Archaeal Ammonia Oxidizers Research Articles

Source, contribution and microbial N-cycle of N-compounds in China fresh snow

The importance and contribution of nitrogen compounds and the related microbial nitrogen cycling processes in fresh snow are not well understood under the current research background. We collected fresh snow samples from 21 cities that 80% are from China during 2016 and 2017. Principal component analysis showed that SO42− were in the first principal component, and N-compounds were the second. Furthermore, the main pollutant ions SO42− and NO3− were from anthropogenic sources, and SO42− contributed (61%) more to the pollution load than NO3− (29%), which were confirmed through a series of precipitation mechanism analysis. We selected five N-cycle processes (consist of oxidation and reduction processes) for molecular biology experiments, including Ammonia-oxidation process, Nitrite-oxidation process, Denitrification process, Anaerobic-ammoxidation process (Anammox) and Dissimilatory nitrate reduction to ammonium process (DNRA). Except ammonia-oxidizing archaeal (AOA) and bacterial (AOB) amoA genes (above 107 copies g−1), molecular assays of key functional genes in various nitrogen conversion processes showed a belowed detection limit number, and AOB abundance was always higher than AOA. The determination of the microbial transformation rate using the 15N-isotope tracer technique showed that the potential rate of five N-conversion processes was very low, which is basically consistent with the results from molecular biology studies. Taken together, our results illustrated that microbial nitrogen cycle processes are not the primary biological processes causing the pollution in China fresh snow.

Regulation of N<sub>2</sub>O emissions from acid organic soil drained for agriculture

Abstract. Organic soils drained for crop production or grazing land are agroecosystems with potentially high but variable emissions of nitrous oxide (N2O). The present study investigated the regulation of N2O emissions in a raised bog area drained for agriculture, which is classified as potentially acid sulfate soil. We hypothesised that pyrite (FeS2) oxidation was a potential driver of N2O emissions through microbially mediated reduction of nitrate (NO3-). Two sites with rotational grass, and two sites with a potato crop, were equipped for monitoring of N2O emissions and soil N2O concentrations at the 5, 10, 20, 50 and 100 cm depth during weekly field campaigns in spring and autumn 2015. Further data acquisition included temperature, precipitation, soil moisture, water table (WT) depth, and soil NO3- and ammonium (NH4+) concentrations. At all sites, the soil was acidic, with pH ranging from 4.7 to 5.4. Spring and autumn monitoring periods together represented between 152 and 174 d, with cumulative emissions of 4–5 kg N2O-N ha−1 at sites with rotational grass and 20–50 kg N2O-N ha−1 at sites with a potato crop. Equivalent soil gas-phase concentrations of N2O at grassland sites varied between 0 and 25 µL L−1 except for a sampling after slurry application at one of the sites in spring, with a maximum of 560 µL L−1 at the 1 m depth. At the two potato sites the levels of below-ground N2O concentrations ranged from 0.4 to 2270 µL L−1 and from 0.1 to 470 µL L−1, in accordance with the higher soil mineral N availability at arable sites. Statistical analyses using graphical models showed that soil N2O concentration in the capillary fringe (i.e. the soil volume above the water table influenced by tension saturation) was the strongest predictor of N2O emissions in spring and, for grassland sites, also in the autumn. For potato sites in autumn, there was evidence that NO3- availability in the topsoil and temperature were the main controls on N2O emissions. Chemical analyses of intact soil cores from the 0 to 1 m depth, collected at adjacent grassland and potato sites, showed that the total reduction capacity of the peat soil (assessed by cerium(IV) reduction) was much higher than that represented by FeS2, and the concentrations of total reactive iron (TRFe) were higher than those of FeS2. Based on the statistical graphical models and the tentative estimates of reduction capacities, FeS2 oxidation was unlikely to be important for N2O emissions. Instead, archaeal ammonia oxidation and either chemodenitrification or nitrifier denitrification were considered to be plausible pathways of N2O production in spring, whereas in the autumn heterotrophic denitrification may have been more important at arable sites.

Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone.

To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70–100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL−1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L−1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.

Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures.

Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (−13–4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20–45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4–8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.

Ammonia Oxidation in a Neutral Purple Soil Measured by the 13C-DNA-SIP Method

Increasing evidence suggests that ammonia oxidation in acidic soils is primarily catalyzed by ammonia-oxidizing archaea (AOA), while ammonia-oxidizing bacteria (AOB) drive ammonia oxidation in neutral and alkaline soils in which AOA overwhelmingly outnumber AOB. Therefore, neutral purple soil with a pH of 7.2 was selected to study the composition of the active ammoxidation microbial community with a stable isotope nucleic acid probe technique combined with cloning sequencing. Results showed that the nitrification rate was 9.68 mg·(kg·d)-1, and AOA and AOB were abundant in neutral purple soils. By using DNA-based stable isotope probing (SIP), we gathered strong evidence of archaeal ammonia oxidation by AOA and AOB. Phylogenetic analysis indicated that the Nitrosospira Cluster 3a.1 AOB was dominant in terms of quantity at 0 days, and the Nitrosospira Cluster 3a.2 only accounted for a small part. After 56 days of cultivation, the Nitrosospira Cluster 3a.2 replaced the Nitrosospira Cluster 3a.1 as the active AOB that dominated ammonia oxidation. The AOA that predominated quantitatively at day 0 was Nitrososphaera Subcluster 9, but after cultivation this became Nitrososphaera Subcluster 3.2/3.3. Thus, the community structure of AOA and AOB changed. Active autotrophic nitrification was found in this neutral purple soil. Sequencing analysis of the 13C-labeled DNA provided robust evidence that both archaea and bacteria played important roles in the nitrification and not all ammonia oxidizers in native soil were active in the nitrification. Phylogenetic analysis clearly showed that the dominant active archaea and bacteria during the incubation were affiliated with Nitrososphaera Subcluster 3.2/3.3 within the soil group 1.1b lineage and Nitrosospira Cluster 3a.2, respectively, which were different from the dominant ammonia oxidizers at the beginning of the incubation. These results suggest that the community structure of ammonia oxidizers can shift quickly upon changes in the substrate availability in soils.

The DNRA-Denitrification Dichotomy Differentiates Nitrogen Transformation Pathways in Mountain Lake Benthic Habitats.

Effects of nitrogen (N) deposition on microbially-driven processes in oligotrophic freshwater ecosystems are poorly understood. We quantified guilds in the main N-transformation pathways in benthic habitats of 11 mountain lakes along a dissolved inorganic nitrogen gradient. The genes involved in denitrification (nirS, nirK, nosZ), nitrification (archaeal and bacterial amoA), dissimilatory nitrate reduction to ammonium (DNRA, nrfA) and anaerobic ammonium oxidation (anammox, hdh) were quantified, and the bacterial 16S rRNA gene was sequenced. The dominant pathways and associated bacterial communities defined four main N-transforming clusters that differed across habitat types. DNRA dominated in the sediments, except in the upper layers of more productive lakes where nirS denitrifiers prevailed with potential N2O release. Loss as N2 was more likely in lithic biofilms, as indicated by the higher hdh and nosZ abundances. Archaeal ammonia oxidisers predominated in the isoetid rhizosphere and rocky littoral sediments, suggesting nitrifying hotspots. Overall, we observed a change in potential for reactive N recycling via DNRA to N losses via denitrification as lake productivity increases in oligotrophic mountain lakes. Thus, N deposition results in a shift in genetic potential from an internal N accumulation to an atmospheric release in the respective lake systems, with increased risk for N2O emissions from productive lakes.

