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Mao Y, Wu J, Yang R, Ma Y, Ye J, Zhong J, Deng N, He X, Hong Y. Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106342. [PMID: 38185001 DOI: 10.1016/j.marenvres.2024.106342] [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: 10/31/2023] [Revised: 12/26/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.
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Affiliation(s)
- Yixiang Mao
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Ruotong Yang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yuexi Ma
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiarui Zhong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Nanling Deng
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Xiang He
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
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2
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Liu Q, Chen Y, Xu XW. Genomic insight into strategy, interaction and evolution of nitrifiers in metabolizing key labile-dissolved organic nitrogen in different environmental niches. Front Microbiol 2023; 14:1273211. [PMID: 38156017 PMCID: PMC10753782 DOI: 10.3389/fmicb.2023.1273211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and complete ammonia oxidizers (comammox) are responsible for nitrification in nature; however, some groups have been reported to utilize labile-dissolved organic nitrogen (LDON) for satisfying nitrogen demands. To understand the universality of their capacity of LDON metabolism, we collected 70 complete genomes of AOA, AOB, NOB, and comammox from typical environments for exploring their potentials in the metabolism of representative LDON (urea, polyamines, cyanate, taurine, glycine betaine, and methylamine). Genomic analyses showed that urea was the most popular LDON used by nitrifiers. Each group harbored unique urea transporter genes (AOA: dur3 and utp, AOB: utp, and NOB and comammox: urtABCDE and utp) accompanied by urease genes ureABC. The differentiation in the substrate affinity of these transporters implied the divergence of urea utilization efficiency in nitrifiers, potentially driving them into different niches. The cyanate transporter (cynABD and focA/nirC) and degradation (cynS) genes were detected mostly in NOB, indicating their preference for a wide range of nitrogen substrates to satisfy high nitrogen demands. The lack of genes involved in the metabolism of polyamines, taurine, glycine betaine, and methylamines in most of nitrifiers suggested that they were not able to serve as a source of ammonium, only if they were degraded or oxidized extracellularly as previously reported. The phylogenetic analyses assisted with comparisons of GC% and the Codon Adaptation Index between target genes and whole genomes of nitrifiers implied that urea metabolic genes dur3 and ureC in AOA evolved independently from bacteria during the transition from Thaumarchaeota to AOA, while utp in terrestrial AOA was acquired from bacteria via lateral gene transfer (LGT). Cyanate transporter genes cynS and focA/nirC detected only in a terrestrial AOA Candidadus Nitrsosphaera gargensis Ga9.2 could be gained synchronously with Nitrospira of NOB by an ancient LGT. Our results indicated that LDON utilization was a common feature in nitrifiers, but metabolic potentials were different among nitrifiers, possibly being intensely interacted with their niches, survival strategies, and evolutions.
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Affiliation(s)
- Qian Liu
- Donghai Laboratory, Zhoushan, Zhejiang, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuhao Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
- Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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3
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Gwak JH, Awala SI, Kim SJ, Lee SH, Yang EJ, Park J, Jung J, Rhee SK. Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica. J Microbiol 2023; 61:967-980. [PMID: 38062325 DOI: 10.1007/s12275-023-00090-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.
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Affiliation(s)
- Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Sang-Hoon Lee
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eun-Jin Yang
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jisoo Park
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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4
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Vipindas PV, Jabir T, Venkatachalam S, Yang EJ, Jain A, Krishnan KP. Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean. Extremophiles 2023; 27:24. [PMID: 37668803 DOI: 10.1007/s00792-023-01310-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
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5
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Guo L, Lin W, Cao C, Li C. Integrated rice-crayfish farming system does not mitigate the global warming potential during rice season. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161520. [PMID: 36646218 DOI: 10.1016/j.scitotenv.2023.161520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Integrated rice-crayfish farming system (RCS) has become increasingly popular in China. However, previous research has largely ignored the effect of trench around the paddy field on GHG emissions, which may cause inaccurate estimation of the global warming potential (GWP) from the system. This study compared the GWP between rice monoculture (RM) and RCS. The results indicated that the field of RCS had significantly lower CH4 emissions compared with RM due to lower mcrA abundance and higher pmoA abundance, while there was no difference in N2O emissions. In addition, the trench resulted in remarkably more CH4 emissions due to higher mcrA abundance and lower pmoA abundance and less N2O emissions than the field in RCS. In general, RCS seems not to mitigate GWP compared with RM due to more CH4 emissions from the trench in the current mode. Furthermore, our results indicate that RCS can reduce GWP relative to RM only when the area ratio of the trench to the system is controlled to be lower than 13.9 %.
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Affiliation(s)
- Lijin Guo
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China; International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 3550002, PR China
| | - Wei Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 3550002, PR China
| | - Cougui Cao
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou 434023, PR China
| | - Chengfang Li
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou 434023, PR China.
