Ammonia-oxidizing Thaumarchaeota Research Articles

Controls on the composition of hydroxylated isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) in cultivated ammonia-oxidizing Thaumarchaeota

Controls on the composition of hydroxylated isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) in cultivated ammonia-oxidizing Thaumarchaeota

Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.

Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core

BackgroundThe hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core.ResultsGenome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins.ConclusionWe provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems.7Emv5x2zFsLcvyRTYGWyYKVideo

Seasonal and multi-annual variation in the abundance of isoprenoid GDGT membrane lipids and their producers in the water column of a meromictic equatorial crater lake (Lake Chala, East Africa)

Isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) are membrane lipids of Archaea. Organic biomarker proxies associated with these lipids, such as the TEX86 paleothermometer and Branched and Isoprenoid Tetraether (BIT) index, are often used in paleoenvironmental reconstructions for the marine environment, but their general applicability in lacustrine settings is hampered by limited understanding of the biological sources and environmental drivers influencing isoGDGT production. To validate the use of isoGDGT proxies in lakes, we studied the occurrence of isoGDGTs in Lake Chala, a permanently stratified (meromictic) crater lake in equatorial East Africa. We analyzed the abundance and distribution of isoGDGTs in 17 depth profiles of suspended particulate matter (SPM) collected monthly between September 2013 and January 2015, and compared this with the abundance and composition of archaea based on 16S rRNA gene and quantitative PCR analysis. Both isoGDGTs and archaeal abundance in the SPM were exceptionally low throughout the study period. In the oxygenated part of the water column, higher fractional abundances of crenarchaeol are matched by a predominance of the ammonia-oxidizing Thaumarchaeota I.1b that are known to produce this GDGT, whereas deep anoxic water layers are characterized by high fractional abundances of GDGT-0 as well as the anaerobic heterotrophic Group C3 MCG Bathyarchaea and specific euryarchaeotal methanogens. Analysis of intact polar lipid (IPL) isoGDGTs using SPM depth profiles from three months representing distinct seasons during the study period revealed the presence of several IPLs of GDGT-0 in the anoxic lower water column, which are rarely found in natural settings. IPL GDGT-0 with a phosphatidylglycerol (PG-), monohexose-phosphatidylglycerol (MH-PG-) and dihexose-phosphatidylglycerol (DH-PG-) head-group was typically only present just above the lake bottom at 90 m depth and probably reflect specific communities of anaerobic archaea. We also determined the flux and distribution of isoGDGTs in settling particles collected monthly between November 2006 and January 2015 from a sediment trap suspended at 35 m water depth to assess seasonal and inter-annual variability in surface-water isoGDGT production, and compared this with the temporal distribution of isoGDGTs in the 25,000-year long sediment record from Lake Chala. Monthly variation of isoGDGTs in the 98-month settling-particles record did not show a strong annual pattern related to seasonal water-column mixing and stratification, likely because the oxycline was regularly situated below sediment-trap depth. Episodes of high GDGT-0 concentrations relative to crenarchaeol in the settling particles can therefore be linked to periods of exceptionally shallow oxycline depth, which suppresses the thaumarchaeotal bloom. During such intervals, TEX86-based paleotemperatures are not reliable because isoGDGT input from other archaeal sources disproportionally influences TEX86 values and creates a cold-temperature bias. Additionally, the abundance of the crenarchaeol isomer relative to crenarchaeol (f[CREN']) gradually increases during such episodes of high GDGT-0/crenarchaeol ratio, suggesting increasing dominance of Group I.1b over Group I.1a Thaumarchaeota, and might prove a good marker for prolonged shallow-oxycline conditions. Most importantly, the associated near-absence of crenarchaeol during times of strong upper-water-column stratification results in high BIT-index values. We propose that this suppression mechanism may be the principal driver of BIT-index variation in the sediment record of Lake Chala, and the main source of observed congruence between the BIT index and climate-driven lake-level variation on long time scales.

