Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota

Holed up, but thriving: Impact of multitrophic cryoconite communities on glacier elemental cycles

Cryoconite holes (water and sediment-filled depressions), found on glacier surfaces worldwide, serve as reservoirs of microbes, carbon, trace elements, and nutrients, transferring these components downstream via glacier hydrological networks. Through targeted amplicon sequencing of carbon and nitrogen cycling genes, coupled with functional inference-based methods, we explore the functional diversity of these mini-ecosystems within Antarctica and the Himalayas. These regions showcase distinct environmental gradients and experience varying rates of environmental change influenced by global climatic shifts. Analysis revealed a diverse array of photosynthetic microorganisms, including Stramenopiles, Cyanobacteria, Rhizobiales, Burkholderiales, and photosynthetic purple sulfur Proteobacteria. Functional inference highlighted the high potential for carbohydrate, amino acid, and lipid metabolism in the Himalayan region, where organic carbon concentrations surpassed those in Antarctica by up to 2 orders of magnitude. Nitrogen cycling processes, including fixation, nitrification, and denitrification, are evident, with Antarctic cryoconite exhibiting a pronounced capacity for nitrogen fixation, potentially compensating for the limited nitrate concentrations in this region. Processes associated with the respiration of elemental sulfur and inorganic sulfur compounds such as sulfate, sulfite, thiosulfate, and sulfide suggest the presence of a complete sulfur cycle. The Himalayan region exhibits a higher potential for sulfur cycling, likely due to the abundant sulfate ions and sulfur-bearing minerals in this region. The capability for complete iron cycling through iron oxidation and reduction reactions was also predicted. Methanogenic archaea that produce methane during organic matter decomposition and methanotrophic bacteria that utilize methane as carbon and energy sources co-exist in the cryoconite, suggesting that these niches support the complete cycling of methane. Additionally, the presence of various microfauna suggests the existence of a complex food web. Collectively, these results indicate that cryoconite holes are self-sustaining ecosystems that drive elemental cycles on glaciers and potentially control carbon, nitrogen, sulfur, and iron exports downstream.

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems

The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.

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.

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Illegal dumping of oil and gas wastewater alters arid soil microbial communities

The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

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.

Association between host nitrogen absorption and root-associated microbial community in field-grown wheat

Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.

Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California

BACKGROUND

Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.

RESULTS

To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.

CONCLUSIONS

These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.

Mainstream nitrogen removal from low temperature and low ammonium strength municipal wastewater using hydrogel-encapsulated comammox and anammox

Application of partial nitritation (PN)-anammox to mainstream wastewater treatment faces challenges in low water temperature and low ammonium strength. In this study, a continuous flow PN-anammox reactor with hydrogel-encapsulated comammox and anammox was designed and operated for nitrogen removal from mainstream wastewater with low temperature. Long-term operation with synthetic and real wastewater as the feed demonstrated nearly complete ammonium and total inorganic nitrogen (TIN) removal by the reactor at temperatures as low as 10 °C. A significantly decreased nitrogen removal performance and biomass activity was observed in the reactor at 4 °C before a selective heating strategy was employed. A novel heating technology using radiation to heat carbon black co-encapsulated in the hydrogel matrix with biomass was used to selectively heat biomass but not water in the treatment system. This selective heating technology enabled nearly complete ammonium removal and 89.4 ± 4.3 % TIN removal at influent temperature of 4 °C and reactor temperature 5 °C. Activity tests suggested selective heating brought the biomass activity at influent temperatures of 4 °C and reactor temperature 5 °C to a level comparable to that at 10 °C. Comammox and anammox were consistently present in the system and spatially organized in the hydrogel beads as revealed by qPCR and fluorescence in-situ hybridization (FISH). The abundance of comammox largely decreased by 3 orders of magnitude during the operation at 4 °C, and rapidly recovered after the application of selective heating. The anammox-comammox technology tested in this study essentially enabled mainstream shortcut nitrogen removal, and the selective heating ensured good performance of the technology at temperature as low as 5 °C.

Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales

Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0-2 cm) and subsurface (18-20 or 22-24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1-5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1-5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1-5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.

Study of Archaeal Diversity in the Arctic Meltwater Lake Region

Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO₂^--N), and nitrate nitrogen (NO₃^--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH₄⁺-N, SiO₃^2--Si, MC, NO₃^--N, and NO₂^--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.

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.

