The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

Comparative analysis of niche adaptation strategies of AOA, AOB, and comammox along a gate-controlled river-estuary continuum

Ammonia oxidizers are key players in the biogeochemical nitrogen cycle. However, in critical ecological zones such as estuaries, especially those affected by widespread anthropogenic dam control, our understanding of their occurrence, ecological performance, and survival strategies remains elusive. Here, we sampled sediments along the Haihe River-Estuary continuum in China, controlled by the Haihe Tidal Gate, and employed a combination of biochemical and metagenomic approaches to investigate the abundance, activity, and composition of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (comammox). We also conducted an extensive comparison of the salinity adaptation mechanisms of different ammonia oxidizers. We found that AOB (57.55 ± 11.46 %) dominated the nitrification process upstream of the tidal gate, while comammox (68.22 ± 14.42 %) played the major role downstream. Redundancy analysis results showed that total nitrogen, ammonium, and salinity were the primary factors influencing the abundance, activity, and contribution of ammonia oxidizers. The abundance and activity of AOB were significantly positively correlated with ammonium. KEGG annotation results showed that AOA Nitrososphaera, AOB Nitrosomonas, and comammox Nitrospira had 7, 31, and 22 genes associated to salinity adaptation, respectively, and were capable of employing both the "salt-in" and "salt-out" strategies. Metagenome assembly results indicated that comammox outperformed AOA primarily in compatible solute accumulation; AOA can synthesize glutamate, whereas comammox Nitrospira can additionally synthesize glycine betaine, choline, and trehalose. The tidal gate caused sharp shifts in ammonium (from 4.10 ± 3.28 mg·kg-1 to 0.45 ± 0.10 mg·kg-1) and salinity (from 1.64 ± 0.48 ppt to 3.26 ± 0.89 ppt), playing a dominant role in driving niche differentiation of ammonia oxidizers along the Haihe River-Estuary continuum. These findings provide profound insights into the nitrogen cycle in freshwater-saltwater transition zones, especially in today's world where estuaries are widely controlled by tidal gates.

Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus

Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N2O) emissions, although biochemical origins of this N2O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus. We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH2OH) to dioxygen (O2) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N2 via reaction with NH2OH and dimerization with itself to yield N2O. These results afford one plausible enzymatic origin for N2O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.

Characterization of prokaryotic communities from Italian super-heated fumaroles

Among extremophiles, thermophile microorganisms from geothermal sites have been widely studied. Nevertheless, our knowledge is still relatively poor on microbial communities colonizing fumaroles, which are super-ephemeral habitats, characterized by an only intermittent presence of water. Here we characterized by metabarcoding both bacterial and archaeal communities from hot spring waters and biofilms, together with dry and wet fumaroles, of a geothermal basin in central Italy. Taxa composition of the analyzed samples mirrored that of previous studies, with Thermoproteota dominating among Archaea, while high percentages of thermophiles and spore-forming organisms were retrieved for Bacteria. Cyanobacteriota were the dominant group in biofilms. Community structure was different in the two domains, with highly selected communities of Archaea, less diversified than bacterial ones. Linear regression analyses highlighted significant correlations between diversity and environmental parameters in dry, but not in wet fumaroles. Although ASV numbers displayed different trends for the two different prokaryotic domains (positive correlation with pH for Bacteria, negative correlation for both pH and T for Archaea), such results indicate that even an extremely ephemeral presence of water can influence the importance of temperature and pH as drivers for microbial community structure.

Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers

Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.

Fusion/fission protein family identification in Archaea

The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.

Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system

The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.

Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans

Introduction

Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions.

Methods

In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria.

Results and Discussion

Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.

Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils

Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.

Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary

The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.

Metabolic potential of Nitrososphaera-associated clades

Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.

Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments

Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.

Growth of soil ammonia-oxidizing archaea on air-exposed solid surface

Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.

Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains

Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.

Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches

Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.

Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil

Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.

Nitrification and beyond: metabolic versatility of ammonia oxidising archaea

Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

BACKGROUND

Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera.

RESULTS

We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species.

CONCLUSIONS

The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.

