Search

Background: For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess–Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes. Results: Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO 2 ) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus. Conclusions: On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes. [ABSTRACT FROM AUTHOR]

Thermodynamic characterization of the relative stabilities of chemical compounds is a pillar of conceptual models in various fields of geosciences. Analogous models applied to genomes can yield new information about the relationship between genomes and their geochemical environments. In this perspective article, we present a chemical and thermodynamic analysis of prokaryotic lineages that have been the target of previous phylogenomic studies of evolutionary adaptation to varying redox conditions. The thermodynamic model development begins by quantifying the effects of hydrogen activity (aH2) and temperature on the relative stabilities of organic compounds with different carbon oxidation state. When applied to proteins instead of metabolites, the same techniques can be used to identify combinations of aH2 and temperature at which reference proteomes for Class I or Class II methanogens are relatively stable. The calculated aH2 values are compatible with reported measurements for habitats of methanogens ranging from highly reducing submarine hydrothermal systems to less reducing environments including methanogenic sediments. In contrast to the transition between the two classes of methanogenic archaea, that between basal and terrestrial groups of Thaumarchaeota (denoting the origin of ammonia‐oxidizing archaea) occurs at a less‐reducing redox boundary. These examples reveal the consequences of energy minimization driving evolution and show how geochemical calculations involving biomolecules can be used to quantify and better understand the coevolution of the geosphere and biosphere. [ABSTRACT FROM AUTHOR]

Aims: Rotational Impoundment Management (RIM) involves summer inundation of impounded mangrove forests for mosquito management. The goal of this study was to investigate the impact of RIM on communities of aerobic ammonia-oxidizing microorganisms in Avicennia germinans dominated mangrove forest soils.Soil samples were collected annually in a managed and an adjacent, non-managed impoundment before and after the start of RIM at three elevation levels with their characteristic mangrove habitats, i.e., dwarf (highest elevation), sparse and dense (lowest elevation). The ammonia-oxidizing communities were studied by qPCR and amplicon analyses based on thaumarchaeal and betaproteobacterial amoA genes.Temporal variations in copy numbers and assemblies of amoA gene amplicons were limited. Thaumarchaeal amoA genes increased in the dwarf and sparse habitat in the non-managed impoundment, and betaproteobacterial amoA genes increased in the dwarf habitat in the RIM impoundment. No copies of the amoA gene of Nitrospirota (comammox bacteria) were detected in either impoundment. Whereas there were no significant effects of RIM on the composition of thaumarchaeal communities, RIM affected the composition of betaproteobacterial amoA assemblies in all habitats in the RIM impoundment.Direct consequences of RIM were reflected in changes in the composition of assemblies of amplicon sequence variants (ASVs) of ammonia-oxidizing Betaproteobacteria in all mangrove habitats of the RIM impoundment. Significant temporal changes at higher elevations in the non-managed impoundment were likely due to groundwater exchange between the impoundments.Methods: Rotational Impoundment Management (RIM) involves summer inundation of impounded mangrove forests for mosquito management. The goal of this study was to investigate the impact of RIM on communities of aerobic ammonia-oxidizing microorganisms in Avicennia germinans dominated mangrove forest soils.Soil samples were collected annually in a managed and an adjacent, non-managed impoundment before and after the start of RIM at three elevation levels with their characteristic mangrove habitats, i.e., dwarf (highest elevation), sparse and dense (lowest elevation). The ammonia-oxidizing communities were studied by qPCR and amplicon analyses based on thaumarchaeal and betaproteobacterial amoA genes.Temporal variations in copy numbers and assemblies of amoA gene amplicons were limited. Thaumarchaeal amoA genes increased in the dwarf and sparse habitat in the non-managed impoundment, and betaproteobacterial amoA genes increased in the dwarf habitat in the RIM impoundment. No copies of the amoA gene of Nitrospirota (comammox bacteria) were detected in either impoundment. Whereas there were no significant effects of RIM on the composition of thaumarchaeal communities, RIM affected the composition of betaproteobacterial amoA assemblies in all habitats in the RIM impoundment.Direct consequences of RIM were reflected in changes in the composition of assemblies of amplicon sequence variants (ASVs) of ammonia-oxidizing Betaproteobacteria in all mangrove habitats of the RIM impoundment. Significant temporal changes at higher elevations in the non-managed impoundment were likely due to groundwater exchange between the impoundments.Results: Rotational Impoundment Management (RIM) involves summer inundation of impounded mangrove forests for mosquito management. The goal of this study was to investigate the impact of RIM on communities of aerobic ammonia-oxidizing microorganisms in Avicennia germinans dominated mangrove forest soils.Soil samples were collected annually in a managed and an adjacent, non-managed impoundment before and after the start of RIM at three elevation levels with their characteristic mangrove habitats, i.e., dwarf (highest elevation), sparse and dense (lowest elevation). The ammonia-oxidizing communities were studied by qPCR and amplicon analyses based on thaumarchaeal and betaproteobacterial amoA genes.Temporal variations in copy numbers and assemblies of amoA gene amplicons were limited. Thaumarchaeal amoA genes increased in the dwarf and sparse habitat in the non-managed impoundment, and betaproteobacterial amoA genes increased in the dwarf habitat in the RIM impoundment. No copies of the amoA gene of Nitrospirota (comammox bacteria) were detected in either impoundment. Whereas there were no significant effects of RIM on the composition of thaumarchaeal communities, RIM affected the composition of betaproteobacterial amoA assemblies in all habitats in the RIM impoundment.Direct consequences of RIM were reflected in changes in the composition of assemblies of amplicon sequence variants (ASVs) of ammonia-oxidizing Betaproteobacteria in all mangrove habitats of the RIM impoundment. Significant temporal changes at higher elevations in the non-managed impoundment were likely due to groundwater exchange between the impoundments.Conclusions: Rotational Impoundment Management (RIM) involves summer inundation of impounded mangrove forests for mosquito management. The goal of this study was to investigate the impact of RIM on communities of aerobic ammonia-oxidizing microorganisms in Avicennia germinans dominated mangrove forest soils.Soil samples were collected annually in a managed and an adjacent, non-managed impoundment before and after the start of RIM at three elevation levels with their characteristic mangrove habitats, i.e., dwarf (highest elevation), sparse and dense (lowest elevation). The ammonia-oxidizing communities were studied by qPCR and amplicon analyses based on thaumarchaeal and betaproteobacterial amoA genes.Temporal variations in copy numbers and assemblies of amoA gene amplicons were limited. Thaumarchaeal amoA genes increased in the dwarf and sparse habitat in the non-managed impoundment, and betaproteobacterial amoA genes increased in the dwarf habitat in the RIM impoundment. No copies of the amoA gene of Nitrospirota (comammox bacteria) were detected in either impoundment. Whereas there were no significant effects of RIM on the composition of thaumarchaeal communities, RIM affected the composition of betaproteobacterial amoA assemblies in all habitats in the RIM impoundment.Direct consequences of RIM were reflected in changes in the composition of assemblies of amplicon sequence variants (ASVs) of ammonia-oxidizing Betaproteobacteria in all mangrove habitats of the RIM impoundment. Significant temporal changes at higher elevations in the non-managed impoundment were likely due to groundwater exchange between the impoundments. [ABSTRACT FROM AUTHOR]

