Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.

Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment

BACKGROUND

The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking.

RESULTS

In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways.

CONCLUSIONS

One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.

Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions

Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.

Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.

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.

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.

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

Heterogeneity of CH4-derived carbon induced by O2:CH4 mediates the bacterial community assembly processes

The mechanism by which O₂:CH₄ controls microbial community assembly in the process of aerobic methane oxidation coupled to denitrification (AMED) remains largely uncharacterized, which hinders the design of engineering microbiomes for the AMED. In this study, the changes in the bacterial community in fed-batch serum bottle reactors under different O₂:CH₄ ratios were systematically characterized. The ratios of CH₄ consumption to the amount of nitrate removal in the treatment with O₂:CH₄ = 1.5:1, O₂:CH₄ = 0.5:1, and O₂:CH₄ = 0.25:1 were 13.1 ± 3.4, 4.7 ± 1.1, and 5.9 ± 3.0 mol-CH₄ mol^-1-NO₃^-, respectively. The α-diversity of the bacterial community increased as O₂:CH₄ decreased. Significantly different selection patterns were found for the high and low O₂:CH₄ ratios. The coherence process dominated the selection at high O₂:CH₄ ratios, while the diversification process played a role when O₂:CH₄ was low. Differences were also observed in the composition of CH₄-derived carbon between treatments with O₂:CH₄ = 1.5:1 and O₂:CH₄ = 0.5:1. Compared with the treatments with O₂:CH₄ = 1.5:1, the concentrations of methanol, formaldehyde, acetate, and ethanol in the treatment with O₂:CH₄ = 0.5:1 were significantly higher, while the concentration of formate was significantly lower. The heterogeneity of CH₄-derived carbon induced by O₂:CH₄ was likely to be responsible for the differences in the selection patterns. Our findings bridge the gaps between the observations of bacterial community perturbations and ecological community assembly theories, highlighting the potential of the bottom-up design approach to improve the nitrate removal rate of the AME-D.

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Wetland soils are the greatest source of nitrous oxide (N₂O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N₂O emissions from wetland soils are poorly understood. Using in situ N₂O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N₂O emissions. We show that N₂O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N₂O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N₂O.

Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils

Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.

Characteristics of microbial community composition and its relationship with carbon, nitrogen and sulfur in sediments

Microorganisms play an important role in the biogeochemical cycles of lacustrine sediments. However, little is known about their vertical responses to sedimentary depths and their contributions to important element cycles such as carbon, nitrogen and sulfur. Here, we investigated the community features of sedimental prokaryotes along with vertical profiles (i.e., sedimental depths of 0-230 cm) in the Dongting watershed. In the entire profile, the bacterial diversity wavelike decreased with increasing sediment depths, whereas archaeal diversity increased monotonically in the deep layer (100-230 cm). Bacteria were more sensitive to sedimental depths than archaea (B: P < 0.001, R = 0.534; A: P < 0.001, R = 0.327). The relative abundance of the primary phylum of bacteria (e.g. Proteobacteria) and archaea (e.g. Thaumarchaeota) changed significantly with sediment layers (P < 0.05). The vertical distribution of prokaryotes in sediments was related to the changes in sediment properties (P < 0.05, e.g., the content of nutrients, pH, texture, etc.). The co-occurrence network analysis further indicated that the superficial (0-40 cm) and deep (100-230 cm) networks contained more tightly connected node groups (more modules number), while the tighter connections (shorter APL) and more complex networks (higher avgK) were seen in sub-deep (40-100 cm) sediments. Based on the FAPROTAX database, we found that the predicted prokaryotic microbial functional groups involved in the N cycle had the highest abundance (87.47%), followed by the C cycle (9.48%) and the S cycle (2.39%). In addition, these groups were enriched in the superficial and deep layers. Taken together, these results reveal a new perspective on the vertical spatial variation in microorganisms at the fine-scale of the lake sediments. Distinct microbiome response patterns may have important implications for carbon, nitrogen and sulfur cycling along with the sediment profile in Dongting lake ecosystems.

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.