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6
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Lu Y, Lv Y, Zhang Y, Liu Q, Xu X, Xiao X, Xu J. Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea. Environ Microbiol 2023; 25:410-427. [PMID: 36448268 DOI: 10.1111/1462-2920.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.
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Affiliation(s)
- Ye Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yongxin Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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7
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Bayer B, McBeain K, Carlson CA, Santoro AE. Carbon content, carbon fixation yield and dissolved organic carbon release from diverse marine nitrifiers. LIMNOLOGY AND OCEANOGRAPHY 2023; 68:84-96. [PMID: 37064272 PMCID: PMC10092583 DOI: 10.1002/lno.12252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Nitrifying microorganisms, including ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and nitrite-oxidizing bacteria, are the most abundant chemoautotrophs in the ocean and play an important role in the global carbon cycle by fixing dissolved inorganic carbon (DIC) into biomass. The release of organic compounds by these microbes is not well quantified, but may represent an as-yet unaccounted source of dissolved organic carbon (DOC) available to marine food webs. Here, we provide measurements of cellular carbon and nitrogen quotas, DIC fixation yields and DOC release of 10 phylogenetically diverse marine nitrifiers. All investigated strains released DOC during growth, representing on average 5-15% of the fixed DIC. Changes in substrate concentration and temperature did not affect the proportion of fixed DIC released as DOC, but release rates varied between closely related species. Our results also indicate previous studies may have underestimated DIC fixation yields of marine nitrite oxidizers due to partial decoupling of nitrite oxidation from CO2 fixation, and due to lower observed yields in artificial compared to natural seawater medium. The results of this study provide critical values for biogeochemical models of the global carbon cycle, and help to further constrain the implications of nitrification-fueled chemoautotrophy for marine food-web functioning and the biological sequestration of carbon in the ocean.
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Affiliation(s)
- Barbara Bayer
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
- Present address:
Department of Microbiology and Ecosystem ScienceUniversity of ViennaViennaAustria
| | - Kelsey McBeain
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
- Present address:
Department of OceanographyUniversity of Hawai'i at ManoaHonoluluHawaii
| | - Craig A. Carlson
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
| | - Alyson E. Santoro
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCalifornia
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8
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Castillo DJ, Dithugoe CD, Bezuidt OK, Makhalanyane TP. Microbial ecology of the Southern Ocean. FEMS Microbiol Ecol 2022; 98:6762916. [PMID: 36255374 DOI: 10.1093/femsec/fiac123] [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: 02/09/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 01/21/2023] Open
Abstract
The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Choaro D Dithugoe
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Oliver K Bezuidt
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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9
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Tian C, Lv Y, Yang Z, Zhang R, Zhu Z, Ma H, Li J, Zhang Y. Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02116-3. [PMID: 36239777 DOI: 10.1007/s00248-022-02116-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.
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Affiliation(s)
- Chen Tian
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yongxin Lv
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhifeng Yang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, USA
| | - Ruifeng Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Zhuoyi Zhu
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Hongmei Ma
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China
| | - Jing Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
- Key Laboratory for Polar Science, MNR, Polar Research Institute of China, Shanghai, People's Republic of China.
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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10
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Pascoal F, Areosa I, Torgo L, Branco P, Baptista MS, Lee CK, Cary SC, Magalhães C. The spatial distribution and biogeochemical drivers of nitrogen cycle genes in an Antarctic desert. Front Microbiol 2022; 13:927129. [PMID: 36274733 PMCID: PMC9583160 DOI: 10.3389/fmicb.2022.927129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.
