Enrichment of marine anammox bacteria from seawater-related samples and bacterial community study

Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments

BACKGROUND

Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.

RESULTS

This study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH₄⁺ and NO₂^- reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.

CONCLUSIONS

This study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication. Video Abstract.

Unraveling the nitrogen removal properties and microbial characterization of "Candidatus Scalindua"-dominated consortia treating seawater-based wastewater

"Candidatus Scalindua", as known as marine anammox bacteria (MAB), was engineered to remove nitrogen from seawater-based wastewater (SWW). In this study, "Candidatus Scalindua" was successfully enriched within 106 days with marine sediments as inoculated sludge. The operating temperature was 20 ± 2 °C, and influent pH was 7.5 ± 0.1. Ammonia (NH₄⁺-N) removal rate (ARR) was 0.53 kg/(m³·d) with the NH₄⁺-N loading rate of 0.68 kg/(m³·d), and nitrite (NO₂^--N) removal rate (NRR) was 0.57 kg/(m³·d) at 0.89 kg/(m³·d) NO₂^--N loading rate. Nitrogen removal was negatively affected at an influent NO₂^- above 224 mg/L, which decreased the ARR and NRR to 0.36 and 0.31 kg/(m³·d), respectively. The genus "Ca. Scalindua" dominated the reactor, and it synergistically coexisted with Marinicella to achieve efficient nitrogen removal. This work would help to better understand the nitrogen removal properties and microbial characterization of MAB in SWW wastewater treatment under low temperature.

Physiological stabilization, community characterization, and nitrogen degradation dynamics in an anammox consortium from estuarine sediments

Anammox is a cost-effective and sustainable process for nitrogen removal; however, the production of a physiologically stable inoculum is a critical point in the start-up process. In this work, estuarine sediments were used as incubation seeds to obtain cultures with stable anammox activity. Assays were performed in batch cultures fed with stoichiometric amounts of ammonium and nitrite, analyzing physiological response variables and the microbial community. Estuarine sediments showed a stable anammox process after 90 days, consuming ammonium and nitrite simultaneously with concomitant generation of N₂ and nitrate in stoichiometric amounts. In kinetic assays, substrates were fully consumed after 210 hr, exhibiting N₂ and nitrate yields of 0.85 and 0.10, respectively. The microbial community analysis using PCR-DGGE indicated the presence of uncultured anammox bacteria and members of the genus Candidatus Jettenia. The results evidenced the achievement of anammox cultures, although their start-up and kinetic characteristics were less favorable than those recorded in man-made systems. PRACTITIONER POINTS: Estuarine sediments were used as incubation seeds to obtain cultures with stable anammox activity. The sediments were fed with stoichiometric amounts of ammonium and nitrite, analyzing the physiological response variables and the microbial community. Sediments showed a stable anammox process after 90 days, converting the substrates into N₂ and nitrate according to stoichiometry. Anammox cultures were achieved although their start-up and kinetic characteristics were less favorable than those recorded in man-made systems. Microbial community analysis using PCR-DGGE indicated the presence of uncultured anaerobic ammonia-oxidizing bacterium and members of genus Candidatus Jettenia.

Changes of nitrogen-removal performance and that of the bacterial community in a mixed culture comprising freshwater and marine anammox bacteria under averaged environmental condition

Nitrogen-removal processes using anammox bacteria are expected to achieve high-rate removal while remaining economical, and their practical applications have been investigated. However, anammox bacteria still have unfavorable characteristics for practical use, including susceptibility to a change in environmental conditions. In this study, with an aim of exploring the adaptability of mixed anammox bacteria to environmental conditions, the shift of nitrogen-removal performance and bacterial community in a mixed culture comprising freshwater anammox bacteria (FAB) and marine anammox bacteria (MAB) were investigated by a continuously stirred tank reactor (CSTR). The CSTR inoculated with the mixed anammox bacteria was operated for 180 days under an averaged condition between freshwater and marine conditions with a temperature of 27.5 °C and a synthetic medium with 15 g/L NaCl was used. Nitrogen-removal performance became stable after 114 days and more than 90% of nitrogen that was loaded into the reactor was removed in the range of nitrogen loading rate 0.07-0.42 kg N/m³/d. After operating at 0.42 kg N/m³/d for one month, a biomass sample was taken and its bacterial community was analyzed by clone-library analysis using a partial sequence of 16S rRNA. Among the clones of anammox bacteria that were made by an anammox-bacteria-specific primer, 97% of them were MAB and only 3% were FAB. These results indicate that the bacterial community including anammox bacteria was evidently changed due to environmental conditions and that the averaged condition in this study was suitable for marine bacteria rather than freshwater bacteria.