Ammonia oxidizing archaea and bacteria respond to different manure application rates during organic vegetable cultivation in Northwest China

Ammonia oxidization is a critical process in nitrogen cycling that involves ammonia oxidizing archaea (AOA) and bacteria (AOB). However, the effects of different manure amounts on ammonia-oxidizing microorganisms (AOMs) over the course of organic vegetables production remains unclear. We used the amoA gene to evaluated AOMs abundance and community structure in organic vegetable fields. Quantitative PCR revealed that AOB were more abundant than AOA. Among them, the amoA copy number of AOB treated with 900 kgN ha^-1 was 21.3 times that of AOA. The potential nitrification rate was significantly correlated with AOB abundance (P < 0.0001) but not with AOA, suggesting that AOB might contribute more to nitrification than AOA. AOB sequences were classified into Nitrosomonas and Nitrosospira, and AOA into Nitrosopumilus and Nitrososphaera. Nitrosomonas and Nitrosopumilus were predominant in treatments that received manure nitrogen at ≥ 900 kg ha^-1 (52.7-56.5%) and when manure was added (72.7-99.8%), respectively, whereas Nitrosospira and Nitrososphaera occupied more than a half percentage in those that received ≤ 600 kg ha^-1 (58.4-84.9%) and no manure (59.6%). A similar manure rate resulted in more identical AOMs' community structures than greater difference manure rate. The bacterial amoA gene abundances and ratios of AOB and AOA showed significantly positive correlations with soil electrical conductivity, total carbon and nitrogen, nitrate, phosphorus, potassium, and organic carbon, indicating that these were potential key factors influencing AOMs. This study explored the AOMs' variation in organic vegetable fields in Northwest China and provided a theoretical basis and reference for the subsequent formulation of proper manure management.

Nitrifying Microorganisms Linked to Biotransformation of Perfluoroalkyl Sulfonamido Precursors from Legacy Aqueous Film-Forming Foams

Drinking water supplies across the United States have been contaminated by firefighting and fire-training activities that use aqueous film-forming foams (AFFF) containing per- and polyfluoroalkyl substances (PFAS). Much of the AFFF is manufactured using electrochemical fluorination by 3M. Precursors with six perfluorinated carbons (C6) and non-fluorinated amine substituents make up approximately one-third of the PFAS in 3M AFFF. C6 precursors can be transformed through nitrification (microbial oxidation) of amine moieties into perfluorohexane sulfonate (PFHxS), a compound of regulatory concern. Here, we report biotransformation of the most abundant C6 sulfonamido precursors in 3M AFFF with available commercial standards (FHxSA, PFHxSAm, and PFHxSAmS) in microcosms representative of the groundwater/surface water boundary. Results show rapid (<1 day) biosorption to living cells by precursors but slow biotransformation into PFHxS (1-100 pM day^-1). The transformation pathway includes one or two nitrification steps and is supported by the detection of key intermediates using high-resolution mass spectrometry. Increasing nitrate concentrations and total abundance of nitrifying taxa occur in parallel with precursor biotransformation. Together, these data provide multiple lines of evidence supporting microbially limited biotransformation of C6 sulfonamido precursors involving ammonia-oxidizing archaea (Nitrososphaeria) and nitrite-oxidizing bacteria (Nitrospina). Further elucidation of interrelationships between precursor biotransformation and nitrogen cycling in ecosystems would help inform site remediation efforts.

Unexpected complexity of the ammonia monooxygenase in archaea

Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.

Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites

Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term “memory of soil”. Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea—among them ammonia-oxidizing and sulphur-related types—are due obviously to former human activities and support the concept of the “ecological memory of soil”.

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.

Antarctic Ardley Island terrace - An ideal place to study the marine to terrestrial succession of microbial communities

