Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents

Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis

Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.

Thermophilic microorganisms involved in the nitrogen cycle in thermal environments: Advances and prospects

Thermophilic microorganisms mediated significant element cycles and material conversion in the early Earth as well as mediating current thermal environments. Over the past few years, versatile microbial communities that drive the nitrogen cycle have been identified in thermal environments. Understanding the microbial-mediated nitrogen cycling processes in these thermal environments has important implications for the cultivation and application of thermal environment microorganisms as well as for exploring the global nitrogen cycle. This work provides a comprehensive review of different thermophilic nitrogen-cycling microorganisms and processes, which are described in detail according to several categories, including nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and dissimilatory nitrate reduction to ammonium. In particular, we assess the environmental significance and potential applications of thermophilic nitrogen-cycling microorganisms, and highlight knowledge gaps and future research opportunities.

A review of anammox metabolic response to environmental factors: Characteristics and mechanisms

Anaerobic ammonium oxidation (anammox) is a promising low carbon and economic biological nitrogen removal technology. Considering the anammox technology has been easily restricted by environmental factors in practical engineering applications, therefore, it is necessary to understand the metabolic response characteristics of anammox bacteria to different environmental factors, and then guide the application of the anammox process. This review presented the latest advances of the research progress of the effects of different environmental factors on the metabolic pathway of anammox bacteria. The effects as well as mechanisms of conventional environmental factors and emerging pollutants on the anammox metabolic processes were summarized. Also, the role of quorum sensing (QS) mediating the bacteria growth, gene expression and other metabolic process in the anammox system were also reviewed. Finally, interaction and cross-feeding mechanisms of microbial communities in the anammox system were discussed. This review systematically summarized the variations of metabolic mechanism response to the external environment and cross-feeding interactions in the anammox process, which would provide an in-depth understanding for the anammox metabolic process and a comprehensive guidance for future anammox-related metabolic studies and engineering applications.

Physiology of anammox adaptation to low temperatures and promising biomarkers: A review

The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.

Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.

Assessment of Ammonia as a Biosignature Gas in Exoplanet Atmospheres

Ammonia (NH₃) in a terrestrial planet atmosphere is generally a good biosignature gas, primarily because terrestrial planets have no significant known abiotic NH₃ source. The conditions required for NH₃ to accumulate in the atmosphere are, however, stringent. NH₃'s high water solubility and high biousability likely prevent NH₃ from accumulating in the atmosphere to detectable levels unless life is a net source of NH₃ and produces enough NH₃ to saturate the surface sinks. Only then can NH₃ accumulate in the atmosphere with a reasonable surface production flux. For the highly favorable planetary scenario of terrestrial planets with hydrogen (H₂)-dominated atmospheres orbiting M dwarf stars (M5V), we find that a minimum of about 5 ppm column-averaged mixing ratio is needed for NH₃ to be detectable with JWST, considering a 10 ppm JWST systematic noise floor. When the surface is saturated with NH₃ (i.e., there are no NH₃-removal reactions on the surface), the required biological surface flux to reach 5 ppm is on the order of 10¹⁰ molecules/(cm²·s), comparable with the terrestrial biological production of methane (CH₄). However, when the surface is unsaturated with NH₃, due to additional sinks present on the surface, life would have to produce NH₃ at surface flux levels on the order of 10¹⁵ molecules/(cm²·s) (∼4.5 × 10⁶ Tg/year). This value is roughly 20,000 times greater than the biological production of NH₃ on the Earth and about 10,000 times greater than Earth's CH₄ biological production. Volatile amines have similar solubilities and reactivities to NH₃ and hence share NH₃'s weaknesses and strengths as a biosignature. Finally, to establish NH₃ as a biosignature gas, we must rule out mini-Neptunes with deep atmospheres, where temperatures and pressures are high enough for NH₃'s atmospheric production.

