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.

Archaeal communities perform an important role in maintaining microbial stability under long term continuous cropping systems

Long-term continuous cropping of soybean can generate the development of disease-suppressive soils. However, whether the changes in microbial communities, especially for archaea, contribute to controlling soil sickness and improving crop yields remains poorly understood. Here, real-time PCR and high-throughput sequencing were employed to investigate the changes in soil archaeal communities in both bulk and rhizosphere soils under four cropping systems, including the continuous cropping of soybeans for a short-term of 3 and 5 years (CC3 and CC5, respectively) and for a long-term of 13 years (CC13), as well as a soybean-maize rotation for 5 years (CR5). The results showed that CC13 and CR5 significantly increased archaeal abundance, reduced the alpha-diversity of archaeal communities, and changed soil archaeal community structures compared to CC3 and CC5. Microbial co-occurrence network analysis revealed that CC13 led to the higher resistant microbial community and lower the relative abundance of potential plant pathogens in the network compared to CC3 and CC5. Correlation analysis showed that the microbial resistance index was negatively correlated with the relative abundance of potential plant pathogens and positively correlated with soybean yields in both bulk and rhizosphere soils. Intriguingly, the random forest (RF) analysis showed that archaea contributed the most to soil microbial resistance even though they were not at the core positions of the network. Overall, structural equation models (SEMs) revealed that high resistant microbial community could directly or indirectly improved soybean yields by regulating the relative abundance of plant pathogens and the soil nutrients, suggesting that the regulation of soil microbial taxa may play an important role in maintaining agricultural productivity under continuous cropping of soybean.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types

Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.

Driving Factors of Microbial Community Abundance and Structure in Typical Forest Soils of Sanjiang Plain, Northeast China

Until recently, a comprehensive evaluation of the environmental drivers on the abundance and structure of the microbial community in typical forest soils has not been thoroughly conducted. In this study, the typical forest soils (Mongolian oak (Quercus mongolica) soil, MOS; white birch (Betula platyphylla) soil, WBS; and white poplar (Populus davidiana) soil, WPS) in the Sanjiang Plain were selected to ascertain the differences and the major environmental factors driving soil microbial community abundance and structure. Results indicated that differences existed in the abundance and structure of the bacterial, archaeal, and fungal community. Co-occurrence network analysis showed that the bacterial and fungal networks were more complex than those of archaeal networks. Unclassified Acidobacteria and unclassified Pyrinomonadaceae were the keystone taxa in the bacterial networks, while Pleotrichocladium and Leotia were the keystone taxa in the fungal networks. Among all environmental factors, pH, SOM, and total N exhibited dominant roles in affecting the abundance of bacteria, archaea, and fungi. The redundancy analysis (RDA) showed that pH was the vital environmental factor responsible for driving the structure of the bacterial, archaeal, and fungal community.

Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species' range in Colby, Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after 10 years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western Kansas as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after 10 years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought. IMPORTANCE In this study, we used a 10-year long reciprocal garden system, and reports that different ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii can maintain or recruit distinct bacterial but not fungal rhizobiomes after 10 years in an arid environment. We used both 16S rRNA and ITS2 amplicons to analyze the bacterial and fungal communities in the rhizospheres of the respective ecotypes. We showed that A. gerardii might regulate the bacterial community to adapt to the arid environment, in which some ecotypes were not adapted to. Our study also suggested a possible tradeoff between the generalist and the specialist bacterial communities in specific environments, which could benefit the plant host. Our study will provide insights into the plant host regulation of the rhizosphere bacterial and fungal communities, especially during frequent drought conditions anticipated in the future.

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

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

High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China

Members of the Thaumarchaeota phylum play a key role in nitrogen cycling and are prevalent in a variety of environments including soil, sediment, and seawater. However, few studies have shown the presence of Thaumarchaeota in the terrestrial deep subsurface. Using high-throughput 16S rRNA gene sequencing, this study presents evidence for the high relative abundance of Thaumarchaeota in a biofilm sample collected from the well of Chinese Continental Scientific Drilling at a depth of 2000 m. Phylogenetic analysis showed a close relationship of these thaumarchaeotal sequences with known ammonia-oxidizing archaea (AOA) isolates, suggesting the presence of AOA in the deep metamorphic environment of eastern China which is believed to be oxic. Based on fluid geochemistry and FAProTax functional prediction, a pathway of nitrogen cycling is proposed. Firstly, heterotrophic nitrogen fixation is executed by diazotrophic bacteria coupled with methane oxidation. Then, ammonia is oxidized to nitrite by AOA, and nitrite is further oxidized to nitrate by bacteria within the phylum Nitrospirae. Denitrification and anaerobic ammonia oxidation occur slowly, leading to nitrate accumulation in the subsurface. With respect to biogeochemistry, the reaction between downward diffusing O2 and upward diffusing CH4 potentially fuels the ecosystem with a high relative abundance of Thaumarchaeota.

Trends in Microbial Community Composition and Function by Soil Depth

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

Microbial communities in rare earth mining soil after in-situ leaching mining

In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.

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.