The study of chronosequences is an effective tool to study the effects of environmental changes or disturbances on microbial community structures, diversity, and the functional properties of ecosystems. Here, we conduct a chronosequence study on the Ardley Island coastal terrace of the Fildes Peninsula, Maritime Antarctica. The results revealed that prokaryotic microorganism communities changed orderly among the six successional stages. Some marine microbial groups could still be found in near-coastal soils of the late stage (lowest stratum). Animal pathogenic bacteria and stress-resistant microorganisms occurred at the greatest level with the longest succession period. The main driving factors for the succession of bacteria, archaea, and fungi along Ardley Island terrace were found through Adonis analysis (PERMANOVA). During analysis, soil elements Mg, Si, and Na were related to the bacterial and archaeal community structure discrepancies, while Al, Ti, K, and Cl were related to the fungal community structure discrepancies. On the other hand, other environmental factors also play an important role in the succession of microbial communities, which could be different among each microorganism. The succession of bacterial communities is greatly affected by pH and water content; archaeal communities are greatly affected by N H 4 + ; fungal communities are affected by nutrients such as N O 3 - . In the analysis of the characteristic microorganisms along terrace, the succession of microorganisms was found to be influenced by complex and comprehensive factors. For instance, environmental instability, relationship with plants and ecological niches, and environmental tolerance. The results found that budding reproduction and/or with filamentous appendages bacteria were enriched in the late stage, which might be connected to its tolerance to rapid changes and barren environments. In addition, the decline in ammonia oxidation capacity of Thaumarchaeota archaeade with succession and the evolution of the fungi-plant relationship throughout classes were revealed. Overall, this research improves the understanding of the effect of the marine-to-terrestrial transition of the Ardley Island terrace on microbial communities. These findings will lay the foundation for more in-depth research regarding microbial adaptations and evolutionary mechanisms throughout the marine-terrestrial transition in the future.

Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture

Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO₂) concentrations aiming to understand the interplay between ammonia oxidation and CO₂ fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO₂ gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μ_max) the biomass to ammonium yield (Y_(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D _crit. Due to changes in Y_(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μ_max. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K _S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.

Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS

Vinegars elaborated in southern Spain are highly valued all over the world because of their exceptional organoleptic properties and high quality. Among the factors which influence the characteristics of the final industrial products, the composition of the microbiota responsible for the process and the raw material used as acetification substrate have a crucial role. The current state of knowledge shows that few microbial groups are usually present throughout acetification, mainly acetic acid bacteria (AAB), although other microorganisms, present in smaller proportions, may also affect the overall activity and behavior of the microbial community. In the present work, the composition of a starter microbiota propagated on and subsequently developing three acetification profiles on different raw materials, an alcohol wine medium and two other natural substrates (a craft beer and fine wine), was characterized and compared. For this purpose, two different "omics" tools were combined for the first time to study submerged vinegar production: 16S rRNA amplicon sequencing, a culture-independent technique, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), a culture-dependent method. Analysis of the metagenome revealed numerous taxa from 30 different phyla and highlighted the importance of the AAB genus Komagataeibacter, which was much more frequent than the other taxa, and Acetobacter; interestingly, also archaea from the Nitrososphaeraceae family were detected by 16S rRNA amplicon sequencing. MALDI-TOF MS confirmed the presence of Komagataeibacter by the identification of K. intermedius. These tools allowed for identifying some taxonomic groups such as the bacteria genera Cetobacterium and Rhodobacter, the bacteria species Lysinibacillus fusiformis, and even archaea, never to date found in this medium. Definitely, the effect of the combination of these techniques has allowed first, to confirm the composition of the predominant microbiota obtained in our previous metaproteomics approaches; second, to identify the microbial community and discriminate specific species that can be cultivated under laboratory conditions; and third, to obtain new insights on the characterization of the acetification raw materials used. These first findings may contribute to improving the understanding of the microbial communities' role in the vinegar-making industry.

Microbial communities associated with mounds of the Orange-footed scrubfowl Megapodius reinwardt

Megapodius reinwardt, the orange-footed scrubfowl, belongs to a small family of birds that inhabits the Indo-Australian region. Megapodes are unique in incubating their eggs in mounds using heat from microbial decomposition of organic materials and solar radiation. Little is known about the microorganisms involved in the decomposition of organic matter in mounds. To determine the source of microbes in the mounds, we used 16S and 18S rRNA gene sequencing to characterize the microbial communities of mound soil, adjacent soil and scrubfowl faeces. We found that the microbial communities of scrubfowl faeces were substantially different from those of the mounds and surrounding soils, suggesting that scrubfowls probably do not use their faeces to inoculate their mounds although a few microbial sequence variants were present in both faeces and mound samples. Further, the mound microbial community structure was significantly different to the adjacent soils. For example, mounds had a high relative abundance of sequence variants belonging to Thermomonosporaceae, a thermophilic soil bacteria family able to degrade cellulose from plant residues. It is not clear whether members of Thermomonosporaceae disproportionately contribute to the generation of heat in the mound, or whether they simply thrive in the warm mound environment created by the metabolic activity of the mound microbial community. The lack of clarity in the literature between designations of heat-producing (thermogenic) and heat-thriving (thermophilic) microbes poses a challenge to understanding the role of specific bacteria and fungi in incubation.

Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils

Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.

Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution

Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.

Responses of Cyanobacterial Crusts and Microbial Communities to Extreme Environments of the Stratosphere

How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at an altitude of 32 km. Freezing and thawing treatments were simulated in the laboratory in terms of the temperature fluctuations during flight. Microbial community composition was characterized by sequencing at the level of DNA and RNA. After exposure to the stratosphere, the RNA relative abundances of Kallotenue and Longimicrobium increased by about 2-fold, while those of several dominant cyanobacteria genera changed slightly. The RNA relative abundances of various taxa declined after freezing, but increased after thawing, whereas cyanobacteria exhibited an opposite change trend. The DNA and RNA relative abundances of Nitrososphaeraceae were increased by 1.4~2.3-fold after exposure to the stratosphere or freezing. Exposure to stratospheric environmental conditions had little impact on the total antioxidant capacity, photosynthetic pigment content, and photosynthetic rate, but significantly increased the content of exopolysaccharides by 16%. The three treatments (stratospheric exposure, freezing, and thawing) increased significantly the activities of N-acetyl-β-D-glucosidase (26~30%) and β-glucosidase (14~126%). Our results indicated cyanobacterial crust communities can tolerate exposure to the stratosphere. In the defense process, extracellular organic carbon degradation and transformation play an important role. This study makes the first attempt to explore the response of microbial communities of cyanobacterial crusts to a Mars-like stratospheric extreme environment, which provides a new perspective for studying the space biology of earth communities.

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.

Hydrazines as Substrates and Inhibitors of the Archaeal Ammonia Oxidation Pathway

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) perform key steps in the global nitrogen cycle, the oxidation of ammonia to nitrite. While the ammonia oxidation pathway is well characterized in AOB, many knowledge gaps remain about the metabolism of AOA. Hydroxylamine is an intermediate in both AOB and AOA, but homologues of hydroxylamine dehydrogenase (HAO), catalyzing bacterial hydroxylamine oxidation, are absent in AOA. Hydrazine is a substrate for bacterial HAO, while phenylhydrazine is a suicide inhibitor of HAO. Here, we examine the effect of hydrazines in AOA to gain insights into the archaeal ammonia oxidation pathway. We show that hydrazine is both a substrate and an inhibitor for AOA and that phenylhydrazine irreversibly inhibits archaeal hydroxylamine oxidation. Both hydrazine and phenylhydrazine interfered with ammonia and hydroxylamine oxidation in AOA. Furthermore, the AOA “Candidatus Nitrosocosmicus franklandus” C13 oxidized hydrazine into dinitrogen (N₂), coupling this reaction to ATP production and O₂ uptake. This study expands the known substrates of AOA and suggests that despite differences in enzymology, the ammonia oxidation pathways of AOB and AOA are functionally surprisingly similar. These results demonstrate that hydrazines are valuable tools for studying the archaeal ammonia oxidation pathway.

IMPORTANCE Ammonia-oxidizing archaea (AOA) are among the most numerous living organisms on Earth, and they play a pivotal role in the global biogeochemical nitrogen cycle. Despite this, little is known about the physiology and metabolism of AOA. We demonstrate in this study that hydrazines are inhibitors of AOA. Furthermore, we demonstrate that the model soil AOA “Ca. Nitrosocosmicus franklandus” C13 oxidizes hydrazine to dinitrogen gas, and this reaction yields ATP. This provides an important advance in our understanding of the metabolism of AOA and expands the short list of energy-yielding compounds that AOA can use. This study also provides evidence that hydrazines can be useful tools for studying the metabolism of AOA, as they have been for the bacterial ammonia oxidizers.

Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient

Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.

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.