Nitrification is a major process within the nitrogen (N) cycle leading to global losses of N, including fertiliser N, from natural and agricultural systems and producing significant nitrous oxide emissions. One strategy for the mitigation of these losses involves nitrification inhibition by plant-derived biological nitrification inhibitors (BNIs). Cultivation-based studies of BNIs, including screening for new compounds, have predominantly investigated inhibition of a single ammonia-oxidising bacterium (AOB), Nitrosomonas europaea, even though ammonia oxidation in soil is usually dominated by ammonia-oxidising archaea (AOA), especially in acidic soils, and AOB Nitrosospira sp., rather than Nitrosomonas, in fertilised soils. This study aimed to assess the sensitivity of ammonia oxidation by a range of AOA and AOB pure cultures to BNIs produced by plant roots (methyl 3-(4-hydroxyphenyl) propionate, sakuranetin and 1,9-decanediol) and shoots (linoleic acid, linolenic acid and methyl linoleate). AOA were generally more sensitive to BNIs than AOB, and sensitivity was greater to BNIs produced by shoots than those produced by roots. Sensitivity also varied within AOA and AOB cultures and between different BNIs. In general, N. europaea was not a good indicator of BNI inhibition, and findings therefore highlight the limitations of use of a single bioassay strain and suggest the use of a broader range of strains that are more representative of natural soil communities. [ABSTRACT FROM AUTHOR]

Nitrification is a central process of the aquatic nitrogen cycle that controls the supply of nitrate used in other key processes, such as phytoplankton growth and denitrification. Through time series observation and modeling of a seasonally stratified, eutrophic coastal basin, we demonstrate that physical dilution of nitrifying microorganisms bywater column mixing can delay and decouple nitrification. The findings are based on a 4-y, weekly time series in the subsurface water of Bedford Basin, Nova Scotia, Canada, that included measurement of functional (amoA) and phylogenetic (16S rRNA) marker genes. In years with colder winters, more intense winter mixing resulted in strong dilution of resident nitrifiers in subsurface water, delaying nitrification for weeks to months despite availability of ammonium and oxygen. Delayed regrowth of nitrifiers also led to transient accumulation of nitrite (3 to 8 µmol · kgsw-1) due to decoupling of ammonia and nitrite oxidation. Nitrite accumulation was enhanced by ammonia-oxidizing bacteria (Nitrosomonadaceae) with fast enzyme kinetics, which temporarily outcompeted the ammonia-oxidizing archaea (Nitrosopumilus) that dominated under more stable conditions. The study reveals how physical mixing can drive seasonal and interannual variations in nitrification through control of microbial biomass and diversity. Variable, mixing-induced effects on functionally specialized microbial communities are likely relevant to biogeochemical transformation rates in other seasonally stratified water columns. The detailed study reveals a complex mechanism through which weather and climate variability impacts nitrogen speciation, with implications for coastal ecosystem productivity. It also emphasizes the value of high-frequency, multiparameter time series for identifying complex controls of biogeochemical processes in aquatic systems. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

"Candidatus Nitrosotenuis uzonensis" is the only cultured moderately thermophilic member of the thaumarchaeotal order Nitrosopumilales (NP) that contains many mesophilic marine strains. We examined its membrane lipid composition at different growth temperatures (37°C, 46°C, and 50°C). Its lipids were all membranespanning glycerol dialkyl glycerol tetraethers (GDGTs), with 0 to 4 cyclopentane moieties. Crenarchaeol (cren), the characteristic thaumarchaeotal GDGT, and its isomer (cren=) were present in high abundance (30 to 70%). The GDGT polar headgroups were mono-, di-, and trihexoses and hexose/phosphohexose. The ratio of glycolipid to phospholipid GDGTs was highest in the cultures grown at 50°C. With increasing growth temperatures, the relative contributions of cren and cren= increased, while those of GDGT-0 to GDGT-4 (including isomers) decreased. TEX86 (tetraether index of tetraethers consisting of 86 carbons)-derived temperatures were much lower than the actual growth temperatures, further demonstrating that TEX86 does not accurately reflect the membrane lipid adaptation of thermophilic Thaumarchaeota. As the temperature increased, specific GDGTs changed relative to their isomers, possibly representing temperature adaption-induced changes in cyclopentane ring stereochemistry. Comparison of a wide range of thaumarchaeotal core lipid compositions revealed that the "Ca. Nitrosotenuis uzonensis" cultures clustered separately from other members of the NP order and the Nitrososphaerales (NS) order. While phylogeny generally seems to have a strong influence on GDGT distribution, our analysis of "Ca. Nitrosotenuis uzonensis" demonstrates that its terrestrial, higher-temperature niche has led to a lipid composition that clearly differentiates it from other NP members and that this difference is mostly driven by its high cren= content. [ABSTRACT FROM AUTHOR]

We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean. [ABSTRACT FROM AUTHOR]

Archaea are important participants in soil biogeochemical cycles. Their membrane lipids are usually composed of isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs), which are ubiquitous in the environments and widely applied as biomarkers for archaeal biogeochemical processes and palaeothermometry. However, the biological sources of iGDGTs and environmental factors controlling their distribution in soils are elusive. We examined the archaeal lipid composition and community structure along an altitudinal soil transect in the Hani terrace wetlands in Southwest of China by combining organic geochemical and high-throughput sequencing approaches. The results show that monoglycosyl -iGDGTs (1G-iGDGTs) are the dominating intact polar lipids (IPLs) and possible precursor of core-iGDGTs preserved in soils. iGDGTs from Hani soils may come from several archaeal lineages based on their significant positive correlations in both core lipids and IPLs. Thaumarchaeota Group I.1b most likely contribute to crenarchaeol and its regio-isomer in non-paddy soils, while Bathyarchaeota , Methanobacteria and Methanomicrobia may predominantly contribute to GDGT-0 in water-saturated paddy soils. Our results indicate that the paleotemperature proxy TEX 86 in soils can be affected by changes in archaeal community structure in addition to environmental variables such as soil water content and pH, but not independently by temperature. In addition, the lower TEX 86 in humid soils may be partly attributed to the insufficient peak separation of iGDGTs with cyclopentyl moieties, which contain abnormally high abundances of shoulder peaks that may be contributed by anaerobic Archaea. This study sheds light on the increasing role of microbial community structure in affecting the fidelity of TEX 86 in terrestrial environment, which should be taken into consideration when applying it to paleo-soil temperature studies. • Archaeal IPLs in soils may represent (recently) living archaea. • iGDGTs in Hani soils are likely to be produced by diverse archaeal populations. • The iGDGT-based terrestrial proxies can be affected by changes in soil archaeal communities. [ABSTRACT FROM AUTHOR]

• High diversity of the archaeal community in the Mediterranean Sea water column. • Dominance of Euryarchaeota Group II and III in upper epipelagic waters (0–100 mbsl). • Shift in archaeal community composition coincided with a change in IPL distribution. • Ratio of GDGT-2/GDGT-3 increased with water depth. • Thaumarchaeota were abundant in the deeper part of the water column. Thaumarchaeota are one of the most abundant groups of Archaea in the marine water column. Their membrane consists of isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) which are applied in the widely used TEX 86 proxy to reconstruct past sea surface temperatures (SSTs). However, in some specific marine systems, such as the Mediterranean Sea, core-top TEX 86 -derived temperatures do not seem to reflect annual mean SSTs. This has been attributed to contributions of deep-water dwelling Thaumarchaeota. Here, we investigate the potential causes of this bias by studying both the archaeal diversity as well as the intact polar lipid (IPL) GDGT composition in the Mediterranean water column by a combined 16S rRNA gene amplicon sequencing and a lipidomic approach on suspended particulate matter (SPM) at different water depths. The archaeal distribution showed a dominance of archaea other than Thaumarchaeota, i.e. Marine Euryarchaeota group II and III in the upper epipelagic waters (0–100 m deep), while Thaumarchaeota (Marine group I; MGI) dominated the subsurface and the deeper waters. This shift in the archaeal community composition coincided with a decrease in IPL GDGT-0 and increase of IPL crenarchaeol. The ratio of GDGT-2/GDGT-3 increased with water depth, but values were lower than observed in deep marine waters of some other regions. The increase of the GDGT-2/GDGT-3 ratio coincided with the high relative abundance of deep-water MGI, which may be linked to the high temperature and salinity found in specific water masses of the Mediterranean Sea. We conclude that these particularities of the Mediterranean Sea are responsible for the overestimated SST based on TEX 86. [ABSTRACT FROM AUTHOR]