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.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

Purification of the key enzyme complexes of the anammox pathway from DEMON sludge

Anaerobic Ammonium Oxidation ("anammox") is a bacterial process in which nitrite and ammonium are converted into nitrogen gas and water, yielding energy for the cell. Anammox is an important branch of the global biological nitrogen cycle, being responsible for up to 50% of the yearly nitrogen removal from the oceans. Strikingly, the anammox process uniquely relies on the extremely reactive and toxic compound hydrazine as a free intermediate. Given its global importance and biochemical novelty, there is considerable interest in the enzymes at the heart of the anammox pathway. Unfortunately, obtaining these enzymes in sufficiently large amounts for biochemical and structural studies is problematic, given the slow growth of pure cultures of anammox bacteria when high cell densities are required. However, the anammox process is being applied in wastewater treatment to remove nitrogenous waste in processes like DEamMONification (DEMON). In plants using such processes, which rely on a combination of aerobic ammonia-oxidizers and anammox organisms, kilogram amounts of anammox bacteria-containing sludge are readily available. Here, we report a protein isolation protocol starting from anammox cells present in DEMON sludge from a wastewater treatment plan that readily yields pure preparations of key anammox proteins in the tens of milligrams, including hydrazine synthase HZS and hydrazine dehydrogenase (HDH), as well as hydroxylamine oxidoreductase (HAO). HDH and HAO were active and of sufficient quality for biochemical studies and for HAO, the crystal structure could be determined. The method presented here provides a viable way to obtain materials for the study of proteins not only from the central anammox metabolism but also for the study of other exciting aspects of anammox bacteria, such as for example, their unusual ladderane lipids.

Whether glycine betaine improves the thermotolerance of mesophilic anammox consortia

While the application of mesophilic anammox process is currently the state of the art, the feasibility of a thermophilic anammox bioprocess is still unclear. In this study, we investigate whether glycine betaine (GB) addition can enhance the thermotolerance of mesophilic anammox biomass in the upflow anaerobic sludge blanket (UASB) reactors fed with synthetic wastewater at a nitrogen loading of approximately 4 kg N m^-3 d^-1. The results showed that during a long-term operation at 45°C with GB (0, 0.1, 1, 2 mM) addition, anammox performance became worse with the final effluent concentrations of NO₂ ^-N of 145 ± 11.6 mg L^-1 and nitrogen removal efficiency decreased from 92.3-6.9%. Specific anammox activity decreased from 392.1 ± 12.1-6.0 ± 0.8 mg N g^-1 VSS d^-1, which were not significantly higher than those in the control reactor. The content of heme c showed a stronger downward trend in T₁ (with GB addition) than in the control reactor T₀. The qPCR results showed that the relative abundance of Candidatus Kuenenia decreased in both the experimental (from 53.5-28.8%) and control reactors (from 54.1-35.1%). Overall, continuous addition of exogenous GB did not improve the thermotolerance of mesophilic anammox consortia at 45°C.

Diversity of sediment associated Planctomycetes and its related phyla with special reference to anammox bacterial community in a high Arctic fjord

The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.

Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes

There is a lack of understanding of the interaction between anammox bacteria and the flanking microbial communities in both freshwater (non-saline) and marine (saline) ecosystems. Here, we present a comparative genome-based exploration of two different anammox bioreactors, through the analysis of 23 metagenome-assembled genomes (MAGs), 12 from freshwater anammox reactor (FWR), and 11 from marine anammox reactor (MWR). To understand the contribution of individual members to community functions, we applied the index of replication (iRep) to determine bacteria that are actively replicating. Using genomic content and iRep information, we provided a potential ecological role for the dominant members of the community based on the reactor operating conditions. In the non-saline system, anammox (Candidatus Brocadia sinica) and auxotrophic neighboring bacteria belonging to the phyla Ignavibacteriae and Chloroflexi might interact to reduce nitrate to nitrite for direct use by anammox bacteria. Whereas, in the saline reactor, anammox bacterium (Ca. Scalindua erythraensis) and flanking community belonging to phyla Planctomycetes (different than anammox bacteria)—which persistently growing in the system—may catabolize detritus and extracellular material and recycle nitrate to nitrite for direct use by anammox bacteria. Despite different microbial communities, there was functional redundancy in both ecosystems. These results signify the potential application of marine anammox bacteria for treating saline N-rich wastewaters.

Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments

Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.

