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Peoples LM, Seixas MH, Evans KA, Bilbrey EM, Ranieri JR, Tappenbeck TH, Dore JE, Baumann A, Church MJ. Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake. Environ Microbiol 2024; 26:e16616. [PMID: 38517638 DOI: 10.1111/1462-2920.16616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.
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Affiliation(s)
- Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Miranda H Seixas
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Evan M Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - John R Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Tyler H Tappenbeck
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Adam Baumann
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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2
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Jacoby DMP, Piper AT. What acoustic telemetry can and cannot tell us about fish biology. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37837176 DOI: 10.1111/jfb.15588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 10/15/2023]
Abstract
Acoustic telemetry (AT) has become ubiquitous in aquatic monitoring and fish biology, conservation, and management. Since the early use of active ultrasonic tracking that required researchers to follow at a distance their species of interest, the field has diversified considerably, with exciting advances in both hydrophone and transmitter technology. Once a highly specialized methodology, however, AT is fast becoming a generalist tool for those wishing to study or conserve fishes, leading to diversifying application by non-specialists. With this transition in mind, we evaluate exactly what AT has become useful for, discussing how the technological and analytical advances around AT can address important questions within fish biology. In doing so, we highlight the key ecological and applied research areas where AT continues to reveal crucial new insights and, in particular, when combined with complimentary research approaches. We provide a comprehensive breakdown of the state of the art for applications of AT, discussing the ongoing challenges, where its strengths lie, and how future developments may revolutionize fisheries management, behavioral ecology and species protection. Through selected papers we illustrate specific applications across the broad spectrum of fish biology. By bringing together the recent and future developments in this field under categories designed to broadly capture many aspects of fish biology, we hope to offer a useful guide for the non-specialist practitioner as they attempt to navigate the dizzying array of considerations and ongoing developments within this diverse toolkit.
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Affiliation(s)
- David M P Jacoby
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Institute of Zoology, Zoological Society of London, London, UK
| | - Adam T Piper
- Institute of Zoology, Zoological Society of London, London, UK
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3
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Dang C, Wu Z, Zhang M, Li X, Sun Y, Wu R, Zheng Y, Xia Y. Microorganisms as bio-filters to mitigate greenhouse gas emissions from high-altitude permafrost revealed by nanopore-based metagenomics. IMETA 2022; 1:e24. [PMID: 38868568 PMCID: PMC10989947 DOI: 10.1002/imt2.24] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 06/14/2024]
Abstract
The distinct climatic and geographical conditions make high-altitude permafrost on the Tibetan Plateau suffer more severe degradation than polar permafrost. However, the microbial responses associated with greenhouse gas production in thawing permafrost remain obscured. Here we applied nanopore-based long-read metagenomics and high-throughput RNA-seq to explore microbial functional activities within the freeze-thaw cycle in the active layers of permafrost at the Qilian Mountain. A bioinformatic framework was established to facilitate phylogenetic and functional annotation of the unassembled nanopore metagenome. By deploying this strategy, 42% more genera could be detected and 58% more genes were annotated to nitrogen and methane cycle. With the aid of such enlarged resolution, we observed vigorous aerobic methane oxidation by Methylomonas, which could serve as a bio-filter to mitigate CH4 emissions from permafrost. Such filtering effect could be further consolidated by both on-site gas phase measurement and incubation experiment that CO2 was the major form of carbon released from permafrost. Despite the increased transcriptional activities of aceticlastic methanogenesis pathways in the thawed permafrost active layer, CH4 generated during the thawing process could be effectively consumed by the microbiome. Additionally, the nitrogen metabolism in permafrost tends to be a closed cycle and active N2O consumption by the topsoil community was detected in the near-surface gas phase. Our findings reveal that although the increased thawed state facilitated the heterotrophic nitrogen and methane metabolism, effective microbial methane oxidation in the active layer could serve as a bio-filter to relieve the overall warming potentials of greenhouse gas emitted from thawed permafrost.