The ecological clusters of soil organisms drive the ecosystem multifunctionality under long-term fertilization

Long-term fertilization is known to impact the biodiversity and community structures of soil organisms, which are responsible for multiple soil ecosystem functions (multifunctionality). However the relationship between the alterations of soil organisms and ecosystem multifunctionality remains unclear, especially in the case of long-term fertilization. To explore the contribution of soil organismal biodiversity and community structures to ecosystem multifunctionality, we took soil samples from a nearly 25-year field fertilization experiment. Organic matter significantly improved the soil ecosystem multifunctionality. Ecosystem multifunctionality was found to be closely linked to the biodiversity and communities of soil organisms within the major ecological clustering of soil organisms (Module 1) according to the trophic co-occurrence network, rather than the entire community of soil organisms. This indicated that ecological clusters of soil organisms within the network were critical in maintaining soil ecosystem multifunctionality. The application of organic fertilization could enrich specialized soil organisms and increase interactions of soil organisms in the ecological cluster. As a result, our findings emphasize the role of ecological clusters in the soil organismal co-occurrence network in controlling soil multifunctionality after long-term fertilization, presenting a novel perspective on the link between soil biodiversity and ecosystem multifunctionality.

Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones

Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.

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

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

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.

Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus

Simple Summary

The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus.

Abstract

The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.

Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.

Nitrosopumilus zosterae sp. nov., an autotrophic ammonia-oxidizing archaeon of phylum Thaumarchaeota isolated from coastal eelgrass sediments of Japan

A novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota, strain NM25^T, was isolated from coastal eelgrass zone sediment sampled in Shimoda (Japan). The cells were rod-shaped with an S-layer cell wall. The temperature range for growth was 20-37 °C, with an optimum at 30 °C. The pH range for growth was pH 6.1-7.7, with an optimum at pH 7.1. The salinity range for growth was 5-40 %, with an optimum range of 15-32 %. Cells obtained energy from ammonia oxidation and used bicarbonate as a carbon source. Utilization of urea was not observed for energy generation and growth. Strain NM25^T required a hydrogen peroxide scavenger, such as α-ketoglutarate, pyruvate or catalase, for sustained growth on ammonia. Growth of strain NM25^T was inhibited by addition of low concentrations of some organic compounds and organic mixtures, including complete inhibition by glycerol, peptone and yeast extract. Phylogenetic analysis of four concatenated housekeeping genes (16S rRNA, rpoB, rpsI and atpD) and concatenated AmoA, AmoB, AmoC amino acid sequences indicated that the isolate is similar to members of the genus Nitrosopumilus. The closest relative is Nitrosopumilus ureiphilus PS0^T with sequence similarities of 99.5 % for the 16S rRNA gene and 97.2 % for the amoA gene. Genome relatedness between strain NM25^T and N. ureiphilus PS0^T was assessed by average nucleotide identity and digital DNA-DNA hybridization, giving results of 85.4 and 40.2 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NM25^T represents a novel species of the genus Nitrosopumilus, for which the name sp. nov, is proposed. The type strain is NM25^T (=NBRC 111181^T=ATCC TSD-147^T).

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction

Soil microbiota are vital for successful revegetation, as they play a critical role in nutrient cycles, soil functions, and plant growth and health. A rehabilitation scenario of the abandoned Kettara mine (Morocco) includes covering acidic tailings with alkaline phosphate mine wastes to limit water infiltration and hence acid mine drainage. Revegetation of phosphate wastes is the final step to this rehabilitation plan. However, revegetation is hard on this type of waste in semi-arid areas and only a few plants managed to grow naturally after 5 years on the store-and-release cover. As we know that belowground biodiversity is a key component for aboveground functioning, we sought to know if any structural problem in phosphate waste communities could explain the almost absence of plants. To test this hypothesis, bacterial and archaeal communities present in these wastes were assessed by 16S rRNA metabarcoding. Exploration of taxonomic composition revealed a quite diversified community assigned to 19 Bacterial and two Archaeal phyla, similar to other studies, that do not appear to raise any particular issues of structural problems. The dominant sequences belonged to Proteobacteria, Bacteroidetes, Actinobacteria, and Gemmatimonadetes and to the genera Massilia, Sphingomonas, and Adhaeribacter. LEfSe analysis identified 19 key genera, and metagenomic functional prediction revealed a broader phylogenetic range of taxa than expected, with all identified genera possessing at least one plant growth-promoting trait. Around 47% of the sequences were also related to genera possessing strains that facilitate plant development under biotic and environmental stress conditions, such as drought and heat.

A standardized archaeal taxonomy for the Genome Taxonomy Database

The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.

Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants

The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon "Candidatus Nitrosocosmicus agrestis"

Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH₃ (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO₂/HCO₃⁻ conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.”

IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N₂O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.

Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin

Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.

