Anammox bacterial diversity in various aquatic ecosystems based on the detection of hydrazine oxidase genes (hzoA/hzoB)

"Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces

Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.

Effects of silver nanoparticles on denitrification and anammox in sediments of hypertrophic and mesotrophic lakes

The abundant production and wide usage of silver nanoparticles (Ag NPs) inevitably lead to their release into aquatic ecosystems. However, it is still unclear about how Ag NPs influence denitrification and anammox (DA) in freshwater sediments. To address this, the sediments of hypertrophic and mesotrophic lakes were exposed to 0.5 and 50 mg/L Ag NPs under anaerobic conditions for 7 days to explore the effects of Ag NPs on environmental variables, including redox potential (Eh), pH, organic matter (OM) and acid volatile sulfide (AVS), and the resulting influence on DA. Experimental results indicated that NO₃^--N and NH₄⁺-N levels were increased by the low (p > 0.05) and high doses of Ag NPs (p < 0.05) in comparison with the non-Ag control, revealing an inhibitive impact on DA. The level of total nitrogen (TN) was notably increased by the low and high doses of Ag NPs (p < 0.05), perhaps due to inhibited enzyme activity and corresponding encoding gene abundance, which were related to generating gaseous nitrogen such as N₂O and N₂. In addition, environmental factor Eh was significantly raised by Ag NPs (p < 0.05), further inhibiting DA. Moreover, the quantitative analysis unveiled that denitrifying and anammox bacteria in hypertrophic lakes evinced a stronger resistance to Ag NPs toxicity than those in mesotrophic lakes. Overall, our study revealed that short-term exposure to Ag NPs could inhibit DA in sediments. These findings provide an understanding enabling evaluation and prediction of the environmental risks of Ag NPs in freshwater lakes.

Microbiomes and Planctomycete diversity in large-scale aquaria habitats

In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1-15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.

Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable

The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N₂O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions.

IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N₂ through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.

Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China

Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 10⁴ to 1.20 × 10⁷ copies L^–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.

Study on the properties of denitrifying carbon sources from cellulose plants and their nitrogen removal mechanisms

Carbon sources of cellulose plants are promising materials that enhance the activities of denitrifying bacteria in the groundwater system. To further verify the denitrification performance of cellulose plants and the main factors of affecting the denitrifying system, six cellulose plants from agricultural wastes (wood chip, corn cob, rice husk, corn straw, wheat straw, and sugar cane) were selected for bioavailable organic matter leaching experiments, carbon denitrification experiments, functional bacteria identification, and analysis experiments. The results show that the extracts of cellulose plants contain a mixed carbon sources system including small molecular organic acids, sugars, nitrogen-containing organic components, and esters. The qPCR results showed that the denitrifying bacteria had obvious advantages compared to anaerobic ammonia-oxidizing bacteria during the stable period; the denitrification experiment showed that each of six cellulose plants removed more than 80% of nitrogen, and the denitrification rates reached 1.00-2.00 mg N cm^-3·d^-1. The supplement of cellulose plants promotes the metabolism rate of denitrifying bacteria, and the additional denitrifying bacteria have little effect on nitrate removal. In summary, the expected denitrification reaction occurred in the cellulose plant system, which is suitable as a carbon source material for water body nitrogen pollution remediation.

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy

The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.

Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China

Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO₃^-, NH₄⁺, DOC/NO₃^-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.

Startup of pilot-scale single-stage nitrogen removal using anammox and partial nitritation (SNAP) reactor for waste brine treatment using marine anammox bacteria

This study is the first to demonstrate the startup of a pilot-scale single-stage nitrogen removal using anammox and partial nitritation (SNAP) reactor utilizing marine anammox bacteria. A complete mixing type reactor, continuously fed with waste brine obtained from a natural gas plant (salinity 3%, NH₄⁺-N 130-180 mg/L) and having an effective volume of 2 m³, achieved stable operation at temperatures of 20-30°C with a maximum nitrogen removal rate of 1.43 kg-N/m³/day. During the startup process, along with a small amount of seed sludge, granular sludge was additionally inoculated as a biomass carrier for the enrichment of ammonia oxidizing bacteria (AOB), followed by the enrichment of anammox bacteria. A mesh screen equipped at the outlet of the reactor facilitated the successful sludge retention in the reactor. Analysis of bacterial community composition indicated that Candidatus Scalindua was successfully enriched in the pilot SNAP reactor. These methods for stable sludge retention in the reactor greatly contributed to the startup of the first pilot-scale SNAP reactor using marine anammox bacteria.