Enhance the treatment of low strength wastewater at low temperature with the coexistence system of AnAOB and heterotrophic bacteria: Performance and bacterial community

The application of anammox process in mainstream wastewater treatment process is still facing challenges especially at the low temperature. To resolve this problem, the coexistence system of anaerobic ammonia-oxidizing bacteria (AnAOB) and heterotrophic bacteria (HB) was built in this study. The nitrogen removal efficiency mainly maintained at above 90% during the process of temperature reducing from 35 °C to 10 °C. The nitrogen removal rate were 0.30 g N·L^-1·d^-1 at both 25 and 15 °C and 0.10 g N·L^-1·d^-1 at 10 °C, respectively. Analysis of 16S rRNA genus sequencing revealed that as the temperature reduced to 10 °C, the Denutrotisoma genera presented a downward trend but Comamonadaceae genera showed an upward trend. At 10 °C, the contrast of anammox activities between granular and flocculent sludge in the system revealed that although the abundance of anammox genera was much lower in flocculent sludge than that in granular sludge, the anammox activities showed no significant discrepancy. And the abundance of Comamonadaceae and Chloroflexales genera were much higher in flocculent sludge than those in granular sludge, presenting their key roles to anammox activity at low temperature. The Circos diagram and Cluster of orthologous Group of protein functional predication showed that the functional abundance related to interaction among microbial communities were higher in flocculent sludge but those related to self-growth was higher in granular sludge. This result indicated the significance of the interactions based on the microbial diversity in the application of annamox process at low temperature.

Adaptation and characterization of thermophilic anammox in bioreactors

Anammox, the oxidation of ammonium with nitrite, is a key microbial process in the nitrogen cycle. Under mesophilic conditions (below 40 °C), it is widely implemented to remove nitrogen from wastewaters lacking organic carbon. Despite evidence of the presence of anammox bacteria in high-temperature environments, reports on the cultivation of thermophilic anammox bacteria are limited to a short-term experiment of 2 weeks. This study showcases the adaptation of a mesophilic inoculum to thermophilic conditions, and its characterization. First, an attached growth technology was chosen to obtain the process. In an anoxic fixed-bed biofilm bioreactor (FBBR), a slow linear temperature increase from 38 to over 48 °C (0.05-0.07 °C d^-1) was imposed to the community over 220 days, after which the reactor was operated at 48 °C for over 200 days. Maximum total nitrogen removal rates reached up to 0.62 g N L^-1 d^-1. Given this promising performance, a suspended growth system was tested. The obtained enrichment culture served as inoculum for membrane bioreactors (MBR) operated at 50 °C, reaching a maximum total nitrogen removal rate of 1.7 g N L^-1 d^-1 after 35 days. The biomass in the MBR had a maximum specific anammox activity of 1.1 ± 0.1 g NH₄⁺-N g^-1 VSS d^-1, and the growth rate was estimated at 0.075-0.19 d^-1. The thermophilic cultures displayed nitrogen stoichiometry ratios typical for mesophilic anammox: 0.93-1.42 g NO₂^--N_removed g^-1 NH₄⁺-N_removed and 0.16-0.35 g NO₃^--N_produced g^-1 NH₄⁺-N_removed. Amplicon and Sanger sequencing of the 16S rRNA genes revealed a disappearance of the original "Ca. Brocadia" and "Ca. Jettenia" taxa, yielding Planctomycetes members with only 94-95% similarity to "Ca. Brocadia anammoxidans" and "Ca. B. caroliniensis", accounting for 45% of the bacterial FBBR community. The long-term operation of thermophilic anammox reactors and snapshot views on the nitrogen stoichiometry, kinetics and microbial community open up the development path of thermophilic partial nitritation/anammox. A first economic assessment highlighted that treatment of sludge reject water from thermophilic anaerobic digestion of sewage sludge may become attractive.