• Suspended particular matter from Lake Malawi was analyzed for isoprenoid GDGTs. • HPH-crenarchaeol concentrations were greatest just below the chlorophyll maximum. • Maximum CL concentrations likely reflect degradation of recently produced IPL GDGTs. • A second, deeper-dwelling Thaumarchaeotal population exists near the chemocline. Several long paleoclimate records generated from Lake Malawi sediments rely on an assumption that the TEX 86 paleothermometer reflects annual mean lake surface temperatures. Thaumarchaeota, the producers of the isoprenoid glycerol dialkyl glycerol tetraether (iGDGT) lipids that are the basis of the TEX 86 proxy, can occupy a wide range of habitats in the upper water column of lacustrine systems, so it is crucial to specifically constrain the ecology of Thaumarchaeota in Lake Malawi to properly interpret its sedimentary TEX 86 record. To investigate the spatial and vertical distribution of Thaumarchaeotal iGDGT production in Lake Malawi, suspended particulate matter (SPM) was collected from the upper water column (>300 m) at three sites spanning the north, central, and south basins of the lake and analyzed for intact polar (IPL) and core (CL) iGDGT lipid abundances. Samples were collected in January during the austral summer when the lake is strongly stratified. Concentrations of the most labile IPL, hexose-phosphohexose (HPH)-crenarchaeol, were greatest just below the deep chlorophyll maximum at ∼50 m water depth in the deeper north and central basins and ∼30 m in the shallow south basin. Maximum CL concentrations occur below the maximum HPH-crenarchaeol concentrations and therefore possibly reflect the accumulation of recently produced IPL GDGT degradation products. If the export of CLs to the sediments is dominated by this CL pool, sedimentary TEX 86 would reflect Thaumarchaeota living within the thermocline during the stratified season and therefore may have a cool bias rather than reflecting true surface water temperatures. An increase in abundances of GDGT-2, crenarchaeol isomer, and monohexose (MH)-crenarchaeol at ∼150–200 m suggests that a secondary Thaumarchaeotal population, likely Group I.1b Thaumarchaeota, inhabits the subsurface water column near the anoxic-suboxic boundary. Total production of iGDGTs by this group appears to be much lower than the surface-dwelling clade, but its imprint on sedimentary TEX 86 is unknown. An analysis of iGDGT production in the water column throughout the annual cycle is needed to resolve the timing and magnitude of export of CLs to the sediments from these two Thaumarchaeotal populations. [ABSTRACT FROM AUTHOR]

Abstract RNA is considered to be a short-lived molecule, indicative of cellular metabolic activity, whereas DNA is thought to turn over more slowly because living cells do not always grow and divide. To explore differences in the rates of synthesis of these nucleic acids, we used H 2 18O quantitative stable isotope probing (qSIP) to measure the incorporation of 18O into 16S rRNA, the 16S rDNA, amoA mRNA and the amoA gene of soil Thaumarchaeota. Incorporation of 18O into the thaumarchaeal amoA mRNA pool was faster than into the 16S rRNA pool, suggesting that Thaumarchaea were metabolically active while using rRNA molecules that were likely synthetized prior to H 2 18O addition. Assimilation rates of 18O into 16S rDNA and amoA genes were similar, which was expected because both genes are present in the same thaumarchaeal genome. The Thaumarchaea had significantly higher rRNA to rDNA ratios than bacteria, though the 18O isotopic signature of thaumarchaeal rRNA was lower than that of bacterial rRNA, further suggesting preservation of old non-labeled rRNA. Through qSIP of soil with H 2 18O, we showed that 18O incorporation into thaumarchaeal nucleic acids was generally low, indicating slower turnover rates compared to bacteria, and potentially suggesting thaumarchaeal capability for preservation and efficient reuse of biomolecules. Highlights • qSIP allows measurement of in situ microbial nucleic acid synthesis rates. • Metabolically active soil Thaumarchaeota use old rRNA. • Genomic DNA is uniformly replicated among the Thaumarchaeota. [ABSTRACT FROM AUTHOR]

Abstract Archaea play an important role in the biogeochemical cycling of elements in the environment. Heavy metals are ubiquitous pollutants in the environment. Previous studies have revealed a considerable influence of metal pollution on the archaeal community, but the short-term response of the archaeal community to metal pollution remains unclear. Hence, the present study investigated the short versus long-term responses of overall archaeal communities in freshwater sediments after exposure to accidental metal pollution caused by the discharge of heavy metal-containing wastewater from an indium-producing factory. Quantitative PCR was used to determine the archaeal abundance, while Illumina MiSeq sequencing was applied to characterize the diversity and structure of the archaeal community. The abundance (2.47 × 105–1.55 × 108 archaeal 16S rRNA gene copies per gram dry sediment), diversity (Shannon diversity index = 2.49–4.45) and structure of overall archaeal community illustrated a drastic temporal change. The archaeal communities mainly comprised the phyla Euryarchaeota , Thaumarchaeota and Bathyarchaeota. The exposure to metal pollution induced an increase in the proportion of Euryarchaeota but lowered the proportion of Thaumarchaeota. The accidental metal pollution exerted a profound impact on the archaeal community in freshwater sediment. This study could contribute our understanding of the short versus long-term response of archaeal communities to metal pollution. Highlights • Metal impact on freshwater sediment archaeal community was investigated. • Metal pollution affected archaeal abundance, diversity and community structure. • Exposure to metal spill increased Euryarchaeota but decreased Thaumarchaeota. [ABSTRACT FROM AUTHOR]

Highlights • Improving green roof nitrogen (N) retention will help reduce N runoff and fertilizer use. • Nitrate runoff and N 2 O losses from several green roofs suggest active nitrification. • Ammonia oxidizing (AO) archaeal sequences were much more prevalent than AO bacteria. • Bacterial orders associated with root nodulation and N fixation were common. • Use of N-fixing plants or nitrification inhibitors may improve green roof N retention. Abstract Green roofs typically consist of an engineered soil paired with drought-tolerant plants installed on a rooftop. These emerging ecosystems are installed for the services they provide, which in many cases depend on plant performance. In terrestrial ecosystems, nitrogen (N) is most often the limiting nutrient for plant productivity and its availability is heavily influenced by soil microorganisms. However, little is known about the green roof microbiome or their influence on N availability. We employed 16S rRNA and nifH gene sequencing to assess the presence of nitrifying and nitrogen-fixing prokaryotes and their relationships to evidence of nitrification (runoff fluxes of nitrate and gaseous fluxes of nitrous oxide) and N fixation (presence of plants with symbiotic nitrogen-fixers) on 6 green roofs near Cincinnati, Ohio, USA. Our data indicate that green roofs in this region are a net source of reactive N: the majority of roofs released elevated nitrate levels in runoff relative to precipitation inputs, and also emitted N 2 O, although at low rates comparable to those in natural ecosystems. We also recovered abundant nifH genes affiliated with Rhizobiales and observed root nodules on leguminous plants on 5 of the 6 studied roofs, together indicating active N fixation. Our findings suggest N loss from green roofs could be alleviated by applying nitrification inhibitors, and that fostering plant-microbe N fixing communities could reduce the need for fertilizer amendments. Our data also highlight the role of microbial N cycling on green roofs and underscore the need for further work to quantify N-processing rates. [ABSTRACT FROM AUTHOR]