Soil Bacterial Communities from Three Agricultural Production Systems in Rural Landscapes of Palmira, Colombia

Soils play important roles in the proper functioning of agroecosystems. Using molecular characterization methods such as metabarcoding, soils from eight farms (57 samples) belonging to three production system types-agroecological (two farms with twenty-two sampling points), organic (three farms with twenty-one sampling points), and conventional (three farms with fourteen sampling points)-were compared from the rural villages of El Arenillo and El Mesón in Palmira, Colombia. Amplification and sequencing of the hypervariable V4 region of the 16S rRNA gene was performed using next-generation sequencing (Illumina MiSeq) to estimate the bacterial composition and the alpha and beta diversity present. Across all soil samples, we found 2 domains (Archaea and Bacteria), 56 phylum, 190 classes, 386 orders, 632 families, and 1101 genera to be present. The most abundant phyla in the three systems were Proteobacteria, (agroecological 28%, organic 30%, and conventional 27%), Acidobacteria (agroecological 22%, organic 21%, and conventional 24%), and Verrucomicrobia (agroecological 10%, organic 6%, and conventional 13%). We found 41 nitrogen-fixing and phosphate-dissolving genera which promote growth and pathogens. Alpha and beta diversity indices were very similar across the three agricultural production systems, as reflected by shared amplicon sequence variants (ASVs) among them, likely due to the proximity of the sampling sites and recent management changes.

Responses of potential ammonia oxidation and ammonia oxidizers community to arsenic stress in seven types of soil

Soil arsenic contamination is of great concern because of its toxicity to human, crops, and soil microorganisms. However, the impacts of arsenic on soil ammonia oxidizers communities remain unclear. Seven types of soil spiked with 0 or 100 mg arsenic per kg soil were incubated for 180 days and sampled at days 1, 15, 30, 90 and 180. The changes in the community composition and abundance of ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis, clone library sequencing, and quantitative PCR (qPCR) targeting amoA gene. Results revealed considerable variations in the potential ammonia oxidation (PAO) rates in different soils, but soil PAO was not consistently significantly inhibited by arsenic, probably due to the low bioavailable arsenic contents or the existence of functional redundancy between AOB and AOA. The variations in AOB and AOA communities were closely associated with the changes in arsenic fractionations. The amoA gene abundances of AOA increased after arsenic addition, whereas AOB decreased, which corroborated the notion that AOA and AOB might occupy different niches in arsenic-contaminated soils. Phylogenetic analysis of amoA gene-encoded proteins revealed that all AOB clone sequences belonged to the genus Nitrosospira, among which those belonging to Nitrosospira cluster 3a were dominant. The main AOA sequence detected belonged to Thaumarchaeal Group 1.1b, which was considered to have a high ability to adapt to environmental changes. Our results provide new insights into the impacts of arsenic on the soil nitrogen cycling.

A New Perspective for Vineyard Terroir Identity: Looking for Microbial Indicator Species by Long Read Nanopore Sequencing

Grapevine is one of the most important fruit crops worldwide, being Portugal one of the top wine producers. It is well established that wine sensory characteristics from a particular region are defined by the physiological responses of the grapevine to its environment and thus, the concept of terroir in viticulture was established. Among all the factors that contribute to terroir definition, soil microorganisms play a major role from nutrient recycling to a drastic influence on plant fitness (growth and protection) and of course wine production. Soil microbiome from four different terroirs in Quinta dos Murças vineyard was analysed through long-read Oxford Nanopore sequencing. We have developed an analytical pipeline that allows the identification of function, ecologies, and indicator species based on long read sequencing data. The Douro vineyard was used as a case study, and we were able to establish microbiome signatures of each terroir.

Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta

Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.

Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior

Despite being the largest freshwater lake system in the world, relatively little is known about the sestonic microbial community structure in the Laurentian Great Lakes. The goal of this research was to better understand this ecosystem using high-throughput sequencing of microbial communities as a function of water depth at six locations in the westernmost Great Lakes of Superior and Michigan. The water column was characterized by gradients in temperature, dissolved oxygen (DO), pH, and other physicochemical parameters with depth. Mean nitrate concentrations were 32 μmol/L, with only slight variation within and between the lakes, and with depth. Mean available phosphorus was 0.07 μmol/L, resulting in relatively large N:P ratios (97:1) indicative of P limitation. Abundances of the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Thaumarchaeota, and Verrucomicrobia differed significantly among the Lakes. Candidatus Nitrosopumilus was present in greater abundance in Lake Superior compared to Lake Michigan, suggesting the importance of ammonia-oxidating archaea in water column N cycling in Lake Superior. The Shannon diversity index was negatively correlated with pH, temperature, and salinity, and positively correlated with DO, latitude, and N₂ saturation. Results of this study suggest that DO, pH, temperature, and salinity were major drivers shaping the community composition in the Great Lakes.

Archaea and their interactions with bacteria in a karst ecosystem

Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 + availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2 -. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.

Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands

Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N₂O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N₂O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N₂O through lab-scale subsurface CWs. The N₂O emission flux of CW at 8 °C was 1.23 mg m^-2·h^-1, significantly lower than that at 25 °C (1.92 mg m^-2·h^-1). The contribution of ammonia oxidation to N₂O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N₂O production from AOA increased from 1.91 ng N·g^-1 at 25 °C to 4.11 ng N·g^-1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N₂O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N₂O at low temperature.

Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine

Ammonia oxidizers (ammonia-oxidizing bacteria (AOB amoA) and ammonia-oxidizing archaea (AOA amoA)) and denitrifiers (encoded by nirS, nirK and nosZ) in the soil nitrogen cycle exist in a variety of natural ecosystems. However, little is known about the contribution of these five N-related functional genes to nitrification and denitrification in the soil profile in severely ecologically degraded areas. Therefore, in the present study, the abundance, diversity and community composition of AOA, AOB, nirS, nirK and nosZ were investigated in the soil profiles of different ecologically degraded areas in the Siding mine. The results indicated that, at the phylum level, the dominant archaea were Crenarchaeota and Thaumarchaeota and the dominant bacteria were Proteobacteria. Heavy metal contents had a great impact on AOA amoA, nirS and nirK gene abundances. AOA amoA contributed more during the ammonia oxidation process and was better adapted for survival in heavy metal-contaminated environments. In addition to heavy metals, the soil organic matter (SOM) content and C/N ratio had strong effects on the AOA and AOB community diversity and structure. In addition, variations in the net ammonification and nitrification rates were proportional to AOA amoA abundance along the soil profile. The soil C/N ratio, soil available phosphorus content and soil moisture influenced the denitrification process. Both soil available phosphorus and moisture were more strongly related to nosZ than to nirS and nirK. In addition, nosZ presented a higher correlation with the nosZ/(nirS + nirK) ratio. Moreover, nosZ/(nirS + nirK) was the key functional gene group that drove the major processes for NH₄⁺-N and NO₃^--N transformation. This study demonstrated the role and importance of soil property impacts on N-related microbes in the soil profile and provided a better understanding of the role and importance of N-related functional genes and their contribution to soil nitrification and denitrification processes in highly degraded areas in the Siding mine.

Response mechanisms of bacterial communities and nitrogen cycle functional genes in millet rhizosphere soil to chromium stress

Introduction

A growing amount of heavy metal contamination in soil disturbs the ecosystem's equilibrium, in which microbial populations play a key role in the nutrient cycle of soils. However, given the different sensitivity of microbial communities to different spatial and temporal scales, microbial community structure and function also have varied response mechanisms to different heavy metal contaminated habitats.

Methods

In this study, samples were taken prior to Cr stress (CK) and 6 h and 6 days after Cr stress (Cr_6h, Cr_6d) in laboratory experiments. High-throughput sequencing revealed trends in the structure and diversity of the bacterial communities, and real-time fluorescence quantitative polymerase chain reaction (qPCR) was used to analyze trends in nitrogen cycle functional genes (AOA-amoA, AOB-amoA, narG, nirK, and nifH).

