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Xin Y, Gao Q, Chen X, Sun S, Liu J, Gao H, Zhou J, Xia X. High biological N fixation potential dominated by heterotrophic diazotrophs in alpine permafrost rivers on the Qinghai‒Tibet Plateau. WATER RESEARCH 2024; 264:122239. [PMID: 39137482 DOI: 10.1016/j.watres.2024.122239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/02/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
Biological nitrogen (N) fixation is a pivotal N source in N-deficient ecosystems. The Qinghai‒Tibet Plateau (QTP) region, which is assumed to be N limited and suboxic, is an ideal habitat for diazotrophs. However, the diazotrophic communities and associated N fixation rates in these high-altitude alpine permafrost QTP rivers remain largely unknown. Herein, we examined diazotrophic communities in the sediment and biofilm of QTP rivers via the nitrogenase (nifH) gene sequencing and assessed their N fixing activities via a 15N isotope incubation assay. Strikingly, anaerobic heterotrophic diazotrophs, such as sulfate- and iron-reducing bacteria, had emerged as dominant N fixers. Remarkably, the nifH gene abundance and N fixation rates increased with altitude, and the average nifH gene abundance (2.57 ± 2.60 × 108 copies g-1) and N fixation rate (2.29 ± 3.36 nmol N g-1d-1) surpassed that documented in most aquatic environments (nifH gene abundance: 1.31 × 105 ∼ 2.57 × 108 copies g-1, nitrogen fixation rates: 2.34 × 10-4 ∼ 4.11 nmol N g-1d-1). Such distinctive heterotrophic diazotrophic communities and high N fixation potential in QTP rivers were associated with low-nitrogen, abundant organic carbon and unique C:N:P stoichiometries. Additionally, the significant presence of psychrophilic bacteria within the diazotrophic communities, along with the enhanced stability and complexity of the diazotrophic networks at higher altitudes, clearly demonstrate the adaptability of diazotrophic communities to extreme cold and high-altitude conditions in QTP rivers. We further determined that altitude, coupled with organic carbon and phosphorus, was the predominant driver shaping diazotrophic communities and their N-fixing activities. Overall, our study reveals high N fixation potential in N-deficient QTP rivers, which provides novel insights into nitrogen dynamics in alpine permafrost rivers.
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Affiliation(s)
- Yuan Xin
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qun Gao
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Xin Chen
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Siyue Sun
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jiao Liu
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hui Gao
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA; School of Biological Sciences, University of Oklahoma, Norman, OK 73019, USA; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; School of Computer Science, University of Oklahoma, Norman, OK, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xinghui Xia
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
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Zhao W, Gu J, Wang X, Song Z, Hu T, Dai X, Wang J. Insights into the associations of copper and zinc with nitrogen metabolism during manure composting with shrimp shell powder. BIORESOURCE TECHNOLOGY 2022; 349:126431. [PMID: 34861387 DOI: 10.1016/j.biortech.2021.126431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/16/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) on heavy metal resistance genes (MRGs), nitrogen functional genes, enzymes, and microorganisms. SSP inhibited nitrification and denitrification via decreasing the abundances of functional genes and key enzymes related to Cu, Zn, and MRGs. The nitrate reductase and nitrous-oxide reductase in the denitrification pathway were lower under H. Phylogenetic trees indicated that Burkholderiales sp. had strong relationships with OTU396 and OTU333, with important roles in the nitrogen cycle and plant growth. Redundancy analysis and structural equation modeling showed the complex response between heavy metal and nitrogen that bio-Cu and bio-Zn had positive significantly relationships with nirK-type and amoA-type bacteria, and amoA-type bacteria might be hotspot of cueO.
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Affiliation(s)
- Wenya Zhao
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Ting Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaoxia Dai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jia Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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Tian L, Yan Z, Wang C, Xu S, Jiang H. Habitat heterogeneity induces regional differences in sediment nitrogen fixation in eutrophic freshwater lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145594. [PMID: 33770866 DOI: 10.1016/j.scitotenv.2021.145594] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Biological nitrogen fixation (BNF) in sediments is an important source of bioavailable nitrogen in aquatic systems. However, the effect of habitat change caused by eutrophication on nitrogen fixation within sediments is still unclear. In this study, nitrogen fixation rates and diazotroph diversities in sediments with heterogeneous ecological status in one eutrophic lake were investigated by using an isotope tracer method and sequencing of nitrogen-fixing (nif) genes. The results showed that both nitrogenase activity (NA) and nifH abundance in sediments of blooms area were higher than those in vegetation-dominated habitats. Correlation analysis showed that NA was correlated closely to nifH abundance, dissolved sulfide, and iron. The diazotrophic assemblage contained mainly Proteobacterial sequences belonging to Cluster I and III, and the variations of diazotrophic community could be explained by total nitrogen content, total phosphorus content, organic matters, sulfides, ammonium and iron content. Moreover, the co-occurrence network analysis showed the Alphaproteobacteria shaped the major interactions in diazotrophic community, and sediment properties had stronger effect on diazotrophic community in cyanobacteria-dominated habitat. This study revealed that habitat heterogeneity in eutrophic lakes shaped different succession of BNF in sediments and cyanobacterial blooms significantly improved the nitrogen-fixing activity in sediments, which broadened our understanding of nitrogen cycle and nutrient management in eutrophic freshwater lakes.
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Affiliation(s)
- Linqi Tian
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shengqi Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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Toussaint E, De Borger E, Braeckman U, De Backer A, Soetaert K, Vanaverbeke J. Faunal and environmental drivers of carbon and nitrogen cycling along a permeability gradient in shallow North Sea sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144994. [PMID: 33550059 DOI: 10.1016/j.scitotenv.2021.144994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Ecosystem functions are driven by abiotic and biotic factors, but due to high collinearity of both, it is often difficult to disentangle the drivers of these ecosystem functions. We studied sedimentological and faunal controls of benthic organic matter mineralization, a crucial ecosystem process provided for by sediments of shelf seas. Subtidal benthic habitats representative of the wide permeability gradient found in the Belgian Part of the North Sea (Northeast Atlantic Shelf) were characterized in terms of sediment descriptors, macrofauna, and sediment biogeochemistry was estimated. Our results confirmed a strong correlation between sediment characteristics and macrofauna, and estimated sediment biogeochemical process rates were clearly linked to both. Results of variance partitioning and statistical modelling showed that oxic mineralization and nitrification were mainly regulated by faunal activities whereas anoxic mineralization was regulated by sediment properties, with permeability as a decisive factor. Both biotic and abiotic factors were needed to explain variability in oxygen consumption and total mineralization estimates, suggesting that macrofaunal activities have different effects across habitats. The statistical models were a useful tool to interpret the impact of anthropogenic activities in the study area and represent a step towards predicting the effects of human activities on crucial ecosystem functions.
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Affiliation(s)
- Elise Toussaint
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and Management, Rue Vautier 29, 1000 Brussels, Belgium.
