded meadow soils. Meadow degradation had a significant effect on bacterial community composition. Soil total nitrogen was the best predictor of bacterial community structure. The beta diversities of the plant and soil bacterial communities were significantly correlated, while their alpha diversities were only weakly correlated. Meadow degradation decreased the potential for nitrogen fixation and denitrification but increased the potential for nitrification. These results have implications for the restoration and reconstruction of subalpine meadow ecosystem on the Loess Plateau.