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Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Inês Areosa
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Luís Torgo
- Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Paula Branco
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON, Canada
| | - Mafalda S. Baptista
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto, Portugal
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
| | - S. Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
- S. Craig Cary,
| | - Catarina Magalhães
- Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- *Correspondence: Catarina Magalhães,
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11
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Ray AE, Zaugg J, Benaud N, Chelliah DS, Bay S, Wong HL, Leung PM, Ji M, Terauds A, Montgomery K, Greening C, Cowan DA, Kong W, Williams TJ, Hugenholtz P, Ferrari BC. Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. THE ISME JOURNAL 2022; 16:2547-2560. [PMID: 35933499 PMCID: PMC9561532 DOI: 10.1038/s41396-022-01298-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
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12
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Wu J, Hong Y, He X, Liu X, Ye J, Jiao L, Li Y, Wang Y, Ye F, Yang Y, Du J. Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea. iScience 2022; 25:104333. [PMID: 35602962 PMCID: PMC9118673 DOI: 10.1016/j.isci.2022.104333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022] Open
Abstract
The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiang He
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lijing Jiao
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiben Li
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yunhua Yang
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Juan Du
- Institute of Environmental Research at Greater Bay Area; Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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13
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Alcamán-Arias ME, Cifuentes-Anticevic J, Díez B, Testa G, Troncoso M, Bello E, Farías L. Surface Ammonia-Oxidizer Abundance During the Late Summer in the West Antarctic Coastal System. Front Microbiol 2022; 13:821902. [PMID: 35401462 PMCID: PMC8992545 DOI: 10.3389/fmicb.2022.821902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 01/04/2023] Open
Abstract
Marine ammonia oxidizers that oxidize ammonium to nitrite are abundant in polar waters, especially during the winter in the deeper mixed-layer of West Antarctic Peninsula (WAP) waters. However, the activity and abundance of ammonia-oxidizers during the summer in surface coastal Antarctic waters remain unclear. In this study, the ammonia-oxidation rates, abundance and identity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were evaluated in the marine surface layer (to 30 m depth) in Chile Bay (Greenwich Island, WAP) over three consecutive late-summer periods (2017, 2018, and 2019). Ammonia-oxidation rates of 68.31 nmol N L−1 day−1 (2018) and 37.28 nmol N L−1 day−1 (2019) were detected from illuminated 2 m seawater incubations. However, high ammonia-oxidation rates between 267.75 and 109.38 nmol N L−1 day−1 were obtained under the dark condition at 30 m in 2018 and 2019, respectively. During the late-summer sampling periods both stratifying and mixing events occurring in the water column over short timescales (February–March). Metagenomic analysis of seven nitrogen cycle modules revealed the presence of ammonia-oxidizers, such as the Archaea Nitrosopumilus and the Bacteria Nitrosomonas and Nitrosospira, with AOA often being more abundant than AOB. However, quantification of specific amoA gene transcripts showed number of AOB being two orders of magnitude higher than AOA, with Nitrosomonas representing the most transcriptionally active AOB in the surface waters. Additionally, Candidatus Nitrosopelagicus and Nitrosopumilus, phylogenetically related to surface members of the NP-ε and NP-γ clades respectively, were the predominant AOA. Our findings expand the known distribution of ammonium-oxidizers to the marine surface layer, exposing their potential ecological role in supporting the marine Antarctic system during the productive summer periods.
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Affiliation(s)
- María E Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Center for Climate and Resilience Research (CR)2, Santiago, Chile.,Escuela de Medicina, Universidad Espíritu Santo, Guayaquil, Ecuador
| | | | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Giovanni Testa
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Programa de Postgrado en Oceanografía, Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Research Center Dynamics of High Latitude Marine Ecosystems (IDEAL), Punta Arenas, Chile
| | | | - Estrella Bello
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile.,Center for Climate and Resilience Research (CR)2, Santiago, Chile
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14
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Martínez-Pérez C, Greening C, Bay SK, Lappan RJ, Zhao Z, De Corte D, Hulbe C, Ohneiser C, Stevens C, Thomson B, Stepanauskas R, González JM, Logares R, Herndl GJ, Morales SE, Baltar F. Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nat Commun 2022; 13:117. [PMID: 35013291 PMCID: PMC8748734 DOI: 10.1038/s41467-021-27769-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
Throughout coastal Antarctica, ice shelves separate oceanic waters from sunlight by hundreds of meters of ice. Historical studies have detected activity of nitrifying microorganisms in oceanic cavities below permanent ice shelves. However, little is known about the microbial composition and pathways that mediate these activities. In this study, we profiled the microbial communities beneath the Ross Ice Shelf using a multi-omics approach. Overall, beneath-shelf microorganisms are of comparable abundance and diversity, though distinct composition, relative to those in the open meso- and bathypelagic ocean. Production of new organic carbon is likely driven by aerobic lithoautotrophic archaea and bacteria that can use ammonium, nitrite, and sulfur compounds as electron donors. Also enriched were aerobic organoheterotrophic bacteria capable of degrading complex organic carbon substrates, likely derived from in situ fixed carbon and potentially refractory organic matter laterally advected by the below-shelf waters. Altogether, these findings uncover a taxonomically distinct microbial community potentially adapted to a highly oligotrophic marine environment and suggest that ocean cavity waters are primarily chemosynthetically-driven systems.
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Affiliation(s)
- Clara Martínez-Pérez
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 8093, Zurich, Switzerland
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, 3800, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, 3800, Australia
| | - Rachael J Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Hulbe
- School of Surveying, University of Otago, Dunedin, New Zealand
| | | | - Craig Stevens
- National Institute of Water and Atmospheric Research, Greta Point, Wellington, 6021, New Zealand
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Blair Thomson
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
| | | | - José M González
- Department of Microbiology, University of La Laguna, ES-38200, La Laguna, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790, AB Den Burg, The Netherlands
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, A-1030, Vienna, Austria
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand.