Evaluating the nitrogen-contaminated groundwater treatment by a denitrifying granular sludge bioreactor: effect of organic matter loading

A sequential bed granular bioreactor was adapted to treat nitrate-polluted synthetic groundwater under anaerobic conditions and agitation with denitrification gas, achieving very efficient performance in total nitrogen removal at influent organic carbon concentrations of 1 g L^-1 (80-90%) and 0.5 g L^-1 (70-80%) sodium acetate, but concentrations below 0.5 g L^-1 caused accumulation of nitrite and nitrate and led to system failure (30-40% removal). Biomass size and settling velocity were higher above 0.5 g L^-1 sodium acetate. Trichosporonaceae dominated the fungal populations at all times, while a dominance of terrestrial group Thaumarchaeota and Acidovorax at 1 and 0.5 g L^-1 passed to a domination of Methanobrevibacter and an unclassified Comamonadaceae clone for NaAc lower than 0.5 g L^-1. The results obtained pointed out that the denitrifying granular sludge technology is a feasible solution for the treatment of nitrogen-contaminated groundwater, and that influent organic matter plays an important role on the conformation of microbial communities within it and, therefore, on the overall efficiency of the system.

Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization

Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.

Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes

Although pyrogenic organic matter (PyOM) generated during wildfires plays a critical role in post-fire ecosystem recovery, the specific mechanisms by which PyOM controls soil microbial community assembly after wildfire perturbation remain largely uncharacterized. Herein we characterized the effect of PyOM on soil bacterial communities at two independent wildfire-perturbed forest sites. We observed that α-diversity of bacterial communities was the highest in wildfire-perturbed soils and that bacterial communities gradually changed along a sequence of unburnt soil → burnt soil → PyOM. The microbial communities reconstructed from unburnt soil and PyOM resembled the real bacterial communities in wildfire-perturbed soils in their α-diversity and community structure. Bacterial specialists in PyOM and soils clustered in phylogenetic coherent lineages with intra-lineage pH-niche conservatism and inter-lineage pH-niche divergence. Our results suggest that PyOM mediates bacterial community assembly in wildfire-perturbed soils by a combination of environmental selection and dispersal of phylogenetic coherent specialists with habitat preference in the heterogeneous microhabitats of burnt soils with distinct PyOM patches.

Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria

Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.

Riparian land-use systems impact soil microbial communities and nitrous oxide emissions in an agro-ecosystem

Riparian buffer systems (RBS) are considered a best management practice (BMP) in agricultural landscapes to intercept soil nitrogen (N) and phosphorus (P) leaching and surface runoff into aquatic ecosystems. However, these environmental benefits could be offset by increased greenhouse gas (GHG) emissions, including nitrous oxide (N₂O). The main sources of N₂O in soil are linked to processes which are mediated by soil microbial communities. These microorganisms play crucial roles in N-cycling and in the reduction of nitrate to N₂, and N₂O gases. This study was conducted to determine the abundance and diversity of microbial communities and functional genes associated with N-cycling and their influence on N₂O emissions in different riparian land-use: undisturbed natural forest (UNF), rehabilitated site (RH), grass buffer (GRB), and an adjacent agricultural land (AGR). Soil was sampled concurrently with N₂O emissions on July 13, 2017. DNA was extracted and used to target key N-cycling genes for N-fixation (nifH), nitrification: (amoA), and denitrification (nirS, nirK, and nosZ) via quantitative PCR, and for high throughput sequencing of total bacterial and fungal communities. Non-metric multidimensional scaling (NMDS) was used to examine microbial community composition and indicated significant differences in bacterial (p < 0.001) and fungal (p < 0.0085) communities between sites. Bacterial abundance differed significantly (p = 0.0005) between RBS and AGR sites with the highest populations occurring in the UNF (2.1 × 10¹⁰ copies g^-1 dry soil), and lowest in AGR (5.3 × 10⁹ copies g^-1 dry soil). However, the AGR site had the highest ammonia-oxidizing bacteria (AOB) abundance, indicating that nitrification is highest at this site. The abundance of the nosZ gene was highest in RH and GRB demonstrating the capacity for complete denitrification at these sites, lowering measured N₂O. These results suggest N-cycling microbial community dynamics differ among RBS and are influencing N₂O emissions in the sites investigated.