Highlights • Crenarchaeol and its isomer were isolated from marine surface sediments. • Structures were studied by ether cleavage and GC–MS using mild ionization. • A tricyclic biphytane stereoisomer is formed from the crenarchaeol isomer. • 13C NMR data suggest the cis stereochemistry of one of the cyclopentane moieties. • This difference likely affects the packing of lipid membranes of Thaumarchaeota. Abstract Isolation of crenarchaeol and its isomer from marine surface sediments, followed by ether cleavage and GC–MS characterization using supersonic molecular beam (SMB) ionization of the biphytanes formed, revealed that the crenarchaeol isomer comprises a tricyclic biphytane that is stereochemically different from the tricyclic biphytane of crenarchaeol. This isomeric tricyclic biphytane was also released from the crenarchaeol isomer in extant Thaumarchaeotal biomass. Reinterpretation of previously obtained 13C NMR data of the crenarchaeol isomer suggested that the cyclopentane moiety adjacent to the cyclohexyl moiety of the tricyclic biphytane of the crenarcheaol isomers possesses the unusual cis stereochemistry in comparison to the trans stereochemistry of all cyclopentane moieties in crenarchaeol. This stereochemical difference likely affects the packing of lipid membranes of Thaumarchaeota and therefore provides a biophysical explanation for the role of the crenarchaeol isomer in the TEX 86 palaeothermometer based on fossilized Thaumarcheotal lipids. [ABSTRACT FROM AUTHOR]

Ammonia is a metabolic waste product excreted by aquatic organisms that causes toxicity when it accumulates. Aquaria and aquaculture systems therefore use biological filters that promote the growth of nitrifiers to convert ammonia to nitrate. Ammonia-oxidizing bacteria (AOB) have been isolated from aquarium biofilters and are available as commercial supplements, but recent evidence suggests that ammonia-oxidizing archaea (AOA) are abundant ammonia-oxidizers in aquarium biofilters. In this study, we report the cultivation and closed genome sequence of novel AOA representative Candidatus Nitrosotenius aquariensis, which was enriched from a freshwater aquarium biofilter. Ca. N. aquariensis oxidizes ammonia stoichiometrically to nitrite with a concomitant increase in thaumarchaeotal cells and a generation time of 34.9 hours. Ca. N. aquariensis has an optimal growth temperature of 33°C, tolerates up to 3 mM NH4Cl, and grows optimally at 0.05% salinity. Transmission electron microscopy revealed that Ca. N. aquariensis cells are rod-shaped, with a diameter of -0.4 µm and lengths ranging from 0.6-3.6 µm. In addition, these cells possess S-layers and multiple proteinaceous appendages. Phylogenetically, Ca. N. aquariensis belongs to group I.1a Thaumarchaeota, clustering with sequences from freshwater aquarium biofilters, aquaculture systems, and wastewater treatment plants. The complete 1.70 Mbp genome encodes for genes involved in ammonia oxidation, bicarbonate assimilation, flagella synthesis, chemotaxis, S-layer production, defense, and protein glycosylation. Incubations with differential inhibitors indicate that Ca. N. aquariensis-like AOA contribute to ammonia oxidation within the isolation source biofilter. [ABSTRACT FROM AUTHOR]

Thaumarchaeota and Bathyarchaeota (formerly named Miscellaneous Crenarchaeotal Group, MCG) are globally occurring archaea playing potential roles in nitrogen and carbon cycling, especially in marine benthic biogeochemical cycle. Information on their distributional and compositional patterns could provide critical clues to further delineate their physiological and biochemical characteristics. Profiles of thaumarchaeotal and the total archaeal community in the northern South China Sea surface sediments revealed a successively transitional pattern of Thaumarchaeota composition using MiSeq sequencing. Shallow-sea sediment enriched phylotypes decreased gradually along the slope from estuarine and coastal marine region to the deep-sea, while deep-sea sediment enriched phylotypes showed a trend of increasing. Proportion of Thaumarchaeota within the total archaea increased with seawater depth. Phylotypes enriched in shallow- and deep-sea sediments were affiliated to OTUs originated from similar niches, suggesting that physiological adaption not geographical distance shaped the distribution of Thaumarchaeota lineages. Quantitative PCR also depicted a successive decrease of thaumarchaeotal 16S rRNA gene abundance from the highest at shallow-sea sites E708S and E709S (2.57 × 106 and 2.73 × 106 gene copies/g of dry sediment) to the lowest at deep-sea sites E525S and E407S (1.97 × 106 and 2.14 × 106 gene copies/g of dry sediment). Both of the abundance fractions of Bathyarchaeota subgroups (including subgroups 1, 6, 8, 10, 13, 15, 17, and ungrouped Bathyarchaeota) and the total Bathyarchaeota in the total archaea showed a negative distribution to seawater depth. Partitioned distribution of Bathyarchaeota fraction in the total archaea is documented for the first time in this study, and the shallow- and deep-sea Bathyarchaeota could account for 17.8 and 0.8%, respectively, on average. Subgroups 6 and 8, enriched subgroups in shallow-sea sediments, largely explained this partitioned distribution pattern according to seawater depth. Their prevalence in shallow-sea and suboxic estuarine sediments rather than deep-sea sediments hints that their metabolic properties of carbon metabolism are adapted to carbon substrates in these environments. [ABSTRACT FROM AUTHOR]

The analysis of ribosomal genes has been applied to study microbiomes of two soils of the solonetzic soil complex in the northern Caspian region. These soils—solonetz and quasigleyic chestnut soil—drastically differ in their salinity characteristics. The specificity of the vertical distribution of prokaryotes by the genetic soil horizons from the surface to the depth of 120 cm in these soils is discussed. The differences in the structure of microbiomes in the upper soil horizons can be related to the differences in the vegetation cover of the two soils, whereas the differentiation of microbiomes along the soil profiles is affected by the soil salinization. The solonetz is characterized by a much sharper decrease in the abundance and diversity of microorganisms down the soil profile in comparison with the leached quasigleyic chestnut soil. The total number of prokaryotes is mainly limited by the organic carbon content. In the upper soil horizons, Archaea from the phylum Thaumarchaeota are relatively abundant; their percentage decreases down the soil profiles. In the lower horizons of the solonetz, the genes of Marinobacter bacteria, which are considered marine inhabitants, have been found. It is probable that they persist in the soil since the previous transgression of the Caspian Sea. [ABSTRACT FROM AUTHOR]

The brown tube sponge Agelas tubulata (cf. Agelas conifera) is an abundant and long-lived sponge on Caribbean reefs. Recently, a disease-like condition, Agelas wasting syndrome (AWS), was described from A. tubulata in the Florida Keys, where prevalence of the syndrome increased from 7 to 35% of the sponge population between 2010 and 2015. In this study, we characterized the prokaryotic symbiont community of A. tubulata for the first time from individuals collected within the same monitoring plots where AWS was described. We also sampled tissue from A. tubulata exhibiting symptoms of AWS to determine its effect on the diversity and structure of prokaryotic symbiont communities. Bacteria from the phyla Chloroflexi and Proteobacteria, particularly the class Gammaproteobacteria, dominated the sponge microbiome in tissue samples of both healthy sponges and those exhibiting AWS. Prokaryotic community structure differed significantly between the diseased and healthy sponge samples, with greater variability among communities in diseased samples compared to healthy samples. These differences in prokaryotic community structure included a shift in relative abundance of the dominant, ammonia-oxidizing (Thaumarchaeota) symbionts present in diseased and healthy sponge samples. Further research is required to determine the functional consequences of this shift in microbial community structure and the causal relationship of dysbiosis and sponge disease in A. tubulata. [ABSTRACT FROM AUTHOR]