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Affiliation(s)
- Chenyuan Dang
- School of Environmental Science and Engineering, College of EngineeringSouthern University of Science and TechnologyShenzhenChina
- Laboratory of High‐Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical PhysicsChinese Academy of Sciences (CAS)DalianChina
| | - Ziqi Wu
- School of Environmental Science and Engineering, College of EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Miao Zhang
- School of Environmental Science and Engineering, College of EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Xiang Li
- School of Environmental Science and Engineering, College of EngineeringSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Marine Archaea Geo‐Omics, Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Yuqin Sun
- Shenzhen Key Laboratory of Marine Archaea Geo‐Omics, Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
- State Environmental Protection Key Laboratory of Integrated Surface Water‐Groundwater Pollution Control, School of Environmental Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Ren'an Wu
- Laboratory of High‐Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical PhysicsChinese Academy of Sciences (CAS)DalianChina
| | - Yan Zheng
- Shenzhen Key Laboratory of Marine Archaea Geo‐Omics, Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
- State Environmental Protection Key Laboratory of Integrated Surface Water‐Groundwater Pollution Control, School of Environmental Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Yu Xia
- School of Environmental Science and Engineering, College of EngineeringSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Key Laboratory of Marine Archaea Geo‐Omics, Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
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Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. mBio 2022; 13:e0237921. [PMID: 35435701 PMCID: PMC9239080 DOI: 10.1128/mbio.02379-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) “Candidatus Nitrotoga” and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.
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Hampel JJ, McCarthy MJ, Aalto SL, Newell SE. Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida). Front Microbiol 2020; 11:1541. [PMID: 32754132 PMCID: PMC7366250 DOI: 10.3389/fmicb.2020.01541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH4+) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R2 = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH4+ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, United States.,Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Mark J McCarthy
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Sanni L Aalto
- Section for Aquaculture, The North Sea Research Centre, DTU Aqua, Technical University of Denmark, Hirtshals, Denmark
| | - Silvia E Newell
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
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Schulhof MA, Allen AE, Allen EE, Mladenov N, McCrow JP, Jones NT, Blanton J, Cavalheri HB, Kaul D, Symons CC, Shurin JB. Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Mol Ecol 2020; 29:2080-2093. [DOI: 10.1111/mec.15469] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/02/2020] [Accepted: 04/28/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Marika A. Schulhof
- Division of Biological Sciences University of California San Diego La Jolla CA USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography University of California San Diego La Jolla CA USA
- Department of Microbial and Environmental Genomics J. Craig Venter Institute La Jolla CA USA
| | - Eric E. Allen
- Division of Biological Sciences University of California San Diego La Jolla CA USA
- Scripps Institution of Oceanography University of California San Diego La Jolla CA USA
| | - Natalie Mladenov
- Department of Civil, Construction, & Environmental Engineering San Diego State University San Diego CA USA
| | - John P. McCrow
- Department of Microbial and Environmental Genomics J. Craig Venter Institute La Jolla CA USA
| | - Natalie T. Jones
- Division of Biological Sciences University of California San Diego La Jolla CA USA
- School of Biological Sciences University of Queensland Brisbane Qld Australia
| | - Jessica Blanton
- Scripps Institution of Oceanography University of California San Diego La Jolla CA USA
| | - Hamanda B. Cavalheri
- Division of Biological Sciences University of California San Diego La Jolla CA USA
| | - Drishti Kaul
- Department of Microbial and Environmental Genomics J. Craig Venter Institute La Jolla CA USA
| | - Celia C. Symons
- Division of Biological Sciences University of California San Diego La Jolla CA USA
- Department of Ecology and Evolutionary Biology University of California Irvine Irvine CA USA
| | - Jonathan B. Shurin
- Division of Biological Sciences University of California San Diego La Jolla CA USA
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7
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Zhou W, Jiang X, Ouyang J, Lu B, Liu W, Liu G. Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai-Tibetan Plateau. Microorganisms 2020; 8:E933. [PMID: 32575850 PMCID: PMC7355592 DOI: 10.3390/microorganisms8060933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/08/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022] Open
Abstract
In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai-Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g-1 and 9.73 × 103 copies g-1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.
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Affiliation(s)
- Wen Zhou
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaoliang Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Ouyang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Research Center for Ecology and Environment of Qinghai–Tibetan Plateau, Tibet University, Lhasa 850000, China
- College of Science, Tibet University, Lhasa 850000, China
| | - Bei Lu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (W.Z.); (X.J.); (J.O.); (B.L.)