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages

Basaltic rocks play a significant role in CO2 sequestration from the atmosphere during their weathering. Moreover, the primary microorganisms that colonize them, by providing mineral elements and nutrients, are shown to promote growth of diverse heterotrophic communities and plants, therefore positively impacting Earth's long-term climate balance. However, the first steps of microbial colonization and subsequent rock weathering remain poorly understood, especially regarding microbial communities over a chronological sequence. Here, we analyzed the microbial communities inhabiting the soil developed in crevices on lava flows derived from different eruptions on Fogo Island. Investigated soils show typically low carbon and nitrogen content and are relatively similar to one another regarding their phylogenetic composition, and similar to what was recorded in large soil surveys with dominance of Actinobacteria and Proteobacteria. Moreover, our results suggest a stronger effect of the organic carbon than the lava flow age in shaping microbial communities as well as the possibility of exogenous sources of bacteria as important colonizers. Furthermore, archaea reach up to 8.4% of the total microbial community, dominated by the Soil Crenarchaeotic Group, including the ammonium-oxidizer Candidatus Nitrososphaera sp. Therefore, this group might be largely responsible for ammonia oxidation under the environmental conditions found on Fogo.

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage

Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO₂ assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.

Abundance, diversity, and distribution patterns along with the salinity of four nitrogen transformation-related microbes in the Yangtze Estuary

Purpose

The abundance and composition of nitrogen transformation-related microbes with certain environmental parameters for living conditions provide information about the nitrogen cycle in the Yangtze Estuary. The aim of this study was to explore the impacts of salinity on four N-related microbes and reveal the phylogenetic characteristics of microorganisms in the Yangtze Estuary ecosystem. A molecular biology method was used for the quantitation and identification of four microbes in the Yangtze River: ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying microbes (nirS-type), and anaerobic ammonia-oxidizing (anammox) bacteria. Sequence identification was performed on the levels of phylum, class, order, family, and genus, and the sequences were then matched to species.

Result

The results showed that the dominant species of AOA were crenarchaeote enrichment cultures, thaumarchaeote enrichment cultures, and Nitrosopumilus maritimus cultures, and the dominant AOB species were betaproteobacterium enrichment cultures and Nitrosomona sp. The denitrifying microbes were identified as the phylum Proteobacteria, classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, and the species Thauera selenatis. The dominant species of the anammox bacteria was Candidatus Brocadia sp. In the estuarine sediments of the Yangtze River, the nirS gene abundance (1.31 × 107–9.50 × 108 copies g−1 sediments) was the highest among all the detected genes, and the abundance of bacterial amoA, archaeal amoA, and nirS was significantly correlated. Closely correlated with the abundance of the bacterial amoA gene, salinity was an important factor in promoting the abundance and restraining the community diversity of AOB. Moreover, the distribution of the AOB species exhibited regional patterns in the estuarine zone.

Conclusions

The results indicated that salinity might promote abundance while limiting the diversity of AOB and that salinity might have reverse impacts on AOA. Denitrifying microbes, which showed a significant correlation with the other genes, were thought to interact with the other genes during nitrogen migration. The results also implied that AOA has a lower potential nitrification rate than AOB and that both the anammox and denitrification processes (defined by nirS gene) account for N2 production.

Indigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic Crust

Ridge flanks represent the major avenue of chemical and heat exchange between the Earth’s oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant archaea and are likely responsible for most of the cycling taking place in the first step of nitrification, a feasible nitrogen cycling step in the oxic basement. The crustal AOA community structure significantly differs from that in deep ocean water but is similar to that of the community in the overlying sediments in close proximity. This report links the occurrence of AOA to their metabolic activity in the oxic subseafloor crust and suggests that ecological selection and in situ proliferation may shape the microbial community structure in the rocky subsurface.

