Denitrification by Anaeromyxobacter dehalogenans, a Common Soil Bacterium Lacking the Nitrite Reductase Genes nirS and nirK

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Maribellus mangrovi sp. nov., an iron-reducing bacterium isolated from mangrove sediment

A novel facultatively anaerobic and Gram-stain-negative bacterium, designated FJH33T, was isolated from mangrove sediment sampled in Zhangzhou, PR China. Cells of strain FJH33T were rod-shaped or slightly curved-shaped, with widths of 0.3-0.5 µm and lengths of 1.0-3.0 µm. Optimum growth of strain FJH33T occurred in the presence of 3 % NaCl (w/v), at 33 °C and at pH 7.0. Oxidase activity was negative, while catalase activity was positive. Its iron-reducing ability was determined. Based on 16S rRNA gene sequence similarity, strain FJH33T was most closely related to Maribellus luteus XSD2T (95.1 %), followed by Maribellus sediminis Y2-1-60T (95.0 %) and Maribellus maritimus 5E3T (94.9 %). Genome analysis of strains FJH33T and M. luteus XSD2T revealed low genome relatedness, with an average nucleotide identity value of 73.8% and a digital DNA-DNA hybridization value of 19.0%. Phylogenetic trees built from 16S rRNA genes and genome sequences showed that strain FJH33T represents a relatively independent phylogenetic lineage within the genus Maribellus. The major cellular fatty acids (≥10 %) were iso-C15 : 0 and C18 : 1  ω9c. The sole respiratory quinone was MK-7. The polar lipids consisted of phosphatidylethanolamine, diphosphatidylcholine, diphosphatidyglycerol and one unidentified lipid. The DNA G+C content was 41.4 mol%. Based on the integrated results of phylogenetic, physiological, biochemical and chemotaxonomic characterizations, we propose that strain FJH33T represents a novel species of the genus Maribellus, for which the name Maribellus mangrovi sp. nov. is proposed. The type strain is FJH33T (=KCTC 102210T=MCCC 1H01459T).

Unlocking bacterial potential to reduce farmland N2O emissions

Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy

Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Two novel Fe(III)-reducing bacteria, Geothrix campi sp. nov. and Geothrix mesophila sp. nov., isolated from paddy soils

In this research, two novel Fe(III)-reducing bacteria, SG10T and SG198T of genus Geothrix, were isolated from the rice field of Fujian Agriculture and Forestry University in Fuzhou, Fujian Province, China. Strains SG10T and SG198T were strictly anaerobic, rod-shaped and Gram-stain-negative. The two novel strains exhibited iron reduction ability, utilizing various single organic acid as the elector donor and Fe(III) as a terminal electron acceptor. Strains SG10T and SG198T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix oryzisoli SG189T (99.0-99.5%) and Geothrix paludis SG195T (99.0-99.7%), respectively. The phylogenetic trees based on the 16S rRNA gene and genome 120 conserved core genes showed that strains SG10T and SG198T belong to the genus Geothrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the phylogenetic neighbors and the two isolated strains were 86.1-94.3% and 30.7-59.5%, respectively. The major fatty acids were iso-C15:0, anteiso-C15:0, C16:0 and iso-C13:0 3OH, and MK-8 was the main respiratory quinone. According to above results, the two strains were assigned to the genus Geothrix with the names Geothrix campi sp. nov. and Geothrix mesophila sp. nov. Type strains are SG10T (= GDMCC 1.3406 T = JCM 39331 T) and SG198T (= GDMCC 62910 T = KCTC 25635 T), respectively.

Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands

Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.

Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil

Three microaerophilic bacterial strains, designated SG22T, SG63T and SG29T were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22T, SG63T and SG29T showed the highest 16S rRNA gene sequence similarities with the members of the genus Anaeromyxobacter. The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus Anaeromyxobacter. The main respiratory menaquinone of SG22T, SG63T and SG29T was MK-8 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. SG22T, SG29T and SG63T not only possessed iron reduction ability but also harboured genes (nifHDK) encoding nitrogenase. The genomic DNA G+C contents of SG22T, SG63T and SG29T ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between SG22T, SG63T and SG29T and the closely related species of the genus Anaeromyxobacter were lower than the cut-off values (dDDH 70 % and ANI 95-96 %) for prokaryotic species delineation. On the basis of these results, strains SG22T, SG63T and SG29T represent three novel species within the genus Anaeromyxobacter, for which the names Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., are proposed. The type strains are SG22T (= GDMCC 1.3185T = JCM 35581T), SG63T (= GDMCC 1.2914T = JCM 35124T) and SG29T (= GDMCC 1.2911T = JCM 35123T).