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
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Wang R, Han R, Long Q, Gao X, Xing J, Shen G, Zhu D. Bacterial and Archaeal Communities within an Ultraoligotrophic, High-altitude Lake in the Pre-Himalayas of the Qinghai-Tibet Plateau. Indian J Microbiol 2020; 60:363-373. [PMID: 32655200 DOI: 10.1007/s12088-020-00881-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/06/2020] [Indexed: 11/25/2022] Open
Abstract
Puma Yumco Lake (PYL) is an ultraoligotrophic freshwater lake that sits an altitude of 5030 m within the Qinghai-Tibet Plateau of China. The bacterial and archaeal diversity of the lake remains poorly understood, despite their potential to inform on biogeochemical cycling and environment-microbial associations in these unique environments. Here, the bacterial and archaeal communities of PYL were investigated using high-throughput sequencing analysis of community 16S rRNA gene sequences. Further, the relationships among dominant taxa and environmental factors were comprehensively evaluated. Bacterial diversity comprised 31 phyla and 371 genera (10,645 operational taxonomic units [OTUs], Shannon index values of 5.21-6.16) and was significantly higher than that of Archaea (five phyla and 24 genera comprising 1141 OTUs and Shannon index values of 1.18-3.28). The bacterial communities were dominated by Proteobacteria (48.42-59.97% relative abundances), followed by Bacteroidetes (12.5-32.51%), Acidobacteria (2.07-11.56%), Firmicutes (0.65-6.32%), Planctomycetes (0.99-3.56%), Gemmatimonadetes (0.38-3.57%), Actinobacteria (1.67-3.52%), Verrucomicrobia (0.87-2.01%), and Chloroflexi (0.5-1.17%). In addition, archaeal communities were dominated by Thaumarchaeota (33.22-93.00%), followed by Euryarchaeota (2.89-35.47%), Woesearchaeota (0.99-31.04%), and Pacearchaeota (0.01-1.14%). The most abundant bacterial genus was Rhodoferax (5.73-26.62%) and the most abundant archaeal genus was the ammonia-oxidizing Nitrososphaera (29.18-91.46%). These results suggest that the Rhodoferax and Nitrososphaera are likely to participate in biogeochemical cycles in these environments through photoheterotrophy and nitrification, respectively. Taken together, these results provide valuable data for better understanding microbial interactions with each other and with these unique environments.
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Affiliation(s)
- Rong Wang
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Rui Han
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016 Qinghai China
| | - Qifu Long
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Xiang Gao
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Jiangwa Xing
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Guoping Shen
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
| | - Derui Zhu
- Research Center of Basic Medical Science, Medical College of Qinghai University, Xining, 810016 Qinghai China
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Alfreider A, Grimus V, Luger M, Ekblad A, Salcher MM, Summerer M. Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes. FEMS Microbiol Ecol 2019; 94:5076030. [PMID: 30137292 PMCID: PMC6118323 DOI: 10.1093/femsec/fiy163] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/02/2022] Open
Abstract
Niche specialization of nitrifying prokaryotes is usually studied with tools targeting molecules involved in the oxidation of ammonia and nitrite. The ecological significance of diverse CO2 fixation strategies used by nitrifiers is, however, mostly unexplored. By analyzing autotrophy-related genes in combination with amoA marker genes based on droplet digitial PCR and CARD-FISH counts targeting rRNA, we quantified the distribution of nitrifiers in eight stratified lakes. Ammonia oxidizing (AO) Thaumarchaeota using the 3-hydroxypropionate/4-hydroxybutyrate pathway dominated deep and oligotrophic lakes, whereas Nitrosomonas-related taxa employing the Calvin cycle were important AO bacteria in smaller lakes. The occurrence of nitrite oxidizing Nitrospira, assimilating CO2 with the reductive TCA cycle, was strongly correlated with the distribution of Thaumarchaeota. Recently discovered complete ammonia-oxidizing bacteria (comammox) belonging to Nitrospira accounted only for a very small fraction of ammonia oxidizers (AOs) present at the study sites. Altogether, this study gives a first insight on how physicochemical characteristics in lakes are associated to the distribution of nitrifying prokaryotes with different CO2 fixation strategies. Our investigations also evaluate the suitability of functional genes associated with individual CO2 assimilation pathways to study niche preferences of different guilds of nitrifying microorganisms based on an autotrophic perspective.