Results

The findings showed that (1) the composition structure of the soil bacterial community changed considerably in Cr-stressed soils; α-diversity showed significant phase transition characteristic from stress to stability (p < 0.05). (2) With an overall rising tendency, the abundance of the nitrogen cycle functional genes (AOA-amoA and AOB-amoA) decreased considerably before increasing, and α-diversity dramatically declined (p < 0.05). (3) The redundancy analysis (RDA) and permutational multivariate analysis of variance (PERMANOVA) tests results showed that the soil physicochemical parameters were significantly correlated with the nitrogen cycle functional genes (r: 0.4195, p < 0.01). Mantel analysis showed that available nitrogen (N), available potassium (K), and available phosphorus (P) were significantly correlated with nifH (p = 0.006, 0.008, 0.004), and pH was highly significantly correlated with nifH (p = 0.026). The PLS-ME (partial least squares path model) model further demonstrated a significant direct effect of the soil physicochemical parameters on the nitrogen cycling functional genes.

Discussion

As a result, the composition and diversity of the bacterial community and the nitrogen cycle functional genes in Cr-stressed agricultural soils changed considerably. However, the influence of the soil physicochemical parameters on the functional genes involved in the nitrogen cycle was greater than that of the bacterial community. and Cr stress affects the N cycling process in soil mainly by affecting nitrification. This research has significant practical ramifications for understanding the mechanisms of microbial community homeostasis maintenance, nitrogen cycle response mechanisms, and soil remediation in heavy metal-contaminated agricultural soils.

Chemolithoautotroph distributions across the subsurface of a convergent margin

Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.

The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils

Nitrification is believed to be one of the primary processes of N₂O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH₄⁺ availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N₂O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N₂O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N₂O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH₄⁺) observably stimulated the production of both AOA and AOB-related N₂O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N₂O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N₂O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N₂O production in purple soils. We speculate that both NH₄⁺ content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N₂O yield led to the different N₂O emission characteristics in purple soils. These results may help inform the development of N₂O reduction strategies in the future.

Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers

Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.

Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments

BACKGROUND

Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water.

RESULTS

A customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO43-, H+, Fe2+, Cu2+) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.

CONCLUSIONS

These findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.

Laboratory-Controlled Experiments Reveal Microbial Community Shifts during Sediment Resuspension Events

In freshwater ecosystems, dynamic hydraulic events (floods or dam maintenance) lead to sediment resuspension and mixing with waters of different composition. Microbial communities living in the sediments play a major role in these leaching events, contributing to organic matter degradation and the release of trace elements. However, the dynamics of community diversity are seldom studied in the context of ecological studies. Therefore, we carried out laboratory-induced leaching experiments, using sediments from the Villerest dam reservoir (Villerest, France). To assess whole microbial community diversity, we sequenced the archaeal and bacterial 16S rRNA genes using Illumina MiSeq. Our results suggest that the degree of dissolved oxygen found in the water during these resuspension episodes influenced community dynamics, with anoxic waters leading to drastic shifts in sedimentary communities compared to oxic waters. Furthermore, the release of microbial cells from sediments to the water column were more favorable to water colonization when events were caused by oxic waters. Most of the bacteria found in the sediments were chemoorganotrophs and most of the archaea were methanogens. Methylotrophic, as well as archaeal, and bacterial chemoorganotrophs were detected in the leachate samples. These results also show that organic matter degradation occurred, likely participating in carbonate dissolution and the release of trace elements during freshwater resuspension events.

Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota

The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.

Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation

Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.

Soil dissolved organic matters mediate bacterial taxa to enhance nitrification rates under wheat cultivation