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Anaerobic Ammonium Oxidation Bacteria in a Freshwater Recirculating Pond Aquaculture System

Anaerobic ammonium oxidation (anammox) is a key biochemical process to reduce nitrogen pollution in aquaculture, especially in water recirculating pond aquaculture system (RPAS). We used 16S RNA and quantified PCR to study the distribution and environmental impacts of anammox bacteria in RPAS. The results show that the anammox bacterial community distributions and diversities that are apparently unit-specific and seasonal have significant (p < 0.05) difference variation in the RPAS. Most of the anaerobic ammonium oxidation bacteria sequences (77.72%) retrieved from the RPAS belong to the Brocadia cluster. The abundance of anammox bacterial in the RPAS ranged from 3.33 × 101 to 41.84 × 101 copies per ng of DNA. The environmental parameter of temperature and nitrogen composition in water could have impacted the anammox bacterial abundance. This study provides more information on our understanding of the anammox bacteria in the RPAS, and provides an important basis for RPAS improvement and regulation.

Effects of submerged vegetation on sediment nitrogen-cycling bacterial communities in Honghu Lake (China)

Sediment nitrogen (N) cycling is an important biological removal process for N permanently and driven by N-cycling microbial community. There is a growing interest in interactions between submerged vegetation (SV) and sediment N-cycling bacterial community, because of the close link between rooted aquatic plants and the sediment microbes. However, the effects of SV on the sediment N-cycling bacterial community are still controversial. Furthermore, the discrimination of direct and indirect effects of SV on the N-cycling bacterial community remains unclear. Here, we investigated the biomass and species richness of SV and determined the corresponding environment factors (water quality and sediment properties) in Honghu Lake (China). We also used functional genes as markers to unveil the bacterial diversity and community composition and abundance in lake sediments. Our results showed that biomass and species richness of SV affected the composition, diversity and abundance of sediment N-cycling bacterial communities through improving lake water quality and sediment properties. With the increasing richness and abundance of SV, the diversity of most N-cycling bacterial assemblages including nitrifying, denitrifying and DNRA bacteria decreased, while the abundance increased. However, the anammox bacterial assemblage in sediments showed inverse trends. Sediment carbon vs. nitrogen (C:N) ratio negatively affected the abundance of amoA and nirS + nirK + nosZ bacterial assemblages. Additionally, due to the presence of SV, positive interactions among N-cycling bacterial assemblages were found, such as amoA and nrfA bacterial assemblages. Overall, our findings confirmed the significant effects of SV on the N-cycling bacterial community structure and abundance. Moreover, the direct effects of SV on the N-cycling bacterial community and the indirect effects through altering the sediment C were clarified in our study. Our results casted a new light on the negative effects of high C:N ratio. From the study, we made a conclusion that the better SV develops, the greater nitrogen removal occurs in lake sediments.

Specific and effective detection of anammox bacteria using PCR primers targeting the 16S rRNA gene and functional genes

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the nitrogen cycle by coupling ammonium and nitrite to produce dinitrogen gas (N₂). Polymerase chain reaction (PCR) is a fast, simple, and sensitive method that is widely used to assess the diversity, abundance, and activity of the slow-growing bacteria. In this review, we summarize and evaluate the wide variety of PCR primers targeting the 16S rRNA gene and functional genes (hzo, nir, and hzs) of anammox bacteria for their effectiveness and efficiencies in detecting this group of bacteria in different sample types. Furthermore, the efficiencies of different universal high-throughput sequencing 16S rRNA gene primers in anammox bacteria investigations were also evaluated to provide a reference for primer selection. Based on our in silico evaluation results, none of the 16S rRNA gene primers could recover all of the known anammox bacteria, but multiple hzo and hzs gene primers could accomplish this task. However, uncertain copies (1-3 copies) of hzo genes were identified in the genomes, and the hydrazine oxidation reaction catalyzed by hydrazine oxidoreductases (HZOs) can also be catalyzed by other hydroxylamine oxidoreductases (HAOs) in anammox bacteria, which can potentially result in large deviations in hzo-based qPCR and RT-qPCR analyses and results. Therefore, the use of optimal primers targeting unique hzs genes are recommended, although the efficiencies of these newly designed primers need further verification in practical applications. This article provides comprehensive information for the effective and specific detection of anammox bacteria using specific primers targeting the 16S rRNA gene and functional genes and serves as a basis for future high-quality primer design.

The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks

The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.

Anaerobic ammonia-oxidizing bacteria in tropical bioaugmented zero water exchange aquaculture ponds