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Affiliation(s)
- Albin Alfreider
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Victoria Grimus
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Martin Luger
- Institute for Water Ecology, Fisheries Biology and Lake Research, Federal Agency for Water Management, Scharfling 18, 5310 Mondsee, Austria
| | - Anja Ekblad
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách, 702/7370 05 Ceské Budejovice, Czech Republic
| | - Monika Summerer
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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10
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Annual nitrification dynamics in a seasonally ice-covered lake. PLoS One 2019; 14:e0213748. [PMID: 30893339 PMCID: PMC6426244 DOI: 10.1371/journal.pone.0213748] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/27/2019] [Indexed: 11/25/2022] Open
Abstract
We investigated the variability in ammonia oxidation (AO) rates and the presence of ammonia-oxidizing archaea and bacteria (AOB and AOA) over an annual cycle in the water column of a small, seasonnally ice covered, temperate shield lake. AO, the first step of nitrification, was measured in situ using 15N-labelled ammonium (NH4+) at 1% and 10% of photosynthetic active radiation during day and at the same depths during night. AO was active across seasons and light levels, ranging from undetectable to 333 nmol L-1 d-1 with peak activity in winter under ice cover. NH4+ concentration was the single most important positive predictor of AO rates. High NH4+ concentrations and reduced chlorophyll a concentrations under ice, which favoured AO, were coherent with high nitrate concentrations and super saturation in nitrous oxide. When targeting the ammonia monooxygenase (amoA) gene in samples from the photic zone, we found AOA to be omnipresent throughout the year while AOB were observed predominantly during winter. Our results demonstrate that AO is an ongoing process in sunlit surface waters of temperate lakes and at all seasons with pronounced nitrification activity observed during winter under ice. The combination of high NH4+ concentrations due to fall overturn, reduced light availability that limited phytoplankton competition, and the presence of AOB together with AOA apparently favoured these elevated rates under ice. We suggest that lake ice could be a control point for nitrification in oligotrophic temperate shield lakes, characterized as a moment and place that exerts disproportionate influence on the biogeochemical behaviour of ecosystems.
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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Kimble JC, Winter AS, Spilde MN, Sinsabaugh RL, Northup DE. A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA. FEMS Microbiol Ecol 2018; 94:5079639. [PMID: 30165514 PMCID: PMC6669814 DOI: 10.1093/femsec/fiy173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/23/2018] [Indexed: 01/03/2023] Open
Abstract
Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected. We hypothesized that within FMD samples we would find the presence of microbial N cycling genes and taxonomy related to N cycling microorganisms. Community DNA were sequenced using Illumina shotgun metagenomics and 16S rRNA gene sequencing. Results suggest a diverse N cycle encompassing several energetic pathways including nitrification, dissimilatory nitrate reduction and denitrification. N cycling genes associated with assimilatory nitrate reduction were also identified. Functional gene sequences and taxonomic findings suggest several bacterial and archaeal phyla potentially play a role in nitrification pathways in FSC and FMD. Thaumarchaeota, a deep-branching archaeal division, likely play an essential and possibly dominant role in the oxidation of ammonia. Our results provide genomic evidence for understanding how microbes are potentially able to acquire and cycle N in a low-nutrient subterranean environment.
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Affiliation(s)
- Jason C Kimble
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Ara S Winter
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael N Spilde
- Institute of Meteoritics, MSC03-2050, University of New Mexico, Albuquerque, NM 87131, USA
| | - Robert L Sinsabaugh
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Diana E Northup
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
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13
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Wilson JM, Litvin SY, Beman JM. Microbial community networks associated with variations in community respiration rates during upwelling in nearshore Monterey Bay, California. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:272-282. [PMID: 29488352 DOI: 10.1111/1758-2229.12635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Respiration of organic material is a central process in the global carbon (C) cycle catalysed by diverse microbial communities. In the coastal ocean, upwelling can drive variation in both community respiration (CR) and the microbial community, but linkages between the two are not well-understood. We measured CR rates and analysed microbial dynamics via 16S rRNA gene sequencing, to assess whether CR correlated with upwelling irrespective of changes in the microbial community, or if the particular microbial community present was a factor in explaining variations in CR. CR varied significantly over time as a function of temperature, dissolved oxygen (DO) and chlorophyll-all of which are altered by upwelling-but also varied with a 'subnetwork' (i.e., a group of microbial taxa that covaried with one another) of the whole community. One subnetwork was associated with higher CR and warmer temperatures, while another was associated with lower CR and DO. Our results suggest that CR in the coastal ocean varies with both environmental variables, and a portion of the microbial community that is not directly correlated with upwelling intensity.