Oceanic ridge flank systems represent one of the largest and least-explored microbial habitats on Earth. Fundamental ecological questions regarding community activity, recruitment, and succession in this environment remain unanswered. Here, we investigated ammonia-oxidizing archaea (AOA) in the sediment-buried basalts on the oxic and young ridge flank at North Pond, a sediment-filled pond on the western flank of the Mid-Atlantic Ridge, and compared them with those in the overlying sediments and bottom seawater. Nitrification in the North Pond basement is thermodynamically favorable and is supported by a reaction-transport model simulating the dynamics of nitrate in the crustal fluids. Nitrification rate is estimated to account for 6% to 7% of oxygen consumption, which is similar to the ratios found in marine oxic sediments, suggesting that aerobic mineralization of organic matter is the major ammonium source for crustal nitrifiers. Using the archaeal 16S rRNA and amoA genes as phylogenetic markers, we show that AOA, composed solely of Nitrosopumilaceae, are the major archaeal dwellers at North Pond. Phylogenetic analysis reveals that the crustal AOA communities are distinct from those in the bottom seawater and the upper oxic sediments but are similar to those in the basal part of the overlying sediment column, suggesting either similar environmental selection or the dispersal of microbes across the sediment-basement interface. Additionally, quantitative abundance data suggest enrichment of the dominant Nitrosopumilaceae clade (Eta clade) in the basement compared to the seawater. This study explored AOA and their activity in the upper oceanic crust, and our results have ecological implications for the biogeochemical cycling of nitrogen in the crustal subsurface.

IMPORTANCE Ridge flanks represent the major avenue of chemical and heat exchange between the Earth’s oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant archaea and are likely responsible for most of the cycling taking place in the first step of nitrification, a feasible nitrogen cycling step in the oxic basement. The crustal AOA community structure significantly differs from that in deep ocean water but is similar to that of the community in the overlying sediments in close proximity. This report links the occurrence of AOA to their metabolic activity in the oxic subseafloor crust and suggests that ecological selection and in situ proliferation may shape the microbial community structure in the rocky subsurface.

Comparative study on archaeal diversity in the sediments of two urban landscape water bodies

Urban lake sediment plays a very important role in waterbody ecosystems. It is the basis of nutrient cycling and material exchange between microorganisms and lake ecosystems. In this study, Illumina high-throughput sequencing technology was employed to detect the structure and species richness of Archaea in anoxic sediments of urban waterbodies (Aohai Lake and Kunming Lake) in Beijing, and the environmental factors (pH level, organic matter, available nitrogen and total nitrogen) affecting the structure and succession of archaeal communities were also investigated. The results showed that there were 13 classified archaeal phyla, and the most frequent archaeal species in the lakes were Bathyarchaeota (MCG), Euryarchaeota, Thaumarchaeota, Aenigmarchaeota, Hadesarchaea, Lokiarchaeota, and Parvarchaeota. The top ten most abundant genera in the two lakes were significantly associated with at least one environmental factor. The results of this study enrich the understanding of microbial diversity in urban eutrophic lake sediments in northern China.

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

Background

Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume.

Results

The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25.

Conclusions

Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.

Extensive interlineage hybridization in the predominantly clonal Hydrilla verticillata

PREMISE

The submersed aquatic plant Hydrilla verticillata ("hydrilla") is important ecologically and economically due to its aggressive growth in both indigenous and nonindigenous regions. Substantial morphological variation has been documented in hydrilla, including the existence of monoecious and dioecious "biotypes." Whereas plastid sequence data have been used previously to explore intraspecific diversity, nuclear data have yet to be analyzed in a phylogenetic context. Molecular and morphological analyses were used to evaluate the genetic diversity and phylogenetic relationships of native and introduced populations.

METHODS

Nuclear (internal transcribed spacer-ITS; phytoene desaturase-PDS) and plastid (trnL-F) sequence data were evaluated phylogenetically using likelihood and Bayesian methods. Leaf morphologies were compared among clades that were identified in phylogenetic analyses.

RESULTS

Data from both ITS and PDS show multiple instances of polymorphic sequences that could be traced to two or more lineages, including both invasive biotypes in the Americas. Leaf morphological data support the distinctness of lineages and provide a metric for distinguishing monoecious and dioecious biotypes in the United States.