Bioaugmented zero water exchange aquaculture production systems (ZWEAPS) maintained with minimal or no water exchange prevent the ammonia accumulation in the system, leading to environmental sustainability and biosecurity. The microbes in the bioaugmented ZWEAPS plays a major role in maintaining low levels of ammonia through ammonia oxidation and nitrite oxidation. The comprehensive understanding on anammox population in the systems will provide an insight on the environmental factors controlling the functional anammox bacterial communities for potential biostimulation and augmented ammonia removal in ZWEAPS. The sediment metagenome of such three tropical bioaugmented ZWE shrimp culture ponds were analysed to determine the diversity, distribution and abundance of anaerobic ammonia-oxidizing (anammox) bacteria based on hydrazine oxidoreductase (hzo) gene as a phylogenetic marker. The restriction fragment length polymorphism (RFLP) phylotypes from the clone libraries were identified with maximum distribution to Candidatus Kuenenia, as the dominant population in the study sites with high ammonia load followed by Candidatus Scalindua. The environmental factors associated with the abundance and diversity of the anammox population were analysed using RDA and Pearson correlation. The samples of final culturing period (75th day) of TCR-S ZWE pond was observed with the highest operational taxonomic unit (OTU)-based diversity, where comparatively higher ammonia (water 0.71 mg L^-1 and sediment 1.21 mg L^-1) was recorded among the study sites. The gene abundance of the anammox population ranged from 10⁶ to 10⁷ copies per gram of sediment, in spite of less diversity. The physiochemical factors such as ammonia, nitrite, redox potential and the total organic carbon indicated a strong and positive correlation to the abundance and distribution of the anammox population, which highlights the importance of anammox communities and the potential of biostimulation for ammonia removal in the aquaculture systems.

Three kinds of ammonia oxidizing microorganisms play an important role in ammonia nitrogen self-purification in the Yellow River

To develop the microbial resources of the Yellow River, seven water samples were collected along the Lanzhou region of the river from upstream to downstream for testing. Analysis of various physico-chemical indexes was conducted, and key parameters influencing the water quality were selected through principal component analysis, after which the decisive factors impacting water quality were determined by correlation and regression analysis. The results indicated that (1) DO, NH₃-N, NO₂^--N, TN, TC, As, Cr⁶⁺ and Pb were the main physico-chemical factors influencing water quality in the Lanzhou region, with NH₃-N having the greatest effect. (2) Ammonia-oxidizing microorganisms [ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and anaerobic ammonia-oxidizing bacteria (AMX)] were found to mediate the transformation of NH₃-N in the studied section. AOA was the primary microbe community among the two aerobic ammonia-oxidizing microorganisms (AOA and AOB) in the Yellow River. (3) Phylogenetic analysis showed that there were some known groups, and there were still many unknown species in the water of the studied section, especially within the AMX population. (4) Correlation analysis revealed that AOA has strong adaptability to unhealthy environments, and that some environmental factors (higher concentrations of carbon, nitrogen and some heavy metals) could increase the AOA gene abundance. Overall, these results suggested there are rich ammonia-oxidizing microbial resources, especially AOA, in the Lanzhou section of the Yellow River, which have the potential for application in nitrogen sewage treatment.

The biological denitrification coupled with chemical reduction for groundwater nitrate remediation via using SCCMs as carbon source

Renewable additional carbon sources for groundwater denitrification, such as sustainable-releasing compound carbon source materials (SCCMs), are required. This work reports long-term groundwater denitrification with permeable reactive barriers filled with SCCMs; the coupling of biological denitrification and chemical reduction avoided the need for a continuous carbon source supply. Four 370-day lab-scale permeable reactive barrier experiments with four SCCMs showed that NO₃^- removal efficiency in zero-valent iron (ZVI) SCCMs was higher than in ZVI-free SCCMs. In the ZVI SCCMs, the NO₃^- removal reaction began quickly in the early stage, owing to ZVI chemical reduction, whereas biological denitrification was lower and incomplete with a NO₂^- concentration of 0.8 mg L^-1 in the ZVI SCCM system. As the chemical reduction efficiency decreased, the biological denitrification efficiency increased, and the highest NO₃^- removal efficiency was 98.8%. Decreasing the Fe²⁺concentration decreased ZVI chemical reduction. High-throughput sequencing indicated that the proportion of denitrifying bacteria attached to the SCCMs was up to 34.4% at the family level, leading to the denitrification gene being predominant. Quantitative PCR indicated increased microbial metabolic activity, richer bacterial community diversity, and more bacteria. Long-term monitoring data for SCCMs will help realize the use of biological denitrification coupled with chemical reduction for groundwater NO₃^- remediation.

Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses

Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NO_x^--N in the sediment, NH₄⁺-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.

Shifts in the anammox bacterial community structure and abundance in sediments from the Changjiang Estuary and its adjacent area

Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria. 16S rRNA and hzo gene fragments affiliating with known anammox bacterial lineages were recovered, and the two major phylotypes belonged to the Candidatus Scalindua (Ca. Scalindua) genus, with >90% sequence similarity. A phylogenetic analysis detected the Scalindua and Brocadia genera together with some anammox-like bacterial clusters, which suggested a higher diversity in the studied ecosystem than in open ocean environment, where only Scalindua genus was detected. A redundancy analysis (RDA) showed that total organic carbon (TOC) and total nitrogen (TN) content in sediments significantly influenced anammox bacterial abundance of. Spearman correlation analyses confirmed that the spatial variation in anammox bacterial abundance was highly correlated with TOC (P<0.01) and TN (P<0.01) contents in sediments.

Is anammox a promising treatment process for nitrogen removal from nitrogen-rich saline wastewater?

Rapidly growing discharge of nitrogen-rich saline wastewater has significantly affect environment. However, due to the inhibition resulting from high salinity on microbes, it is still a challenge to treat nitrogen-rich saline wastewater efficiently. Anammox process, as a cost-effective and environment-friendly nitrogen removal approach, has shown a potential in treating nitrogen-rich saline wastewater. This review is conducted from a critical perspective and provides a comprehensive overview on the performance of anammox process treating nitrogen-rich saline wastewater. Two strategies including freshwater-derived anammox bacteria acclimatization and marine anammox bacteria enrichment are evaluated. Second, effects resulting from salinity on the performance of anammox reactor, the microbial communities and sludge characteristics are discussed. Third, salinity-tolerant mechanism of anammox bacteria is analyzed. This review also reveals some critical knowledge gaps and future research needs, which benefits application of anammox process to treat nitrogen-rich saline wastewater.

Autofluorescent characteristics of Candidatus Brocadia fulgida and the consequences for FISH and microscopic detection

An enrichment culture of Candidatus Brocadia fulgida was identified by three independent methods: analysis of autofluorescence using different microscope filter blocks and a fluorescence spectrometer, fluorescence in situ hybridization (FISH) with anammox-specific probes and partial sequencing of the 16S rDNA, hydrazine synthase hzsA and hydrazine oxidoreductase hzo. The filter block BV-2A (400-440, 470 LP, Nikon) was suitable for preliminary detection of Ca. B. fulgida. An excitation-emission matrix revealed three pairs of excitation-emission maxima: 288-330 nm, 288-478 nm and 417-478 nm. Several autofluorescent cell clusters could not be stained with DAPI or by FISH, suggesting empty but intact cells (ghost cells) or inhibited permeability. Successful staining of autofluorescent cells with the FISH probes Ban162 and Bfu613, even at higher formamide concentrations, suggested insufficient specificity of Ban162. Under certain conditions, Ca. B. fulgida lost its autofluorescence, which reduced the reliability of autofluorescence for identification and detection. Non-fluorescent Ca. Brocadia cells could not be stained with Ban162, but with Bfu613 at higher formamide concentrations, suggesting a dependency between both parameters. The phylogenetic analysis showed only good taxonomical clustering of the 16S rDNA and hzsA. In conclusion, careful consideration of autofluorescent characteristics is recommended when analysing and presenting FISH observations of Ca. B. fulgida to avoid misinterpretations and misidentifications.

Nitrogen fate in a subtropical mangrove swamp: Potential association with seawater-groundwater exchange

Coastal mangrove swamps play an important role in nutrient cycling at the land-ocean boundary. However, little is known about the role of periodic seawater-groundwater exchange in the nitrogen cycling processes. Seawater-groundwater exchange rates and inorganic nitrogen concentrations were investigated along a shore-perpendicular intertidal transect in Daya Bay, China. The intertidal transect comprises three hydrologic subzones (tidal creek, mangrove and bare mudflat zones), each with different physicochemical characteristics. Salinity and hydraulic head measurements taken along the transect were used to estimate the exchange rates between seawater and groundwater over a spring-neap tidal cycle. Results showed that the maximum seawater-groundwater exchange occurred within the tidal creek zone, which facilitated high-oxygen seawater infiltration and subsequent nitrification. In contrast, the lowest exchange rate found in the mangrove zone caused over-loading of organic matter and longer groundwater residence times. This created an anoxic environment conducive to nitrogen loss through the anammox and denitrification processes. Potential oxidation rates of ammonia and nitrite were measured by the rapid and high-throughput method and rates of denitrification and anammox were measured by the modified membrane inlet mass spectrometry (MIMS) with isotope pairing, respectively. In the whole transect, denitrification accounted for 90% of the total nitrogen loss, and anammox accounted for the remaining 10%. The average nitrogen removal rate was about 2.07g per day per cubic meter of mangrove sediments.

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH₄⁺ and NO₂^- biochemically to form N₂ gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.

Nitrogen removal capacity and bacterial community dynamics of a Canon biofilter system at different organic matter concentrations

Three Canon bench-scale bioreactors with a volume of 2 L operating in parallel were configured as submerged biofilters. In the present study we investigated the effects of a high ammonium concentration (320 mgNH₄⁺· L^-1) and different concentrations of organic matter (0, 100 and 400 mgCOD·L^-1) on the nitrogen removal capacity and the bacterial community structure. After 60 days, the Canon biofilters operated properly under concentrations of 0 and 100 mgCOD·L^-1 of organic matter, with nitrogen removal efficiencies up to 85%. However, a higher concentration of organic matter (400 mgCOD·L^-1) produced a partial inhibition of nitrogen removal (68.1% efficiency). The addition of higher concentrations of organic matter a modified the bacterial community structure in the Canon biofilter, increasing the proliferation of heterotrophic bacteria related to the genera of Thauera, Longilinea, Ornatilinea, Thermomarinilinea, unclassified Chlorobiales and Denitratisoma. However, heterotrophic bacteria co-exist with Nitrosomonas and Candidatus Scalindua. Thus, our study confirms the co-existence of different microbial activities (AOB, Anammox and denitrification) and the adaptation of a fixed-biofilm system to different concentrations of organic matter.