Studies have shown that dissolved organic matters (DOMs) may affect soil nutrient availability to plants due to their effect on microbial communities; however, the relationships of soil DOM-bacterial community-N function in response to root exudates remains poorly understand. Here, we evaluated the DOM composition, bacterial taxonomic variation and nitrogen transformation rates in both acidic and alkaline soils, with or without the typical nitrate preference plant (wheat, Triticum aestivum L.). After 30 days' cultivation, DOM compositions such as sugars, amines, amino acids, organic acid, and ketone were significantly increased in soil with wheat vs. bare soil, and these compounds were mainly involved in nitrogen metabolism pathways. Soil core bacterial abundance was changed while bacterial community diversity decreased in response to wheat planting. Function prediction analysis based on FAPROTAX software showed that the bacterial community were significantly (p < 0.05) affiliated with nitrification and organic compound degradation. Additionally, db-RDA and VPA analysis suggested that the contribution of soil DOM to the variance of bacterial community was stronger than that of soil available nutrients. Furthermore, the N-transformation related bacteria like Burkholderiales and ammonia-oxidizing bacteria (AOB) were positively correlated with soil gross nitrification rate, confirming that the soil N transformation was enhanced in both acidic and alkaline soils. Our results provide insight into how soil DOM affects the community structure and function of bacteria to regulate the process of nitrogen transformation in plant-soil system.

Optimization of plant harvest and management patterns to enhance the carbon sink of reclaimed wetland in the Yangtze River estuary

Estuarine wetlands are often located in economically developed and densely populated estuarine deltas, which are frequently disturbed and threatened by human activities. Reclamation, as an important way to alleviate the demand for local land resources, can lead to habitat destruction of natural coastal wetlands and weakening of ecological service functions, including carbon sink capacity. Research has shown that poor plant growth and weakened carbon fixation were the main reasons for the reduced carbon sequestration in a reclaimed wetland. This study aimed to examine the impacts of plant management on the improvement or restoration of carbon sink function in Chongming Dongtan reclaimed wetland, located in the Yangtze River Estuary, China. A management pattern that could effectively enhance the carbon sink function of the reclaimed wetland was selected based on analyses of the effects of different plant harvesting and management patterns (no harvesting, harvesting without returning to the field, direct straw return, and charred straw return) on the plant growth, carbon fixation, and soil respiration, combined with whole-life-cycle carbon footprint evaluation from straw harvest to field return. Compared with no harvesting, the aboveground biomass of direct straw return and charred straw return increased by about 12.3% and 15.5%, respectively (P < 0.05). Simultaneously, straw charring released the least amount of CO₂ (1.94 μmol m^-2 s^-1) and inhibited degradation of soil organic carbon through affecting its microbial community structure. Moreover, considering the carbon budget of different patterns, the charred straw return pattern also most effectively enhanced the carbon sink function and thus could be used for subsequent improvement of carbon sequestration in reclaimed wetlands.

Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems

Thaumarchaeota (now the class Nitrososphaeria in the phylum Thermoproteota in GTDB taxonomy) are abundant across marine and soil habitats; however, their genomic diversity and evolutionary history in freshwater environments remain elusive. Here, we reconstructed 17 high-quality metagenome-assembled genomes of Nitrososphaeria from a deep lake and two great rivers, and compared all available genomes between freshwater and marine habitats regarding their phylogenetic positions, relative abundance, and genomic content. We found that freshwater Nitrososphaeria were dominated by the family Nitrosopumilaceae and could be grouped into three distinct clades closely related to the genera Nitrosopumilus, Nitrosoarchaeum, and Nitrosotenuis. The Nitrosopumilus-like clade was exclusively from deep lakes, while the Nitrosoarchaeum-like clade was dominated by species from deep lakes and rivers, and the Nitrosotenuis-like clade was mainly from rivers, deep lakes, and estuaries. Interestingly, there was vertical niche separation between two clades in deep lakes, showing that the Nitrosopumilus-like species dominated shallow layers, whereas the relative abundance of the Nitrosoarchaeum-like clade increased toward deep waters. Phylogenetic clustering patterns in the Nitrosopumilaceae supported at least one freshwater-to-marine and two marine-to-freshwater transitions, the former of which refined the potential terrestrial-to-marine evolutionary path as previously proposed. The occurrence of the two marine-to-freshwater transitions were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation, and cell motility during their colonization to freshwater habitats. Specifically, the Nitrosopumilus-like clade showed losses of genes encoding flagella assembly and ion transport, whereas the Nitrosoarchaeum-like clade had losses of intact genes involved in urea uptake and utilization and gains of genes encoding osmolarity-mediated mechanosensitive channels. Collectively, our results reveal for the first time the high genomic diversity of the class Nitrososphaeria across freshwater ecosystems and provide novel insights into their adaptive mechanisms and evolutionary histories.

Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea

The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.

Intercropping Pinto Peanut in Litchi Orchard Effectively Improved Soil Available Potassium Content, Optimized Soil Bacterial Community Structure, and Advanced Bacterial Community Diversity

Intercropping is widely used in agricultural production due to its capability of raising land productivity and providing an opportunity to achieve sustainable intensification of agriculture. In this study, soil samples from 10 to 20 cm depth of intercropping Pinto peanut in litchi orchard and litchi monoculture mode were established to determine soil attributes, enzyme activities, as well as the effect on soil bacterial diversity. On this basis, 16S rRNA V4-V5 region of soil bacterial communities in litchi/Pinto peanut intercropping (LP) mode and litchi monoculture mode (CK) was detected by the Illumina MiSeq sequencing platform. The results showed that the content of available potassium (AK) in LP was significantly higher than that in CK by 138.9%, and the content of available nitrogen (AN) in LP was significantly lower than that in CK by 19.6%. The soil enzyme activities were higher in LP as a whole, especially sucrase (SC) and acid protease (PT) were significantly higher by 154.4 and 76.5%, respectively. The absolute abundance and alpha diversity of soil microbiota were significantly higher in the intercropping group. Most importantly, endemic species with a significant difference in LP was higher by ~60 times compared to CK treatment. In the aspect of soil bacterial community structure, the dominant phyla of the two groups were Acidobacteria, Proteobacteria, Chloroflexi, and Actinobacteria. At the genus level, the absolute abundance of Flavobacterium and Nitrososphaera was significantly higher by 79.20 and 72.93%, respectively, while that of Candidatus_Koribacter was significantly lower with an amplitude of 62.24% in LP than in CK. Furthermore, the redundancy analysis (RDA) suggested that AK, which was highly associated with the dominant genera and phyla, is the vitally dominating environmental factors in LP groups, while in CK groups, it is AN and pH. In addition, PICRUSt2 analysis indicated that intercropping improved the metabolic activity of bacteria which can be correlated to the resistance of litchi root systems to soil-borne diseases. Overall, this study is expected to provide a theoretical basis and technical support for the healthy intercropping cultivation of litchi.

Glycyrrhiza uralensis Fisch. Root-associated microbiota: the multifaceted hubs associated with environmental factors, growth status and accumulation of secondary metabolites

Glycyrrhiza uralensis Fisch. is an important, perennial medicinal plant whose root microbiome is considered to play an important role in promoting accumulation of effective medicinal ingredients (liquiritin and glycrrhizic acid). Here, we report a comprehensive analysis of the microbial community structural composition and metabolite-plant-microbes association of G. uralensis Fisch. We collected both soil and rhizosphere samples of G. uralensis from different environmental conditions (cultivated and wild) and growth years (grown for one year and three years). Our data revealed higher species diversity in the wild group than in the cultivated group. The core rhizosphere microbiome of G. uralensis comprised 78 genera, including Bacillus, Pseudomonas, Rhizobium, some of which were potential plant beneficial microbes. Our results suggest that the growth of G. uralensis has a correlation with the root-associated microbiota assemblage. Integrated analysis among rhizosphere microbial taxa, plant gene expressions, and liquiritin and glycrrhizic acid accumulation showed that the liquiritin and glycrrhizic acid accumulation exhibited associations with the rhizosphere microbial composition at the genus level. The results provide valuable information to guide cultivation of G. uralensis, and potentially to harness the power of the root-associated microbiota to improve medicinal plant production.

Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers

Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil

Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha^-1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.

Salt tolerance-based niche differentiation of soil ammonia oxidizers

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined ¹³C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol_c exchangeable Na⁺ kg^-1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na⁺ extrusion/H⁺ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na⁺ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms

Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO₃ by the activity of nitrifying bacteria.

Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers

The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH₄ ⁺-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N₂ production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH₄ ⁺, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.

Can moderate heavy metal soil contaminations due to cement production influence the surrounding soil bacterial communities?