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands

Biogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil, while the subsoil is assumed to have microbial diversity patterns similar to those of the topsoil. Here we compared patterns and drivers of microbial alpha and beta diversity in and between topsoils (0 to 10 cm) and subsoils (30 to 50 cm) of temperate grasslands in Inner Mongolia of China, covering an ∼1,500-km transect along an aridity gradient. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity remains constant or increases with increasing aridity in topsoil and decreases in subsoil, archaeal diversity decreases in topsoil and remains constant in subsoil. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation and contemporary climate but is most strongly influenced by the factor historical temperature anomaly since the Last Glacial Maximum (LGM) and by soil pH in the subsoil. Moreover, the biogeographic patterns of topsoil-subsoil community dissimilarities vary for different microbial groups and are overall most strongly influenced by soil fertility differences between depths for bacteria and by contemporary climate for archaea. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the spatial variation of bacterial diversity. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth.IMPORTANCE Exploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from an ∼1,500-km temperate grassland transect, we find divergent patterns of microbial diversity and its determinants in the topsoil versus the subsoil. Furthermore, we find important and direct legacy effects of historical climate change on the microbial diversity of subsoil yet indirect effects on topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with various climate histories.

Metagenomic and chemical characterization of soil cobalamin production

Cobalamin (vitamin B₁₂) is an essential enzyme cofactor for most branches of life. Despite the potential importance of this cofactor for soil microbial communities, the producers and consumers of cobalamin in terrestrial environments are still unknown. Here we provide the first metagenome-based assessment of soil cobalamin-producing bacteria and archaea, quantifying and classifying genes encoding proteins for cobalamin biosynthesis, transport, remodeling, and dependency in 155 soil metagenomes with profile hidden Markov models. We also measured several forms of cobalamin (CN-, Me-, OH-, Ado-B₁₂) and the cobalamin lower ligand (5,6-dimethylbenzimidazole; DMB) in 40 diverse soil samples. Metagenomic analysis revealed that less than 10% of soil bacteria and archaea encode the genetic potential for de novo synthesis of this important enzyme cofactor. Predominant soil cobalamin producers were associated with the Proteobacteria, Actinobacteria, Firmicutes, Nitrospirae, and Thaumarchaeota. In contrast, a much larger proportion of abundant soil genera lacked cobalamin synthesis genes and instead were associated with gene sequences encoding cobalamin transport and cobalamin-dependent enzymes. The enrichment of DMB and corresponding DMB synthesis genes, relative to corrin ring synthesis genes, suggests an important role for cobalamin remodelers in terrestrial habitats. Together, our results indicate that microbial cobalamin production and repair serve as keystone functions that are significantly correlated with microbial community size, diversity, and biogeochemistry of terrestrial ecosystems.

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO₂ emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO₂ production.

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.

Temperature-Dependent Network Modules of Soil Methanogenic Bacterial and Archaeal Communities

Temperature is an important factor regulating the production of the greenhouse gas CH₄. Structure and function of the methanogenic microbial communities are often drastically different upon incubation at 45°C versus 25°C or 35°C, but are also different in different soils. However, the extent of taxonomic redundancy within each functional group and the existence of different temperature-dependent microbial community network modules are unknown. Therefore, we investigated paddy soils from Italy and the Philippines and a desert soil from Utah (United States), which all expressed CH₄ production upon flooding and exhibited structural and functional differences upon incubation at three different temperatures. We continued incubation of the pre-incubated soils (Liu et al., 2018) by changing the temperature in a factorial manner. We determined composition, abundance and function of the methanogenic archaeal and bacterial communities using HiSeq Illumina sequencing, qPCR and analysis of activity and stable isotope fractionation, respectively. Heatmap analysis of operational taxonomic units (OTU) from the different incubations gave detailed insights into the community structures and their putative functions. Network analysis showed that the microbial communities in the different soils were all organized within modules distinct for the three incubation temperatures. The diversity of Bacteria and Archaea was always lower at 45°C than at 25 or 35°C. A shift from 45°C to lower temperatures did not recover archaeal diversity, but nevertheless resulted in the establishment of structures and functions that were largely typical for soil at moderate temperatures. At 25 and 35°C and after shifting to one of these temperatures, CH₄ was always produced by a combination of acetoclastic and hydrogenotrophic methanogenesis being consistent with the presence of acetoclastic (Methanosarcinaceae, Methanotrichaceae) and hydrogenotrophic (Methanobacteriales, Methanocellales, Methanosarcinaceae) methanogens. At 45°C, however, or after shifting from moderate temperatures to 45°C, only the Philippines soil maintained such combination, while the other soils were devoid of acetoclastic methanogens and consumed acetate instead by syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Syntrophic acetate oxidation was apparently achieved by Thermoanaerobacteraceae, which were especially abundant in Italian paddy soil and Utah desert soil when incubated at 45°C. Other bacterial taxa were also differently abundant at 45°C versus moderate temperatures, as seen by the formation of specific network modules. However, the archaeal OTUs with putative function in acetoclastic or hydrogenotrophic methanogenesis as well as the bacterial OTUs were usually not identical across the different soils and incubation conditions, and if they were, they suggested the existence of mesophilic and thermophilic ecotypes within the same OTUs. Overall, methanogenic function was determined by the bacterial and/or archaeal community structures, which in turn were to quite some extent determined by the incubation temperature, albeit largely individually in each soil. There was quite some functional redundancy as seen by different taxonomic community structures in the different soils and at the different temperatures.

Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China

Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 10⁷ to 26.18 × 10⁷ 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions.