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Lawson CE, Lücker S. Complete ammonia oxidation: an important control on nitrification in engineered ecosystems? Curr Opin Biotechnol 2018; 50:158-165. [PMID: 29414055 DOI: 10.1016/j.copbio.2018.01.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/09/2018] [Accepted: 01/15/2018] [Indexed: 11/17/2022]
Abstract
Nitrification has long been considered to be mediated by two distinct microbial guilds, the ammonia-oxidizing bacteria and archaea, and the nitrite-oxidizing bacteria. The process has been widely applied as an environmental biotechnology for ammonium removal during water and wastewater treatment. Recently, bacteria capable of complete nitrification of ammonia to nitrate (a process termed complete ammonia oxidation, or comammox) have been discovered. These novel nitrifiers have been identified in a range of engineered, natural freshwater and terrestrial ecosystems, challenging previously held knowledge on the key microorganisms and biochemical pathways controlling nitrification. This paper discusses the distribution of comammox bacteria with a focus on engineered ecosystems, as well as emerging insights from recent genomic and experimental studies on their ecophysiology.
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Affiliation(s)
- Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
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353
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Cáceres R, Malińska K, Marfà O. Nitrification within composting: A review. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 72:119-137. [PMID: 29153903 DOI: 10.1016/j.wasman.2017.10.049] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 10/24/2017] [Accepted: 10/28/2017] [Indexed: 05/23/2023]
Abstract
Composting could be regarded as a process of processes because it entails a number of complex chemical and microbiological reactions and transformations. Nitrification is one of such processes that normally takes place during the curing phase. This process has been studied in detail for wastewater treatment, and it is becoming an extensively studied topic within composting. In the past, nitrate presence in compost has been clearly perceived as a maturation indicator; however, nowadays, nitrate formation is also conceived as a way of conserving nitrogen in compost. Nitrification is a process closely linked to other processes such as ammonification and the possible loss of ammonia (NH3). Nitrification is defined as conversion of the most reduced form of nitrogen (NH3) to its most oxidized form (i.e. nitrate) and it is performed in two steps which are carried out by two different groups of microorganisms: the ammonia-oxidizing bacteria or archaea (AOB/AOA) and the nitrite-oxidizing bacteria (NOB). The objectives of this review are: a) to gather relevant information on nitrification, which can specifically occur during composting, b) to outline ultimate findings described by the literature in order to increase the understanding and the application of nitrification within composting, and c) to outline future research direction.
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Affiliation(s)
- Rafaela Cáceres
- GIRO Unit, Institute of Agriculture and Food Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain.
| | - Krystyna Malińska
- Institute of Environmental Engineering, Częstochowa University of Technology, Brzeźnicka 60A, 42-200 Częstochowa, Poland
| | - Oriol Marfà
- GIRO Unit, Institute of Agriculture and Food Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
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354
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Ushiki N, Fujitani H, Shimada Y, Morohoshi T, Sekiguchi Y, Tsuneda S. Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity. Front Microbiol 2018; 8:2637. [PMID: 29375506 PMCID: PMC5767232 DOI: 10.3389/fmicb.2017.02637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/18/2017] [Indexed: 02/02/2023] Open
Abstract
The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira, we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10–C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira.
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Affiliation(s)
- Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yu Shimada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, Tochigi, Japan
| | - Yuji Sekiguchi
- Bio-Measurement Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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355
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Laanbroek HJ, Veenhuizen PTM, Keijzer RM, Hefting MM. Numerical Relationships Between Archaeal and Bacterial amoA Genes Vary by Icelandic Andosol Classes. MICROBIAL ECOLOGY 2018; 75:204-215. [PMID: 28707145 PMCID: PMC5742608 DOI: 10.1007/s00248-017-1032-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/30/2017] [Indexed: 05/26/2023]
Abstract
Bacterial amoA genes had not been detectable by qPCR in freshly sampled Icelandic Andosols thus far. Hence, a new primer set yielding shorter gene fragments has been designed to verify the absence of ammonia-oxidizing bacteria in different Icelandic Andosol classes. At the same time, a new primer set was also constructed for archaeal amoA genes that should improve the quality of PCR products. Although a large part of the soil samples were found to be amoA-negative, bacterial amoA genes were detectable with new as well as old primer sets. The same results were obtained for the archaeal amoA genes. The relative distribution of archaeal and bacterial amoA genes varied between Andosol classes. Archaeal amoA genes were significantly more abundant in Brown than in Histic Andosols, while the opposite was observed for bacterial amoA genes. The numbers of archaeal and bacterial amoA genes in Gleyic Andosols were not significantly different from those in Histic and Brown Andosols. The numbers of bacterial amoA genes, but not the numbers of archaeal amoA genes, correlated significantly and positively with potential ammonia oxidation activities. The presence of the bacterial nitrification inhibitor allylthiourea inhibited the potential ammonia oxidation activities during the first 12 h of incubation. Hence, it was concluded that ammonia-oxidizing bacteria profited most from the conditions during the measurements of potential ammonia oxidation activities.
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Affiliation(s)
- Hendrikus J Laanbroek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands.
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands.
| | - Peter T M Veenhuizen
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Rosalinde M Keijzer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, the Netherlands
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
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356
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Semblante GU, Phan HV, Hai FI, Xu ZQ, Price WE, Nghiem LD. The role of microbial diversity and composition in minimizing sludge production in the oxic-settling-anoxic process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:558-567. [PMID: 28704678 DOI: 10.1016/j.scitotenv.2017.06.253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
The oxic-settling-anoxic (OSA) process, which involves an aerobic tank attached to oxygen- and substrate-deficient external anoxic reactors, minimizes sludge production in biological wastewater treatment. In this study, the microbial community structure of OSA was determined. Principal coordinate analysis showed that among the three operational factors, i.e., (i) redox condition, (ii) external reactor sludge retention time (SRText), and (iii) sludge interchange between aerobic and anoxic reactors, redox condition had the greatest impact on microbial diversity. Generally, reactors with lower oxidation-reduction potential had higher microbial diversity. The main aerobic sequencing batch reactor of OSA (SBROSA) that interchanged sludge with an external anoxic reactor had greater microbial diversity than SBRcontrol which did not have sludge interchange. SBROSA sustained high abundance of the slow-growing nitrifying bacteria (e.g., Nitrospirales and Nitrosomondales) and consequently exhibited reduced sludge yield. Specific groups of bacteria facilitated sludge autolysis in the external reactors. Hydrolyzing (e.g., Bacteroidetes and Chloroflexi) and fermentative (e.g., Firmicutes) bacteria, which can break down cellular matter, proliferated in both the external aerobic/anoxic and anoxic reactors. Sludge autolysis in the anoxic reactor was enhanced with the increase of predatory bacteria (e.g., order Myxobacteriales and genus Bdellovibrio) that can contribute to biomass decay. Furthermore, β- and γ-Proteobacteria were identified as the bacterial phyla that primarily underwent decay in the external reactors.
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Affiliation(s)
- Galilee U Semblante
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Hop V Phan
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Faisal I Hai
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - Zhi-Qiang Xu
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - William E Price
- Strategic Water Infrastructure Laboratory, School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Long D Nghiem
- Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
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357
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Chen H, Li A, Cui D, Wang Q, Wu D, Cui C, Ma F. N-Acyl-homoserine lactones and autoinducer-2-mediated quorum sensing during wastewater treatment. Appl Microbiol Biotechnol 2017; 102:1119-1130. [DOI: 10.1007/s00253-017-8697-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/16/2022]
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358
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Han S, Luo X, Liao H, Nie H, Chen W, Huang Q. Nitrospira are more sensitive than Nitrobacter to land management in acid, fertilized soils of a rapeseed-rice rotation field trial. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 599-600:135-144. [PMID: 28475907 DOI: 10.1016/j.scitotenv.2017.04.086] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/04/2017] [Accepted: 04/09/2017] [Indexed: 06/07/2023]
Abstract
Nitrite oxidation is recognized as an essential process of biogeochemical nitrogen cycling in agricultural ecosystems. How nitrite-oxidizing bacteria (NOB) respond to land managements (the effect from the long-term straw incorporation and environmental variability caused by the shift from the upland stage to the paddy stage) in a rapeseed-rice rotation field remains unclear. We found the nitrite oxidation (NO) in soils increased from the upland stage to the paddy stage. An inhibitory effect of the long-term straw incorporation on NO was detectable in the upland stage. The abundance of Nitrospira was always greater than Nitrobacter, and it was affected by the rice-growing and straw incorporation while Nitrobacter was not. NO correlated positively with the abundance of Nitrospira and with soluble sulfate (SO42-), soil moisture, pH and NH4+. The high-throughput sequencing analysis of the nitrite oxidoreductase nxrA and nxrB genes for Nitrobacter- and Nitrospira-like NOB was performed respectively. The dominating (relative abundance>1%) operational taxonomic units (OTUs) from Nitrobacter were closely related to Nitrobacter hamburgensis, whereas those from Nitrospira were affiliated with or related to lineage II, lineage V and several unknown groups. Heatmap analysis showed that a few dominant Nitrobacter OTUs were affected by the straw treatment or the rice-growing, and half of the dominant Nitrospira ones were explained by at least one of the variables. Multi-response permutation procedure (MRPP) and redundancy analyses showed that the Nitrospira-like NOB community changes were significantly shaped by the land managements and the soil chemical properties, including pH, moisture and NH4+, whereas that of the Nitrobacter-like NOB community was not. These results suggested that Nitrospira are more sensitive than Nitrobacter to land management in acid and fertilized soils of a rapeseed-rice rotation field trial.
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Affiliation(s)
- Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailing Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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359
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Füssel J, Lücker S, Yilmaz P, Nowka B, van Kessel MAHJ, Bourceau P, Hach PF, Littmann S, Berg J, Spieck E, Daims H, Kuypers MMM, Lam P. Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus. SCIENCE ADVANCES 2017; 3:e1700807. [PMID: 29109973 PMCID: PMC5665590 DOI: 10.1126/sciadv.1700807] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 10/13/2017] [Indexed: 05/22/2023]
Abstract
Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences.
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Affiliation(s)
- Jessika Füssel
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, UK
| | - Sebastian Lücker
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Pelin Yilmaz
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Boris Nowka
- Section Microbiology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Patric Bourceau
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Philipp F. Hach
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jasmine Berg
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Eva Spieck
- Section Microbiology, Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | | | - Phyllis Lam
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton SO14 3ZH, UK
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360
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Speirs LBM, Dyson ZA, Tucci J, Seviour RJ. Eikelboom filamentous morphotypes 0675 and 0041 embrace members of the Chloroflexi: resolving their phylogeny, and design of fluorescence in situ hybridisation probes for their identification. FEMS Microbiol Ecol 2017; 93:4107108. [DOI: 10.1093/femsec/fix115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/05/2017] [Indexed: 11/13/2022] Open
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361
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Adaptation of soil nitrifiers to very low nitrogen level jeopardizes the efficiency of chemical fertilization in west african moist savannas. Sci Rep 2017; 7:10275. [PMID: 28860500 PMCID: PMC5578973 DOI: 10.1038/s41598-017-10185-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/07/2017] [Indexed: 12/05/2022] Open
Abstract
The moist savanna zone covers 0.5 × 106 km2 in West Africa and is characterized by very low soil N levels limiting primary production, but the ecology of nitrifiers in these (agro)ecosystems is largely unknown. We compared the effects of six agricultural practices on nitrifier activity, abundance and diversity at nine sites in central Ivory Coast. Treatments, including repeated fertilization with ammonium and urea, had no effect on nitrification and crop N status after 3 to 5 crop cycles. Nitrification was actually higher at low than medium ammonium level. The nitrifying community was always dominated by ammonia oxidizing archaea and Nitrospira. However, the abundances of ammonia oxidizing bacteria, AOB, and Nitrobacter increased with fertilization after 5 crop cycles. Several AOB populations, some affiliated to Nitrosospira strains with urease activity or adapted to fluctuating ammonium levels, emerged in fertilized plots, which was correlated to nitrifying community ability to benefit from fertilization. In these soils, dominant nitrifiers adapted to very low ammonium levels have to be replaced by high-N nitrifiers before fertilization can stimulate nitrification. Our results show that the delay required for this replacement is much longer than ever observed for other terrestrial ecosystems, i.e. > 5 crop cycles, and demonstrate for the first time that nitrifier characteristics jeopardize the efficiency of fertilization in moist savanna soils.
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362
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Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature 2017; 549:269-272. [PMID: 28847001 PMCID: PMC5600814 DOI: 10.1038/nature23679] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/28/2017] [Indexed: 01/31/2023]
Abstract
Nitrification, the oxidation of ammonia (NH3) via nitrite
(NO2-) to nitrate (NO3-), is a
key process of the biogeochemical nitrogen cycle. For decades, ammonia and
nitrite oxidation were thought to be separately catalyzed by ammonia-oxidizing
bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The
recent discovery of complete ammonia oxidizers (comammox) in the NOB genus
Nitrospira1,2, which alone convert ammonia to nitrate,
raised questions about the ecological niches where comammox
Nitrospira successfully compete with canonical nitrifiers.
Here we isolated the first pure culture of a comammox bacterium,
Nitrospira inopinata, and show that it is adapted to slow
growth in oligotrophic and dynamic habitats based on a high affinity for
ammonia, low maximum rate of ammonia oxidation, high growth yield compared to
canonical nitrifiers, and genomic potential for alternative metabolisms. The
nitrification kinetics of four AOA from soil and hot springs were determined for
comparison. Their surprisingly poor substrate affinities and lower growth yields
reveal that, in contrast to earlier assumptions, not all AOA are most
competitive in strongly oligotrophic environments and that N.
inopinata has the highest substrate affinity of all analyzed
ammonia oxidizer isolates except the marine AOA Nitrosopumilus
maritimus SCM13. These
results suggest a role of comammox organisms for nitrification under
oligotrophic and dynamic conditions.
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363
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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364
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Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment. Appl Environ Microbiol 2017; 83:AEM.00549-17. [PMID: 28500038 DOI: 10.1128/aem.00549-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km ) and the generation time were determined to be 25 μM NO2- and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of NitrotogaIMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.
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365
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Kinnunen M, Gülay A, Albrechtsen HJ, Dechesne A, Smets BF. Nitrotogais selected overNitrospirain newly assembled biofilm communities from a tap water source community at increased nitrite loading. Environ Microbiol 2017; 19:2785-2793. [DOI: 10.1111/1462-2920.13792] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Marta Kinnunen
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Arda Gülay
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Hans-Jørgen Albrechtsen
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
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366
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Coskun D, Britto DT, Shi W, Kronzucker HJ. Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition. NATURE PLANTS 2017; 3:17074. [PMID: 28585561 DOI: 10.1038/nplants.2017.74] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/25/2017] [Indexed: 05/20/2023]
Abstract
The nitrogen (N)-use efficiency of agricultural plants is notoriously poor. Globally, about 50% of the N fertilizer applied to cropping systems is not absorbed by plants, but lost to the environment as ammonia (NH3), nitrate (NO3-), and nitrous oxide (N2O, a greenhouse gas with 300 times the heat-trapping capacity of carbon dioxide), raising agricultural production costs and contributing to pollution and climate change. These losses are driven by volatilization of NH3 and by a matrix of nitrification and denitrification reactions catalysed by soil microorganisms (chiefly bacteria and archaea). Here, we discuss mitigation of the harmful and wasteful process of agricultural N loss via biological nitrification inhibitors (BNIs) exuded by plant roots. We examine key recent discoveries in the emerging field of BNI research, focusing on BNI compounds and their specificity and transport, and discuss prospects for their role in improving agriculture while reducing its environmental impact.
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Affiliation(s)
- Devrim Coskun
- Department of Biological Sciences and Canadian Centre for World Hunger Research (CCWHR), University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Dev T Britto
- Department of Biological Sciences and Canadian Centre for World Hunger Research (CCWHR), University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Herbert J Kronzucker
- Department of Biological Sciences and Canadian Centre for World Hunger Research (CCWHR), University of Toronto, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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367
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Wang Y, Ma L, Mao Y, Jiang X, Xia Y, Yu K, Li B, Zhang T. Comammox in drinking water systems. WATER RESEARCH 2017; 116:332-341. [PMID: 28390307 DOI: 10.1016/j.watres.2017.03.042] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 03/18/2017] [Accepted: 03/18/2017] [Indexed: 05/04/2023]
Abstract
The discovery of complete ammonia oxidizer (comammox) has fundamentally upended our perception of the global nitrogen cycle. Here, we reported four metagenome assembled genomes (MAGs) of comammox Nitrospira that were retrieved from metagenome datasets of tap water in Singapore (SG-bin1 and SG-bin2), Hainan province, China (HN-bin3) and Stanford, CA, USA (ST-bin4). Genes of phylogenetically distinct ammonia monooxygenase subunit A (amoA) and hydroxylamine dehydrogenase (hao) were identified in these four MAGs. Phylogenetic analysis based on ribosomal proteins, AmoA, hao and nitrite oxidoreductase (subunits nxrA and nxrB) sequences indicated their close relationships with published comammox Nitrospira. Canonical ammonia-oxidizing microbes (AOM) were also identified in the three tap water samples, ammonia-oxidizing bacteria (AOB) in Singapore's and Stanford's samples and ammonia-oxidizing archaea (AOA) in Hainan's sample. The comammox amoA-like sequences were also detected from some other drinking water systems, and even outnumbered the AOA and AOB amoA-like sequences. The findings of MAGs and the occurrences of AOM in different drinking water systems provided a significant clue that comammox are widely distributed in drinking water systems.
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Affiliation(s)
- Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Liping Ma
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Ke Yu
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong.
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368
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Alfreider A, Baumer A, Bogensperger T, Posch T, Salcher MM, Summerer M. CO 2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs. Environ Microbiol 2017; 19:2754-2768. [PMID: 28474482 PMCID: PMC5619642 DOI: 10.1111/1462-2920.13786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 11/23/2022]
Abstract
While mechanisms of different carbon dioxide (CO2) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO2 fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.
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Affiliation(s)
- Albin Alfreider
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andreas Baumer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M Salcher
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Monika Summerer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
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369
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Miao Y, Zhang L, Li B, Zhang Q, Wang S, Peng Y. Enhancing ammonium oxidizing bacteria activity was key to single-stage partial nitrification-anammox system treating low-strength sewage under intermittent aeration condition. BIORESOURCE TECHNOLOGY 2017; 231:36-44. [PMID: 28192724 DOI: 10.1016/j.biortech.2017.01.045] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/21/2017] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
Intermittent aeration and bio-augmentation were integrated to enhance single-stage partial nitrification-anammox (SPN/A) stability over 235-day operational period treating low-strength sewage. The effect of bio-augmentation sludge (with different abundances of ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB)) was determined. Partial nitrification sludge based bio-augmentation increased the total nitrogen (TN) removal efficiency from 29.1% to 70%, followed by the nitrification sludge (from 38.1% to 65.4%), then the denitrifying phosphorus sludge (from 42.1% to 54.4%). The evolution of bacteria activity and communities showed that anammox activity increased with the enhancement of AOB activity, and higher AOB abundance led to higher anammox bacterial abundance despite high NOB abundance. The enhancement of AOB activity produced more nitrite, anammox bacteria gained more nitrite than NOB since intermittent aeration selectively inhibited NOB, thus the reactor stability enhanced substantially. This study highlights the significance of enhancing AOB activity to ensure long-term operational stability of SPN/A processes.