High-throughput analysis of anammox bacteria in wetland and dryland soils along the altitudinal gradient in Qinghai-Tibet Plateau

This study investigated the diversity, community composition, and abundance of anaerobic ammonium oxidation (anammox) bacteria along the altitudinal gradient in Qinghai–Tibet Plateau. Two types of soil samples (wetland and dryland soils, n = 123) were collected from 641 m to 5,033 m altitudes. Polymerase chain reaction (PCR) screening showed that anammox were not widespread, and were only detected in 9 sampling sites of the 50 sites tested by amplifying the 16S rRNA genes. Then, only samples collected from Linzhi (2,715 m), Rikaze (4,030 m), and Naqu (5,011 m), which were positive for the presence of anammox, were further processed to explore the biogeography of anammox bacteria in Qinghai–Tibet Plateau. Results of high‐throughput sequencing targeting the hydrazine synthesis β‐subunit (hzsB) gene revealed the presence of three known anammox genera (Candidatus Brocadia, Candidatus Jettenia, and Candidatus Kuenenia) in both soil types. Their diversity, community composition, and abundance did not show significant variation with altitude at large scale. However, it was the small‐scale environmental heterogeneities between wetland and dryland soils that determined their biogeographical distribution. Specifically, the dryland soils had higher diversity of anammox bacteria than the wetland soils, but their abundance patterns varied. The community composition of anammox bacteria were found to be influenced by soil nitrate content.

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats

Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0–2, 2–4, and 4–6 mm). To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%), followed by Archaea (∼4%) and Eukarya (∼1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0–2 mm) than in the lower layers (2–4 and 4–6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat.

Effects of various fertilization regimes on abundance and activity of anaerobic ammonium oxidation bacteria in rice-wheat cropping systems in China

Anaerobic ammonium oxidation (anammox) is an important process in many marine and paddy ecosystems. However, few studies have reported on the contribution to the nitrogen cycle of anammox and its dynamics in rice-wheat cropping systems with different fertilization regimes. Here, isotope tracing and molecular techniques were used to determine the potential rates of anammox and their association with bacterial abundance, diversity, and activity. Rice-wheat cropping systems at two sites in Jiangsu Province, China were selected and the treatments at each site were: 1) no fertilization (CK), 2) 100% chemical fertilization (CF), 3) pig manure compost plus 50% chemical fertilization (PMCF), and 4) straw plus 100% chemical fertilization (SRCF). The results revealed that anammox bacteria with high abundance were detected in both the wheat and rice seasons. The abundance of anammox in PMCF treatment was higher than that in SRCF treatment in both Changshu and Jintan. Moreover, the abundance of anammox bacteria in CF treatment was significantly higher than that in CK in Changshu. Analysis of anammox hydrazine synthase β subunit (hzs-β) gene sequences showed that in the rice season, the anammox bacteria Ca. Brocadia, Ca. Scalindua, and Ca. Jettenia were present. In contrast, all of the anammox hydrazine oxidase (hzo) genes were affiliated with Ca. Brocadia, suggesting that hzs genes are more representative of anammox biological diversity compared to hzo. Sequences from the PMCF treatment where affiliated with both Ca. Jettenia and Ca. Brocadia, and showed the highest diversity. Anammox activity was detected in both the wheat and rice seasons, but there were significant differences between seasons. The anammox rates were in the range 0.34 to 1.04nmol dinitrogen gas∙g^-1 dry soil∙h^-1, and 3.15 to 9.62% of dinitrogen gas emissions were attributed to anammox. However, no significant difference among the fertilizer treatments for anammox activity was found in the study.

Novel anammox bacteria and nitrogen loss from Lake Superior

Anaerobic ammonium oxidizing (anammox) bacteria own a central position in the global N-cycle, as they have the ability to oxidize NH₄⁺ to N₂ under anoxic conditions using NO₂⁻. They are responsible for up to 50% of all N₂ released from marine ecosystems into the atmosphere and are thus indispensible for balancing the activity of N-fixing bacteria and completing the marine N-cycle. The contribution, diversity, and impact of anammox bacteria in freshwater ecosystems, however, is largely unknown, confounding assessments of their role in the global N-cycle. Here we report the activity and diversity of anammox bacteria in the world’s largest freshwater lake—Lake Superior. We found that anammox performed by previously undiscovered bacteria is an important contributor to sediment N₂ production. We observed striking differences in the anammox bacterial populations found at different locations within Lake Superior and those described from other locations. Our data thus reveal that novel anammox bacteria underpin N-loss from Lake Superior, and if more broadly distributed across inland waters would play an important role in continental N-cycling and mitigation of fixed nitrogen transfer from land to the sea.

Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes

Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5–4.7 nmol L⁻¹ d⁻¹, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L⁻¹ oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes

Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd ₁-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.

Metagenomic potential for and diversity of N-cycle driving microorganisms in the Bothnian Sea sediment

The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N₂, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.

New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria

PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH₄⁺ and NH₄⁺/Σ(NO₃^- + NO₂^-) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox bacteria within wider coverage of genera in Mai Po wetland indicates this unique niche is very complex, and species of anammox bacteria are niche-specific with different physiological properties towards substrates competing and chemical tolerance capability.

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.

Diversity, Community Composition and Abundance of Anammox Bacteria in Sediments of the North Marginal Seas of China

Over the past few decades, anammox bacteria have been recognized as key players that contribute significantly to the release of large amounts of nitrogen in the global marine nitrogen cycle. In the present study, the diversity, community composition, and abundance of anammox bacteria from the sediments of four diverse regions in the north marginal seas in China were determined via clone library construction and a quantitative PCR analysis. The clone libraries retrieved by the 16S rRNA gene and Hzo gene markers indicated that “Candidatus Scalindua” was the predominant group throughout the sites examined. The 16S rRNA gene clone libraries revealed exceptional diversity by identifying two potential novel anammox clades, as evidenced by the high sequence similarities between these two clades and known anammox genera, and their unique phylogenetic positions with high bootstrap values. However, their potential roles in the anammox reaction need to be validated. Six novel members of Planctomycetes, divergent from the known genera of anammox bacteria, were also detected. A phylogenetic analysis by Hzo protein sequences revealed the existence of two known genera, i.e., “Candidatus Jettenia” and “Candidatus Anammoxoglobus”, which are rarely captured from marine sediments. Among all ecological parameters investigated, the distribution patterns and composition of anammox bacteria were found to be influenced by salinity, total organic matter, and temperature. The abundance of the anammox bacterial 16S rRNA gene from the sites examined ranged between 3.95×10⁵ and 9.21×10⁵ copies g⁻¹ wet sediment and positively correlated with the median size of the sediment sample.

Redox zones stratification and the microbial community characteristics in a periphyton bioreactor

Bioremediation techniques based on microorganisms have been widely applied to treat polluted surface water, but the efficiencies have been limited, especially in deep and static waters. Microbial aggregates, known as periphyton, were introduced into a tank bioreactor to improve pollutants removal and a periphyton bioreactor with an 84 cm column was built to investigate microbe-wastewater interactions. Periphyton greatly improved water quality and produced a distinct stratification in the water column into five redox zones with slight overlaps. From top to bottom these were: oxygen reduction, nitrate reduction, iron reduction, sulfate reduction and methanogenic zone. Periphyton communities had high species diversities (767-947 OTUs) with the facultative zone (middle layer) having higher species richness and functional diversity than the aerobic (top layer) and anaerobic zones (bottom layer). A good knowledge of interactions between periphyton and water column stratification could benefit from integration of periphyton to improve bioremediation of deep and static water.

In situ expression of nitrite-dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer

Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here, we used environmental metaproteomics to obtain information about the identity of subsurface microbial populations in coal tar-contaminated groundwater and the metabolic processes they catalyze. Metaproteomic libraries (two shotgun and seven slices from one SDS-PAGE gel) were generated from replicate samples of microbial biomass. Peptide fragment analysis using nano-liquid chromatography (LC)-mass spectrometry (MS)/MS of the three protein pools generated a total of 95,725 mass spectra. When analyzed using mascot v.2.3.02 and searched against the NCBInr bacterial database [confidence interval 99% (P < 0.01)], a total of 1,270 proteins had at least two peptide matches. Replication of identified proteins across the three libraries was low (3.3%); however, in each library, the most frequently identified protein host was Candidatus Methylomirabilis oxyfera (15, 12 and 62 proteins for each shotgun and the gel-slice library respectively). Remarkably, eight of the nine proteins in the nitrite-dependent anaerobic methane oxidation pathway were found. Additionally, 39 proteins were matched to known anammox bacteria including hydroxylamine and hydrazine oxidase. Metaproteomics thus revealed a microbial population, closely related to Ca. Methylomirabilis oxyfera, actively engaged in nitrite-dependent anaerobic methane oxidation and likely competing for nitrite with anammox bacteria.