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15
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Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA, Mahon AR, Halanych KM, Learman DR. Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. mSphere 2021; 6:e0077021. [PMID: 34817234 PMCID: PMC8612310 DOI: 10.1128/msphere.00770-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.
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Affiliation(s)
- Arkadiy I. Garber
- Biodesign Center for Mechanisms for Evolution, Arizona State University, Tempe, Arizona, USA
| | | | - Cody S. Sheik
- Biology Department and Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Michael W. Henson
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, USA
- Department of Marine Biology, Haifa University, Haifa, Israel
| | - Andrew R. Mahon
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
| | - Kenneth M. Halanych
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Deric R. Learman
- Department of Biology, Central Michigan University, Mt. Pleasant, Michigan, USA
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16
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Lu S, Liu X, Liu C, Cheng G, Zhou R, Li Y. A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China. Front Microbiol 2021; 12:775794. [PMID: 34917055 PMCID: PMC8671037 DOI: 10.3389/fmicb.2021.775794] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.
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Affiliation(s)
- Shimin Lu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Xingguo Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Chong Liu
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Guofeng Cheng
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Runfeng Zhou
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yayuan Li
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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17
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Ortiz M, Bosch J, Coclet C, Johnson J, Lebre P, Salawu-Rotimi A, Vikram S, Makhalanyane T, Cowan D. Microbial Nitrogen Cycling in Antarctic Soils. Microorganisms 2020; 8:E1442. [PMID: 32967081 PMCID: PMC7564152 DOI: 10.3390/microorganisms8091442] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (M.O.); (J.B.); (C.C.); (J.J.); (P.L.); (A.S.-R.); (S.V.); (T.M.)
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18
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Cholet F, Ijaz UZ, Smith CJ. Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts. Environ Microbiol 2020; 22:2383-2402. [PMID: 32285609 DOI: 10.1111/1462-2920.15017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/08/2020] [Indexed: 12/28/2022]
Abstract
Reverse-transcriptase-quantitative PCR (RT-Q-PCR) and RT-PCR amplicon sequencing, provide a convenient, target-specific, high-sensitivity approach for gene expression studies and are widely used in environmental microbiology. Yet, the effectiveness and reproducibility of the reverse transcription step has not been evaluated. Therefore, we tested a combination of four commercial reverse transcriptases with two priming techniques to faithfully transcribe 16S rRNA and amoA transcripts from marine sediments. Both enzyme and priming strategy greatly affected quantification of the exact same target with differences of up to 600-fold. Furthermore, the choice of RT system significantly changed the communities recovered. For 16S rRNA, both enzyme and priming had a significant effect with enzyme having a stronger impact than priming. Inversely, for amoA only the change in priming strategy resulted in significant differences between the same samples. Specifically, more OTUs and better coverage of amoA transcripts diversity were obtained with GS priming indicating this approach was better at recovering the diversity of amoA transcripts. Moreover, sequencing of RNA mock communities revealed that, even though transcript α diversities (i.e., OTU counts within a sample) can be biased by the RT, the comparison of β diversities (i.e., differences in OTU counts between samples) is reliable as those biases are reproducible between environments.
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Affiliation(s)
- Fabien Cholet
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, Glasgow, Scotland, G12 8LT, UK
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, Glasgow, Scotland, G12 8LT, UK
| | - Cindy J Smith
- Infrastructure and Environment Research Division, James Watt School of Engineering, University of Glasgow, Glasgow, Scotland, G12 8LT, UK
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19
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Barnard S, Van Goethem MW, de Scally SZ, Cowan DA, van Rensburg PJ, Claassens S, Makhalanyane TP. Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils. FEMS Microbiol Ecol 2020; 96:5818763. [DOI: 10.1093/femsec/fiaa065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measured to assess a warming scenario. Soil warming to 15°C for 30 days triggered a significant decrease in microbial biomass compared to baseline soils (0°C; P < 0.05) after incubations had induced an initial increase. These changes coincided with increases in extracellular enzymatic activity for peptide hydrolysis and phenolic oxidation at higher temperatures, but not for the degradation of carbon substrates. Shifts in ammonia-oxidising bacteria (AOB) community composition related most significantly to changes in soil carbon content (P < 0.05), which gradually increased in microcosms exposed to a persistently elevated temperature relative to baseline incubations, while temperature did not influence AOBs. The concentration of soil ammonium (NH4+) decreased significantly at higher temperatures subsequent to an initial increase, possibly due to higher conversion rates of NH4+ to nitrate by nitrifying bacteria. We show that higher soil temperatures may reduce viable microbial biomass in cold environments but stimulate their activity over a short period.
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Affiliation(s)
- Sebastian Barnard
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Storme Z de Scally
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Peet Jansen van Rensburg
- Focus Area Human Metabolomics, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Sarina Claassens
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
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20
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Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica. Microorganisms 2020; 8:microorganisms8030404. [PMID: 32183078 PMCID: PMC7143839 DOI: 10.3390/microorganisms8030404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 01/07/2023] Open
Abstract
Polar ecosystems are generally limited in nitrogen (N) nutrients, and the patchy availability of N is partly determined by biological pathways, such as nitrification, which are carried out by distinctive prokaryotic functional groups. The activity and diversity of microorganisms are generally strongly influenced by environmental conditions. However, we know little of the attributes that control the distribution and activity of specific microbial functional groups, such as nitrifiers, in extreme cold environments and how they may respond to change. To ascertain relationships between soil geochemistry and the ecology of nitrifying microbial communities, we carried out a laboratory-based manipulative experiment to test the selective effect of key geochemical variables on the activity and abundance of ammonia-oxidizing communities in soils from the McMurdo Dry Valleys of Antarctica. We hypothesized that nitrifying communities, adapted to different environmental conditions within the Dry Valleys, will have distinct responses when submitted to similar geochemical disturbances. In order to test this hypothesis, soils from two geographically distant and geochemically divergent locations, Miers and Beacon Valleys, were incubated over 2 months under increased conductivity, ammonia concentration, copper concentration, and organic matter content. Amplicon sequencing of the 16S rRNA gene and transcripts allowed comparison of the response of ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) to each treatment over time. This approach was combined with measurements of 15NH4+ oxidation rates using 15N isotopic additions. Our results showed a higher potential for nitrification in Miers Valley, where environmental conditions are milder relative to Beacon Valley. AOA exhibited better adaptability to geochemical changes compared to AOB, particularly to the increase in copper and conductivity. AOA were also the only nitrifying group found in Beacon Valley soils. This laboratorial manipulative experiment provided new knowledge on how nitrifying groups respond to changes on key geochemical variables of Antarctic desert soils, and we believe these results offer new insights on the dynamics of N cycling in these ecosystems.
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21
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Pinto OHB, Silva TF, Vizzotto CS, Santana RH, Lopes FAC, Silva BS, Thompson FL, Kruger RH. Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. BMC Microbiol 2020; 20:13. [PMID: 31941452 PMCID: PMC6964070 DOI: 10.1186/s12866-020-1698-x] [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: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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Affiliation(s)
- Otávio H B Pinto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Thais F Silva
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Carla S Vizzotto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.,Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil
| | | | - Fabyano A C Lopes
- Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil
| | - Bruno S Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Ricardo H Kruger
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.
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22
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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23
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Alcamán-Arias ME, Farías L, Verdugo J, Alarcón-Schumacher T, Díez B. Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer. FEMS Microbiol Lett 2019; 365:4961137. [PMID: 29788084 DOI: 10.1093/femsle/fny090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/03/2018] [Indexed: 12/19/2022] Open
Abstract
Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.
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Affiliation(s)
- María E Alcamán-Arias
- Department of Oceanography, Universidad de Concepción, 4070386 Concepción, Chile.,Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
| | - Laura Farías
- Department of Oceanography, Universidad de Concepción, 4070386 Concepción, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
| | - Josefa Verdugo
- Alfred-Wegener-Institute Helmholtz-Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 6513677 Santiago, Chile.,Center for Climate and Resilience Research (CR) 2, Universidad de Chile, 8370448 Santiago, Chile
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24
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Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019; 21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, Moss Landing, CA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA
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25
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Yasong C, Junling L, Zheng Z, Huiping C, Yuke P, Lin X. Nitrogen removal and responses of bacterial communities in activated sludge under different operational manipulations. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:607-618. [PMID: 30975927 DOI: 10.2166/wst.2019.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Operational conditions are often manipulated to improve the nitrogen removal performance of wastewater treatment, yet the impacts of operational conditions on microbial communities were still not well understood. There is a pressing need to understand the microbial mechanisms that link operation manipulation and nitrogen removal performance. In this study, high-throughput analysis of 16S rDNA and quantitative polymerase chain reaction of functional genes were used to identify the microbial response to operational manipulations. The results showed that alteration of operational parameters could change the bacterial communities at the genera level and denitrification guild gradually dominated in the activated sludge bacterial communities. Heterotrophic Hyphomicrobium and Chromatiaceae drove the kinetic of dominant genera and denitrification guild. Carbon source supplement was the most efficient strategy for improving nitrogen removal, and greatly increased the abundance of denitrifiers and denitrification genes. However, carbon source supplement inhibited expression activities of denitrification genes, as well as the proliferation of autotrophic denitrifiers, and it was supposed to be unfavorable in terms of cost over the long term. The result should bring new inspiration for improving the effect of WWTP performance through the manipulation of operational parameters.