| | - Emil De Borger
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Netherlands Institute of Sea Research (NIOZ), Department of Estuarine and Delta Systems,Korringaweg 7, P.O. Box 140, 4401, NT, Yerseke, the Netherlands; Utrecht University, Heidelberglaan 8, 3584, CS, Utrecht, the Netherlands
| | - Ulrike Braeckman
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium
| | - Annelies De Backer
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Aquatic Environment and Quality, Ankerstraat 1, 8400 Oostende, Belgium
| | - Karline Soetaert
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Netherlands Institute of Sea Research (NIOZ), Department of Estuarine and Delta Systems,Korringaweg 7, P.O. Box 140, 4401, NT, Yerseke, the Netherlands; Utrecht University, Heidelberglaan 8, 3584, CS, Utrecht, the Netherlands
| | - Jan Vanaverbeke
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and Management, Rue Vautier 29, 1000 Brussels, Belgium
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Cabello AM, Turk‐Kubo KA, Hayashi K, Jacobs L, Kudela RM, Zehr JP. Unexpected presence of the nitrogen-fixing symbiotic cyanobacterium UCYN-A in Monterey Bay, California. JOURNAL OF PHYCOLOGY 2020; 56:1521-1533. [PMID: 32609873 PMCID: PMC7754506 DOI: 10.1111/jpy.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/10/2020] [Indexed: 05/20/2023]
Abstract
In the last decade, the known biogeography of nitrogen fixation in the ocean has been expanded to colder and nitrogen-rich coastal environments. The symbiotic nitrogen-fixing cyanobacteria group A (UCYN-A) has been revealed as one of the most abundant and widespread nitrogen-fixers, and includes several sublineages that live associated with genetically distinct but closely related prymnesiophyte hosts. The UCYN-A1 sublineage is associated with an open ocean picoplanktonic prymnesiophyte, whereas UCYN-A2 is associated with the coastal nanoplanktonic coccolithophore Braarudosphaera bigelowii, suggesting that different sublineages may be adapted to different environments. Here, we study the diversity of nifH genes present at the Santa Cruz Municipal Wharf in the Monterey Bay (MB), California, and report for the first time the presence of multiple UCYN-A sublineages, unexpectedly dominated by the UCYN-A2 sublineage. Sequence and quantitative PCR data over an 8-year time-series (2011-2018) showed a shift toward increasing UCYN-A2 abundances after 2013, and a marked seasonality for this sublineage which was present during summer-fall months, coinciding with the upwelling-relaxation period in the MB. Increased abundances corresponded to positive temperature anomalies in MB, and we discuss the possibility of a benthic life stage of the associated coccolithophore host to explain the seasonal pattern. The dominance of UCYN-A2 in coastal waters of the MB underscores the need to further explore the habitat preference of the different sublineages in order to provide additional support for the hypothesis that UCYN-A1 and UCYN-A2 sublineages are different ecotypes.
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Affiliation(s)
- Ana M. Cabello
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
- Centro Oceanográfico de MálagaInstituto Español de OceanografíaFuengirolaMálaga29001Spain
| | - Kendra A. Turk‐Kubo
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Kendra Hayashi
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Lucien Jacobs
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Raphael M. Kudela
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
| | - Jonathan P. Zehr
- Ocean Sciences DepartmentUniversity of California, Santa CruzSanta CruzCalifornia95064USA
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Pedersen JN, Bombar D, Paerl RW, Riemann L. Diazotrophs and N 2-Fixation Associated With Particles in Coastal Estuarine Waters. Front Microbiol 2018; 9:2759. [PMID: 30505296 PMCID: PMC6250843 DOI: 10.3389/fmicb.2018.02759] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Putative heterotrophic bacteria carrying out N2-fixation, so-called non-cyanobacterial diazotrophs (NCDs), are widely distributed in marine waters, but details of how the O2-inhibited N2-fixation process is promoted in the oxic water column remains ambiguous. Here we carried out two experiments with water from a eutrophic temperate fjord to examine whether low-oxygen microenvironments within particulate organic matter could be loci suitable for N2-fixation. First, water enriched with natural particles or sediment showed higher N2-fixation rates than bulk water, and nitrogenase genes (nifH) revealed that specific diazotrophs were affiliated with the particulate matter. Second, pristine artificial surfaces were rapidly colonized by diverse bacteria, while putative diazotrophs emerged relatively late (after 80 h) during the colonization, and phylotypes related to Pseudomonas and to anaerobic bacteria became dominant with time. Our study pinpoints natural particles as sites of N2-fixation, and indicates that resuspension of sediment material can elevate pelagic N2-fixation. Moreover, we show that diverse natural diazotrophs can colonize artificial surfaces, but colonization by “pioneer” bacterioplankton that more rapidly associate with surfaces appears to be a prerequisite. Whereas our experimental study supports the idea of pelagic particles as sites of N2-fixation by heterotrophic bacteria, future in situ studies are needed in order to establish identity, activity and ecology of particle associated NCDs as a function of individual particle characteristics.
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Affiliation(s)
- Jeppe N Pedersen
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Deniz Bombar
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ryan W Paerl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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Chen R, Deng M, He X, Hou J. Enhancing Nitrate Removal from Freshwater Pond by Regulating Carbon/Nitrogen Ratio. Front Microbiol 2017; 8:1712. [PMID: 28943869 PMCID: PMC5596099 DOI: 10.3389/fmicb.2017.01712] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/24/2017] [Indexed: 11/13/2022] Open
Abstract
Nitrogen accumulation is a serious environmental problem in freshwater ponds, which can lead to massive death of fish and shrimps as well as the eutrophication. The removal of nitrate by regulating the carbon to nitrogen (C/N) ratio and the underlying mechanisms were investigated. The nitrate removal system comprised 530-mL medium containing 5 mg/L NO3−-N and 0–66.6 mg/L COD (i.e., C/N ratio of 0–13.3) and 20 g ponds sediments. When the C/N ratio was higher than 8, the nitrate removal efficiency nearly reached 100% during the incubation period and the accumulation of nitrite was negligible. When the C/N ratio was below 8, the nitrate removal efficiency was lower and significant nitrite accumulation occurred. The nitrate removal rate increased with the C/N ratio increased, which was ascribed to the increase in the absolute abundance of denitrifiers (nirS, nirK, and nosZ). Although both nirS-type and nirK-type denitrifiers were found in the sediments of freshwater pond, nirS-type denitrifiers were predominant. Dechloromonas was the major nirS-type denitrifier for nitrate removal in nirS-type with the C/N ratios above 5.33, while the majority of the nirK-type denitrifiers were unclassified. Thus, this study implied that the appropriate C/N ratio played an important role on the removal of excess nitrate from freshwater ponds.
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Affiliation(s)
- Rong Chen
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China.,School of Environmental Studies, China University of GeosciencesWuhan, China
| | - Min Deng
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China
| | - Xugang He
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceWuhan, China.,Hubei Provincial Engineering Laboratory for Pond AquacultureWuhan, China
| | - Jie Hou
- College of Fisheries, Huazhong Agricultural UniversityWuhan, China
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Preisner EC, Fichot EB, Norman RS. Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance. Front Microbiol 2016; 7:1632. [PMID: 27799927 PMCID: PMC5066559 DOI: 10.3389/fmicb.2016.01632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/30/2016] [Indexed: 11/13/2022] Open
Abstract
The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011-2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help elucidate factors connecting disturbance, biodiversity, and ecosystem function that may enhance ecosystem models.
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Affiliation(s)
| | | | - Robert S. Norman
- Department of Environmental Health Sciences, University of South Carolina, ColumbiaSC, USA
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Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers. BMC Genomics 2016; 17:155. [PMID: 26923558 PMCID: PMC4770552 DOI: 10.1186/s12864-016-2465-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/12/2016] [Indexed: 01/09/2023] Open
Abstract
Background Copper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to primer coverage limitations that can be attributed to their broad taxonomic diversity and enormous nirK sequence divergence. Therefore, we revisited reported analyses on partial NirK sequences using a taxonomically diverse, full-length NirK sequence dataset. Results Division of NirK sequences into two phylogenetically distinct clades was confirmed, with Clade I mainly comprising Alphaproteobacteria (plus some Gamma- and Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae, Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta and Gamma). Failure of currently available primer sets to target diverse NirK-type denitrifiers in environmental surveys could be attributed to mismatches over the whole length of the primer binding regions including the 3′ site, with Clade II sequences containing higher sequence divergence than Clade I sequences. Simultaneous presence of both the denitrification and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers. Conclusion The previously reported division of NirK into two distinct phylogenetic clades was confirmed using a taxonomically diverse set of full-length NirK sequences. Enormous sequence divergence of nirK gene sequences, probably due to variable nirK evolutionary trajectories, will remain an issue for covering diverse NirK-type denitrifiers in amplicon-based environmental surveys. The potential of a single organism to partition nitrate to either denitrification or dissimilatory nitrate reduction to ammonium appeared to be more widespread than originally anticipated as more than half of all NirK-type denitrifiers were shown to contain both pathways in their genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2465-0) contains supplementary material, which is available to authorized users.
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