The first report of a microdiverse anammox bacteria community in waters of Colombian Pacific, a transition area between prominent oxygen minimum zones of the eastern tropical Pacific

Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen-deficient marine ecosystems such as oxygen minimum zones (OMZ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the Colombian Pacific, a transition area between the prominent South and North Pacific OMZs. Anammox bacteria were detected in the coastal and oceanic areas of the Colombian Pacific in low oxygen (< 22 μM), high nitrate (25–35 μM) and low nitrite (< 0.07 μM), and ammonium (< 1 μM) waters. In these waters, anammox bacteria were rich [∼ 7 operational taxonomic units (OTUs), 98% cut-off) and microdiverse (Shannon index H′ < 1.24), in comparison with the observed at the prominent OMZ of the Eastern Tropical South Pacific, Arabian Sea and Black Sea. Anammox bacteria-like sequences from the Colombian Pacific were grouped together with sequences retrieved from the distinct OMZ's marine subclusters (Peru, Northern Chile and Arabian Sea) within Candidatus ‘Scalindua spp’. Moreover, some anammox bacteria OTUs shared a low similarity with environmental phylotypes (86–94%). Our results indicated that a microdiverse anammox community inhabits the Colombian Pacific, generating new questions about the ecological and biogeochemical differences influencing its community structure.

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N₂ gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.

Impact of inocula and operating conditions on the microbial community structure of two anammox reactors

The microbial community structure of the biomass selected in two distinctly inoculated anaerobic oxidation of ammonium (anammox) reactors was investigated and compared with the help of data obtained from 454-pyrosequencing analyses. The anammox reactors were operated for 550 days and seeded with different sludges: sediment from a constructed wetland (reactor I) and biomass from an aerated lagoon part of the oil-refinery wastewater treatment plant (reactor II). The anammox diversity in the inocula was evaluated by 16S rRNA gene-cloning analysis. The diversity of anammox bacteria was greater in the sludge from the oil-refinery (three of the five known genera of anammox were detected) than in the wetland sludge, in which only Candidatus Brocadia was observed. Pyrosequencing analysis demonstrated that the community enriched in both reactors had differing compositions despite the nearly similar operational conditions applied. The dominant phyla detected in both reactors were Proteobacteria, Chloroflexi, Planctomycetes, and Acidobacteria. The phylum Bacteroidetes, which is frequently observed in anammox reactors, was not detected. However, Acidobacteria and GN04 phyla were observed for the first time, suggesting their importance for this process. Our results suggest that, under similar operational conditions, anammox populations (Ca. Brocadia sinica and Ca. Brocadia sp. 40) were selected in both reactors despite the differences between the two initial inocula. Taken together, these results indicated that the type of inoculum and the culture conditions are key determinants of the general microbial composition of the biomass produced in the reactors. Operational conditions alone might play an important role in anammox selection.

Diversity and distribution of planktonic anaerobic ammonium-oxidizing bacteria in the Dongjiang River, China

Anaerobic ammonium-oxidizing (anammox) process has recently been recognized as an important pathway for removing fixed nitrogen (N) from aquatic ecosystems. Anammox organisms are widely distributed in freshwater environments. However, little is known about their presence in the water column of riverine ecosystems. Here, the existence of a diverse anammox community was revealed in the water column of the Dongjiang River by analyzing 16S rRNA and hydrazine oxidation (hzo) genes of anammox bacteria. Phylogenetic analyses of hzo genes showed that Candidatus Jettenia related clades of anammox bacteria were dominant in the river, suggesting the ecological microniche distinction from freshwater/estuary and marine anammox bacteria with Ca. Brocadia and Kuenenia genera mainly detected in freshwater/estuary ecosystems, and Ca. Scalindua genus mainly detected in marine ecosystems. The abundance and diversity of anammox bacteria along the river were both significantly correlated with concentrations of NH4(+)-N based on Pearson and partial correlation analyses. Redundancy analyses showed the contents of NH4(+)-N, NO3(-)-N and the ratio of NH4(+)-N to NO2(-)-N significantly influenced the spatial distributions of anammox bacteria in the water column of the Dongjiang River. These results expanded our understanding of the distribution and potential roles of anammox bacteria in the water column of the river ecosystem.

Impact of volcanic ash on anammox communities in deep sea sediments

Subaerial explosive volcanism contributes substantial amounts of material to the oceans, but little is known about the impact of volcanic ash on sedimentary microbial activity. We have studied anammox communities in deep sea sediments near the volcanically active island of Montserrat, Lesser Antilles. The rates of anammox and denitrification in the sediments were measured using (15)N isotope pairing incubation experiments, while 16S rRNA genes were used to examine anammox community structures. The higher anammox rates were measured in sediment containing the lower accumulation of volcanic ash in the surface sediments, while the lowest activities were found in sediments with the highest ash deposit. 16S rRNA gene analysis revealed the presence of 'Candidatus Scalindua spp.' in the sediments. The lowest diversity of anammox bacteria was observed in the sediments with the highest ash deposit. Overall, this study demonstrates that the deposition of volcanic material in deep sea sediments has negative impacts on activity and diversity of the anammox community. Since anammox may account for up to 79% of N2 production in marine ecosystems, periods of extensive explosive volcanism in Earth history may have had a hitherto unrecognized negative impact on the sedimentary nitrogen removal processes.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria--anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species--in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca-anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.