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Affiliation(s)
- Chen Yasong
- School of Environment, Nanjing University, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University Xianlin Campus, Xianlin Avenue 163, Nanjing 210023, China E-mail: ; BCEG Environment Development Co., Ltd, 2nd Floor, Building 4 Yiyuan, Anhui Beili, Chaoyang District, Beijing 100101, China
| | - Lu Junling
- School of Environment, Nanjing University, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University Xianlin Campus, Xianlin Avenue 163, Nanjing 210023, China E-mail:
| | - Zhao Zheng
- BCEG Environment Development Co., Ltd, 2nd Floor, Building 4 Yiyuan, Anhui Beili, Chaoyang District, Beijing 100101, China
| | - Chen Huiping
- School of Environment, Nanjing University, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University Xianlin Campus, Xianlin Avenue 163, Nanjing 210023, China E-mail:
| | - Peng Yuke
- School of Environment, Nanjing University, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University Xianlin Campus, Xianlin Avenue 163, Nanjing 210023, China E-mail:
| | - Xiao Lin
- School of Environment, Nanjing University, State Key Laboratory for Pollution Control and Resource Reuse (SKL-PCRR), Nanjing University Xianlin Campus, Xianlin Avenue 163, Nanjing 210023, China E-mail:
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26
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Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column. ISME JOURNAL 2019; 13:1144-1158. [PMID: 30610232 DOI: 10.1038/s41396-018-0311-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 01/09/2023]
Abstract
Ecological factors contributing to depth-related diversification of marine Thaumarchaeota populations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity-water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters-were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeota and heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobia and Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and Nitrospina OTUs. Even at depths where WCB-like Thaumarchaeota dominated, Nitrospina OTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.
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27
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Bowman JS. Identification of Microbial Dark Matter in Antarctic Environments. Front Microbiol 2018; 9:3165. [PMID: 30619224 PMCID: PMC6305705 DOI: 10.3389/fmicb.2018.03165] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Numerous studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI's Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumina platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6%. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2%, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0% for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.
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Affiliation(s)
- Jeff S. Bowman
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
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28
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Carini P, Dupont CL, Santoro AE. Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environ Microbiol 2018; 20:2112-2124. [PMID: 29626379 DOI: 10.1111/1462-2920.14107] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139-fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery.
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Affiliation(s)
- Paul Carini
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | | | - Alyson E Santoro
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
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29
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Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun 2018; 9:1517. [PMID: 29666365 PMCID: PMC5904100 DOI: 10.1038/s41467-018-03861-1] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/19/2018] [Indexed: 12/30/2022] Open
Abstract
Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.
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Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Campus Vienna Biocenter 5, Dr. Bohr Gasse 9, 1030, Vienna, Austria
- Ecology and Evolution, Research School of Biology, Australian National University, 2601, Canberra, ACT, Australia
| | - Tim Urich
- Institute of Microbiology, Ernst-Moritz-Arndt University, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Campus Vienna Biocenter 5, Dr. Bohr Gasse 9, 1030, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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30
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Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight. ISME JOURNAL 2018; 12:1473-1485. [PMID: 29445129 PMCID: PMC5956005 DOI: 10.1038/s41396-018-0066-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/26/2017] [Accepted: 01/13/2018] [Indexed: 11/08/2022]
Abstract
Mid-summer peaks in the abundance of Thaumarchaeota and nitrite concentration observed on the Georgia, USA, coast could result from in situ activity or advection of populations from another source. We collected data on the distribution of Thaumarchaeota, ammonia-oxidizing betaproteobacteria (AOB), Nitrospina, environmental variables and rates of ammonia oxidation during six cruises in the South Atlantic Bight (SAB) from April to November 2014. These data were used to examine seasonality of nitrification in offshore waters and to test the hypothesis that the bloom was localized to inshore waters. The abundance of Thaumarchaeota marker genes (16S rRNA and amoA) increased at inshore and nearshore stations starting in July and peaked in August at >107 copies L-1. The bloom did not extend onto the mid-shelf, where Thaumarchaeota genes ranged from 103 to 105 copies L-1. Ammonia oxidation rates (AO) were highest at inshore stations during summer (to 840 nmol L-1 d-1) and were always at the limit of detection at mid-shelf stations. Nitrite concentrations were correlated with AO (R = 0.94) and were never elevated at mid-shelf stations. Gene sequences from samples collected at mid-shelf stations generated using Archaea 16S rRNA primers were dominated by Euryarchaeota; sequences from inshore and nearshore stations were dominated by Thaumarchaeota. Thaumarchaeota were also abundant at depth at the shelf-break; however, this population was phylogenetically distinct from the inshore/nearshore population. Our analysis shows that the bloom is confined to inshore waters during summer and suggests that Thaumarchaeota distributions in the SAB are controlled primarily by photoinhibition and secondarily by water temperature.