Functional relationship between ammonia-oxidizing bacteria and ammonia-oxidizing archaea populations in the secondary treatment system of a full-scale municipal wastewater treatment plant

The abundance of ammonia-oxidizing bacteria and archaea and their amoA genes from the aerobic activated sludge tanks, recycled sludge and anaerobic digesters of a full-scale wastewater treatment plant (WWTP) was determined. Polymerase chain reaction and denaturing gradient gel electrophoresis were used to generate diversity profiles, which showed that each population had a consistent profile although the abundance of individual members varied. In the aerobic tanks, the ammonia-oxidizing bacterial (AOB) population was more than 350 times more abundant than the ammonia-oxidizing archaeal (AOA) population, however in the digesters, the AOA population was more than 10 times more abundant. Measuring the activity of the amoA gene expression of the two populations using RT-PCR also showed that the AOA amoA gene was more active in the digesters than in the activated sludge tanks. Using batch reactors and ddPCR, amoA activity could be measured and it was found that when the AOB amoA activity was inhibited in the anoxic reactors, the expression of the AOA amoA gene increased fourfold. This suggests that these two populations may have a cooperative relationship for the oxidation of ammonia.

Nitrification inhibitors effectively target N2 O-producing Nitrosospira spp. in tropical soil.

SummaryThe nitrification inhibitors (NIs) 3,4‐dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2O‐producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite‐oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co‐varying variables with nitrifier operational taxonomic units (OTUs): the N2O‐producing AOB Nitrosospira with N2O, NO3 −, NH4 +, water‐filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 −, NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 +, which suggests different drivers. These results support the co‐occurrence of non‐N2O‐producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2O‐producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.

Distinct pattern of nitrogen functional gene abundances in top- and subsoils along a 120,000-year ecosystem development gradient

Soil microorganisms are key players of the nitrogen cycle and relevant for soil development. While the community structure of nitrogen-cycling microorganisms during initial soil development is already well investigated, knowledge about the patterns during long-term ecosystem development is limited. In this study, nitrogen functional genes of ammonia-oxidizers (amoA), nitrate-reducers (narG), and chitin-degraders (chiA) were determined via quantitative PCR and the functional community composition of archaeal ammonia-oxidizers was analyzed via clone libraries and DNA sequencing (amoA) in soil depth profiles along the 120,000-year Franz Josef chronosequence (New Zealand). The results show that absolute nitrogen functional gene abundances change significantly during long-term soil development. In organic layers, narG and chiA gene abundances were highest in young to intermediate-aged soils and then decreased following progressive and retrogressive development of the vegetation. While relative archaeal amoA gene abundance (proportional to total cell counts) decreased in the oldest phosphorus-limited topsoils, relative narG and chiA gene abundances remained constant. In subsoils, archaeal amoA and narG gene abundances also decreased with ecosystem retrogression that coincided with the increasing content of iron and aluminum oxides as well as other clay-sized minerals. In contrast, subsoil chiA gene abundances were hardly affected by soil age. The analysis of the archaeal amoA community revealed a compositional shift during long-term ecosystem development. Our study provides evidence that the community structure of nitrogen-cycling microorganisms in top- and subsoils is significantly affected by long-term ecosystem development and suggests an important role of the mineral phase in subsoils.

Response of the Soil N2O Emission and Ammonia-oxidizing Microorganism Community to the Maize Straw Return with Reducing Fertilizer in Purple Soil

Crop straw is an important agricultural source, which can replace chemical fertilizers. A field experiment with six different amounts of fertilization combined with maize straw residues was carried out in purple soil, including the control (CK), conventional fertilizing (F), straw return with conventional fertilizing (100FS), straw return with 70% conventional fertilizing (70FS), straw return with 60% conventional fertilizing (60FS), and straw return with 50% regular fertilizing (50FS), to determine the response of the soil N2O emission and ammonia-oxidizing microorganism community distribution to straw return with reducing fertilizer. The dynamic characteristics of the N2O emission in purple soil were observed using an in situ closed chamber and gas chromatography-based system. The ammonia-oxidizing microorganism community distribution was analyzed with multiple molecular techniques (DNA-based clone library and qPCR) linked to physical-chemical soil properties. The results show that the combination of straw with fertilizer increases the N2O emission and cumulative N2O emission. The highest N2O emission[57.59-6238.02 μg·(m2·h)-1]and cumulative N2O emission (60.76 kg·hm-2) were observed for the 100FS treatment. Compared with the F treatment, the soil ammonium nitrogen and nitrate nitrogen contents are reduced and the soil organic matter increases after crop straw return with chemical fertilizer. However, significant changes of the soil total nitrogen and pH were not observed. The bacterial ammonia oxidizer (AOB) amoA gene abundance is higher than that of the archaeal ammonia oxidizer (AOA). The AOA amoA gene abundance during F treatment (50.9×103 copies·g-1) is significantly higher than that of others, while the AOB amoA abundance gene of the F treatment is the lowest (1.36×105 copies·g-1). The 100FS reduces the community diversity and Pielou index of AOA and AOB amoA gene. Their amoA gene abundance significantly declines during 100FS treatment. However, the increment of the AOA and AOB amoA gene diversity and dominant increment of AOB amoA gene abundance are significant when applying straw with reducing fertilizer. The specific AOA indicator OTU1 may be most important with respect to the direct and indirect production of N2O in purple soil. The redundancy analysis (RDA) shows that the community structure of AOA is remarkably relevant to the soil ammonium nitrogen, organic matter, and available phosphorus (P<0.05) and that the community structure of AOB is remarkably relevant to the soil dissolved organic nitrogen, total nitrogen, available potassium, and available phosphorus (P<0.05). The tolerance to different environments and ecological niches of AOB is weaker than that of AOA. Our results illustrate that the maize straw return with 60%-70% regular fertilizing dramatically increases the community diversity and abundance of the AOA and AOB amoA genes and partly mitigates the soil N2O emission without significantly decreasing the vegetable yields.

Archaeal ammonia oxidation plays a part in late Quaternary nitrogen cycling in the South China Sea

Thaumarchaeota, as an ammonia oxidizing archaea (AOA), is crucial for modern marine nitrogen cycling; however, little is known about its history during the Quaternary climate change. Here, isoprenoidal glycerol dialkyl glycerol tetraethers (GDGTs), biomarkers of Thaumarchaeota, were used to trace the role of AOA in the South China Sea (SCS) for the past 160 kyr. The GDGT-[2]/[3] ratio was firstly argued as an indicator of contribution of shallow Thaumarchaeota cluster that is more active in ammonia oxidization (AO) than the deep cluster, and then, was used to reconstruct AO in the past. The inferred AO exhibited intensification in the interglacials, and moreover, showed strong precessional cycles with enhancements at the precessional maxima when boreal winter insolation was the highest. The AOA record varied in line with isotope record of organic nitrogen (δ15Norg) that is modulated by the strength of diazotroph N2 fixation (NF), suggesting a close coupling of increased AO with enhanced NF during periods of weak east Asian winter monsoon (EAWM) and hence increase of upper water stratification. AO intensification, a step of a series of dissolved oxygen consuming processes, is hereby hypothesized to encourage NF when the EAWM weakens. This result might be a reference for the future NF trend in the current situation of enhanced ocean deoxygenation due to global warming.

Exploring anammox bacteria ecology to improve nitrogen removal in wastewater treatment

Exploring anammox bacteria ecology to improve nitrogen removal in wastewater treatment

Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups.