Thaumarchaeota synthesize specific glycerol dibiphytanyl glycerol tetraethers (GDGTs), the distribution of which is affected by temperature, thereby forming the basis of the paleotemperature proxy, TEX 86 . Lipids in marine surface sediments are believed to be derived mainly from pelagic Thaumarchaeota; however, some studies have evaluated the possibility that benthic Archaea also contribute to the lipid fossil record. Here, we compared the archaeal abundance and composition from DNA-based methods with the archaeal intact polar lipid (IPL) diversity in surface sediments of a seasonally hypoxic marine lake to determine the potential biological sources of the sedimentary archaeal IPLs under changing environmental conditions. The archaeal community changed from March (oxic conditions) to August (euxinic) from a Thaumarchaeota-dominated community (up to 82%) to an archaeal community dominated by the DPANN super phylum (up to 95%). This marked change coincided with a one order of magnitude decrease in the total IPL-GDGT abundance. In addition, IPL-GDGTs with a glyco polar head group increased. This may indicate a transition to Thaumarchaeota growing in stationary phase or selective preservation of the GDGT pool. In addition, considering the apparent inability of the DPANN Archaea to synthesize their own membrane lipids, we hypothesize that the dominant DPANN Archaea population present in August use the lipids synthesized previously by the Thaumarchaeota or other Archaea to form their own cell membranes, which would indicate an active recycling of fossil IPLs in the marine surface sediment. [ABSTRACT FROM AUTHOR]

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. These findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes. [ABSTRACT FROM AUTHOR]

To characterize the archaeal community composition in soil originating iron-manganese nodules, four types of soils—brown soil, yellow-cinnamon soil, yellow brown soil and red soil—and their associated iron-manganese nodules were collected from Queyu (QY), Zaoyang (ZY), Wuhan (WH) and Guiyang (GY), China, respectively, and subjected to quantitative polymerase chain reaction, cloning and sequencing analyses. The results showed that the archaeal 16S rRNA gene copy numbers in nodules, ranging between 3.59 × 102and 4.17 × 103copies g−1dry nodule, were about 50–1000 times lower than those in their corresponding soils (1.87 × 105to 1.08 × 106copies g−1dry soil), correlating with the low organic matter in the nodules, while archaea accounted for a relatively higher proportion of total prokaryote in nodules than in soils. Community composition analysis suggested that the archaeal diversity in both soils and nodules were much lower than bacterial, but archaeal community structures were similar to each other among the soils and nodules from the same location but varied among four locations, converse to the previous observation that bacterial community shifted markedly between nodules and soils as the result of habitat filtering. The archaeal communities in both soils and nodules were predominated byThaumarchaeotaGroup I.1b with the relative abundance ranging between 73.88 and 94.17%, except thatEuryarchaeotadominated the archaeal community in one nodule sample (WHn) developed from lake sediment. The finding shed new light on the archaeal diversity and their ecophysiology in different habitats, and further supported the opinion that archaea are more adaptable to stress and unfavorable conditions. [ABSTRACT FROM PUBLISHER]

Thaumarchaeota and Nitrospinae are the main drivers of nitrification in global oceans. However, their vertical and horizontal distributions throughout seawater columns remain unclear. Here, we conducted high-throughput sequencing of 16S rRNA genes and quantified putative nitrifying genes of microbial communities within seawater samples from the full depths of the Central Indian Ocean and the Western Pacific Ocean waters. Thaumarchaeota and Nitrospinae exhibited clear compositional distinctions between the two oceanic regions. Vertical variation in their assemblages was also apparent among all samples and within regions. However, their core operational taxonomic units (OTUs) were shared between the two regions and belonged to diverse phylogenetic clades that coincided with specific vertical niches. Further, their relative abundances were significantly and positively associated with Acidobacteriota, SAR324, Chloroflexi, and SAR406 phyla across and within regions, suggesting potential metabolic interactions. Regardless of oceanic regions, the maximal copy numbers of Thaumarchaeotal 16S rRNA and ammonia monooxygenase subunit A genes were both observed at 150–200 m depth, approximately overlapping with the primary nitrite maximum (PNM, 150 m), just below the deep chlorophyll a maximum (DCM, 125 m and 150 m); the maximal Nitrospina 16S rRNA gene copy numbers were located deeper (500 m), where nitrate concentrations had already increased. • The community composition of Thaumarchaeota and Nitrospinae varied regionally and vertically. • The core Thaumarchaeota and Nitrospinae were shared across oceanic regions. • Co-occurring of Thaumarchaeota with specific bacterial lineages could act as global sinks for nitrous oxide greenhouse gase. • The copy numbers of nitrifying genes were coincided with specific vertical niches.M [ABSTRACT FROM AUTHOR]

Nitrification represents one of the key steps in the global nitrogen cycle. While originally considered an exclusive metabolic capability of bacteria, the identification of the Thaumarchaeota revealed that ammonia-oxidizing archaea (AOA) are also important contributors to this process, particularly in acidic environments. Nonetheless, the relative contribution of AOA to global nitrification remains difficult to ascertain, particularly in underexplored neutrophilic and alkalinophilic terrestrial systems. In this study we examined the contribution of AOA to nitrification within alkaline (pH 8.3–8.7) cave environments using quantitative PCR, crenarchaeol lipid identification and measurement of potential nitrification rates. Our results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments. The dominance of Thaumarchaeota in the archaeal communities was confirmed by both archaeal 16S rRNA gene clone library and membrane lipid analyses, while potential nitrification rates suggest that Thaumarchaeota may contribute up to 100% of ammonia oxidation in these sediments. Phylogenetic analysis of ThaumarchaeotaamoAgene sequences demonstrated similarity toamoAclones across a range of terrestrial habitats, including acidic ecosystems. These data suggest that despite the alkaline conditions within the cave, the low NH3concentrations measured continue to favor growth of AOA over AOB populations. In addition to providing important information regarding niche differentiation within Thaumarchaeota, these data may provide important clues as to the factors that have historically led to nitrate accumulation within cave sediments. [ABSTRACT FROM PUBLISHER]

Organisms within all domains of life require the cofactor cobalamin (vitamin B12), which is produced only by a subset of bacteria and archaea. On the basis of genomic analyses, cobalamin biosynthesis in marine systems has been inferred in three main groups: select heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, and photoautotrophic Cyanobacteria. Culture work demonstrates that many Cyanobacteria do not synthesize cobalamin but rather produce pseudocobalamin, challenging the connection between the occurrence of cobalamin biosynthesis genes and production of the compound in marine ecosystems. Here we show that cobalamin and pseudocobalamin coexist in the surface ocean, have distinct microbial sources, and support different enzymatic demands. Even in the presence of cobalamin, Cyanobacteria synthesize pseudocobalamin—likely reflecting their retention of an oxygen-independent pathway to produce pseudocobalamin, which is used as a cofactor in their specialized methionine synthase (MetH). This contrasts a model diatom, Thalassiosira pseudonana, which transported pseudocobalamin into the cell but was unable to use pseudocobalamin in its homolog of MetH. Our genomic and culture analyses showed that marine Thaumarchaeota and select heterotrophic bacteria produce cobalamin. This indicates that cobalamin in the surface ocean is a result of de novo synthesis by heterotrophic bacteria or via modification of closely related compounds like cyanobacterially produced pseudocobalamin. Deeper in the water column, our study implicates Thaumarchaeota as major producers of cobalamin based on genomic potential, cobalamin cell quotas, and abundance. Together, these findings establish the distinctive roles played by abundant prokaryotes in cobalamin-based microbial interdependencies that sustain community structure and function in the ocean. [ABSTRACT FROM AUTHOR]

• The distribution and concentration of OH-GDGTs in soil profiles were investigated. • OH-GDGT and crenarchaeol concentration decreased with soil depth. • OH-GDGT-2 dominated in soils, differing from that in aquatic settings. • RI-OH and RI-OH′ were higher in soils than in marine environments. Hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (OH-GDGTs), a class of lipids that widely occur in global marine and lacustrine environments, have been used as tools for temperature reconstruction. Reports on their occurrence in soils, however, are rare. Here, we report the downward variation in distribution and concentration of OH-GDGTs in three soil profiles (SP) from Mount Yujiashan in Wuhan, central China. The OH-GDGT concentrations show significant correlations with that of crenarchaeol and decreased with soil depth, likely in relation to the decreased oxygen availability of OH-GDGT-producing archaea with depth. Crenarchaeol was likely to be produced primarily by several thaumarchaeotal lineages, e.g. group I.1a, I.1b, and SAGMCG (South Africa Gold Mine Crenarchaeotal Group)-1, whereas OH-GDGTs were presumed to be contributed primarily by SAGMCG-1 and to a lesser extent, by group I.1a Thaumarchaeota based on 16S rRNA gene amplicon sequencing. OH-GDGTs were dominated by OH-GDGT-2, differing significantly from aquatic settings. This results in markedly higher RI-OH and RI-OH′ (both expressing the ring index of OH-GDGTs) values in soils than in marine sediments, suggesting a different response of terrestrial OH-GDGTs to temperature and (or) a significant bias towards summer temperature in RI-OH and RI-OH′ for soils. [ABSTRACT FROM AUTHOR]

Shifts in microbial communities driven by anthropogenic nitrogen (N) addition have broad-scale ecological consequences. However, responses of microbial groups to exogenous N supply vary considerably across studies, hindering efforts to predict community changes. We used meta-analytical techniques to explore how amoA gene abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) respond to N addition, and found that N addition increased AOA and AOB abundances by an average of 27% and 326%, respectively. Responses of AOB varied by study type, ecosystem, fertilizer type, and soil pH, and were strongest in unmanaged wildland soils and soils fertilized with inorganic N sources. Increases in nitrification potential with N addition significantly correlated with only AOB. Our analyses suggest that elevated N supply enhances soil nitrification potential by increasing AOB populations, and that this effect may be most pronounced in unmanaged wildland soils. [ABSTRACT FROM AUTHOR]

Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate.We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R2 = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol.cell-1.d-1 increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86. Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature. [ABSTRACT FROM AUTHOR]

Background: Peptidyl-prolyl isomerases (PPIases) are present in all forms of life and play a crucial role in protein folding and regulation. They catalyze the cis-trans isomerization of the peptide bond that precedes proline residues in numerous proteins. The parvulins, which is one family of PPIases, have been extensively investigated in several eukaryotes. However, nothing is known about their expression, function and localization in archaea. Results: Here, we describe the endogenous expression, molecular structure, function and cellular localization of NmPin, a single-domain parvulin-type PPIase from Nitrosopumilus maritimus. This marine chemolithoautotrophic archaeon belongs to the globally abundant phylum Thaumarchaeota. Using high resolution NMR spectroscopy we demonstrate that the 3D structure of NmPin adopts a parvulin fold and confirmed its peptidyl-prolyl isomerase activity by protease-coupled assays and mutagenesis studies. A detailed topological analysis revealed a positively charged lysine-rich patch on the protein surface, which is conserved in all known parvulin sequences of thaumarchaeotes and targets NmPin to lipids in vitro. Immunofluorescence microscopy confirms that the protein is attached to the outer archaeal cell membrane in vivo. Transmission electron microscopy uncovered that NmPin has a uniform distribution at the membrane surface, which is correlated with a native cell shape of the prokaryote. Conclusion: We present a novel solution structure of a catalytically active thaumarchaeal parvulin. Our results reveal that a lysine-rich patch in NmPin mediates membrane localization. These findings provide a model whereby NmPin is located between the archaeal membrane and the surface layer and hence suggest proteins of the S-layer as the key target substrates of this parvulin. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs), major membrane lipids in some Archaea, have been widely used to examine past archaeal activity and infer ancient paleotemperature in aquatic environments. However, it is still unclear whether soil thaumarchaeotal iGDGTs also record temperature, and how thaumarchaeotal iGDGTs in the different climatic zones respond to temperature. Here we investigated iGDGTs in soils along an altitudinal transect of Mt. Shennongjia in central China, and determined the response of thaumarchaeotal membrane lipids to temperature in soils from a typical subtropical region. The TEX86proxy, reflecting the number of GDGT cyclopentyl moieties, in these soils is significantly correlated with mean annual air temperature (MAT) at a given site, apparently recording a temperature response by Thaumarchaeota that dominate in soils. However, the TEX86values are similar both at Mt. Shennongjia where a warm and humid climate prevails and at Mt. Xiangpi where a cold and dry climate is predominant. This could result from the seasonality of thaumarchaeotal production in soils from cold and (or) dry regions, and a local calibration is required if the TEX86proxy is to be applied to reconstruct paleoaltimetry or paleotemperature in paleosols from cold and (or) dry regions. The TEX86for soils from Mt. Rungwe (Tanzania), Mt. Jianfengling (China) and another climatic transect generally follows the rising trend of TEX86vs. MAT for Mt. Shennongjia, suggesting that the thaumarchaeotal iGDGTs in soils from subtropical and tropical regions respond to temperature similarly among sites. However, the different calibrations of TEX86paleothermometer among sites also reveal factors other than MAT may affect the TEX86values in soils. [ABSTRACT FROM AUTHOR]

Methanogens define the archaeal communities involved in anaerobic digestion. Recently, non-methanogen archaeal populations have been unexpectedly identified in anaerobic digestion processes. To gain insight into the ecophysiology of these uncharacterized archaeal populations, for the first time, a phylogenetic analysis was performed on a collection of non-methanogen archaeal 16S rRNA gene sequences from anaerobic digesters of broad geographic distribution, revealing a distinct clade formed by these sequences in subgroup 6 of the Miscellaneous Crenarchaeotal Group in the newly proposed archaeal phylum Bathyarchaeota. This exclusive phylogenetic assemblage enabled the development of a real-time quantitative PCR (qPCR) assay specifically targeting these non-methanogen archaeal populations in anaerobic digestion. Application of the qPCR assay in continuous anaerobic digesters indicated that these archaeal populations were minor constituents of the archaeal communities, and the abundance of these populations remained relatively constant irrespective of process perturbations. Analysis of the archaeal populations in methanogenic communities further revealed the co-occurrence of these non-methanogen archaea with acetoclastic methanogens. Nevertheless, the low abundance of non-methanogen archaea as compared with acetoclastic methanogens suggests that the non-methanogen archaeal populations were not major players in animal waste-fed methanogenic processes investigated in this study and the functions of these archaeal populations remain to be identified. [ABSTRACT FROM AUTHOR]

Macroecological patterns are found in animals and plants, but also in micro-organisms. Macroecological and biogeographic distribution patterns in marine Archaea, however, have not been studied yet. Ammonia-oxidizing Archaea ( AOA) show a bipolar distribution (i.e. similar communities in the northernmost and the southernmost locations, separated by distinct communities in the tropical and gyral regions) throughout the Atlantic, detectable from epipelagic to upper bathypelagic layers (<2000 m depth). This tentatively suggests an influence of the epipelagic conditions of organic matter production on bathypelagic AOA communities. The AOA communities below 2000 m depth showed a less pronounced biogeographic distribution pattern than the upper 2000 m water column. Overall, AOA in the surface and deep Atlantic waters exhibit distance-decay relationships and follow the Rapoport rule in a similar way as bacterial communities and macroorganisms. This indicates a major role of environmental conditions in shaping the community composition and assembly (species sorting) and no, or only weak limits for dispersal in the oceanic thaumarchaeal communities. However, there is indication of a different strength of these relationships between AOA and Bacteria, linked to the intrinsic differences between these two domains. [ABSTRACT FROM AUTHOR]

Marine ammonia-oxidizing archaea (AOA) are among the most abundant of marine microorganisms, spanning nearly the entire water column of diverse oceanic provinces. Historical patterns of abundance are preserved in sediments in the form of their distinctive glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids. The correlation between the composition of GDGTs in surface sediment and the overlying annual average sea surface temperature forms the basis for a paleotemperature proxy (TEX86) that is used to reconstruct surface ocean temperature as far back as the Middle Jurassic. However, mounting evidence suggests that factors other than temperature could also play an important role in determining GDGT distributions. We here use a study set of four marine AOA isolates to demonstrate that these closely related strains generate different TEX86--temperature relationships and that oxygen (O2) concentration is at least as important as temperature in controlling TEX86 values in culture. All of the four strains characterized showed a unique membrane compositional response to temperature, with TEX86-inferred temperatures varying as much as 12 °C from the incubation temperatures. In addition, both linear and nonlinear TEX86-- temperature relationships were characteristic of individual strains. Increasing relative abundance of GDGT-2 and GDGT-3 with increasing O2 limitation, at the expense of GDGT-1, led to significant elevations in TEX86-derived temperature. Although the adaptive significance of GDGT compositional changes in response to both temperature and O2 is unclear, this observation necessitates a reassessment of archaeal lipid-based paleotemperature proxies, particularly in records that span low-oxygen events or underlie oxygen minimum zones. [ABSTRACT FROM AUTHOR]

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. [ABSTRACT FROM AUTHOR]

Crenarchaeol is a unique glycerol dialkyl glycerol tetraether (GDGT) lipid specific to Thaumarchaeota, which play an important role in the global C and N cycles. GDGTs from Thaumarchaeota have been used to develop proxies for paleoclimate or paleoenvironment studies in aquatic environments. However, our understanding of their response to environmental change in soil remains poor. We addressed this question by investigating the change in archaeal lipid composition and community structure in the context of other environmental variables over a period of 12 months in a subtropical soil from Chongming Island, China. The results showed that Nitrososphaera spp. were the dominant archaeal population producing crenarchaeol in the soil. The relative abundance of GDGTs with one and three cyclopentane moieties, and crenarchaeol and its isomer in the core lipid (CL) fraction correlated with seasonal pH change in the soil. We therefore propose a molecular fossil proxy, the thaumarchaeota index (TI), which significantly related to pH in not only Chongming Island soil ( R 2 0.56, RMSE 0.14, P < 0.05), but also global soils ( R 2 0.51, RMSE 1.39, P < 0.001) and five thaumarchaeotal enrichments ( R 2 0.99, RMSE 0.04, P < 0.001). This suggests that TI could be a useful proxy for soil pH, which may corroborate the use of the bacterial GDGT proxy for soil pH, the cyclisation ratio of branched tetraethers (CBT). [ABSTRACT FROM AUTHOR]

Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. [ABSTRACT FROM AUTHOR]

Relatively little is known of the archaeal communities associated with endolithic environments, compared to other microbial groups such as bacteria and fungi. Analyzing the pyrosequenced archaeal 16S ribosomal RNA (rRNA) gene V1-V3 region, we investigated the archaeal community associated with aboveground-exfoliated weathering layers of a granite gneiss, and of the saprolite derived from this rock at 1 m depth below the soil surface, in a forested hilly area south of Seoul, South Korea. In both these sites, an archaeal community dominated by the phylum Thaumarchaeota was identified. The archaeal community in all cases closely resembled that of the surface layer of acidic soils in temperate climates of Korea. It appears that there is no clear distinction in archaeal community composition between a soil and a rock and a saprolite despite a tremendous difference in the concentration of total nitrogen and organic carbon. Of the chemical properties we measured, pH was the best predictor of the archaeal community composition and relative abundance of thaumarchaeal subphyla. These findings reinforce the view that soil archaea are mostly generalists, whose ecology is not closely dependent on nitrogen concentration or soil organic matter status, the presence of living roots, or the abundant presence of any other biota. [ABSTRACT FROM AUTHOR]

In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability. [ABSTRACT FROM AUTHOR]

Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of thaumarchaeal ammonia monooxygenase subunit A (AOA- amoA) gene. Different primer sets targeting 16S rRNA and AOA- amoA gene were used for the detection of AOA in FPETPs. Phylogenetic analysis of the gene revealed that the AOA was affiliated with thaumarchaeal group 1.1a lineage (marine cluster). Quantitative real time PCR of amoA gene was used to study the copy number of AOA and AOB in FPETPs. The AOA- amoA and AOB- amoA gene copy numbers of sludge samples ranged from 2.2 × 10 to 4.2 × 10 and 1.1 × 10 to 8.5 × 10 mg sludge respectively. Primer sets Arch-amoAF/Arch-amoAR and 340F/1000R were found to be useful for the sensitive detection of AOA- amoA and Archaeal 16S rRNA genes respectively in FPETPs. Their presence suggests the widespread occurrence and possible usefulness in removing ammonia from FPETPs which is in line with reports from other waste water treatment plants. [ABSTRACT FROM AUTHOR]

Abstract: PCR-DGGE, qPCR and sequencing highlighted a quite homogenous archaeal community prevailing in secondary calcite deposits, so-called moonmilk, within the cold alpine Hundalm cave in Tyrol (Austria). Furthermore, the depth profile of this moonmilk could prove that the Archaea are located in oxygen-rich near- and oxygen-depleted sub-surface layers. To gather these communities we therefore applied an aerobic and anaerobic cultivation approach in oligotrophic and methanotrophic media. The mixed moonmilk community was analyzed with a combination of molecular methods using qPCR, PCR-DGGE and sequencing. Anaerobic and aerobic cultures were additionally investigated with GC and HPLC analyses. It was possible to initially cultivate and enrich the supposed aerobic/microaerophilic and anaerobic archaeal fraction, representing the natural archaeal community. While the naturally less abundant near-surface Archaea are closely related to members of the Thaumarchaeota (Nitrosopumilus maritimus), the highly abundant anaerobic Archaea are more distantly related to members within the Euryarchaeota. It is possible that these cultivable moonmilk-born Archaea represent new ecotypes or are so far undescribed. Based on the sequencing results and the production of very low amounts of methane, a corresponding methanogenic community is thought to represent only a minor abundant archaeal fraction. On a physiological level the cultivated moonmilk community is cold-adapted and basically of oligotrophic and organotrophic character. [Copyright &y& Elsevier]