Synergetic effect of nitrate on dissolved organic carbon attenuation through dissimilatory iron reduction during aquifer storage and recovery

Aquifer storage and recovery (ASR) is a promising water management technique in terms of quantity and quality. During ASR, iron (Fe) (hydr)oxides contained in the aquifer play a crucial role as electron acceptors in attenuating dissolved organic carbon (DOC) in recharging water through dissimilatory iron reduction (DIR). Considering the preference of electron acceptors, nitrate (NO3⁻), possibly coexisting with DOC as the prior electron acceptor to Fe (hydr)oxides, might influence DIR by interrupting electron transfer. However, this phenomenon is yet to be clarified. In this study, we systematically investigated the potential effect of NO3⁻ on DOC attenuation during ASR using a series of sediment columns representing typical aquifer conditions. The results suggest that DOC attenuation could be enhanced by the presence of NO3⁻. Specifically, total DOC attenuation was notably higher than that from the stoichiometric calculation simply employing NO3⁻ as the additional electron acceptor to Fe (hydr)oxides, implying a synergetic effect of NO3⁻ in the overall reactions. X-ray photoelectron spectroscopy analyzes revealed that the Fe(II) ions released from DIR transformed the Fe (hydr)oxides into a less bioavailable form, inhibiting further DIR. In the presence of NO3⁻, however, no aqueous Fe(II) was detected, and another form of Fe (hydr)oxide appeared on the sediment surface. This may be attributed to nitrate-dependent Fe(II) oxidation (NDFO), in which Fe(II) is (re)oxidized into Fe (hydr)oxide, which is available for the subsequent DOC attenuation. These mechanisms were supported by the dominance of DIR-relevant bacteria and the growth of NDFO-related bacteria in the presence of NO3⁻.

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback

Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH4, was most sensitive to N2O, with inhibitory constants (KI) in the range of 18-25 μM, followed by hydrogenotrophic (KI, 60-90 μM) and methylotrophic (KI, 110-130 μM) methanogenesis. Dissolved N2O concentrations exceeding these KI values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N2O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation

As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.

Inhibition of Methylmercury and Methane Formation by Nitrous Oxide in Arctic Tundra Soil Microcosms

Climate warming causes permafrost thaw predicted to increase toxic methylmercury (MeHg) and greenhouse gas [i.e., methane (CH₄), carbon dioxide (CO₂), and nitrous oxide (N₂O)] formation. A microcosm incubation study with Arctic tundra soil over 145 days demonstrates that N₂O at 0.1 and 1 mM markedly inhibited microbial MeHg formation, methanogenesis, and sulfate reduction, while it slightly promoted CO₂ production. Microbial community analyses indicate that N₂O decreased the relative abundances of methanogenic archaea and microbial clades implicated in sulfate reduction and MeHg formation. Following depletion of N₂O, both MeHg formation and sulfate reduction rapidly resumed, whereas CH₄ production remained low, suggesting that N₂O affected susceptible microbial guilds differently. MeHg formation strongly coincided with sulfate reduction, supporting prior reports linking sulfate-reducing bacteria to MeHg formation in the Arctic soil. This research highlights complex biogeochemical interactions in governing MeHg and CH₄ formation and lays the foundation for future mechanistic studies for improved predictive understanding of MeHg and greenhouse gas fluxes from thawing permafrost ecosystems.

Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency

Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.

Effect of Rice Straw and Stubble Burning on Soil Physicochemical Properties and Bacterial Communities in Central Thailand

Rice straw and stubble burning is widely practiced to clear fields for new crops. However, questions remain about the effects of fire on soil bacterial communities and soil properties in paddy fields. Here, five adjacent farmed fields were investigated in central Thailand to assess changes in soil bacterial communities and soil properties after burning. Samples of soil prior to burning, immediately after burning, and 1 year after burning were obtained from depths of 0 to 5 cm. The results showed that the pH, electrical conductivity, NH4-N, total nitrogen, and soil nutrients (available P, K, Ca, and Mg) significantly increased immediately after burning due to an increased ash content in the soil, whereas NO3-N decreased significantly. However, these values returned to the initial values. Chloroflexi were the dominant bacteria, followed by Actinobacteria and Proteobacteria. At 1 year after burning, Chloroflexi abundance decreased remarkably, whereas Actinobacteria, Proteobacteria, Verrucomicrobia, and Gemmatimonadetes abundances significantly increased. Bacillus, HSB OF53-F07, Conexibacter, and Acidothermus abundances increased immediately after burning, but were lower 1 year after burning. These bacteria may be highly resistant to heat, but grow slowly. Anaeromyxobacter and Candidatus Udaeobacter dominated 1 year after burning, most likely because of their rapid growth and the fact that they occupy areas with increased soil nutrient levels after fires. Amidase, cellulase, and chitinase levels increased with increased organic matter levels, whereas β-glucosidase, chitinase, and urease levels positively correlated with the soil total nitrogen level. Although clay and soil moisture strongly correlated with the soil bacterial community’s composition, negative correlations were found for β-glucosidase, chitinase, and urease. In this study, rice straw and standing stubble were burnt under high soil moisture and within a very short time, suggesting that the fire was not severe enough to raise the soil temperature and change the soil microbial community immediately after burning. However, changes in soil properties due to ash significantly increased the diversity indices, which was noticeable 1 year after burning.

Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil

An anaerobic, Gram-staining-negative, rod-shaped, Fe(III)-reducing strain, designated SG189^T, was isolated from paddy soil in Fujian Province, China. Growth occurred at 20-35 ℃ (optimum 30 ℃), pH 6.5-8.0 (optimum 7.0) and 0-0.2% (w/v) NaCl (optimum 0%). The strain SG189^T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix fermentans DSM 14018^T (98.9%), "Geothrix terrae" SG184^T (99.0%) and "Geothrix alkalitolerans" SG263^T (99.3%). ANI and dDDH values between strain SG189^T and the most closely related Geothrix species were 86.5-87.1% and 31.5-32.9%, which lower than the cut-off values (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Further, genome-based phylogenomic trees constructed using 81 core genes (UBCG2) and 120 conserved genes (GTDB) showed that strain SG189^T formed a clade with members of the genus Geothrix. The menaquinone was shown to be MK-8, and the major fatty acids were iso-C_15:0 and iso-C_13:0 3OH. The genomic DNA G + C content was 68.2%. Additionally, we found that strain SG189^T possessed ability to reduce ferric iron, and strain SG189^T could reduce 10 mM of ferric citrate in 10 days with lactate as the sole electron donor. Based on the observed physiological and biochemical properties, chemotaxonomic characteristics, ANI and dDDH values, SG189^T represents a novel species of the genus Geothrix, for which the name Geothrix oryzisoli sp. nov. is proposed. The type strain is SG189^T (= GDMCC 1.3408^T = JCM 39324^T).

Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands

Atmospheric nitrous oxide (N2O) is a potent greenhouse gas thought to be mainly derived from microbial metabolism as part of the denitrification pathway. Here we report that in unexplored peat soils of Central and South America, N2O production can be driven by abiotic reactions (≤98%) highly competitive to their enzymatic counterparts. Extracted soil iron positively correlated with in situ abiotic N2O production determined by isotopic tracers. Moreover, we found that microbial N2O reduction accompanied abiotic production, essentially closing a coupled abiotic-biotic N2O cycle. Anaerobic N2O consumption occurred ubiquitously (pH 6.4-3.7), with proportions of diverse clade II N2O reducers increasing with consumption rates. Our findings show that denitrification in tropical peat soils is not a purely biological process but rather a 'mosaic' of abiotic and biotic reduction reactions. We predict that hydrological and temperature fluctuations differentially affect abiotic and biotic drivers and further contribute to the high N2O flux variation in the region.

Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia

Anaerobic microorganisms are thought to play a critical role in regulating the flux of short-chain gaseous alkanes (SCGAs; including ethane, propane and butane) from terrestrial and aquatic ecosystems to the atmosphere. Sulfate has been confirmed to act as electron acceptor supporting microbial anaerobic oxidation of SCGAs, yet several other energetically more favourable acceptors co-exist with these gases in anaerobic environments. Here, we show that a bioreactor seeded with biomass from a wastewater treatment facility can perform anaerobic propane oxidation coupled to nitrate reduction to dinitrogen gas and ammonium. The bioreactor was operated for more than 1000 days, and we used ¹³C- and ¹⁵N-labelling experiments, metagenomic, metatranscriptomic, metaproteomic and metabolite analyses to characterize the microbial community and the metabolic processes. The data collectively suggest that a species representing a novel order within the bacterial class Symbiobacteriia is responsible for the observed nitrate-dependent propane oxidation. The closed genome of this organism, which we designate as 'Candidatus Alkanivorans nitratireducens', encodes pathways for oxidation of propane to CO₂ via fumarate addition, and for nitrate reduction, with all the key genes expressed during nitrate-dependent propane oxidation. Our results suggest that nitrate is a relevant electron sink for SCGA oxidation in anaerobic environments, constituting a new microbially-mediated link between the carbon and nitrogen cycles.

Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils

Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of Anaeromyxobacter species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of Anaeromyxobacter , Anaeromyxobacter dehalogenans 2CP-1T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in A. dehalogenans 2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.

The inhibitory effects and underlying mechanism of high ammonia stress on sulfide-driven denitrification process

Sulfide-driven denitrification (SD) process has been widely studied for treating wastewater containing sulfate and ammonia in recent years. But influence of high ammonia stress on the SD process and microbial community remained unclear. In this work, a series of tests were conducted to investigate effects of different ammonia stress (200-3000 mg-total ammonia nitrogen (TAN)/L) on denitrification efficiency, byproduct accumulation and microbial community of the SD process. According to our results, the SD process was severely inhibited, and 32.67 ± 5.15 mg/L NO₂^--N was accumulated when ammonia stress reached 3000 mg TAN/L. But the inhibited SD process could recover in about 40 days when ammonia stress was decreased to 200 mg TAN/L. After analyzing the microbial community, Thiobacillus sp. (Thiobacillus sp. 65-29, Thiobacillus sp. SCN 64-317, Thiobacillus sp. 63-78 and Thiobacillus denitrificans) was confirmed as dominant bacteria responsible for the SD process. Further, expression of narG, napA, nirK and nirS were inhibited under high ammonia stress, thus making the SD process stuck in NO₃^- and NO₂^- reduction step. This study reveals the inhibitory effects of high ammonia stress on the SD process and its possible underlying mechanism with discussion in gene level.

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs. rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications.

Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils

Five strictly anaerobic strains, designated RG2^T, RG3, RG10^T, RF4^T, and RG29, were isolated from paddy soils in China. Strains RG2^T, RF4^T, RG10^T, RG3, and RG29 grew at temperatures ranging 5–42°C and pH ranging 5.5–8.5. Strains RG2^T, RF4^T, RG3, and RG29 could tolerate NaCl up to 0–0.7% (w/v) while strain RG10^T could tolerate NaCl up to 0–0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of Geomonas terrae Red111^T and Geomonas paludis Red736^T. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus Geomonas. Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C_15:1 ω6c, C_16:0, iso-C_15:0, and Summed Feature 3. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cutoff value (ANI 95–96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2^T, RG10^T, and RF4^T could easily be differentiated with the members of the genus Geomonas. Additionally, all the isolated strains possessed nifHDK clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus Geomonas, for which the names Geomonas oryzisoli sp. nov., Geomonas subterranea sp. nov., and Geomonas nitrogeniifigens sp. nov. are proposed. The type strains are RG10^T (= GDMCC1.2537^T = KCTC 26318^T), RG2^T (= GDMCC1.2536^T = KCTC 25317^T), and RF4^T (= GDMCC 1.2547^T = KCTC 25316^T).

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

Insight of bacteria and archaea in Feammox community enriched from different soils

Anaerobic ammonium oxidation coupled to Fe(III) reduction, known as Feammox, is a newly discovered nitrogen-cycling process, which serves an important role in the pathways of nitrogen loss in the environment. However, the specific types of microorganisms involved in Feammox currently remain unclear. In this study, we selected two groups of soil samples (paddy and mine), from considerably different habitats in South China, to acclimate Feammox colonies. The Paddy Group had a shorter lag period than the Mine Group, while the ammonium transformation rate was nearly equal in both groups in the mature period. The emergence of the Feammox activity was found to be associated with the increased abundance of iron-reducing bacteria, especially Clostridium_sensu_stricto_12, Desulfitobacterium, Thermoanaerobaculum, Anaeromyxobacter and Geobacter. Ammonium oxidizing archaea and methanogens were dominant among the known archaea. These findings extend our knowledge of the microbial community composition of the potential Feammox microbes from soils under different environmental conditions, which broadens our understanding of this important Fe/N transformation process.

Fe(II) enhances simultaneous phosphorus removal and denitrification in heterotrophic denitrification by chemical precipitation and stimulating denitrifiers activity

Using Fe(II) salt as the precipitant in heterotrophic denitrification achieves improved TP removal, and enhancement in denitrification was often observed. This study aimed to obtain a better understanding of Fe(II)-enhanced denitrification with sufficient carbon source supply. Laboratory-scale experiments were conducted in SBRs with or without Fe(II) addition. Remarkably improved TP removal was experienced. TP removal efficiency in Fe(II) adding reactor was 85.8 ± 3.4%; whereas, that in the reactor without Fe(II) addition was 31.1 ± 2.8%. Besides improved TP removal, better TN removal efficiency (94.1 ± 1.1%) were recorded when Fe(II) was added, and that in the reactor without Fe(II) addition was 89 ± 0.8%. The specific denitrification rate were observed increase by 12.6% when Fe(II) was added. Further microbial analyses revealed increases in the abundances of typical denitrifiers (i.e. Niastella, Opitutus, Dechloromonas, Ignavibacterium, Anaeromyxobacter, Pedosphaera, and Myxococcus). Their associated denitrifying genes, narG, nirS, norB, and nosZ, were observed had 14.2%, 19.4%, 21.6%, and 9.9% elevation, respectively. Such enhancement in denitrification shall not be due to nitrate-dependent ferrous oxidation, which prevails in organic-deficient environments. In an environment with a continuous supply of Fe(II) and plenty of carbon sources, a cycle of denitrifying enzyme activity enhancement in the presence of Fe(II) facilitating nitrogen substrate utilization, stimulating denitrifier metabolism and growth, elevating denitrifying genes abundance, and increasing denitrifying enzymes expression were thought to be responsible for the Fe(II)-enhanced heterotrophic denitrification. Fe(II) salt is often a less expensive precipitant and has recently become attractive for TP removal in wastewater. The findings of this study solidify previous observation of enhancement of both TP and TN removal by adding Fe(II) in denitrification, and would be helpful for developing cost-effective pollutant removal processes.

A Novel Regulator Participating in Nitrogen Removal Process of Bacillus subtilis JD-014

Aerobic denitrification is considered as a promising biological method to eliminate the nitrate contaminants in waterbodies. However, the molecular mechanism of this process varies in different functional bacteria. In this study, the nitrogen removal characteristics for a newly isolated aerobic denitrifier Bacillus subtilis JD-014 were investigated, and the potential functional genes involved in the aerobic denitrification process were further screened through transcriptome analysis. JD-014 exhibited efficient denitrification performance when having sodium succinate as the carbon source with the range of nitrate concentration between 50 and 300 mg/L. Following the transcriptome data, most of the up-regulated differentially expressed genes (DEGs) were associated with cell motility, carbohydrate metabolism, and energy metabolism. Moreover, gene nirsir annotated as sulfite reductase was screened out and further identified as a regulator participating in the nitrogen removal process within JD-014. The findings in present study provide meaningful information in terms of a comprehensive understanding of genetic regulation of nitrogen metabolism, especially for Bacillus strains.

Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Many biotic and abiotic processes contribute to nitrous oxide (N₂ O) production in the biosphere, but N₂ O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N₂ O reductase enzyme, NosZ, responsible for N₂ O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N₂ O reducers could play an important, previously unrecognized role in controlling N₂ O emissions for several reasons, including: (1) the consumption of N₂ O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N₂ O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N₂ O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N₂ O reducers in regulating soil N₂ O emissions.

Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N₂O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N₂O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N₂O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO₂ and the largest natural source of N₂O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.

The impacts of straw substrate on biofloc formation, bacterial community and nutrient removal in shrimp ponds

This study explored biofloc technology for shrimp culture based on straw substrates with a size of 40 mu, 80 mu, and 120 mu. Straw substrates utilization stimulated shrimp growth compared to control. Treatment with 40 mu had the best ammonium (71.60%) and nitrite nitrogen (77.78%) removal rates generally. In all biofloc treatments, Proteobacteria (4.10-56.1%) was the most dominant phylum, followed by Bacteroidetes (2.44-38.21%), Planctomycetes (0.45-21.41%), and Verrucomicrobia (1.2-10.30%). Redundancy analysis showed that salinity was a significant factor closely related to the microbial community in biofloc. The environmental parameters (DO > pH > TN > NH₄⁺-N > COD > Salinity > EC), nitrification, and denitrification genes (amoA > napA > nirK) were significant factors that interrelated with the bacterial genus in the network analysis. This study highlighted a novel technology of reusing agricultural waste that transformed inorganic nitrogen using nutrient recycling to control water quality in the culture system and produced microbial proteins that served as a natural nutritional supplement to enhance shrimp growth.

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

Aerobic Denitrification and Heterotrophic Sulfur Oxidation in the Genus Halomonas Revealed by Six Novel Species Characterizations and Genome-Based Analysis

Bacteria of Halomonas are widely distributed in various environments and play a substantial role in the nutrient cycle. In this report, 14 strains capable of aerobic denitrification and heterotrophic sulfur oxidation were isolated from different habitats. Based on the phenotypic, genotypic, and chemotaxonomic analyses, these strains were considered to represent six novel species of the genus Halomonas, for which the names Halomonas zhangzhouensis sp. nov. type strain CXT3-11T ( = MCCC 1A11036T = KCTC 72087T), Halomonas aerodenitrificans sp. nov. CYD-9T ( = MCCC 1A11058T = KCTC 72088T), Halomonas sulfidoxydans sp. nov. CYN-1-2T ( = MCCC 1A11059T = KCTC 72089T), Halomonas ethanolica sp. nov. CYT3-1-1T ( = MCCC 1A11081T = KCTC 72090T), Halomonas sulfidivorans sp. nov. NLG_F1ET ( = MCCC 1A13718T = KCTC 72091T), and Halomonas tianxiuensis sp. nov. BC-M4-5T ( = MCCC 1A14433T = KCTC 72092T) are proposed. Intriguingly, they formed a unique group with 11 other species designated as the "H. desiderata group." To better understand their featured metabolisms, genes involved in denitrification and sulfur oxidation were analyzed, along with 193 other available genomes of the whole genus. Consistently, complete denitrification pathways were confirmed in the "H. desiderata group," in which napA, narG, nirS, norB, and nosZ genes coexist. Their nitrite reductase NirS formed a unique evolutionary lineage, distinguished from other denitrifiers in Halomonas. In addition, diverse occurrence patterns of denitrification genes were also observed in different phylogenetic clades of Halomonas. With respect to sulfur oxidation, fccAB genes involved in sulfide oxidation commonly exist in the "H. desiderata group," while sqr genes are diverse and can be found in more species; sqr genes co-occurred with fccAB in eight strains of this study, contributing to more active sulfide oxidation. Besides, the tsdA gene, which encodes an enzyme that oxidizes thiosulfate to tetrathionate, is ubiquitous in the genus Halomonas. The widespread presence of sqr/fccAB, pdo, and tsdA in Halomonas suggests that many Halomonas spp. can act as heterotrophic sulfur oxidizers. These results provide comprehensive insights into the potential of denitrification and sulfur oxidation in the whole genus of Halomonas. With regard to the global distribution of Halomonas, this report implies their unneglectable role in the biogeochemical cycle.

The nitrogen removal characterization of a cold-adapted bacterium: Bacillus simplex H-b

The removal efficacy of biological nitrogen removal process is inhibited by low temperatures. Herein, a psychrotrophic bacterium strain, Bacillus simplex H-b, was isolated and identified with the potential to conduct heterotrophic nitrification and aerobic denitrification in the temperature range from 5 to 37 °C. At 10 °C, the removal efficiencies of initial nitrate-N (63 mg/L), nitrite-N (10 mg/L) and ammonium-N (60 mg/L) were 67.29%, 78.69% and 82.16%, with the maximum removal rate of 0.56, 0.18 and 0.74 mg/L/h, respectively. Additionally, both the accumulation level of ATP (adenosine triphosphate) and the formation of extracellular polymeric substances was found to increase with the decrease of temperature from 37 °C to 10 °C, indicating strain H-b might resist low temperature stress through its cellular extreme environment resistant mechanism and further suggesting the newly isolated strain could serve as a promising candidate for nitrogen contaminated wastewater treatment, especially under low-temperature condition.

Diazotrophic Anaeromyxobacter Isolates from Soils

Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N₂-dependent growth and acetylene reduction activity (ARA) in vitro Transcriptional activity of the nif gene was also detected when both strains were cultured with N₂ gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N₂ gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium.IMPORTANCE Anaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N₂-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.

Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov

Bacteria of the family Geobacteraceae are particularly common and deeply involved in many biogeochemical processes in terrestrial and freshwater environments. As part of a study to understand biogeochemical cycling in freshwater sediments, three iron-reducing isolates, designated as Red96^T, Red100^T, and Red88^T, were isolated from the soils of two paddy fields and pond sediment located in Japan. The cells were Gram-negative, strictly anaerobic, rod-shaped, motile, and red-pigmented on agar plates. Growth of these three strains was coupled to the reduction of Fe(III)-NTA, Fe(III) citrate, and ferrihydrite with malate, methanol, pyruvate, and various organic acids and sugars serving as alternate electron donors. Phylogenetic analysis based on the housekeeping genes (16S rRNA gene, gyrB, rpoB, nifD, fusA, and recA) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family Geobacteraceae. Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly differentiated the strains Red96^T, Red100^T, and Red88^T from other species in the family Geobacteraceae, with values below the thresholds for species delineation. Along with the genomic comparison, the chemotaxonomic features further helped distinguish the three isolates from each other. In addition, the lower values of average amino acid identity and percentage of conserved protein, as well as biochemical differences with their relatives, indicated that the three strains represented a novel genus in the family Geobacteraceae. Hence, we concluded that strains Red96^T, Red100^T, and Red88^T represented three novel species of a novel genus in the family Geobacteraceae, for which the names Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. are proposed, with type strains Red96^T (= NBRC 114286^T = MCCC 1K04376^T), Red100^T (= NBRC 114287^T = MCCC 1K04377^T), and Red88^T (= MCCC 1K03694^T = JCM 33033^T), respectively.

Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism

Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.

Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum

In tropical iron ore regions, biologically mediated reduction of crystalline iron oxides drives ongoing iron cycling that contributes to the stability of surface duricrusts. This represents a biotechnological opportunity with respect to post-mining rehabilitation attempts, requiring re-formation of these duricrusts. However, cultivated dissimilatory iron reducing bacteria typically reduce crystalline iron oxides quite poorly. A glucose-fermenting microbial consortium capable of reducing at least 27 mmol/L goethite was enriched from an iron duricrust region. Metagenome analysis led to the recovery of a metagenome assembled genome (MAG) of an iron reducer belonging to the alphaproteobacterial genus Telmatospirillum. This is the first report of iron reduction within the Telmatospirillum and the first reported genome of an iron-reducing, neutrophilic member of the Alphaproteobacteria. The Telmatospirillum MAG encodes putative metal transfer reductases (MtrA, MtrB) and a novel, multi-heme outer membrane cytochrome for extracellular electron transfer. In the presence of goethite, short chain fatty acid production shifted significantly in favor of acetate rather than propionate, indicating goethite is a hydrogen sink in the culture. Therefore, the presence of fermentative bacteria likely promotes iron reduction via hydrogen production. Stimulating microbial fermentation has potential to drive reduction of crystalline iron oxides, the rate limiting step for iron duricrust re-formation.

Changes in microbial communities of a passive coal mine drainage bioremediation system

Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%–43%), Bacteroidetes (12%–37%), Firmicutes (3%–11%), and Verrucomicrobia (6%–11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.

Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov

In paddy soil, bacteria from the family Geobacteraceae have been shown to strongly contribute to the biogeochemical cycle. However, no Geobacteraceae species with validly published names have been isolated from paddy soil. In this study, we isolated and characterized four novel ferric reducing bacteria in the family Geobacteraceae from the paddy soils of three different fields in Japan. The four strains, S43T, Red53T, S62T, and Red111T, were Gram-stain negative, strictly anaerobic, chemoheterotrophic, and motile with peritrichous flagella. Phylogenetic studies based on 16S rRNA gene sequences, five concatenated housekeeping genes (fusA, rpoB, recA, nifD, and gyrB) and 92 concatenated core genes revealed that the four strains belong to the family Geobacteraceae and are most closely related to Geobacter bemidjiensis BemT (97.4-98.2%, 16S rRNA gene sequence similarities) and Geobacter bremensis Dfr1T (97.1-98.0%). Genomic analysis with average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) calculations clearly distinguished the four isolated strains from other species of the family Geobacteraceae and indicated that strains S43T, Red53T, S62T, and Red111T represent independent species, with values below the thresholds for species delineation. Chemotaxonomic characteristics, including major fatty acid and whole cell protein profiles, showed differences among the isolates and their closest relatives, which were consistent with the results of DNA fingerprints and physiological characterization. Additionally, each of the four isolates shared a low 16S rRNA gene sequence similarity (92.4%) and average amino acid identity (AAI) with the type strain of the type species Geobacter metallireducens. Overall, strains S43T, Red53T, S62T, and Red111T represent four novel species, which we propose to classify in a novel genus of the family Geobacteraceae, and the names Geomonas oryzae gen. nov., sp. nov. (type strain S43T), Geomonas edaphica sp. nov. (type strain Red53T), Geomonas ferrireducens sp. nov. (type strain S62T), and Geomonas terrae sp. nov. (type strain Red111T) are proposed. Based on phylogenetic and genomic analyses, we also propose the reclassification of Geobacter bremensis as Geomonas bremensis comb. nov., Geobacter pelophilus as Geomonas pelophila comb. nov., and Geobacter bemidjiensis as Geomonas bemidjiensis comb. nov.