Biogeographic pattern of the nirS gene-targeted anammox bacterial community and composition in the northern South China Sea and a coastal Mai Po mangrove wetland

Functional genes, namely hzo/hao, nirS, hzs, and ccs gene, are efficient with high specificity for detecting anammox bacteria. Sc-nirS and An-nirS primer sets were proposed for targeting Scalindua/non-Scalindua anammox bacterial groups; previously, they have not been assessed for biogeographic study on marine-terrestrial transitional systems, specifically marine and terrestrial ecosystems. Here, we report phylogenetic distribution pattern of anammox bacteria in both northern South China Sea (nSCS) and Mai Po wetland (a coastal mangrove) using nirS gene-based primers. A well-delineated biogeographic distribution pattern from ocean to continental shelf was evident by combining both gene-based analyses as previously depicted using 16S rRNA as the biomarker. Furthermore, factors affecting the abundance and composition of An-nirS genes in Mai Po wetland were identified as substrate (NO₃^-/NO₂^- concentration) and anoxic/oxic condition in association to depth. An-nirS gene abundance was from 2.6 × 10³ to 1.2-1.4 × 10⁴ copies/g dry sediment in nSCS; and it was around 5 × 10³ and 1-2 × 10⁴ copies/g dry sediment in surface and subsurface sediments of Mai Po wetland, respectively. In addition, nirS gene abundance and distribution pattern of denitrifiers and anammox bacteria in the wetland indicates a competition relationship between them. Mangrove vegetation affected the community composition of An-nirS gene considerably, and a more homogeneous distribution pattern was observed in the mangrove forest than intertidal mudflats. Sc/An-nirS gene-based biogeographic insights on anammox bacteria have shed lights on the compositional and potential functional dynamics and emphasized the importance of molecular tools on refining the current microbial ecological patterns.

Unique Solid Phase Microextraction Sampler Reveals Distinctive Biogeochemical Profiles among Various Deep-Sea Hydrothermal Vents

Current methods for biochemical and biogeochemical analysis of the deep-sea hydrothermal vent ecosystems rely on water sample recovery, or in situ analysis using underwater instruments with limited range of analyte detection and limited sensitivity. Even in cases where large quantities of sample are recovered, labile dissolved organic compounds may not be detected due to time delays between sampling and preservation. Here, we present a novel approach for in situ extraction of organic compounds from hydrothermal vent fluids through a unique solid phase microextraction (SPME) sampler. These samplers were deployed to sample effluent of vents on sulphide chimneys, located on Axial Seamount in the North-East Pacific, in the Urashima field on the southern Mariana back-arc, and at the Hafa Adai site in the central Mariana back-arc. Among the compounds that were extracted, a wide range of unique organic compounds, including labile dissolved organic sulfur compounds, were detected through high-resolution LC-MS/MS, among which were biomarkers of anammox bacteria, fungi, and lower animals. This report is the first to show that SPME can contribute to a broader understanding of deep sea ecology and biogeochemical cycles in hydrothermal vent ecosystems.

Anammox and partial denitrification coupling: a review

As a new wastewater biological nitrogen removal process, anammox and partial denitrification coupling not only plays a significant role in the nitrogen cycle, but also holds high engineering application value. Because anammox and some denitrifying bacteria are coupled under harsh living conditions, certain operating conditions and mechanisms of the coupling process are not clear; thus, it is more difficult to control the process, which is why the process has not been widely applied. This paper analyzes the research focusing on the coupling process in recent years, including anammox and partial denitrification coupling process inhibitors such as nitrogen (NH₄⁺, NO₂⁻), organics (toxic and non-toxic organics), and salts. The mechanism of substrate removal in anammox and partial denitrification coupling nitrogen removal is described in detail. Due to the differences in process methods, experimental conditions, and sludge choices between the rapid start-up and stable operation stages of the reactor, there are significant differences in substrate inhibition. Multiple process parameters (such as pH, temperature, dissolved oxygen, redox potential, carbon-to-nitrogen ratio, and sludge) can be adjusted to improve the coupling of anammox and partial denitrification to modify nitrogen removal performance.

As a new wastewater biological nitrogen removal process, anammox and partial denitrification coupling not only plays a significant role in the nitrogen cycle, but also holds high engineering application value.

Performance of Anammox Processes for Wastewater Treatment: A Critical Review on Effects of Operational Conditions and Environmental Stresses

The anaerobic ammonium oxidation (anammox) process is well-known as a low-energy consuming and eco-friendly technology for treating nitrogen-rich wastewater. Although the anammox reaction was widely investigated in terms of its application in many wastewater treatment processes, practical anammox application at the pilot and industrial scales is limited because nitrogen removal efficiency and anammox activity are dependent on many operational factors such as temperature, pH, dissolved oxygen concentration, nitrogen loading, and organic matter content. In practical application, anammox bacteria are possibly vulnerable to non-essential compounds such as sulfides, toxic metal elements, alcohols, phenols, and antibiotics that are potential inhibitors owing to the complexity of the wastewater stream. This review systematically summarizes up-to-date studies on the effect of various operational factors on nitrogen removal performance along with reactor type, mode of operation (batch or continuous), and cultured anammox bacterial species. The effect of potential anammox inhibition factors such as high nitrite concentration, high salinity, sulfides, toxic metal elements, and toxic organic compounds is listed with a thorough interpretation of the synergistic and antagonistic toxicity of these inhibitors. Finally, the strategy for optimization of anammox processes for wastewater treatment is suggested, and the importance of future studies on anammox applications is indicated.

The performance of an anaerobic ammonium oxidation upflow anaerobic sludge blanket reactor during natural periodic temperature variations

An anaerobic ammonium oxidation-upflow anaerobic sludge blanket (anammox-UASB) reactor was operated without temperature control during the four seasons and was therefore subjected to natural periodic temperature variations between 9 and 28 ℃. The anammox reactor had a high nitrogen removal ability at intermediate and low temperatures. The total nitrogen (TN) concentration of the influent increased from 200 to 1200 mg/L, the nitrogen removal efficiency was maintained at 90%, and the nitrogen removal rate (NRR) increased to 9.15 ± 0.35 kg N/m³/d. The enrichment of anammox bacteria in the UASB granular sludge reached 53.8%, and the dominant bacteria changed from Candidatus Brocadia to Candidatus Kuenenia after several seasons of cultivation. Dynamics analysis revealed that the maximum reaction rate of the anammox-UASB sludge was 62.5 kg N/m³/d, reflecting the high potential nitrogen removal ability of the reactor.

Impacts of diel temperature variations on nitrogen removal and metacommunity of anammox biofilm reactors

The influence of diel temperature variations (DTVs) on nitrogen removal and bacterial communities was investigated in two parallel anammox reactors (i.e., control and DTV reactors). The control reactor was operated at a constant temperature of 30 °C, whereas the DTV reactor was operated in a temperature fluctuation mode with a cycle of 12/12 h of high/low temperatures. Nine water temperature variations for the day/night periods were set from 30/30 °C (i.e., Δ0 °C) to 38/22 °C (i.e., Δ16 °C). An increase in DTVs from Δ8 °C (34/26 °C) to Δ16 °C (38/22 °C) caused a significant decline in reactor performance and a shift in bacterial diversity. Compared to the control reactor, for instance, nitrogen removal efficiency decreased (P < 0.05) when temperature fluctuations exceeded Δ8 °C in the DTV reactor with a decreasing ΔNO₃^-/ΔNH₄⁺ ratio (from 0.21 ± 0.15 to 0.16 ± 0.04). The results of 16S rRNA gene sequencing showed that the initial disturbance of temperature variations led to increased levels of bacterial diversity (i.e., alpha diversity) and decreased community levels of anammox consortia whereas they slightly recovered at the end of each DTV phase. Notably, Candidatus Jettenia was more sensitive to strong water temperature fluctuations, with the lower relative abundance at Δ14 °C (17.11 ± 5.01%) and Δ16 °C (17.83 ± 7.22%) than at Δ4 °C (39.82 ± 0.01%). In contrast, Ca. Brocadia and Ca. Kuenenia had higher relative abundance at Δ14 °C (i.e., 0.24 ± 0.07% and 0.09 ± 0.02%, respectively) and Δ16 °C (i.e., 0.28 ± 0.05% and 0.12 ± 0.03%, respectively) compared to that at Δ4 °C (i.e., 0.15 ± 0.04% and 0.04 ± 0.01%, respectively). Nitrifiers (i.e., unidentified_Nitrospiraceae and Nitrosomonas) and denitrifiers (i.e., Denitratisoma) were also capable of tolerating high temperature perturbations. Overall this study furthers our knowledge of responses of the microbial ecology of anammox bacteria to DTVs in anammox processes, which could aid us in optimizing anammox-related wastewater treatment systems and in understanding the nitrogen cycles of natural ecosystems.

Increased salinity improves the thermotolerance of mesophilic anammox consortia

While the application of anammox-based process for mesophilic sidestream treatment is at present the state of the art and mainstream treatment at ambient temperature is also in development, the feasibility of thermophilic anammox process is still unclear. This study investigated the effects of salinity on the thermotolerance of mesophilic anammox sludge. In batch activity tests, 45 °C seems to be the critical temperature for the tolerance of mesophilic anammox consortia without acclimatization or amendments. The optimal anammox activity at 40, 42.5, and 45 °C can be achieved with the amendment of salt at 5-8, 8-10, and ~12 g NaCl L^-1, respectively. However, this improvement effect was limited at 50 °C or when the shock duration was longer than 24 h even at 45 °C. In continuous-flow bioreactors, mesophilic anammox consortia could gradually adapt to 40-50 °C under a transition of 2.5 °C, and the performance was enhanced by an increase in salinity, which may be associated with the increase in extracellular polymeric substances. A nitrogen removal rate of 0.53 kgN m^-3 d^-1 was finally obtained at 50 °C. Overall, these interesting results facilitate further opportunities for thermophilic anammox process.

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields

The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.

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.

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.

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.

Influence of temperature and pH on the anammox process: A review and meta-analysis

The anammox (anaerobic ammonium oxidation) process was considered a very efficient and economic wastewater treatment technology immediately after its discovery in 1995, thus research in this field was intensified. The anammox process is characterised by a high temperature optimum and is very sensitive to both temperature and pH fluctuations. The process can also be inhibited by many factors, including by its substrates, i.e. nitrite and ammonium (or its unionised forms: free ammonia and free nitrous acid). This paper presents a comprehensive study of the most important and recent findings on the influence of two parameters that are crucial in wastewater treatment, i.e. temperature and pH. Because both parameters may influence the anammox process simultaneously, a meta-analysis was conducted of the data from the literature. Although meta-analysis is commonly used in medical research, mathematical analysis of the literature data has become an interesting and important step in the environmental sciences. This paper presents information on the influence of both temperature and pH on process efficiency and microbial composition. Additionally, the responses of different operating systems on both temperature and pH changes are described. Moreover, the role of both adaptation to changed conditions and of pH control as well as indicated areas of process operation are discussed.

Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores

Menez Gwen, Lucky Strike and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through chemoautotrophy, feeding and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. In this study, we provide for the first time a comparative survey of the sediment-associated microbial communities from these three neighbouring vent fields. Sediment samples collected in the Menez Gwen, Lucky Strike and Rainbow vent fields showed significant differences in trace-metal concentrations and associated microbiomes. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene-tag pyrosequencing, identified anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggesting sediment communities potentially enriched in sub-seafloor microbes rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Elemental contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.

Nitrogen removal performance and operation strategy of anammox process under temperature shock

Sequencing batch reactors were used to study anaerobic ammonium oxidation (anammox) process under temperature shock. Both long-term (15-35 °C) and short-term (10-50 °C) temperature effects on nitrogen removal performance were performed. In reactor operation test, the results indicated that ammonium removal rate decreased from 0.35 kg/(m³ day) gradually to 0.059 kg/(m³ day) when temperature dropped from 35 to 15 °C. Although bacteria morphology was not modified, sludge settling velocity decreased with decreasing temperature. In batch test, apparent activation energy (E_a) increased with decreasing temperature, which suggested the activity decrease of anaerobic ammonium oxidizing bacteria (AAOB). Low temperature inhibited AAOB and weakened nitrogen removal performance. The cardinal temperature model with inflection was first used to describe temperature effect on anammox process. Simulated results revealed that anammox reaction could occur at 10.52-50.15 °C with maximum specific anammox activity of 0.50 kg/(kg day) at 36.72 °C. The cold acclimatization of AAOB could be achieved and glycine betaine could slightly improve nitrogen removal performance at low temperature.