Nitrogen removal properties in a continuous marine anammox bacteria reactor under rapid and extensive salinity changes

Salinity tolerance is one of the most important factors for the application of bioreactors to high-salinity wastewater. Although marine anammox bacteria (MAB) might be expected to tolerate higher salinities than freshwater anammox bacteria, there is little information on the effects of salinity on MAB activity. This study aimed to reveal the nitrogen removal properties in a continuous MAB reactor under conditions of rapid and extensive salinity changes. The reactor demonstrated stable nitrogen removal performance with a removal efficiency of over 85% under salinity conditions ranging from 0 to 50 g/L NaCl. The reactor performance was also well maintained, even though the salinity was rapidly changed from 30 to 50 g/L and from 30 to 0 g/L. Other evidence suggested that the seawater medium used contained components essential for effective MAB performance. Bacterial community analysis using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) showed that planctomycete UKU-1, the dominant MAB species in the inoculum, was the main contributor to anammox activity under all conditions. The PCR-DGGE using a universal bacterial primer set showed different DNA band patterns between the reactor biomass sample collected under conditions of 75 g/L NaCl and all other conditions (0, 30, 50 and freshwater-medium). All DNA sequences determined were very similar to those of bacterial species from marine environments, anaerobic environments, or wastewater-treatment facilities.

Biomass yield efficiency of the marine anammox bacterium, "Candidatus Scalindua sp.," is affected by salinity

The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium "Candidatus Scalindua sp." is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of "Ca. Scalindua sp." enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0-10 mM) were observed under varying salinities (0.5%-4%). Anammox activity was high at 0.5%-3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%-3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium "Ca. Scalindua sp." was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency.

Physiological characterization of an anaerobic ammonium-oxidizing bacterium belonging to the "Candidatus scalindua" group

The phylogenetic affiliation and physiological characteristics (e.g., Ks and maximum specific growth rate [μmax]) of an anaerobic ammonium oxidation (anammox) bacterium, "Candidatus Scalindua sp.," enriched from the marine sediment of Hiroshima Bay, Japan, were investigated. "Candidatus Scalindua sp." exhibits higher affinity for nitrite and a lower growth rate and yield than the known anammox species.

Anammox--growth physiology, cell biology, and metabolism

Anaerobic ammonium-oxidizing (anammox) bacteria are the last major addition to the nitrogen-cycle (N-cycle). Because of the presumed inert nature of ammonium under anoxic conditions, the organisms were deemed to be nonexistent until about 15 years ago. They, however, appear to be present in virtually any anoxic place where fixed nitrogen (ammonium, nitrate, nitrite) is found. In various mar`ine ecosystems, anammox bacteria are a major or even the only sink for fixed nitrogen. According to current estimates, about 50% of all nitrogen gas released into the atmosphere is made by these bacteria. Besides this, the microorganisms may be very well suited to be applied as an efficient, cost-effective, and environmental-friendly alternative to conventional wastewater treatment for the removal of nitrogen. So far, nine different anammox species divided over five genera have been enriched, but none of these are in pure culture. This number is only a modest reflection of a continuum of species that is suggested by 16S rRNA analyses of environmental samples. In their environments, anammox bacteria thrive not just by competition, but rather by delicate metabolic interactions with other N-cycle organisms. Anammox bacteria owe their position in the N-cycle to their unique property to oxidize ammonium in the absence of oxygen. Recent research established that they do so by activating the compound into hydrazine (N(2)H(4)), using the oxidizing power of nitric oxide (NO). NO is produced by the reduction of nitrite, the terminal electron acceptor of the process. The forging of the N-N bond in hydrazine is catalyzed by hydrazine synthase, a fairly slow enzyme and its low activity possibly explaining the slow growth rates and long doubling times of the organisms. The oxidation of hydrazine results in the formation of the end product (N(2)), and electrons that are invested both in electron-transport phosphorylation and in the regeneration of the catabolic intermediates (N(2)H(4), NO). Next to this, the electrons provide the reducing power for CO(2) fixation. The electron-transport phosphorylation machinery represents another unique characteristic, as it is most likely localized on a special cell organelle, the anammoxosome, which is surrounded by a glycerolipid bilayer of ladder-like ("ladderane") cyclobutane and cyclohexane ring structures. The use of ammonium and nitrite as sole substrates might suggest a simple metabolic system, but the contrary seems to be the case. Genome analysis and ongoing biochemical research reveal an only partly understood redundancy in respiratory systems, featuring an unprecedented collection of cytochrome c proteins. The presence of the respiratory systems lends anammox bacteria a metabolic versatility that we are just beginning to appreciate. A specialized use of substrates may provide different anammox species their ecological niche.

Anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties

Anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. Among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. Here we review our current knowledge about anammox cell biology. The anammox cell is divided into three separate compartments by bilayer membranes. The anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, and anammoxosome. Not much is known about the composition or function of both the anammox cell wall and the paryphoplasm compartment. The cell wall is proposed to be proteinaceous and to lack both peptidoglycan and an outer membrane typical of Gram-negative bacteria. The function of the paryphoplasm is unknown, but it contains the cell division ring. The riboplasm resembles the standard cytoplasmic compartment of other bacteria; it contains ribosomes and the nucleoid. The anammoxosome occupies most of the cell volume and is a so-called "prokaryotic organelle" analogous to the eukaryotic mitochondrion. This is the site where the anammox reaction takes place, coupled over the curved anammoxosome membrane, possibly giving rise to a proton motive force and subsequent ATP synthesis. With these unique properties, anammox bacteria are food for thought concerning the early evolution of the domains Bacteria, Archaea, and Eukarya.