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Affiliation(s)
- Yuanyuan Miao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Baikun Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Qian Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Simeng Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China.
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370
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Stein LY. Accessories make the microbe. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:21-22. [PMID: 27775875 DOI: 10.1111/1758-2229.12492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6H 2E9, Canada
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371
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Bartelme RP, McLellan SL, Newton RJ. Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira. Front Microbiol 2017; 8:101. [PMID: 28194147 PMCID: PMC5276851 DOI: 10.3389/fmicb.2017.00101] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/13/2017] [Indexed: 01/04/2023] Open
Abstract
Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while supporting multiple ammonia oxidation lifestyles within the nitrifying consortium.
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Affiliation(s)
- Ryan P Bartelme
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
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372
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Fan XY, Gao JF, Pan KL, Li DC, Dai HH. Temporal dynamics of bacterial communities and predicted nitrogen metabolism genes in a full-scale wastewater treatment plant. RSC Adv 2017. [DOI: 10.1039/c7ra10704h] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dynamics of bacterial communities and nitrogen metabolism genes in a full-scale WWTP as revealed by Illumina sequencing and PICRUSt.
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Affiliation(s)
- Xiao-Yan Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Kai-Ling Pan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology
- Beijing University of Technology
- Beijing 100124
- China
| | - Hui-Hui Dai
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology
- Beijing University of Technology
- Beijing 100124
- China
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373
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Kartal B, Keltjens JT. Anammox Biochemistry: a Tale of Heme c Proteins. Trends Biochem Sci 2016; 41:998-1011. [DOI: 10.1016/j.tibs.2016.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
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374
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Levipan HA, Molina V, Anguita C, Rain-Franco A, Belmar L, Fernandez C. Variability of nitrifying communities in surface coastal waters of the Eastern South Pacific (∼36° S). ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:851-864. [PMID: 27487247 DOI: 10.1111/1758-2229.12448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/06/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
We report the seasonal and single-diurnal variability of potentially active members of the prokaryote community in coastal surface waters off central Chile and the relationship between nitrifiers and solar radiation by combining 16S cDNA-based pyrosequencing, RT-qPCR of specific gene markers for nitrifiers (amoA, for general AOA, AOA-A, AOA-B, Nitrosopumilus maritimus and beta-AOB; and 16S rRNA gene for Nitrospina-like NOB), and solar irradiance measurements. We also evaluated the effects of artificial UVA-PAR and PAR spectra on nitrifiers by RT-qPCR. All nitrifiers (except AOA-B ecotype) were detected via RT-qPCR but AOA was the only group detected by pyrosequencing. Results showed high variability in their transcriptional levels during the day which could be associated to sunlight intensity thresholds in winter although AOA and Nitrospina-like NOB transcript number were also potentially related with environmental substrate availability. Only N. maritimus amoA transcripts showed a significant negative correlation with solar irradiances in both periods. During spring-summer, Nitrospina transcripts decreased at higher sunlight intensities, whereas the opposite was found during winter under natural (in situ) and artificial light experiments. In summary, a nitrifying community with variable tolerance to solar radiation is responsible for daily nitrification, and was particularly diverse during winter in the study area.
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Affiliation(s)
- Héctor A Levipan
- Programa de Postgrados en Oceanografía, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Chile, Valparaíso
- Interdisciplinary Center for Aquaculture Research (INCAR), Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
| | - Verónica Molina
- Programa de Biodiversidad and Departamento de Biología. Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Avda. Leopoldo Carvallo 270, Playa Ancha, Valparaíso, Chile
| | - Cristóbal Anguita
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Chile, Valparaíso
| | - Angel Rain-Franco
- Programa de Postgrados en Oceanografía, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
| | - Lucy Belmar
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Camila Fernandez
- Interdisciplinary Center for Aquaculture Research (INCAR), Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
- COPAS SUR-AUSTRAL, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, Banyuls/Mer, F-66650, France
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