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.

Bacterial diversity in medication-related osteonecrosis of the jaw

OBJECTIVE

The aim was to study the association between microflora and medication-related osteonecrosis of the jaw (MRONJ) by using culture-independent molecular techniques to detect bacteria in necrotic bone lesions.

STUDY DESIGN

Included were 18 consecutive patients with MRONJ, 10 with osteoporosis and 8 cancer patients. Bone biopsies were retrieved from the center of the necrotic bone and from visually healthy bone, and 16 S rRNA gene fragments from bacterial DNA were amplified with polymerase chain reaction.

RESULTS

The study revealed a diversity of bacteria represented by 16 S rRNA sequences in all the necrotic bone samples and in 60% of the visually healthy bone. Eight dominating taxa groups were identified at the genus level: Porphyromonas, Lactobacillus, Tannerella, Prevotella, Actinomyces, Treponema, Streptococcus, and Fusobacterium.

CONCLUSIONS

The necrotic bone lesions contained mainly anaerobic bacteria, representative of periodontal microflora, suggesting that a periodontal infection in combination with antiresorptive treatment could initiate osteonecrosis.

The diversity and distribution of anammox bacteria in the marine aquaculture zones

The accumulation of toxic inorganic nitrogen is one of the major water quality problems in intensive aquaculture systems, thus the N removal in aquaculture systems is an important issue for the sustainable development of aquaculture. To understand one of the major microbial N removal processes, anaerobic ammonium oxidation (anammox), phylogenetic diversity, and distribution of anammox bacteria in sediments of four different marine aquaculture zones in Hong Kong (HK) were investigated. The 16S rRNA genes analysis indicated that sequences detected from Cheung Sha Wan (CSW) and Sok Kwu Wan (SKW) were closely related to several clusters within the Scalindua genus of anammox bacteria, including a new habitat-specific group, while only several sequences related to Scalindua and Kuenenia were detected in Sham Wan (SW) and Yim Tin Tsai East (YTTE). Most of the sequences obtained in SW and YTTE with the same PCR primers showed a low similarity to the known anammox bacteria, forming several novel groups within the Planctomycetes. However, results from the hydrazine oxidoreductase (HZO) encoding gene showed that only sequences from SW were related to the genus of Kuenenia, and sequences from other three sites were closely related to the genus of Scalindua. The community analysis showed that CSW and SKW share similar anammox bacterial community structures while SW and YTTE contain a unique anammox bacterial community. Furthermore, correlations reflect that organic matter is positively correlated with Kuenenia-like anammox bacteria, while the redox potential is significantly correlated with Scalindua-like anammox bacteria in marine aquaculture zones. Our results extend the knowledge of anammox bacteria in marine aquaculture systems and highlight the importance of environmental factors in shaping the community structures of anammox bacteria.

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.

Iron Transformation Pathways and Redox Micro-Environments in Seafloor Sulfide-Mineral Deposits: Spatially Resolved Fe XAS and δ(57/54)Fe Observations

Hydrothermal sulfide chimneys located along the global system of oceanic spreading centers are habitats for microbial life during active venting. Hydrothermally extinct, or inactive, sulfide deposits also host microbial communities at globally distributed sites. The main goal of this study is to describe Fe transformation pathways, through precipitation and oxidation-reduction (redox) reactions, and examine transformation products for signatures of biological activity using Fe mineralogy and stable isotope approaches. The study includes active and inactive sulfides from the East Pacific Rise 9°50'N vent field. First, the mineralogy of Fe(III)-bearing precipitates is investigated using microprobe X-ray absorption spectroscopy (μXAS) and X-ray diffraction (μXRD). Second, laser-ablation (LA) and micro-drilling (MD) are used to obtain spatially-resolved Fe stable isotope analysis by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Eight Fe-bearing minerals representing three mineralogical classes are present in the samples: oxyhydroxides, secondary phyllosilicates, and sulfides. For Fe oxyhydroxides within chimney walls and layers of Si-rich material, enrichments in both heavy and light Fe isotopes relative to pyrite are observed, yielding a range of δ(57)Fe values up to 6‰. Overall, several pathways for Fe transformation are observed. Pathway 1 is characterized by precipitation of primary sulfide minerals from Fe(II)aq-rich fluids in zones of mixing between vent fluids and seawater. Pathway 2 is also consistent with zones of mixing but involves precipitation of sulfide minerals from Fe(II)aq generated by Fe(III) reduction. Pathway 3 is direct oxidation of Fe(II) aq from hydrothermal fluids to form Fe(III) precipitates. Finally, Pathway 4 involves oxidative alteration of pre-existing sulfide minerals to form Fe(III). The Fe mineralogy and isotope data do not support or refute a unique biological role in sulfide alteration. The findings reveal a dynamic range of Fe transformation pathways consistent with a continuum of micro-environments having variable redox conditions. These micro-environments likely support redox cycling of Fe and S and are consistent with culture-dependent and -independent assessments of microbial physiology and genetic diversity of hydrothermal sulfide deposits.

Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei.

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.

Membrane Distillation Bioreactor (MDBR) - A lower Green-House-Gas (GHG) option for industrial wastewater reclamation

A high-retention membrane bioreactor system, the Membrane Distillation Bioreactor (MDBR) is a wastewater reclamation process which has the potential to tap on waste heat generated in industries to produce high quality product water. There are a few key factors which could make MDBR an attractive advanced treatment option, namely tightening legal requirements due to increasing concerns on the micropollutants in industrial wastewater effluents as well as concerns over the electrical requirement of pressurized advanced treatment processes and greenhouse gas emissions associated with wastewater reclamation. This paper aims to provide a consolidated review on the current state of research for the MDBR system and to evaluate the system as a possible lower Green House Gas (GHG) emission option for wastewater reclamation using the membrane bioreactor-reverse osmosis (MBR-RO) system as a baseline for comparison. The areas for potential applications and possible configurations for MDBR applications are discussed.

Occurrence, activity and contribution of anammox in some freshwater extreme environments

Anaerobic ammonium oxidation (anammox) widely occurs in marine ecosystems, and it plays an important role in the global nitrogen cycle. But in freshwater ecosystems its occurrence, distribution and contribution, especially in extreme environments, are still not well known. In this study, anammox process was investigated in some extreme environments of freshwater ecosystems, such as those with high (above 75°C) and low (below -35°C) temperature, high (pH > 8) and low (pH < 4) pH and eutrophy (the concentration of NH4 (+) -N > 300 mg kg(-1) ). The polymerase chain reaction (PCR) screening results showed that anammox bacteria were widespread in the examined sediments from freshwater extreme environments. Quantitative PCR showed that the abundance of anammox bacteria ranged from 6.94 × 10(4) to 8.05 × 10(6) hydrazine synthase (hzsB) gene copies g(-1) dry soil. (15) N-labelled incubation experiments indicated the occurrence of anammox in all examined sediments and the potential anammox rates ranged from 0.02 to 6.24 nmol N g(-1)  h(-1) , with a contribution of 3.45-58.74% of the total N2 production. In summary, these results demonstrate the occurrence of anammox in these extreme environments, inferring that anammox may harbour a wide ecological niche in the freshwater ecosystems.

Microbial community shifts on an anammox reactor after a temperature shock using 454-pyrosequencing analysis

To explore the changes in the microbial community structure during the recovery process of an anammox reactor after a temperature shock, the 454-pyrosequencing technique was used. The temperature shock reduced the nitrogen removal rate up to 92% compared to that just before the temperature shock, and it took 70 days to recover a similar nitrogen removal rate to that before the temperature shock (ca. 0.30 g N L(-1) d(-1)). Pyrosequencing results indicated that microbial diversity in the reactor decreased as the reactor progressively recovered from the temperature shock. Anammox bacteria were accounted as 6%, 35% and 46% of total sequence reads in samples taken 13, 45 and 166 days after the temperature shock. These results were in agreement with N-removal performance results and anammox activity measured in the reactor during the recovery process. An anammox specific primer was used to precisely determine the anammox species in the biomass samples.

Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture

Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.

Assessing the global phylum level diversity within the bacterial domain: A review

Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.