CONCLUSIONS

Nuclear molecular data indicate far greater genetic diversity than could be estimated using plastid markers. Substantially divergent copies of nuclear genes, found in multiple populations worldwide, likely result from interlineage hybridization. Invasive monoecious and dioecious hydrilla biotypes in the Americas are genetically distinct, with both biotypes resulting from admixture among Eurasian progenitors. Genetic similarity to populations in India and South Korea, respectively, implicates these as likely origins for the dioecious and monoecious biotypes.

Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands

Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.

Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.

The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

BACKGROUND

Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments in phylogenetic methodology, provides the potential for better analysis of microbial niche specialisation. This study aimed to develop an approach for sequencing of bacterial and archaeal amoA genes amplified from soil using bioinformatics pipelines developed for general analysis of functional genes and employed sequence data to reassess phylogeny and niche specialisation in terrestrial bacterial ammonia oxidisers.

RESULTS

amoA richness and community composition differed with bioinformatics approaches used but analysis of MiSeq sequences was reliable for both archaeal and bacterial amoA genes and was used for subsequent assessment of potential niche specialisation of soil bacteria ammonia oxidisers. Prior to ecological analysis, phylogenetic analysis of Nitrosospira, which dominates soil AOB, was revisited using a phylogenetic analysis of 16S rRNA and amoA genes in available AOB genomes. This analysis supported congruence between phylogenies of the two genes and increased previous phylogenetic resolution, providing support for additional gene clusters of potential ecological significance. Analysis of environmental sequences using these new sequencing, bioinformatics and phylogenetic approaches demonstrated, for the first time, similar niche specialisation in AOB to that in AOA, indicating pH as a key ecological factor controlling the composition of soil ammonia oxidiser communities.

CONCLUSIONS

This study presents the first bioinformatics pipeline for optimal analysis of Illumina MiSeq sequencing of a functional gene and is adaptable to any amplicon size (even genes larger than 500 bp). The pipeline was used to provide an up-to-date phylogenetic analysis of terrestrial betaproteobacterial amoA genes and to demonstrate the importance of soil pH for their niche specialisation and is broadly applicable to other ecosystems and diverse microbiomes.

Dynamics of archaeal community in soil with application of composted tannery sludge

Application of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7^th year by using different rates (0, 2.5, 5, 10 and 20 ton ha⁻¹). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front

Ultraslow spreading ridges account for one-third of the global mid-ocean ridges. Their impact on the diversity and connectivity of benthic deep-sea microbial assemblages is poorly understood, especially for hydrothermally inactive, magma-starved ridges. We investigated bacterial and archaeal diversity in sediments collected from an amagmatic segment (10°–17°E) of the Southwest Indian Ridge (SWIR) and in the adjacent northern and southern abyssal zones of similar water depths within one biogeochemical province of the Indian Ocean. Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. Our results show significant differences in microbial communities between stations outside and inside the SWIR, which were mostly explained by environmental selection. Community similarity correlated significantly with differences in chlorophyll a content and with the presence of upward porewater fluxes carrying reduced compounds (e.g., ammonia and sulfide), suggesting that trophic resource availability is a main driver for changes in microbial community composition. At the stations in the SWIR axial valley (3,655–4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g., SEEP-SRB1, Dehalococcoida, Atribacteria, and Woesearchaeota) and chemosynthetic environments (mainly Helicobacteraceae). The abyssal stations outside the SWIR communities (3,760–4,869 m water depth) were dominated by OM1 clade, JTB255, Planctomycetaceae, and Rhodospirillaceae. We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats.

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems

Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach.

Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers

Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.

Diversity and distribution of Archaea in global estuarine ecosystems

Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.

Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam

Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.

Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils

Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and archaea and their potential to perform nitrogen transformation processes. The results indicate significant dissimilarities in the structure of soil bacterial and archaeal communities as well as nirK, nirS, nosZ, nifH and archaeal amoA gene-possessing microbial communities. The reduced denitrification and N₂-fixing potential was detected in the drained tropical peatland soil. In undisturbed peatland soil, the N₂O emission was primarily related to nirS-type denitrifiers and dissimilatory nitrate reduction to ammonium, while the conversion of N₂O to N₂ was controlled by microbes possessing nosZ clade I genes. The denitrifying microbial community of the drained site differed significantly from the natural site community. The main reducers of N₂O were microbes harbouring nosZ clade II genes in the drained site. Additionally, the importance of DNRA process as one of the controlling mechanisms of N₂O fluxes in the natural peatlands of the tropics revealed from the results of the study.

Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China

Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.

Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi

Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics

Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.

Anaerobic digestion of pig manure supernatant at high ammonia concentrations characterized by high abundances of Methanosaeta and non-euryarchaeotal archaea

We examined the effect of ammonium and temperature on methane production in high rate upflow anaerobic sludge bed reactors treating pig manure supernatant. We operated four reactors at two ammonium concentrations (‘low’ at 1.9, ‘high’ at 3.7 g L⁻¹, termed LA and HA reactors, respectively) and at variable temperatures over 358 days. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons. Ammonium was a major selective factor for bacterial and archaeal community structure. After ~200 days of adaptation to high ammonium levels, acetate and propionate removal and methane production improved substantially in HA reactors. Aceticlastic Methanosaeta was abundant and positively correlated to methane yield in the HA reactors, whereas Methanosarcina was more abundant in LA reactors. Furthermore, a group of monophyletic OTUs that was related to Thaumarchaeota in phylogenetic analysis was highly abundant in the archaeal communities, particularly in the HA reactors. The most abundant bacterial OTU in LA reactors, representing Syntrophomonadaceae, was also positively correlated to methane yield in the HA reactors, indicating its importance in methane production under ammonia stress. In conclusion, efficient methane production, involving aceticlastic methanogenesis by Methanosaeta took place in the reactors at free ammonia concentrations as high as 1 g L⁻¹.

Comparison of Archaeal Communities in Mineral Soils at a Boreal Forest in Finland and a Cold-Temperate Forest in Japan

Archaeal communities in mineral soils were compared between a boreal forest in Finland and cold-temperate forest in Japan using 16S rRNA gene-targeted high-throughput sequencing. In boreal soils, Thaumarchaeota Group 1.1c archaea predominated and Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were also detected. In temperate soils, Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were dominant members at the subsurface, whereas their dominancy was replaced by Thermoplasmata archaea at the subsoil. An analysis of the ammonia monooxygenase subunit A gene of Archaea also indicated the distribution of Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea in these soils.

Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites

Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic‐ring‐hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil‐impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished. Based on a deduced ARHD peptide sequences consensus phylogeny, we examined trends and divergences in the sequence phylogenetic clustering from the different sites. The taxonomic affiliation of the OPF revealed that Pseudomonas, Streptomyces, Variovorax, Bordetella and Rhodococcus were the five most abundant genera, considering all sites. The functional diversity analysis showed the enzymatic prevalence of benzene 1,2‐dioxygenase, 3‐phenylpropionate dioxygenase and naphthalene 1,2‐dioxygenase, in addition to 10.98% of undefined category ARHDs. The ARHD gene correlation analysis among different sites was essentially important to gain insights on spatial distribution patterns, genetic congruence and ecological coherence of the bacterial groups found. This work revealed the genetic potential from the mangrove sediment for AH biodegradation and a considerable evolutionary proximity among the dioxygenase OPFs found in Antarctica and South America sites, in addition to high level of endemism in each continental region.

Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils

The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils reconstructed 20 to 30 years previously and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal forest soils subject to wildfire disturbance. Prokaryotic α-diversity and β-diversity were assessed using massively parallel sequencing of 16S rRNA genes. The β-diversity, but not the α-diversity, differed between reconstructed and natural soils. Bacteria associated with an oligotrophic lifestyle were more abundant in natural forest soils, whereas bacteria associated with a copiotrophic lifestyle were more abundant in reconstructed soils. Ammonia-oxidizing archaea were most abundant in reconstructed soils planted with grasses. Plant species were the main factor influencing α-diversity in natural and in reconstructed soils. Nitrogen deposition, pH, and plant species were the main factors influencing the β-diversity of the prokaryotic communities in natural and reconstructed soils. The results highlight the importance of nitrogen deposition and aboveground-belowground relationships in shaping soil microbial communities in natural and reconstructed soils.IMPORTANCE Covering over 800 km², land disturbed by the exploitation of the oil sands in Canada has to be restored. Here, we take advantage of the proximity between these reconstructed ecosystems and the boreal forest surrounding the oil sand mining area to study soil microbial community structure and processes in both natural and nonnatural environments. By identifying key characteristics shaping the structure of soil microbial communities, this study improved our understanding of how vegetation, soil characteristics and microbial communities interact and drive soil functions.

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

Ongoing elimination efforts have altered the global distribution of Onchocerca volvulus, the agent of river blindness, and further population restructuring is expected as efforts continue. Therefore, a better understanding of population genetic processes and their effect on biogeography is needed to support elimination goals. We describe O. volvulus genome variation in 27 isolates from the early 1990s (before widespread mass treatment) from four distinct locales: Ecuador, Uganda, the West African forest and the West African savanna. We observed genetic substructuring between Ecuador and West Africa and between the West African forest and savanna bioclimes, with evidence of unidirectional gene flow from savanna to forest strains. We identified forest:savanna-discriminatory genomic regions and report a set of ancestry informative loci that can be used to differentiate between forest, savanna and admixed isolates, which has not previously been possible. We observed mito-nuclear discordance possibly stemming from incomplete lineage sorting. The catalogue of the nuclear, mitochondrial and endosymbiont DNA variants generated in this study will support future basic and translational onchocerciasis research, with particular relevance for ongoing control programmes, and boost efforts to characterize drug, vaccine and diagnostic targets.

Plant-Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere

A major challenge facing agriculture in the 21st century is the need to increase the productivity of cultivated land while reducing the environmentally harmful consequences of mineral fertilization. The microorganisms thriving in association and interacting with plant roots, the plant microbiota, represent a potential resource of plant probiotic function, capable of conjugating crop productivity with sustainable management in agroecosystems. However, a limited knowledge of the organismal interactions occurring at the root-soil interface is currently hampering the development and use of beneficial plant-microbiota interactions in agriculture. Therefore, a comprehensive understanding of the recruitment cues of the plant microbiota and the molecular basis of nutrient turnover in the rhizosphere will be required to move toward efficient and sustainable crop nutrition. In this chapter, we will discuss recent insights into plant-microbiota interactions at the root-soil interface, illustrate the processes driving mineral dynamics in soil, and propose experimental avenues to further integrate the metabolic potential of the plant microbiota into crop management and breeding strategies for sustainable agricultural production.

Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Studies of the distribution of ammonia oxidising archaea (AOA) and bacteria (AOB) suggest distinct ecological niches characterised by ammonia concentration and pH, arising through differences in substrate affinity and ammonia tolerance. AOA form five distinct phylogenetic clades, one of which, the 'Nitrososphaera sister cluster', has no cultivated isolate. A representative of this cluster, named 'Candidatus Nitrosocosmicus franklandus', was isolated from a pH 7.5 arable soil and we propose a new cluster name:'Nitrosocosmicus' While phylogenetic analysis of amoA genes indicates its association with the Nitrososphaera sister cluster, analysis of 16S rRNA genes provided no support for a relative branching that is consistent with a 'sister cluster', indicating placement within a lineage of the order Nitrososphaerales 'Ca.N. franklandus' is capable of ureolytic growth and its tolerances to nitrite and ammonia are higher than in other AOA and similar to those of typical soil AOB. Similarity of other growth characteristics of 'Ca.N. franklandus' with those of typical soil AOB isolates reduces support for niche differentiation between soil AOA and AOB and suggests that AOA have a wider physiological diversity than previously suspected. In particular, the high ammonia tolerance of 'Ca.N. franklandus' suggests potential contributions to nitrification in fertilised soils.

The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors

Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75–1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray–Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors.