A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils

15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.

Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary

In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.

Co-immobilization of AOA strains with anammox bacteria in three different synthetic bio-granules maintained under two substrate-level conditions

Hydrogel encapsulation of ammonium oxidizing archaea (AOA) along with anammox bacteria holds potential to enable mainstream partial nitritation (PN)-anammox process attributing to AOA's high affinity to ammonia and oxygen. This study explored the growth of AOA and anammox in hydrogel-based synthetic biogranules by testing two AOA strains, three types of hydrogel beads and two substrate levels, to identify the optimal combination favoring the concomitant growth of AOA and anammox. The AOA Nitrososphaera viennensis (AOA-NV) exhibited higher abundance (10-2.3±0.6 AOA/16S) than the AOA-DW (10-4.7±0.8 AOA/16S) during the entire experimental period. Amongst the three types of hydrogel beads, the PVA-SA-BaCl2 (140 days) and PVA-SA-H3BO3 beads (>180 days) exhibited better long-term structural stability than the PEGDMA-SA-CaCl2 beads. The PVA-SA-H3BO3 beads exhibited the best long-term stability and both the PVA/SA BaCl2 and PVA-SA-H3BO3 beads had comparable ability to retain AOA, anammox and the overall microbial community. Substrate conditions rather than the bead type primarily controlled the microbial community structure. Modest substrate concentrations (1 mM NH4+-N in the feed and 0.8 mg/L dissolved oxygen (DO) in the reactor during aeration phase) followed by low substrate conditions (0.1 mM NH4+-N and 0.2 mg DO/L) both supported the growth of AOA and anammox, while the low substrate condition also suppressed the growth of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), with AOA /AOB and anammox/NOB ratio of 0.7 and 0.4 at moderate substrate condition and 16.5 and 2.6 at low substrate condition.

Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone

The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.

The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers

Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.

Elucidating the Role of Biofilm-Forming Microbial Communities in Fermentative Biohydrogen Process: An Overview

Amongst the biofuels described in the literature, biohydrogen has gained heightened attention over the past decade due to its remarkable properties. Biohydrogen is a renewable form of H2 that can be produced under ambient conditions and at a low cost from biomass residues. Innovative approaches are continuously being applied to overcome the low process yields and pave the way for its scalability. Since the process primarily depends on the biohydrogen-producing bacteria, there is a need to acquire in-depth knowledge about the ecology of the various assemblages participating in the process, establishing effective bioaugmentation methods. This work provides an overview of the biofilm-forming communities during H2 production by mixed cultures and the synergistic associations established by certain species during H2 production. The strategies that enhance the growth of biofilms within the H2 reactors are also discussed. A short section is also included, explaining techniques used for examining and studying these biofilm structures. The work concludes with some suggestions that could lead to breakthroughs in this area of research.

Divergent responses of soil microbial functional groups to long-term high nitrogen presence in the tropical forests

A massive rise in atmospheric nitrogen deposition (ND) has threatened ecosystem health through accelerating soil nitrogen (N) cycling rates. While soil microbes serve a crucial function in soil N transformation, it remains poorly understood on how excess ND affects microbial functional populations regulating soil N transformation in tropical forests. To address this gap, we conducted 13-year N (as NH₄NO₃) addition experiments in one N-rich tropical primary forest (PF) and two N-poor tropical reforested forests (rehabilitated and disturbed) in South China. Based on our data, 13-year N introduction markedly enhanced soil N₂O generation in all forests, regardless of soil N status, but microbial functional groups showed divergent responses to excess N addition among the studied forests. In the PF, long-term N introduction markedly decreased presence of bacterial 16S rRNA gene, nitrifier (amoA) and denitrifier genes (nirK, nirS and nosZ) and bacteria/fungi ratio, which could be attributed to the decreases in soil pH, dissolved organic carbon to N ratio and understory plant richness. In the two reforested forests, however, long-term N introduction generally did neither alter soil properties nor the abundance of most microbial groups. We further found that the elevated N₂O generation was related to the increased soil N availability and decreased nosZ abundance, and the PF has the highest N₂O generation than the other two forests. Overall, our data indicates that the baseline soil N status may dominate response of microbial functional groups to ND in tropical forests, and N-rich forests are more responsive to excess N inputs, compared to those with low-N status. Forests with high soil N status can produce more N₂O than those with low-N status. With the spread of elevated ND from temperate to tropical zones, tropical forests should merit more attention because ecosystem N saturation may be common and high N₂O emission will occur.

Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input

Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

Functional structures of soil microbial community relate to contrasting N2O emission patterns from a highly acidified forest

Nitrous oxide (N₂O) is an important greenhouse gas contributing to global climate change. Emissions of N₂O from acidic forests are increasing rapidly; however, little is known about the mechanisms driving these emissions. We analyzed soil samples from a high N₂O emission area (HEA, 224-601 μg N m^-2 h^-1) and an adjacent low emission area (LEA, 20-30 μg N m^-2 h^-1) of a highly acidified forest. HEA showed similar carbon and nitrogen (N) pools and microbial biomass to LEA, but significantly higher moisture and extractable nutrients than LEA did. GeoChip 4 detected 298 gene families (unadjusted P < 0.05; 94, adjusted P < 0.05) showing significantly different structures between HEA and LEA. Both areas had highly diverse N cycling functional genes. However, HEA had higher relative abundances of nor, P450nor, and archaeal nitrifier nirK, which provided evidence for the importance of denitrifiers in N₂O emission. HEA also showed significantly higher relative abundances of lignin- and cellulose-degrading genes, oxygen-limitation-response genes and denitrifier ppk, but lower abundances of N- and phosphorus (P) -limitation-response genes especially denitrifier pstS, corresponding to the higher moisture and extractable nutrients conducive to denitrification. The moisture, extractable nutrients and pH explained over 50% variation in microbial communities, and extractable P appeared as the key factor driving community variation and consequently regulated N₂O production. CAPSULE ABSTRACT: N₂O emission in highly acidified forest soils was related to the diverse N functional genes, especially denitrification genes, and was affected by soil properties.

An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake

Ammonium-oxidizing archaea (AOA) and bacteria (AOB) play crucial roles in ammonium oxidation in freshwater lake sediment. However, previous reports on the predominance of AOA and AOB in the surface sediment of Lake Taihu have been based on DNA levels, detecting the total abundance of microbiota (including inactive cells), and have resulted in numerous contradictory conclusions. Existing RNA-level studies detecting active transcription are very limited. The current study, using RNA-based real-time quantification and clone library analysis, demonstrated that the amoA gene abundance of active AOB was higher than that of active AOA, despite conflicting results at the DNA level. Further exploration revealed a significant positive correlation between the potential nitrification rate (PNR) and the abundance of AOA and AOB at the RNA level, with irregular or contradictory correlation found at the DNA level. Ultimately, using quantitative analysis of RNA levels, we show AOB to be the active dominant contributor to ammonium oxidation. Our investigations also indicated that AOB were more diverse in high-ammonium lake regions, with Nitrosomonas being the active and dominating cluster, but that AOA had an advantage in the low-ammonium lake regions.

Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests

Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al³⁺, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.

Microbial adaptation to long-term N supply prevents large responses in N dynamics and N losses of a subtropical forest

Atmospherically-deposited nitrogen (N) can stimulate complex soil N metabolisms and accumulations over time. Whether long-term (decadal) N deposition effects on soil N transformations and functional microbes differ from the short-term (annual) effects has rarely been assessed. Here we conducted a laboratory ¹⁵N tracing study with soil samples from a short-term (one year) N addition site and a long-term (12 years) site in a subtropical forest. The effects of simulated N deposition on soil N₂O emissions, N transformation rates and microbial nitrifying and denitrifying genes were determined. Our results showed that: (1) long-term N addition did not change soil N₂O fluxes significantly in comparison to the short-term N addition. Denitrification, heterotrophic nitrification and autotrophic nitrification contributed 53%, 28% and 18% to total N₂O emissions, respectively. (2) Autotrophic nitrification was the dominant N transformation process, except for the high-N treatment at the long-term site. The magnitude of soil N transformation rates was significantly different among N addition treatments but not between short- and long-term N addition sites. However, long-term N addition changed the responses of specific N transformation rates to N addition markedly, especially for the rates of nitrification, organic N mineralization to NH₄⁺, NO₃^- immobilization and dissimilatory NO₃^- reduction to NH₄⁺ (DNRA). (3) Responses of ammonia oxidizing archaea and bacteria (AOA and AOB) were more variable than those of denitrifying N₂O-producers (nirK) and denitrifying N₂O-reducers (nosZ), particularly at the long-term site. (4) The close correlations among N₂O flux, functional genes and soil properties observed at the short-term site were weakened at the long-term site, posing a decreased risk for N losses in the acid subtropical forest soil. There is evidence for an adaptation of functional microbial communities to the prevailing soil conditions and in response to long-term natural and anthropogenic N depositions.