Abundance and composition of airborne archaea during springtime mixed dust and haze periods in Beijing, China

Archaea have an important role in the elemental biogeochemical cycle and human health. However, characteristics of airborne archaea affected by anthropogenic and natural processes are unclear. In this study, we investigated the abundance, structures, influencing factors and assembly processes of the archaeal communities in the air samples collected from Beijing in springtime using quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology and statistical analysis. The concentrations of airborne archaea ranged from 10¹ to 10³ copies m^-3 (455 ± 211 copies m^-3), accounting for 0.67% of the total prokaryote (sum of archaea and bacteria). An increase in airborne archaea was seen when the air quality shifted from clean to slightly polluted conditions. Sandstorm dust imported a large number of archaea to the local atmosphere. Euryarchaeota, Thaumarchaeota and Crenarchaeota were the dominant phyla, revealing the primary role of soil in releasing archaea to the ambient environment. Dispersal-related neutral processes play an important role in shaping the structure of airborne archaeal assembly. Of all phyla, methanogenic Euryarchaeota were most abundant in the air parcels come from the south of Beijing. Air masses from the west of Beijing, which brought sandstorm to Beijing, carried large amounts of ammonia oxidizing archaea Nitrososphaera. The results demonstrate the importance of air mass sources and local weather conditions in shaping the local airborne archaea community.

Metagenomics approach and canonical correspondence analysis of novel nitrifiers and ammonia-oxidizing archaea in full scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes

Various microorganisms are involved in nitrogen removal, and their group compositions depend closely on operating parameters. The structures and functions of nitrification microorganisms in full-scale anaerobic-anoxic-oxic (A2/O) and oxidation ditch processes were analyzed using metagenomics and canonical correspondence analysis. The community structure of ammonia-oxidizing archaea in the oxidation ditch was 3.8 (winter) - 6.3 (summer) times higher than in A2/O, and the complete ammonia oxidizer was only found in the oxidation ditch process. The canonical correspondence analysis of various environmental variables showed that Nitrosomonadales, Crenarchaeota, and Nitrospira inopinata correlate highly with nitrification, and Nitrospira was involved in NO₂^--N oxidation rather than Nitrobacter. The longer solid and hydraulic retention times in the oxidation ditch were more effective in achieving a wider range of novel nitrification than A2/O. This result indicates that microbial communities of novel nitrifiers and ammonia-oxidizing archaea improved in the oxidation ditch process, significantly contributing to stable nitrogen removal.

Tailoring the distribution of microbial communities and gene expressions to achieve integrating nitrogen transformation in a gravity-driven submerged membrane bioreactor

A pilot-scale upgraded gravity-driven submerged membrane (GDSM) reactor was constructed to enhance nitrogen removal. It was artificially formed multiple stratified environments (dissolved oxygen (DO) and substrate supply (TOC, TN, COD, NH₄⁺-N, NO₂^--N, and NO₃^--N)) by embedding moving water baffles to control water-flow process in bulk liquid with slow-flowing liquid state. Significant diversity and relative abundance of microorganisms associated with nitrogen transformation paths (i.e., ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite oxidizing bacteria, and denitrifying bacteria) were tailored to distribute on different spatial and temporal regions, and performed their dominant functions. The process simultaneously integrated diverse and effective nitrogen transformation paths (i.e., nitrification, partial nitrification, denitrification, anammox, and dissimilatory nitrate reduction) to achieve high nitrogen removal, with NH₄⁺-N, TN, and COD eliminated by 94.68 ± 2.55%, 55.16 ± 5.53%, and 80.17 ± 6.75%, respectively. Gene expressions involved in the nitrogen transformations were estimated by qPCR to explore the shifts of dominant nitrogen transforming bioreactions in multiple stratified environments. Pearson correlation coefficients supported that the functional genes had more stable and active ability by complementing each other. As a result, an endogenous integration of diverse nitrogen transformation paths was achieved in a single system by artificially tailoring the distributions of microbial communities and gene expressions with enhanced nitrogen removal.

Biologically mediated release of endogenous N2O and NO2 gases in a hydrothermal, hypoxic subterranean environment

The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO₂-rich fluids. Anomalous concentrations of N₂O and NO₂ were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO₂ and CH₄ during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O₂, temperature, and GHG concentration. Both the N₂O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N₂O and NO₂ emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH₂OH, NO, and NO₂^- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.