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Affiliation(s)
- Jesse M Wilson
- Life and Environmental Sciences and Environmental Systems, University of California, Merced, Merced, CA, 95343, USA
| | - Steven Y Litvin
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, 93950, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA
| | - J Michael Beman
- Life and Environmental Sciences and Environmental Systems, University of California, Merced, Merced, CA, 95343, USA
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14
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Molina V, Dorador C, Fernández C, Bristow L, Eissler Y, Hengst M, Hernandez K, Olsen LM, Harrod C, Marchant F, Anguita C, Cornejo M. The activity of nitrifying microorganisms in a high-altitude Andean wetland. FEMS Microbiol Ecol 2018; 94:4969675. [DOI: 10.1093/femsec/fiy062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
| | - Camila Fernández
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
- Interdisciplinary Center for Aquaculture Research (INCAR), COPAS SUR-AUSTRAL Program, Barrio Universitario s/n, Universidad de Concepción, Concepción, Chile
| | - Laura Bristow
- Nordic Center for Earth Evolution (NordCEE), Department of Biology, University of Southern Denmark, Campusvej 55-5230, Odense, Denmark
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte. Av Angamos 0610 Antofagasta, Chile
| | - Klaudia Hernandez
- Centro de Investigacion Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Avenida República 440, Santiago, Chile10
| | | | - Chris Harrod
- Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisca Marchant
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
| | - Cristobal Anguita
- Departamento de Ecologia y Biodiversidad, Facultad de Ecologia y Recursos Naturales, Universidad Andres Bello, Av. Republica 440, Santiago, Chile
| | - Marcela Cornejo
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía , Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile, Altamirano 1480, Valparaíso
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15
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Abstract
Ammonia is a widespread pollutant in aquatic ecosystems originating directly and indirectly from human activities, which can strongly affect the structure and functioning of the aquatic foodweb. The biological oxidation of NH4+ to nitrite, and then nitrate is a key part of the complex nitrogen cycle and a fundamental process in aquatic environments, having a profound influence on ecosystem stability and functionality. Environmental studies have shown that our current knowledge of physical and chemical factors that control this process and the abundance and function of involved microorganisms are not entirely understood. In this paper, the efficiency and the transformation velocity of ammonium into oxidised compounds in 14 south-alpine lakes in northern Italy, with a similar origin, but different trophic levels, are compared with lab-scale experimentations (20 °C, dark, oxygen saturation) that are performed in artificial microcosms (4 L). The water samples were collected in different months to highlight the possible effect of seasonality on the development of the ammonium oxidation process. In four-liter microcosms, concentrations were increased by 1 mg/L NH4+ and the process of ammonium oxidation was constantly monitored. The time elapsed for the decrease of 25% and 95% of the initial ion ammonium concentration and the rate for that ammonium oxidation were evaluated. Principal Component Analysis and General Linear Model, performed on 56 observations and several chemical and physical parameters, highlighted the important roles of total phosphorus and nitrogen concentrations on the commencement of the oxidation process. Meanwhile, the natural concentration of ammonium influenced the rate of nitrification (µg NH4+/L day). Seasonality did not seem to significantly affect the ammonium transformation. The results highlight the different vulnerabilities of lakes with different trophic statuses.
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16
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Zhao D, He X, Huang R, Yan W, Yu Z. Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments. J Basic Microbiol 2017; 57:625-632. [DOI: 10.1002/jobm.201700035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/31/2017] [Accepted: 04/30/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
| | - Xiaowei He
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
| | - Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
| | - Wenming Yan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering; Hohai University; Nanjing China
- College of Hydrology and Water Resources; Hohai University; Nanjing China
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17
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Yang Y, Li N, Zhao Q, Yang M, Wu Z, Xie S, Liu Y. Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:15358-15369. [PMID: 27109114 DOI: 10.1007/s11356-016-6707-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Abstract
Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qun Zhao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Mengxi Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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18
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Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79. Appl Environ Microbiol 2016; 82:4776-4788. [PMID: 27235442 DOI: 10.1128/aem.01171-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCE Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbe-microbe interactions, in particular between ammonia oxidizers and their neighboring microbial community.
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19
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Zhang Y, Chen L, Sun R, Dai T, Tian J, Zheng W, Wen D. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay. Appl Microbiol Biotechnol 2016; 100:6035-45. [PMID: 26960319 DOI: 10.1007/s00253-016-7421-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge.
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Affiliation(s)
- Yan Zhang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Lujun Chen
- School of Environment, Tsinghua University, Beijing, 100084, China.,Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, 314050, China
| | - Renhua Sun
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.,Rural Energy & Environment Agency, Ministry of Agriculture, Beijing, 100125, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jinping Tian
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Wei Zheng
- Zhejiang Provincial Key Laboratory of Water Science and Technology, Department of Environmental Technology and Ecology, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang, 314050, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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20
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Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:590434. [PMID: 26379473 PMCID: PMC4561949 DOI: 10.1155/2015/590434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/17/2015] [Indexed: 01/05/2023]
Abstract
Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.
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