Cell biology of unique anammox bacteria that contain an energy conserving prokaryotic organelle

Anammox bacteria obtain their energy for growth from the anaerobic oxidation of ammonium with nitrite to dinitrogen gas. This property has made anammox bacteria very valuable for industry where they are applied for the removal of nitrogen compounds from industrial and domestic wastewaters. Anammox bacteria are also important in nature where they contribute significantly to oceanic nitrogen loss. Further, anammox bacteria have similarities to both Archaea and Eukarya, making them extremely interesting from a cell biological perspective. The anammox cell does not conform to the typical prokaryotic cell plan: single bilayer membranes divide the anammox cell into three distinct cellular compartments that possibly also have distinct cellular functions. The innermost and largest compartment, the anammoxosome, is the location of the energy metabolism. The middle compartment, the riboplasm, contains the nucleoid and ribosomes and thus has a genetic, information processing function. Finally, the outermost compartment, the paryphoplasm, has an as yet unknown function. In addition, anammox bacteria are proposed to have an atypical cell wall devoid of both peptidoglycan and a typical outer membrane. Here, I review the current knowledge on the cell biology of this enigmatic group of bacteria.

Community structures and distribution of anaerobic ammonium oxidizing and nirS-encoding nitrite-reducing bacteria in surface sediments of the South China Sea

Anaerobic ammonium oxidation (anammox) and denitrification are two important processes responsible for nitrogen loss; monitoring of microbial communities carrying out these two processes offers a unique opportunity to understand the microbial nitrogen cycle. The aim of the current study was to characterize community structures and distribution of anammox and nirS-encoding nitrite-reducing bacteria in surface sediments of the northern South China Sea (SCS). The consistent phylogenetic results of three biomarkers of anammox bacteria, including 16S rRNA, hzo, and Scalindua-nirS genes, showed that Scalindua-like bacteria were the only anammox group presenting in surface sediments of the SCS. However, a relatively high micro-diversity was found within this group, including several SCS habitat-specific phylotypes, Candidatus "Scalindua zhenghei". Comparing to 16S rRNA gene, hzo and Scalindua-nirS genes provided a relatively higher resolution to elucidate anammox bacteria. For the nirS-encoding nitrite-reducing bacteria, the detected nirS gene sequences were closely related to various marine nirS denitrifiers, especially those which originated from coastal and estuarine sediments with a much higher diversity than anammox bacteria. Anammox bacterial communities shifted along with the seawater depth, while nirS-encoding nitrite-reducing bacteria did not. Although nirS-encoding nitrite-reducing bacteria have a much higher abundance and diversity than anammox bacteria, they showed similar abundance variation patterns in research sites, suggesting the two microbial groups might be affected by the similar environmental factors. The significant correlations among the abundance of the two microbial groups with the molar ratio of NH4 (+) to (NO2 (-) + NO3 (-)), pH, and organic matters of sediments strongly supported this hypothesis.

Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China

The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named "Ca. Scalindua pacifica". Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were active for the in situ N transforming process and maintained a versatile life style well adapted to the varying environmental conditions of the studied coastal ocean.

More refined diversity of anammox bacteria recovered and distribution in different ecosystems

A newly reported 16S rRNA gene-based PCR primer set was successfully applied to detect anammox bacteria from four ecosystem samples, including sediments from marine, reservoir, mangrove wetland, and wastewater treatment plant sludge. This primer set showed ability to amplify a much wider coverage of all reported anammox bacterial genera. Based on the phylogenetic analyses of 16S rRNA gene of anammox bacteria, two new clusters were obtained, one closely related to Candidatus Scalindua, and the other in a previously reported novel genus related to Candidatus Brocadia. In the Scalindua cluster, four new subclusters were also found in this study, mainly by sequences of the South China Sea sediments, presenting a higher diversity of Candidatus Scalindua in marine environment. Community structure analyses indicated that samples were grouped together based on ecosystems, showing a niche-specific distribution. Phylogenetic analyses of anammox bacteria in samples from the South China Sea also indicated distinguished community structure along the depth. Pearson correlation analysis showed that the amount of anammox bacteria in the detected samples was positively correlated with the nitrate concentration. According to Canonical Correspondence Analysis, pH, temperature, nitrite, and nitrate concentration strongly affected the diversity and distribution of anammox bacteria in South China Sea sediments. Results collectively indicated a promising application of this new primer set and higher anammox bacteria diversity in the marine environment.