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges

River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firmicutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeota in G15Y and G15DS, indicating Yamuna River's influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem.

The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats

Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N₂O release. Loss as N₂ was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N₂O emissions from productive lakes.

Ecological and physiological implications of nitrogen oxide reduction pathways on greenhouse gas emissions in agroecosystems

Microbial reductive pathways of nitrogen (N) oxides are highly relevant to net emissions of greenhouse gases (GHG) from agroecosystems. Several biotic and abiotic N-oxide reductive pathways influence the N budget and net GHG production in soil. This review summarizes the recent findings of N-oxide reduction pathways and their implications to GHG emissions in agroecosystems and proposes several mitigation strategies. Denitrification is the primary N-oxide reductive pathway that results in direct N2O emissions and fixed N losses, which add to the net carbon footprint. We highlight how dissimilatory nitrate reduction to ammonium (DNRA), an alternative N-oxide reduction pathway, may be used to reduce N2O production and N losses via denitrification. Implications of nosZ abundance and diversity and expressed N2O reductase activity to soil N2O emissions are reviewed with focus on the role of the N2O-reducers as an important N2O sink. Non-prokaryotic N2O sources, e.g. fungal denitrification, codenitrification and chemodenitrification, are also summarized to emphasize their potential significance as modulators of soil N2O emissions. Through the extensive review of these recent scientific advancements, this study posits opportunities for GHG mitigation through manipulation of microbial N-oxide reductive pathways in soil.

An evaluation of primers for detecting denitrifiers via their functional genes

Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.

Nitrous Oxide Is a Potent Inhibitor of Bacterial Reductive Dechlorination

Organohalide-respiring bacteria are key players for the turnover of organohalogens. At sites impacted with chlorinated ethenes, bioremediation promotes reductive dechlorination; however, stoichiometric conversion to environmentally benign ethene is not always achieved. We demonstrate that nitrous oxide (N₂O), a compound commonly present in groundwater, inhibits organohalide respiration. N₂O concentrations in the low micromolar range decreased dechlorination rates and resulted in incomplete dechlorination of tetrachloroethene (PCE) in Geobacter lovleyi strain SZ and of cis-1,2-dichloroethene ( cDCE) and vinyl chloride (VC) in Dehalococcoides mccartyi strain BAV1 axenic cultures. Presumably, N₂O interferes with reductive dechlorination by reacting with super-reduced Co(I)-corrinoids of reductive dehalogenases, which is supported by the finding that N₂O did not inhibit corrinoid-independent fumarate-to-succinate reduction in strain SZ. Kinetic analyses revealed a best fit to the noncompetitive Michaelis-Menten inhibition model and determined N₂O inhibitory constants, K_I, for PCE and cDCE dechlorination of 40.8 ± 3.8 and 21.2 ± 3.5 μM in strain SZ and strain BAV1, respectively. The lowest K_I value of 9.6 ± 0.4 μM was determined for VC to ethene reductive dechlorination in strain BAV1, suggesting that this crucial dechlorination step for achieving detoxification is most susceptible to N₂O inhibition. Groundwater N₂O concentrations exceeding 100 μM are not uncommon, especially in watersheds impacted by nitrate runoff from agricultural sources. Thus, dissolved N₂O measurements can inform about cDCE and VC stalls at sites impacted with chlorinated ethenes.

Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan

Nitrous oxide (N₂O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N₂O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N₂O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N₂O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N₂O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N₂O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N₂O only. Collectively, these results suggest that the N₂O-reducing microbiome in eelgrass meadows is largely responsible for coastal N₂O mitigation.

Nitrous oxide from chemodenitrification: A possible missing link in the Proterozoic greenhouse and the evolution of aerobic respiration

The potent greenhouse gas nitrous oxide (N₂ O) may have been an important constituent of Earth's atmosphere during Proterozoic (~2.5-0.5 Ga). Here, we tested the hypothesis that chemodenitrification, the rapid reduction of nitric oxide by ferrous iron, would have enhanced the flux of N₂ O from ferruginous Proterozoic seas. We empirically derived a rate law, d N 2 O d t = 7.2 × 10 - 5 [ Fe 2 + ] 0.3 [ NO ] 1 , and measured an isotopic site preference of +16‰ for the reaction. Using this empirical rate law, and integrating across an oceanwide oxycline, we found that low nM NO and μM-low mM Fe²⁺ concentrations could have sustained a sea-air flux of 100-200 Tg N₂ O-N year^-1 , if N₂ fixation rates were near-modern and all fixed N₂ was emitted as N₂ O. A 1D photochemical model was used to obtain steady-state atmospheric N₂ O concentrations as a function of sea-air N₂ O flux across the wide range of possible pO₂ values (0.001-1 PAL). At 100-200 Tg N₂ O-N year^-1 and >0.1 PAL O₂ , this model yielded low-ppmv N₂ O, which would produce several degrees of greenhouse warming at 1.6 ppmv CH₄ and 320 ppmv CO₂ . These results suggest that enhanced N₂ O production in ferruginous seawater via a previously unconsidered chemodenitrification pathway may have helped to fill a Proterozoic "greenhouse gap," reconciling an ice-free Mesoproterozoic Earth with a less luminous early Sun. A particularly notable result was that high N₂ O fluxes at intermediate O₂ concentrations (0.01-0.1 PAL) would have enhanced ozone screening of solar UV radiation. Due to rapid photolysis in the absence of an ozone shield, N₂ O is unlikely to have been an important greenhouse gas if Mesoproterozoic O₂ was 0.001 PAL. At low O₂ , N₂ O might have played a more important role as life's primary terminal electron acceptor during the transition from an anoxic to oxic surface Earth, and correspondingly, from anaerobic to aerobic metabolisms.

Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors

Bacteria of the genus Paracoccus are common components of the microbiomes of many naturally- and anthropogenically shaped environments. One species, Paracoccus yeei, is unique within the genus because it is associated with opportunistic human infections. Therefore, strains of P. yeei may serve as an interesting model to study the transition from a saprophytic to a pathogenic lifestyle in environmental bacteria. Unfortunately, knowledge concerning the biology, genetics and genomic content of P. yeei is fragmentary; also the mechanisms of pathogenicity of this bacterium remain unclear. In this study we provide the first insight into the genome composition and metabolic potential of a clinical isolate, P. yeei CCUG 32053. This strain has a multipartite genome (4,632,079 bp) composed of a circular chromosome plus eight extrachromosomal replicons pYEE1–8: 3 chromids and 5 plasmids, with a total size of 1,247,173 bp. The genome has been significantly shaped by the acquisition of genomic islands, prophages (Myoviridae and Siphoviridae phage families) and numerous insertion sequences (ISs) representing seven IS families. Detailed comparative analysis with other complete genomic sequences of Paracoccus spp. (including P. yeei FDAARGOS_252 and TT13, as well as non-pathogenic strains of other species in this genus) enabled us to identify P. yeei species-specific genes and to predict putative determinants of virulence. This is the first attempt to identify pathoadaptive genetic information of P. yeei and to estimate the role of the mobilome in the evolution of pathogenicity in this species.

Nitrogen removal performance and functional genes distribution patterns in solid-phase denitrification sub-surface constructed wetland with micro aeration

An up-flow vertical flow constructed wetland (AC-VFCW) filled with ceramsite and 5% external carbon source poly(3-hydroxybutyrate-hydroxyvalerate) (PHBV) as substrate was set for nitrogen removal with micro aeration. Simultaneous nitrification and denitrification process was observed with 90.4% NH₄⁺-N and 92.1% TN removal efficiencies. Nitrification and denitrification genes were both preferentially enriched on the surface of PHBV. Nitrogen transformation along the flow direction showed that NH₄⁺-N was oxidized to NO₃^--N at the lowermost 10 cm of the substrate and NO₃^--N gradually degraded over the depth. AmoA gene was more enriched at -10 and -50 cm layers. NirS gene was the dominant functional gene at the bottom layer with the abundance of 2.05 × 10⁷ copies g^-1 substrate while nosZ gene was predominantly abundant with 7.51 × 10⁶ and 2.64 × 10⁶ copies g^-1 substrate at the middle and top layer, respectively, indicating that functional division of dominant nitrogen functional genes forms along the flow direction in AC-VFCW.

Nitrogen Addition Decreases Dissimilatory Nitrate Reduction to Ammonium in Rice Paddies

Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.

Environmental Controls on Soil Microbial Communities in a Seasonally Dry Tropical Forest

Several studies have shown that rainfall seasonality, soil heterogeneity, and increased nitrogen (N) deposition may have important effects on tropical forest function. However, the effects of these environmental controls on soil microbial communities in seasonally dry tropical forests are poorly understood. In a seasonally dry tropical forest in the Yucatan Peninsula (Mexico), we investigated the influence of soil heterogeneity (which results in two different soil types, black and red soils), rainfall seasonality (in two successive seasons, wet and dry), and 3 years of repeated N enrichment on soil chemical and microbiological properties, including bacterial gene content and community structure. The soil properties varied with the soil type and the sampling season but did not respond to N enrichment. Greater organic matter content in the black soils was associated with higher microbial biomass, enzyme activities, and abundances of genes related to nitrification (amoA) and denitrification (nirK and nirS) than were observed in the red soils. Rainfall seasonality was also associated with changes in soil microbial biomass and activity levels and N gene abundances. Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria were the most abundant phyla. Differences in bacterial community composition were associated with soil type and season and were primarily detected at higher taxonomic resolution, where specific taxa drive the separation of communities between soils. We observed that soil heterogeneity and rainfall seasonality were the main correlates of soil bacterial community structure and function in this tropical forest, likely acting through their effects on soil attributes, especially those related to soil organic matter and moisture content.IMPORTANCE Understanding the response of soil microbial communities to environmental factors is important for predicting the contribution of forest ecosystems to global environmental change. Seasonally dry tropical forests are characterized by receiving less than 1,800 mm of rain per year in alternating wet and dry seasons and by high heterogeneity in plant diversity and soil chemistry. For these reasons, N deposition may affect their soils differently than those in humid tropical forests. This study documents the influence of rainfall seasonality, soil heterogeneity, and N deposition on soil chemical and microbiological properties in a seasonally dry tropical forest. Our findings suggest that soil heterogeneity and rainfall seasonality are likely the main factors controlling soil bacterial community structure and function in this tropical forest. Nitrogen enrichment was likely too low to induce significant short-term effects on soil properties, because this tropical forest is not N limited.