Archaea are the least understood members of the microbial community in Antarctic mineral soils. Although their occurrence in Antarctic coastal soils has been previously documented, little is known about their distribution in soils across the Mc Murdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (t- RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of soil physicochemical properties to characterize archaeal diversity and identify environmental factors that might shape and maintain archaeal communities in soils of the three southern most Mc Murdo Dry Valleys (Garwood, Marshall, and Miers Valley). Archaea were successfully detected in all inland and coastal mineral soils tested, revealing a low overall richness (mean of six operational taxonomic units [ OTUs] per sample site). However, OTU richness was higher in some soils and this higher richness was positively correlated with soil water content, indicating water as a main driver of archaeal community richness. In total, 18 archaeal OTUs were detected, predominately Thaumarchaeota affiliated with Marine Group 1.1b (> 80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were loosely related to members of the phylum Euryarchaeota. This is the first comprehensive study showing a widespread presence and distribution of Archaea in inland Antarctic soils. [ABSTRACT FROM AUTHOR]

Abstract: Acid soils, extensively used for nitrogen-fertilized agriculture and agroforestry, have important roles in maintaining global biogeochemical cycling and ecosystem functions. Huge inputs of nitrogen-based fertilizers into terrestrial ecosystems accelerate soil acidification, concomitantly altering the nitrogen transformation processes. Nitrification, as a critical component of the nitrogen cycle, is a microbially mediated process from ammonia to nitrate via nitrite, contributing to enormous losses of fertilizers through atmospheric emissions of greenhouse gas N2O and nitrate leaching to groundwater. However, the functionally dominant nitrifiers and underlying mechanisms for the acid soil nitrification are a long-standing mystery, which have confused scientists for more than 100 years. This century-long paradox originated from the early observations of active nitrification activity in acid soils, intensified by the failure of ammonia-oxidizing bacteria (AOB) cultures to sustain the nitrification in liquid batch under acid conditions, might be resolved by the recent progress in metagenomic, isotopic probing studies, and isolation of acidophilic ammonia-oxidizing archaea (AOA). Emerging evidence led to the supposition of the predominant role of AOA in controlling the autotrophic ammonia oxidation of acid soils, which has radically revised the previous perception that this oxidative reaction was exclusively regulated by autotrophic AOB and occasionally by heterotrophic nitrifiers. In this chapter, we review the recent progress in our understanding of the pH-impacted distribution of ammonia oxidizers, the niche differentiation of AOA and AOB shaped by acid stress, and the possible mechanisms of autotrophic nitrification in acid soils. The unveiling of this key process in widely distributed acid soils would help to identify effective biological strategies for better management of terrestrial nitrogen turnover and balance. [Copyright &y& Elsevier]

Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success. [ABSTRACT FROM PUBLISHER]

The marine planktonic archaea are dominated by Thaumarchaeotal Marine Group I, which is characterized by the lipid biomarker thaumarchaeol. The marine benthic archaea are characterized by greater diversity of currently unknown species whose lipid biomarker signatures are uncertain. In this study, a sediment core from the northwestern part of the South China Sea (SCS) (water depth 1474 m) was analyzed using molecular DNA and lipid biomarker approaches. While 16S rRNA gene analysis showed changing archaeal community structures with sediment depth, this change had little impact on the fossil record of archaeal lipids that are characteristic of the planktonic community. As a result, the fossil archaeal lipids recorded paleo sea surface temperature of the SCS since the last glacial maxima by the TEX86proxy, which agreed generally with the winter temperature recorded by planktonic foraminiferas collected from the same area of the SCS that hosted mass-transported deposits. This suggests that this deep water deposit may have partially preserved paleoclimate record reflecting seasonal temperature variation in a near shore setting, which is in contrast to annual sea surface temperature or sub sea surface temperature variation recorded by TEX86in the open ocean. [ABSTRACT FROM AUTHOR]

Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T- RFLP and cloning/sequencing) of archaeal genes ( mcrA, amoA, 16S rRNA gene). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota proliferated only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome. [ABSTRACT FROM AUTHOR]

Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of p H values. DNA was PCR-amplified for the V1- V3 region of the 16S r RNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by q PCR) also decreased at higher p H. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units ( OTUs), there was clear evidence of niche partitioning by p H. No individual OTU occurred across the entire range of p H values. Overall, the results of this study show that p H plays a major role in structuring tropical soil archaeal communities. [ABSTRACT FROM AUTHOR]

DNA fingerprinting methods provide a means to rapidly compare microbial assemblages from environmental samples without the need to first cultivate species in the laboratory. The profiles generated by these techniques are able to identify statistically significant temporal and spatial patterns, correlations to environmental gradients, and biological variability to estimate the number of replicates for clone libraries or next generation sequencing (NGS) surveys. Here we describe an improved DNA fingerprinting technique that combines terminal restriction fragment length polymorphisms (TRFLP) and single stranded conformation polymorphisms (SSCP) so that both can be used to profile a sample simultaneously rather than requiring two sequential steps as in traditional two-dimensional (2-D) gel electrophoresis. For the purpose of profiling Archaeal 16S rRNA genes from soil, the dynamic range of this combined 1-D TRFLP-SSCP approach was superior to TRFLP and SSCP. 1-D TRFLP-SSCP was able to distinguish broad taxonomic clades with genetic distances greater than 10%, such as Euryarchaeota and the Thaumarchaeal clades g_Ca. Nitrososphaera (formerly 1.1b) and o_NRP-J (formerly 1.1c) better than SSCP. In addition, 1-D TRFLP-SSCP was able to simultaneously distinguish closely related clades within a genus such as s_SCA1145 and s_SCA1170 better than TRFLP. We also tested the utility of 1-D TRFLP-SSCP fingerprinting of environmental assemblages by comparing this method to the generation of a 16S rRNA clone library of soil Archaea from a restored Tallgrass prairie. This study shows 1-D TRFLP-SSCP fingerprinting provides a rapid and phylogenetically informative screen of Archaeal 16S rRNA genes in soil samples. [ABSTRACT FROM AUTHOR]

The composition of prokaryotic communities was determined in the meso- and bathypelagic waters funneled through the Romanche Fracture Zone ( RFZ, 2°7′S, 31°79′W to 0°6′N, 14°33′W) in the tropical Atlantic. Distinct water masses were identified based on their physical and chemical characteristics. The bacterial and archaeal communities were depth-stratified with a total of 116 and 25 operational taxonomic units ( OTUs), respectively, distributed among the distinct water masses as revealed by terminal restriction fragment length polymorphism, and cloning and sequencing. The relative abundance of Thaumarchaeota, determined by catalyzed reporter deposition-fluorescence in situ hybridization, was significantly higher in deeper layers ( Antarctic Bottom Water, AABW, > 4000 m depth), contributing up to 31% to the total prokaryotic community, than in the mesopelagic and lower euphotic layer. Although the contribution of SAR11 to bacterial abundance did not increase with depth, SAR202, SAR324, SAR406 and Alteromonas did increase with depth. Terminal restriction fragment length polymorphism analysis revealed successional changes in the bacterial and archaeal community composition of the North Atlantic Deep Water ( NADW) with a passage time through the RFZ of c. 4 months but not in the under- and overlying water masses. Our results indicate that specific water masses harbor distinct bacterial and archaeal communities and that the prokaryotic community of the NADW undergoes successional changes in this conduit between the western and eastern Atlantic basin. Apparently, in the absence of major input of organic matter to specific deep-water masses, the indigenous prokaryotic community adapts to subtle physical and biogeochemical changes in the water mass within a time frame of weeks, similar to the reported seasonal changes in surface water prokaryotic communities. [ABSTRACT FROM AUTHOR]