Sediment nitrogen cycling is a network of microbially mediated biogeochemical processes that are vital in regulating ecosystem functioning. Mucopolysaccharides (mucus) are produced by many invertebrates and have the potential to be an important source of organic carbon and nitrogen to sediment microorganisms. At present, we have limited understanding of how mucopolysaccharide moderates total sediment microbial communities and specific microbial functional groups that drive nitrogen cycling processes. To start addressing this knowledge gap, sediment slurries were incubated with and without Hediste diversicolor mucus. Changes in dissolved inorganic nitrogen (ammonia, nitrite and nitrate) concentrations and bacterial and archaeal community diversity were assessed. Our results showed that mucopolysaccharide addition supported a more abundant and distinct microbial community. Moreover, mucus stimulated the growth of bacterial and archaeal ammonia oxidisers, with a concomitant increase in nitrite and nitrate. Hediste diversicolor mucopolysaccharide appears to enhance sediment nitrification rates by stimulating and fuelling nitrifying microbial groups. We propose that invertebrate mucopolysaccharide secretion should be considered as a distinct functional trait when assessing invertebrate contributions to sediment ecosystem function. By including this additional trait, we can improve our mechanistic understanding of invertebrate-microbe interactions in nitrogen transformation processes and provide opportunity to generate more accurate models of global nitrogen cycling.

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

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

Abundance, contribution, and possible driver of ammonia-oxidizing archaea (AOA) in various types of aquatic ecosystems

In some habitats, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA), which are therefore important for studying biogeochemical nitrogen cycling. However, the behavior and distribution of AOA in aquatic ecosystems are not well characterized, especially on a global scale. We sampled 66 sites across all five continents to analyze the global abundance of AOA. Ammonium oxidation rates were measured using the dicyandiamide (DCD) and octyne inhibition method to separately evaluate the contributions of AOA to ammonium oxidation. High-throughput pyrosequencing and phylogenetic analysis were applied to study AOA community compositions, combined with DNA-stable isotope probing (DNA-SIP). The archaeal amoA gene was widespread and abundant across all aquatic ecosystem types. The average abundance was 3.59 × 108 copies g−1, with the highest values in lake samples and the lowest in river samples. The AOA abundance was influenced by pH. Archaeal ammonia oxidation rates were 0.81 ± 0.45 mg (NO3−-N) kg−1 day−1, corresponding to 63.75% of the total ammonia oxidation rate. Pyrosequencing analysis showed that the AOA community was dominated by the Group I.1b lineage (65.8%). Candidatus Nitrosocosmicus franklandus showed the highest positive correlation with archaeal ammonium oxidation rates and had the highest carbon use efficiency. Abundance, activity, and community composition of AOA were highly heterogeneous. pH negatively impacted the abundance of the archaeal amoA functional gene. AOA were the main ammonia oxidators in aquatic ecosystems. Ca. N. franklandus was found to dominate archaeal ammonium oxidation.

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing.

Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [13C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural 13C-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [13C]bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (>50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [13C]bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with 13C-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from "dark" primary production.IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ "dark" primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.

High contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation related to a potential active AOA species in various arable land soils

Ammonia oxidation is the limiting step in soil nitrification and critical in the global nitrogen cycle. The discovery of ammonia-oxidizing archaea (AOA) has improved our knowledge of microbial mechanisms for ammonia oxidation in complex soil environments. However, the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation remain unclear. In this study, through large geographical scale sampling in China, totally nine samples representing various types of arable land soils were selected for analyzing the ammonia oxidation activity. The AOA and AOB activities were separately determined by using the dicyandiamide and 1-octyne inhibition method. High-throughput pyrosequencing and DNA stable-isotope probing (DNA-SIP) analysis were applied to investigate the distribution and activity of Candidatus Nitrosocosmicus franklandus in the arable land soils. In this study, AOA abundance (3.2 × 107–3.4 × 109 copies g−1) and activity (0.01–1.33 mg N kg−1 dry soil day−1) were evaluated for nine selected arable land soils and accounted for 4–100% of ammonia oxidation. By separately determining AOA and AOB rates, we observed that archaeal ammonia oxidation dominated the ammonia oxidation process in six soils, revealing a considerable contribution of AOA in ammonia oxidation in arable land soils. Based on high-throughput pyrosequencing analysis, the AOA species Ca. N. franklandus with relatively low abundance (0.6–13.5% in AOA) was ubiquitously distributed in all the tested samples. Moreover, according to the DNA-SIP analysis for Urumqi sample, the high activity and efficiency of Ca. N. franklandus in using CO2 suggests that this species plays an important role in archaeal ammonia oxidation in arable land soils. Through determining the AOA activity and analyzing the potential predominant functional AOA species, this study greatly improves our understanding of ammonia oxidation in arable land soils.

