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Meng S, Peng T, Wang H, Huang T, Gu JD, Hu Z. Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments. Appl Microbiol Biotechnol 2022; 106:5811-5822. [PMID: 35941255 DOI: 10.1007/s00253-022-12104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2-, and NO3-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2-, and NO3- are important shapers of nitrifier communities in mangroves.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China.,Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China.
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Gantt SE, McMurray SE, Stubler AD, Finelli CM, Pawlik JR, Erwin PM. Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges. MICROBIOME 2019; 7:124. [PMID: 31466521 PMCID: PMC6716902 DOI: 10.1186/s40168-019-0739-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO4, NOx, NH4) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart). RESULTS Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO4, and NOx flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH4 flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH4 flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum. CONCLUSIONS Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.
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Affiliation(s)
- Shelby E Gantt
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Steven E McMurray
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Amber D Stubler
- Biology Department, Occidental College, 1600 Campus Road, Los Angeles, CA, 90041, USA
| | - Christopher M Finelli
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Joseph R Pawlik
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Patrick M Erwin
- Center for Marine Science and Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28409, USA.
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Monteiro M, Séneca J, Magalhães C. The history of aerobic ammonia oxidizers: from the first discoveries to today. J Microbiol 2014; 52:537-47. [PMID: 24972807 DOI: 10.1007/s12275-014-4114-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 12/31/2022]
Abstract
Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.
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Affiliation(s)
- Maria Monteiro
- EcoBioTec Laboratory, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, P 4050-123, Porto, Portugal
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Liu W, Li L, Khan MA, Zhu F. Popular molecular markers in bacteria. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2012. [DOI: 10.3103/s0891416812030056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Junier P, Molina V, Dorador C, Hadas O, Kim OS, Junier T, Witzel JP, Imhoff JF. Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment. Appl Microbiol Biotechnol 2010; 85:425-40. [PMID: 19830422 PMCID: PMC2802487 DOI: 10.1007/s00253-009-2228-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 08/28/2009] [Accepted: 08/28/2009] [Indexed: 12/17/2022]
Abstract
The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.
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Affiliation(s)
- Pilar Junier
- Laboratory of Microbial Ecology, University of Neuchatel, Neuchatel, Switzerland.
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Physiological and molecular biological characteristics of heterotrophic ammonia oxidation by Bacillus sp. LY. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0336-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Junier P, Kim OS, Junier T, Ahn TS, Imhoff JF, Witzel KP. Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon. Appl Microbiol Biotechnol 2009; 83:175-88. [PMID: 19274459 PMCID: PMC2845890 DOI: 10.1007/s00253-009-1923-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 02/17/2009] [Accepted: 02/17/2009] [Indexed: 01/03/2023]
Abstract
The genes and intergenic regions of the amoCAB operon were analyzed to establish their potential as molecular markers for analyzing ammonia-oxidizing betaproteobacterial (beta-AOB) communities. Initially, sequence similarity for related taxa, evolutionary rates from linear regressions, and the presence of conserved and variable regions were analyzed for all available sequences of the complete amoCAB operon. The gene amoB showed the highest sequence variability of the three amo genes, suggesting that it might be a better molecular marker than the most frequently used amoA to resolve closely related AOB species. To test the suitability of using the amoCAB genes for community studies, a strategy involving nested PCR was employed. Primers to amplify the whole amoCAB operon and each individual gene were tested. The specificity of the products generated was analyzed by denaturing gradient gel electrophoresis, cloning, and sequencing. The fragments obtained showed different grades of sequence identity to amoCAB sequences in the GenBank database. The nested PCR approach provides a possibility to increase the sensitivity of detection of amo genes in samples with low abundance of AOB. It also allows the amplification of the almost complete amoA gene, with about 300 bp more sequence information than the previous approaches. The coupled study of all three amo genes and the intergenic spacer regions that are under different selection pressure might allow a more detailed analysis of the evolutionary processes, which are responsible for the differentiation of AOB communities in different habitats.
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Affiliation(s)
- Pilar Junier
- Ecole Polytechnique Fédérale de Lausanne (EPFL ENAC ISTE EML), CE 1 644 (Centre Est), Station 6, 1015 Lausanne, Switzerland.
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Park JJ, Byun IG, Park SR, Park TJ. Nitrifying bacterial communities and its activities in aerobic biofilm reactors under different temperature conditions. KOREAN J CHEM ENG 2008. [DOI: 10.1007/s11814-008-0238-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Park JJ, Park SR, Ju DJ, An JK, Byun IG, Park TJ. Application of spent sulfidic caustics for autotrophic denitrification in a MLE process and their microbial characteristics by fluorescence in situ hybridization. KOREAN J CHEM ENG 2008. [DOI: 10.1007/s11814-008-0091-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Junier P, Kim OS, Molina V, Limburg P, Junier T, Imhoff JF, Witzel KP. Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria. FEMS Microbiol Ecol 2008; 64:141-52. [PMID: 18248438 DOI: 10.1111/j.1574-6941.2007.00437.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study.
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Affiliation(s)
- Pilar Junier
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
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Ida T, Kugimiya M, Kogure M, Takahashi R, Tokuyama T. Phylogenetic relationships among ammonia-oxidizing bacteria as revealed by gene sequences of glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase. J Biosci Bioeng 2005; 99:569-76. [PMID: 16233833 DOI: 10.1263/jbb.99.569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 03/11/2005] [Indexed: 11/17/2022]
Abstract
The three previously recognized genera of 'Nitrosolobus', Nitrosospira and 'Nitrosovibrio' were combined into one genus, Nitrosospira, on the basis of 16S rDNA sequence similarities. However, this classification has been controversial for some time, since the marked differences in their shapes suggest that they are not closely related. In this study, the phylogenetic analyses of the three groups using two genotypical markers, glyceraldehyde-3-phosphate dehydrogenase (GAP, gap), and 3-phosphoglycerate kinase (PGK, pgk), were performed. In the phylogenetic tree inferred from gap and pgk, the three genera appeared as clearly separated clusters. This is the first study of markers that are able to reveal the precise phylogenetic relationship among 'Nitrosolobus', Nitrosospira and 'Nitrosovibrio'.
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Affiliation(s)
- Takeshi Ida
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
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