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31
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La Cono V, Ruggeri G, Azzaro M, Crisafi F, Decembrini F, Denaro R, La Spada G, Maimone G, Monticelli LS, Smedile F, Giuliano L, Yakimov MM. Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO 2-Fixing Bathypelagic Prokaryotic Consortia. Front Microbiol 2018; 9:3. [PMID: 29403458 PMCID: PMC5780414 DOI: 10.3389/fmicb.2018.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022] Open
Abstract
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m-3 d-1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m-2 d-1. This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.
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Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gioachino Ruggeri
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Maurizio Azzaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Franco Decembrini
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Giovanna Maimone
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Luis S. Monticelli
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Laura Giuliano
- Mediterranean Science Commission (CIESM), Monaco, Monaco
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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32
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Duff AM, Zhang LM, Smith CJ. Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Sci Rep 2017; 7:13200. [PMID: 29038459 PMCID: PMC5643298 DOI: 10.1038/s41598-017-13583-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022] Open
Abstract
While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2- µg-1 g-1 day-1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.
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Affiliation(s)
- Aoife M Duff
- Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Science, Chinese Academy of Sciences, 18 Shuangqing Rd., Haidan Beijing, 100085, P.R. China
| | - Cindy J Smith
- Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland.
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom.
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33
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Danovaro R, Rastelli E, Corinaldesi C, Tangherlini M, Dell'Anno A. Marine archaea and archaeal viruses under global change. F1000Res 2017; 6:1241. [PMID: 29034077 PMCID: PMC5532796 DOI: 10.12688/f1000research.11404.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 01/08/2023] Open
Abstract
Global change is altering oceanic temperature, salinity, pH, and oxygen concentration, directly and indirectly influencing marine microbial food web structure and function. As microbes represent >90% of the ocean’s biomass and are major drivers of biogeochemical cycles, understanding their responses to such changes is fundamental for predicting the consequences of global change on ecosystem functioning. Recent findings indicate that marine archaea and archaeal viruses are active and relevant components of marine microbial assemblages, far more abundant and diverse than was previously thought. Further research is urgently needed to better understand the impacts of global change on virus–archaea dynamics and how archaea and their viruses can interactively influence the ocean’s feedbacks on global change.
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Affiliation(s)
- Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Eugenio Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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34
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Parada AE, Fuhrman JA. Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. ISME JOURNAL 2017; 11:2510-2525. [PMID: 28731479 DOI: 10.1038/ismej.2017.104] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 05/16/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022]
Abstract
Marine archaea are critical contributors to global carbon and nitrogen redox cycles, but their temporal variability and microbial associations across the water column are poorly known. We evaluated seasonal variability of free living (0.2-1 μm size fraction) Thaumarchaea Marine Group I (MGI) and Euryarchaea Marine Group II (MGII) communities and their associations with the microbial community from surface to seafloor (890 m) over 5 years by 16S rRNA V4-V5 gene sequencing. MGI and MGII communities demonstrated distinct compositions at different depths, and seasonality at all depths. Microbial association networks at 150 m, 500 m and 890 m, revealed diverse assemblages of MGI (presumed ammonia oxidizers) and Nitrospina taxa (presumed dominant nitrite oxidizers, completing the nitrification process), suggesting distinct MGI-Nitrospina OTUs are responsible for nitrification at different depths and seasons, and depth- related and seasonal variability in nitrification could be affected by alternating MGI-Nitrospina assemblages. MGII taxa also showed distinct correlations to possibly heterotrophic bacteria, most commonly to members of Marine Group A, Chloroflexi, Marine Group B, and SAR86. Thus, both MGI and MGII likely have dynamic associations with bacteria based on similarities in activity or other interactions that select for distinct microbial assemblages over time. The importance of MGII taxa as members of the heterotrophic community previously reported for photic zone appears to apply throughout the water column.