The distribution of sediment and water column nitrification potential in the hyper-turbid Ems estuary

Estuaries, being transition zones between land and ocean, act as sink or source of nitrate and thus influence the conditions in adjacent coastal waters. Hence, nitrification, which is the process oxidizing ammonium via nitrite to nitrate and simultaneously consuming oxygen, is important in estuaries. The process has been studied in sediment and water column of many estuaries, but seldom in both estuarine compartments at the same time. In August 2014, we collected water and sediment samples during a sampling trip along the salinity gradient of the hyper-turbid Ems estuary, which ends up in the North Sea. We conducted nitrification incubations in microcosms to determine nitrification potentials and we measured a suite of abiotic factors like oxygen saturation, salinity, and dissolved inorganic nitrogen (DIN). Two approaches were used, one isotope dilution method for net (NNP) and gross (GNP) nitrification potentials and one method with substrate addition for substrate induced nitrification potentials (SNP). The long-term incubation set-ups of several days include inseparably nitrification-coupled processes like remineralization and nitrate consumption, as well as cell growth, and hence they do not represent in-situ rates of nitrification. DNA was also isolated and used for quantitative PCR of the archaeal and bacterial amoA genes, which encode for the ammonia-oxidizing enzyme ammonia monooxygenase (AMO). Nitrification varied over the salinity gradient of the estuary. GNP in water and sediments decreased with increasing salinity. No NNP could be measured in the sediments of the oligohaline part of the estuary, while SNP was four-fold higher than GNP in this part of the estuary. Generally, the gene abundance of the amoA gene was higher in the oligohaline/mesohaline area than in the polyhaline area, and archaea dominated the ammonia-oxidizing communities in all samples. The local similarity in partitioning of archaeal and bacterial amoA genes over the water column and sediment at each sampling station along the estuarine gradient implied a link between the archaeal and bacterial ammonia oxidizers in both compartments, which is likely due to resuspension of sediment particles in the water column of this hyper-turbid estuary.

Field-aged biochar stimulated N2O production from greenhouse vegetable production soils by nitrification and denitrification

Evidence suggests that biochar is among ideal strategies for climate change mitigation and sustainable agriculture. However, the effects of soil aging on the physicochemical characteristics of biochar and nitrous oxide (N2O) production remain elusive. We set up a microcosm experiment with two greenhouse vegetable production (GVP) (alkaline and acid) soils by using the 15N tracing technique and quantitative polymerase chain reaction (qPCR) to investigate the mechanisms of N2O production as affected by fresh (FB) and aged biochar (AB) amendment. The results showed that AB increased the specific surface area, organic C, ammonium sorption capacity and cation exchange capacity, whereas decreased the pore size and pH relative to the FB. Results also demonstrated that FB effectively decreased N2O emissions from both soils while it enhanced the abundance of nirK and nosZI genes in alkaline soil and reduced the abundance of ammonia-oxidizing bacteria (AOB) amoA and increased nirK and nosZII genes in acid soil. In contrast, AB significantly stimulated nitrification and denitrification in both soils and thus significantly increased the N2O emissions by 43–78%. Furthermore, AB induced increases in ammonia-oxidizing archaeal (AOA) amoA and nirK gene abundances in alkaline soil and fungal nirK gene abundances in acid soil. These results suggest that AB may not be suitable for the mitigation of soil N2O emissions in GVP soils thus improving our understanding of the potential mechanism of biochar in N2O emissions.

Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea.

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.