Events of soil contamination by heavy metals are mostly related to human activities that release these metals into the environment as emissions or effluents. Among the industrial activities related to heavy metal pollution, cement production plants are considered one of the most common sources. In this work we applied the High-throughput sequencing approach called 16 S rDNA metabarcoding to perform the taxonomic characterization of the prokaryotic communities of the soil surrounding three cement plants as well as two areas outside the influence of the cement plants that represented agricultural production environments free of heavy metal contamination (control areas). We applied the environmental genomics approaches known as "structural community metrics" (α- and β-diversity metrics) and "functional community metrics" (PICRUSt2 approach) to verify whether or not the effects of heavy metal contamination in the study area generated impacts on soil bacterial communities. We found that the impact related to the elevation of heavy metal concentration due to the operation of cement plants in the surrounding soil can be considered smooth according to globally recognized indices such as Igeo. However, we identified that both the taxonomic and functional structures of the communities surrounding cement plants were different from those found in the control areas. We consider that our findings contribute significantly to the general understanding of the effects of heavy metals on the soil ecosystem by showing that light contamination can disturb the dynamics of ecosystem services provided by soil, specifically those associated with microbial metabolism.

Supplying silicon alters microbial community and reduces soil cadmium bioavailability to promote health wheat growth and yield

Soil amendments of black bone (BB), biochar (BC), silicon fertilizer (SI), and leaf fertilizer (LF) play vital roles in decreasing cadmium (Cd) availability, thereby supporting healthy plant growth and food security in agroecosystems. However, the effect of their additions on soil microbial community and the resulting soil Cd bioavailability, plant Cd uptake and health growth are still unknown. Therefore, in this study, BB, BC, SI, and LF were selected to evaluate Cd amelioration in wheat grown in Cd-contaminated soils. The results showed that relative to the control, all amendments significantly decreased both soil Cd bioavailability and its uptake in plant tissues, promoting healthy wheat growth and yield. This induced-decrease effect in seeds was the most obvious, wherein the effect was the highest in SI (52.54%), followed by LF (43.31%), and lowest in BC (35.24%) and BB (31.98%). Moreover, the induced decrease in soil Cd bioavailability was the highest in SI (29.56%), followed by BC (28.85%), lowest in LF (17.55%), and BB (15.30%). The significant effect in SI likely resulted from a significant increase in both the soil bioavailable Si and microbial community (Acidobacteria and Thaumarchaeota), which significantly decreased soil Cd bioavailability towards plant roots. In particular, a co-occurrence network analysis indicated that soil microbes played a substantial role in wheat yield under Si amendment. Therefore, supplying Si alters the soil microbial community, positively and significantly interacting with soil bioavailable Si and decreasing Cd bioavailability in soils, thereby sustaining healthy crop development and food quality.

Dynamics of Soil Microbial N-Cycling Strategies in Response to Cadmium Stress

Globally increasing trace metal contamination of soils requires a better mechanistic understanding of metal-stress impacts on microbially mediated nutrient cycling. Herein, a 5-month laboratory experiment was employed to assess the effects of cadmium (Cd) on soil microbial N-cycling processes and associated functional gene abundance, with and without urea amendment. In non-N-amended soils, Cd progressively stimulated microbial populations for N acquisition from initial dissolved organic N (DON) to later recalcitrant organic N. The acceleration of N catabolism was synchronously coupled with C catabolism resulting in increased CO₂/N₂O fluxes and adenosine triphosphate (ATP) contents. The abundance of microbes deemed inefficient in N catabolism was gradually repressed after an initial stimulation period. We posit that enhanced exergonic N processes diminished the need for endergonic activities as a survival strategy for N communities experiencing metal stress. With urea amendment, Cd exhibited an initial stimulation effect on soil nitrification and a later a promotion effect on mineralization, along with an increase in the associated microbial populations. In N-amended soils, Cd accelerated N/C transformation processes, but decreased N₂O and CO₂ fluxes by 19 and 14%, respectively. This implies that under eutrophic conditions, Cd synchronously altered microbial C/N metabolism from a dominance of catabolic to anabolic processes. These results infer a nutrient-based adjustment of microbial N-cycling strategies to enhance their metal resistance.