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Affiliation(s)
- Alma E Parada
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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35
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Hollibaugh JT. Oxygen and the activity and distribution of marine Thaumarchaeota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:186-188. [PMID: 28401690 DOI: 10.1111/1758-2229.12534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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36
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Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environ Microbiol 2017; 19:2434-2452. [PMID: 28418097 DOI: 10.1111/1462-2920.13768] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 11/29/2022]
Abstract
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes. The PT modification genes and an adjacent putative restriction enzyme (RE) operon likely form a restriction modification (RM) system for defence from foreign DNA. PacBio sequencing showed >98% methylation at two motifs, and inferred PT guanine modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals the putative virus region and PT modification and RE genes are present in 18-26%, 9-14% and <1.5% of natural populations at 150 m with ≥85% identity to strain SPOT01. The presence of multiple probable RM systems in a highly streamlined genome suggests a surprising importance for defence from foreign DNA for dilute populations that infrequently encounter viruses or other cells. This new strain provides new insights into the ecology, including viral interactions, of this important group of marine microbes.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yangyang Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Alma E Parada
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Vickie Trinh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ting Chen
- Bioinformatics Division, TNLIST, Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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37
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Schaefer SC, Hollibaugh JT. Temperature Decouples Ammonium and Nitrite Oxidation in Coastal Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3157-3164. [PMID: 28225262 DOI: 10.1021/acs.est.6b03483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nitrification is a two-step process linking the reduced and oxidized sides of the nitrogen cycle. These steps are typically tightly coupled with the primary intermediate, nitrite, rarely accumulating in coastal environments. Nitrite concentrations can exceed 10 μM during summer in estuarine waters adjacent to Sapelo Island, Georgia, U.S.A. Similar peaks at other locations have been attributed to decoupling of the two steps of nitrification by hypoxia; however, the waters around Sapelo Island are aerobic and well-mixed. Experiments examining the response to temperature shifts of a nitrifying assemblage composed of the same organisms found in the field indicate that ammonia- and nitrite-oxidation become uncoupled between 20 and 30 °C, leading to nitrite accumulation. This suggests that nitrite peaks in coastal waters might be explained by differences in the responses of ammonia- and nitrite-oxidizers to increased summer temperatures. Analysis of field data from 270 stations in 29 temperate and subtropical estuaries and lagoons show transient accumulation of nitrite driven primarily by water temperatures, rather than by hypoxia. Increased climate variability and warming coastal waters may therefore increase the frequency of these nitrite peaks, with potential ecosystem consequences that include increased N2O production, NO2- toxicity, and shifts in phytoplankton community composition.
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Affiliation(s)
- Sylvia C Schaefer
- Department of Marine Sciences, University of Georgia , Athens, Georgia 30602-3636, United States
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia , Athens, Georgia 30602-3636, United States
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38
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Luria CM, Amaral-Zettler LA, Ducklow HW, Rich JJ. Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula. Front Microbiol 2016; 7:1731. [PMID: 27857708 PMCID: PMC5093341 DOI: 10.3389/fmicb.2016.01731] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023] Open
Abstract
The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
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Affiliation(s)
- Catherine M Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence RI, USA
| | - Linda A Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods HoleMA, USA; Department of Earth, Environmental and Planetary Sciences, Brown University, ProvidenceRI, USA
| | - Hugh W Ducklow
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory of Columbia University, Palisades NY, USA
| | - Jeremy J Rich
- School of Marine Sciences and Darling Marine Center, University of Maine, Walpole ME, USA
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39
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Tolar BB, Wallsgrove NJ, Popp BN, Hollibaugh JT. Oxidation of urea-derived nitrogen by thaumarchaeota-dominated marine nitrifying communities. Environ Microbiol 2016; 19:4838-4850. [PMID: 27422798 DOI: 10.1111/1462-2920.13457] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Urea nitrogen has been proposed to contribute significantly to nitrification by marine thaumarchaeotes. These inferences are based on distributions of thaumarchaeote urease genes rather than activity measurements. We found that ammonia oxidation rates were always higher than oxidation rates of urea-derived N in samples from coastal Georgia, USA (means ± SEM: 382 ± 35 versus 73 ± 24 nmol L-1 d-1 , Mann-Whitney U-test p < 0.0001), and the South Atlantic Bight (20 ± 8.8 versus 2.2 ± 1.7 nmol L-1 d-1 , p = 0.026) but not the Gulf of Alaska (8.8 ± 4.0 versus 1.5 ± 0.6, p > 0.05). Urea-derived N was relatively more important in samples from Antarctic continental shelf waters, though the difference was not statistically significant (19.4 ± 4.8 versus 12.0 ± 2.7 nmol L-1 d-1 , p > 0.05). We found only weak correlations between oxidation rates of urea-derived N and the abundance or transcription of putative Thaumarchaeota ureC genes. Dependence on urea-derived N does not appear to be directly related to pH or ammonium concentrations. Competition experiments and release of 15 NH3 suggest that urea is hydrolyzed to ammonia intracellularly, then a portion is lost to the dissolved pool. The contribution of urea-derived N to nitrification appears to be minor in temperate coastal waters, but may represent a significant portion of the nitrification flux in Antarctic coastal waters.
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Affiliation(s)
- Bradley B Tolar
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Natalie J Wallsgrove
- Department of Geology and Geophysics, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Brian N Popp
- Department of Geology and Geophysics, University of Hawai'i, Honolulu, HI, 96822, USA
| | - James T Hollibaugh
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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