Genome-centered omics insight into the competition and niche differentiation of Ca. Jettenia and Ca. Brocadia affiliated to anammox bacteria
Although the niche differentiation of anammox bacteria has been extensively observed in a lab-scale reactor, the inherent mechanism for this ecological phenomenon is still elusive. Here, we combined the long-term reactor operation, genome-centered metagenome, and metatranscriptome analyses to gain insight into the substrate competition and niche differentiation of Candidatus Jettenia and Candidatus Brocadia. After 146 days of operation, we found the anammox bacterial population shifted from Ca. Jettenia to Ca. Brocadia in the immobilization-anaerobic baffled reactor (I-ABR) with the ammonium and nitrite concentrations of 30 mg/L. Importantly, the genome and transcript comparisons of Ca. Jettenia and Ca. Brocadia showed that Ca. Brocadia harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system and more redundant function in nitrite reduction, in which the genes were also highly expressed. Ca. Brocadia out-competed Ca. Jettenia at the mainstream condition. Meanwhile, though the highest biomass concentration led to the highest nitrogen removal rate (NRR) in the first compartment (C1), the competition of Ca. Jettenia and Ca. Brocadia could also affect the NRR of different compartments through affecting the bacterial activity. Substrate competition of anammox bacteria led to higher transcript activity of Ca. Jettenia and Ca. Brocadia in the second (C2) and fourth (C4) compartments, respectively. Further, high transcript activity of Ca. Brocadia led to the higher NRR in C4. A comparison of metabolic potential based on the metagenome-assembled genome adds a different dimension for understanding the discrepantly physiological characteristics and competition of anammox bacteria for wastewater treatment.
KeywordsAnammox bacteria Genome-centered omics Genome comparison Competition Niche differentiation
This study was financially supported by the National Natural Science Foundations of China (Nos. 51878008 and 91647211).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
This article does not contain any studies involving human participants or animals performed by any of the authors.
- Allard MF, Schönekess BO, Henning SL, English DR, Lopaschuk GD, Allard F, Schonekess B, Tg A (1994) Contribution of oxidative metabolism and glycolysis to ATP production in hypertrophied hearts. Am J Physiol Heart Circ Physiol 267:H742–H750. https://doi.org/10.1152/ajpheart.1994.267.2.H742 CrossRefGoogle Scholar
- APHA (1995) Standard methods for the examination of water and wastewater, 19th edn. American Public Health Association, New YorkGoogle Scholar
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336. https://doi.org/10.1038/nmeth.f.303 CrossRefGoogle Scholar
- Hira D, Toh H, Migita CT, Okubo H, Nishiyama T, Hattori M, Furukawa K, Fujii T (2012) Anammox organism KSU-1 expresses a NirK-type copper-containing nitrite reductase instead of a NirS-type with cytochrome cd1. FEBS Lett 586(11):1658–1663. https://doi.org/10.1016/j.febslet.2012.04.041 CrossRefGoogle Scholar
- John JSt (2011) SeqPrep: tool for stripping adaptors and/or merging paired reads with overlap into single reads. Available at https://github.com/jstjohn/SeqPrep. Accessed Oct 2018
- Kartal B, Rattray J, Niftrik LAVA, van de Vossenberg JC, Schmid MI, Webb R, Stefan Schouten A, Fuerst J, Sinninghe Damsté JSM, Jetten M, Strous M (2007) Candidatus ‘Anammoxoglobus propionicusʼ a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria. Syst Appl Microbiol 30:39–49. https://doi.org/10.1016/j.syapm.2006.03.004 CrossRefGoogle Scholar
- Kartal B, Van Niftrik L, Rattray J, Van De Vossenberg JLCM, Schmid MC, Sinninghe Damsté J, Jetten MSM, Strous M (2008) Candidatus ‘Brocadia fulgidaʼ: An autofluorescent anaerobic ammonium oxidizing bacterium. FEMS Microbiol Ecol 63:46–55. https://doi.org/10.1111/j.1574-6941.2007.00408.x CrossRefGoogle Scholar
- Laureni M, Falås P, Robin O, Wick A, Weissbrodt DG, Nielsen JL, Ternes TA, Morgenroth E, Joss A (2016) Mainstream partial nitritation and anammox: Long-term process stability and effluent quality at low temperatures. Water Res 101:628–639. https://doi.org/10.1016/j.watres.2016.05.005 CrossRefGoogle Scholar
- Liu W, Yang D, Chen W, Gu X (2017) High-throughput sequencing-based microbial characterization of size fractionated biomass in an anoxic anammox reactor for low-strength wastewater at low temperatures. Bioresour Technol 231:45–52. https://doi.org/10.1016/j.biortech.2017.01.050 CrossRefGoogle Scholar
- Ljungdhal LG (1986) The autotrophic pathway of acetate synthesis in acetogenic bacteria. Annu Rev Microbiol 40:415–450. https://doi.org/10.1146/annurev.mi.40.100186.002215 CrossRefGoogle Scholar
- Oshiki M, Mizuto K, Kimura ZI, Kindaichi T, Satoh H, Okabe S (2017) Genetic diversity of marine anaerobic ammonium-oxidizing bacteria as revealed by genomic and proteomic analyses of ‘Candidatus Scalindua japonicaʼ. Environ Microbiol Rep 9:550–561. https://doi.org/10.1111/1758-2229.12586 CrossRefGoogle Scholar
- Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, Le Paslier D (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790–794. https://doi.org/10.1038/nature04647 CrossRefGoogle Scholar
- Wang D, Wang G, Yang F, Liu C, Kong L, Liu Y (2018) Treatment of municipal sewage with low carbon-to-nitrogen ratio via simultaneous partial nitrification, anaerobic ammonia oxidation, and denitrification (SNAD) in a non-woven rotating biological contactor. Chemosphere 208:854–861. https://doi.org/10.1016/j.chemosphere.2018.06.061 CrossRefGoogle Scholar
- Zhao Y, Liu S, Jiang B, Feng Y, Zhu T, Tao H, Tang X, Liu S (2018b) Genome-centered metagenomics analysis reveals the symbiotic organisms possessing ability to cross-feed with anammox bacteria in anammox consortia. Environ Sci Technol 52:11285–11296. https://doi.org/10.1021/acs.est.8b02599 CrossRefGoogle Scholar
- Zhou X, Liu X, Huang S, Cui B, Liu Z, Yang Q (2018) Total inorganic nitrogen removal during the partial/complete nitrification for treating domestic wastewater: removal pathways and main influencing factors. Bioresour Technol 256:285–294. https://doi.org/10.1016/j.biortech.2018.01.131 CrossRefGoogle Scholar