Lipidomics in archaeal membrane adaptation to environmental stresses and growth conditions: A review of culture-based physiological studies

Membrane lipids are thought to be a crucial part of the homeoviscous adaptation of archaea to extreme conditions. This article reviews the recent lipidomic studies of physiological membrane adaptations of archaea, assesses the biomolecular basis of an organic paleothermometer, TEX86, and contemplates the future directions of archaeal lipidomics. The studies of extremophilic archaea have revealed that at least three different molecular mechanisms are involved in membrane adaptation of archaea: (1) regulation of the number of cyclopentane rings of caldarchaeol, (2) alteration of the diether-to-tetraether lipid ratio, and (3) variation of the proportion of saturated and unsaturated lipids. However, most of the studies have focused on a limited number of archaeal ether-linked lipids, such as glycerol dialkyl glycerol tetraethers (GDGTs), which only represent a fraction of the entire lipidome. Environmental factors such as growth temperature and pH have been most frequently reported, but biotic factors, including growth phases, nutrition, and enzymatic activities affecting the membrane lipid composition are often overlooked. Membrane lipids of mesophilic ammonia-oxidizing marine Thaumarchaeota have been applied in the reconstruction of past sea surface temperatures. However, recent culture-based physiological studies have demonstrated that non-thermal biotic factors, including dissolved oxygen, ammonia oxidation rate and the growth rate, are the main drivers of GDGT cyclization in Nitrosopumilus maritimus . Moreover, other related strains or ecotypes exhibit a markedly different set of stress adaptations. A trend is now developing to examine the whole lipid profile (lipidome) for studies of archaeal physiology and biochemistry related to lipid biosynthesis (lipidomics) to gain a better understanding of the biological mechanisms underpinning the applications of membrane lipid-based proxies in biogeochemical or ecological research.

A single Thaumarchaeon drives nitrification in deep oligotrophic Lake Constance.

Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.

CO2-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) pathway of carbon fixation is found in thermophilic Crenarchaeota of the order Sulfolobales and in aerobic, ammonia-oxidizing Thaumarchaeota. Unlike all other known autotrophic carbon metabolisms, this pathway exclusively uses HCO_3- rather than CO_2 as the substrate for carbon fixation. Biomass produced by the 3HB/4HP pathway is relatively ^(13)C-enriched compared to biomass fixed by other autotrophic pathways, with total biosynthetic isotope effects (e_(Ar)) of ca. 3‰ in the Sulfolobales and ca. 20‰ in the Thaumarchaeota. Explanations for the difference between these values usually invoke the dual effects of thermophily and growth at low pH (low [HCO_3-]) for the former group vs. mesophily and growth at pH > 7 (high [HCO_3-]) for the latter group. Here we examine the model taxa Metallosphaera sedula and Nitrosopumilus maritimususing an isotope flux-balance model to argue that the primary cause of different e_(Ar) values more likely is the presence of carbonic anhydrase in M. sedula and its corresponding absence in N. maritimus. The results suggest that the pool of HCO_3-inside N. maritimus is out of isotopic equilibrium with CO_2 and that the organism imports < 10% HCO_3- from the extracellular environment. If correct and generalizable, the aerobic, ammonia-oxidizing marine Thaumarchaeota are dependent on passive CO_2 uptake and a slow rate of intracellular conversion to HCO_3-. Values of e_(Ar) should therefore vary in response to growth rate (μ) and CO_2 availability, analogous to eukaryotic algae, but in the opposite direction: e_(Ar) becomes smaller as [CO_(2(aq))] increases and/or μ decreases. Such an idea represents a testable hypothesis, both in the laboratory and in natural systems. Sensitivity to μ and CO_2 implies that measurements of e_(Ar) may hold promise as a pCO_2 paleobarometer.

Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment.

Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4-6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7-10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.

Utilization of urea and cyanate in waters overlying and within the eastern tropical north Pacific oxygen deficient zone.

In marine oxygen deficient zones (ODZs), which contribute up to half of marine N loss, microbes use nitrogen (N) for assimilatory and dissimilatory processes. Here, we examine N utilization above and within the ODZ of the Eastern Tropical North Pacific Ocean, focusing on distribution, uptake and genes for the utilization of two simple organic N compounds, urea and cyanate. Ammonium, urea and cyanate concentrations generally peaked in the oxycline while uptake rates were highest in the surface. Within the ODZ, concentrations were lower, but urea N and C and cyanate C were taken up. All identified autotrophs had an N assimilation pathway that did not require external ammonium: ODZ Prochlorococcus possessed genes to assimilate nitrate, nitrite and urea; nitrite oxidizers (Nitrospina) possessed genes to assimilate nitrite, urea and cyanate; anammox bacteria (Scalindua) possessed genes to utilize cyanate; and ammonia-oxidizing Thaumarchaeota possessed genes to utilize urea. Urease genes were present in 20% of microbes, including SAR11, suggesting the urea utilization capacity was widespread. In the ODZ core, cyanate genes were largely (∼95%) associated with Scalindua, suggesting that, within this ODZ, cyanate N is primarily used for N loss via anammox (cyanammox), and that anammox does not require ammonium for N loss.

Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics

Marine and brackish surface waters are highly dynamic habitats that undergo repeated seasonal variations in microbial community composition and function throughout time. While succession of the various microbial groups has been well investigated, little is known about the underlying gene-expression of the microbial community. We investigated microbial interactions via metatranscriptomics over a spring to fall seasonal cycle in the brackish Baltic Sea surface waters, a temperate brackish water ecosystem periodically promoting massive cyanobacterial blooms, which have implications for e.g. primary production, nutrient cycling, and expansion of hypoxic zones. Network analysis of the gene expression of all microbes from 0.22 - 200 µm in size and of the major taxonomic groups dissected the seasonal cycle into four components that comprised genes peaking during different periods of the bloom. Photoautotrophic nitrogen-fixing Cyanobacteria displayed the highest connectivity among the microbes, in contrast to chemoautotrophic ammonia-oxidizing Thaumarchaeota, while heterotrophs dominated connectivity among pre- and post-bloom peaking genes. The network was also composed of distinct functional connectivities, with an early season balance between carbon metabolism and ATP synthesis shifting to a dominance of ATP synthesis during the bloom, while carbon degradation, specifically through the glyoxylate shunt, characterized the post-bloom period, driven by Alphaproteobacteria as well as by Gammaproteobacteria of the SAR86 and SAR92 clusters. Our study stresses the exceptionally strong biotic driving force executed by cyanobacterial blooms on associated microbial communities in the Baltic Sea and highlights the impact cyanobacterial blooms have on functional microbial community composition.

Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

Oxygenated derivative is more influential than unsubstituted polycyclic aromatic hydrocarbon on ammonia-oxidizing archaea in an acidic soil

Oxygenated polycyclic aromatic hydrocarbons (PAHs) often co-occur with their parent compounds and may be chemically more reactive due to increased hydrophilicity and polarity. However, the influences of oxygenated PAH on soil functions and involved microbes, for example, nitrification and ammonia-oxidizing microorganisms, are largely unknown. Benz(a)anthracene (BaA) and benz(a)anthracene-7,12-dione (BaAD) were selected to represent unsubstituted and oxygenated PAHs, respectively. A microcosm experiment was performed with an acidic agricultural soil following the ISO 14238 method. Each microcosm was spiked with varied concentration (1, 10, and 100 mg kg−1) of either pollutants, with the unamended as the control. Ammonium was added to all microcosms to stimulate soil nitrification. After 28 days of incubation, abundance and composition of both bacterial and archaeal amoA genes were determined using quantitative PCR and denaturing gradient gel electrophoresis (DGGE). In addition, the growth inhibition of an ammonia-oxidizing Thaumarchaeota by both PAHs were examined. Neither BaA nor BaAD suppressed soil nitrate production and reduced the abundance of ammonia-oxidizing archaea. DGGE analysis of archaeal amoA genes revealed the enrichment of a few I.1b Thaumarchaeota in the ammonium fertilized control treatment; however, no such succession was observed in all BaAD and in 100 mg kg−1 BaA microcosms. Ammonia-oxidizing bacteria appeared to be less responsive to the ammonium fertilization and PAH stress. The cultivation experiment indicated the growth of the archaeal enrichment YT7-2 was more sensitive to BaAD than to BaA. These findings indicate inhibitory potency of BaAD to soil ammonia-oxidizing I.1b Thaumarchaeota, thus implicating potential ecological risks of the widely occurred oxygenated PAHs.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields

Currently, little is known about the microbial diversity in the sediments of Pacmanus and Desmos hydrothermal fields in Manus Basin. In this study, Illumina-based sequencing of 16S rRNA gene amplicons and metagenomic analysis were conducted to investigate the microbial populations and metabolic profiles in the sediments from four different regions in Pacmanus and Desmos hydrothermal fields. It was found that Gammaproteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal populations, respectively. The autotrophic prokaryotes in the four communities probably fixed CO2 via four major pathways, i.e. Calvin-Benson-Bassham cycle, reductive acetyl-CoA cycle, rTCA cycle, and 3-hydroxypropionate/4-hydroxybutyrate cycle. Ammonia-oxidizing Thaumarchaeota, nitrifiers, denitrifiers, and sulfur oxidizers belonging to the subgroups of Proteobacteria (e.g., alpha, beta, gamma, and epsilon), Nitrospira, and Nitrospina, and sulfate-reducing Desulfobacterales likely played critical roles in nitrogen and sulfur cycling, in which ammonia, sulfur compounds, and hydrogen could be utilized as potential energy sources. These findings revealed new insights into the operational mechanism of the microbial communities associated with Pacmanus and Desmos hydrothermal fields.

Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils.

Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea.

Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity.

Maintaining soil fertility and the microbial communities that determine fertility is critical to sustainable agricultural strategies, and the use of different organic fertilizer (OF) regimes represents an important practice in attempts to preserve soil quality. However, little is known about the dynamic response of bacterial communities to fertilization regimes across crop growth stages. In this study, we examined microbial community structure and diversity across eight representative growth stages of wheat-rice rotation under four different fertilization treatments: no nitrogen fertilizer (NNF), chemical fertilizer (CF), organic–inorganic mixed fertilizer (OIMF), and OF. Quantitative PCR (QPCR) and high-throughput sequencing of bacterial 16S rRNA gene fragments revealed that growth stage as the best predictor of bacterial community abundance and structure. Additionally, bacterial community compositions differed between wheat and rice rotations. Relative to soils under wheat rotation, soils under rice rotation contained higher relative abundances (RA) of anaerobic and mesophilic microbes and lower RA of aerophilic microbes. With respect to fertilization regime, NNF plots had a higher abundance of nitrogen–fixing Cyanobacteria. OIMF had a lower abundance of ammonia-oxidizing Thaumarchaeota compared with CF. Application of chemical fertilizers (CF and OIMF treatments) significantly increased the abundance of some generally oligotrophic bacteria such those belonging to the Acidobacteria, while more copiotrophic of the phylum Proteobacteria increased with OF application. A high correlation coefficient was found when comparing RA of Acidobacteria based upon QPCR vs. sequence analysis, yet poor correlations were found for the α- and β- Proteobacteria, highlighting the caution required when interpreting these molecular data. In total, crop, fertilization scheme and plant developmental stage all influenced soil microbial community structure, but not total levels of alpha diversity.

Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy

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 (R(2) = 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.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes.

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential.

(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea.

Natural CO2 venting systems can mimic conditions that resemble intermediate to high pCO2 levels as predicted for our future oceans. They represent ideal sites to investigate potential long-term effects of ocean acidification on marine life. To test whether microbes are affected by prolonged exposure to pCO2 levels, we examined the composition and diversity of microbial communities in oxic sandy sediments along a natural CO2 gradient. Increasing pCO2 was accompanied by higher bacterial richness and by a strong increase in rare members in both bacterial and archaeal communities. Microbial communities from sites with CO2 concentrations close to today's conditions had different structures than those of sites with elevated CO2 levels. We also observed increasing sequence abundance of several organic matter degrading types of Flavobacteriaceae and Rhodobacteraceae, which paralleled concurrent shifts in benthic cover and enhanced primary productivity. With increasing pCO2 , sequences related to bacterial nitrifying organisms such as Nitrosococcus and Nitrospirales decreased, and sequences affiliated to the archaeal ammonia-oxidizing Thaumarchaeota Nitrosopumilus maritimus increased. Our study suggests that microbial community structure and diversity, and likely key ecosystem functions, may be altered in coastal sediments by long-term CO2 exposure to levels predicted for the end of the century.