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Hu X, Huang Y, Gu G, Hu H, Yan H, Zhang H, Zhang R, Zhang D, Wang K. Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China. ENVIRONMENTAL MICROBIOME 2023; 18:75. [PMID: 37805516 PMCID: PMC10560434 DOI: 10.1186/s40793-023-00530-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises. RESULTS The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study. CONCLUSIONS Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.
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Affiliation(s)
- Xuya Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yujie Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Gaoke Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hanjing Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huizhen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China.
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Exploring the Diversity of Active Ureolytic Bacteria in the Rumen by Comparison of cDNA and gDNA. Animals (Basel) 2020; 10:ani10112162. [PMID: 33233592 PMCID: PMC7699693 DOI: 10.3390/ani10112162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Ureolytic bacteria produce urease that hydrolyzes dietary or recycled urea to ammonia, which can then be converted into microbial proteins. The diversity of ruminal ureolytic bacteria benefits N utilization efficiency in ruminants. However, there is no information at the complementary DNA (cDNA) level to reflect the active status of ureolytic bacteria. To reveal the diversity of active ureolytic bacteria in the rumen, we compared ureC amplicons between genomic DNA (gDNA) and cDNA. These results revealed distinct ureolytic bacterial community profiles based on gDNA and cDNA. The dominant ureolytic bacterial had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance. Abstract In this study we revealed the diversity of active ureolytic bacteria in the rumen by compared ureC amplicons between gDNA and cDNA. Rumen fluid was collected from four Holstein dairy cows with rumen fistulas at 0, 2, and 6 h after morning feeding. Total microbial gDNA and RNA were isolated, and the RNA was reverse-transcribed into cDNA. The ureC gene amplicons of gDNA and cDNA were produced and sequenced by MiSeq. These results revealed that the sampling time had no significant difference on the alphssa and beta diversity indices of the ureolytic bacteria. The Shannon diversity of the ureC gene for cDNA was greater than that for gDNA (p < 0.05). There were significant difference in the beta diversity of ureolytic bacteria between gDNA and cDNA (p < 0.01), which indicates a shift in the community of active ureolytic bacteria. Approximately 67% of ureC sequences from cDNA could not be confidently classified at the genus level. The active ureolytic bacteria were mainly from Helicobacter, Herbaspirillum, Clostridium, Paenibacillus, Synechococcus, and Sphingobacterium sp. Changes in the operational taxonomic units revealed that the top abundant ureC genes were mostly consistent between gDNA and cDNA, and most differences occurred in the ureC genes with lower abundances. These results revealed distinct ureolytic bacteria community profiles based on gDNA and cDNA. The dominant ureolytic bacteria had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance.
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Li X, Gao D, Hou L, Liu M. Salinity stress changed the biogeochemical controls on CH 4 and N 2O emissions of estuarine and intertidal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 652:593-601. [PMID: 30368188 DOI: 10.1016/j.scitotenv.2018.10.294] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Elevated salinity is expected to drive changes in biogeochemical cycling and microbial communities in estuarine and intertidal wetlands. However, limited information regarding the role of salinity in shaping biogeochemical controls and mediating greenhouse gas emissions is currently available. In this study, we used incubation experiment across salinity gradients of the estuarine and intertidal sediments to reveal the underlying interconnections of CH4 and N2O emissions, biogeochemical controls and salinity gradients. Our results indicated that sediment biogeochemical properties were significantly affected by the increasing salinity, which were attributed to the accelerated sediment enzyme activities. The increasing salinity promoted CH4 and N2O emission rates by stimulating organic carbon decomposition and nitrogen transformation rates. In addition, the copy number of mcrA, nirS and nirK genes increased along with the salinity gradients, which strongly mediated the CH4 and N2O emission rates. Stepwise regression analysis suggested that labile organic carbon and denitrification were the most crucial determinants of CH4 and N2O emission rates, respectively. Overall, salinity could enhance CH4 and N2O emission mainly by altering sediment geochemical variables, microbial activity and functional gene abundance in estuarine and intertidal environments. Furthermore, increasing salinity could enhance the carbon and nitrogen export, which may pose a threat to the ecological function of estuarine and intertidal ecosystems. This study may contribute to the knowledge about the importance of biogeochemical controls induced by salinity in mediating greenhouse gas emissions.
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Affiliation(s)
- Xiaofei Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou 350007, China; School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China.
| | - Dengzhou Gao
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Costal Research, East China Normal University, Shanghai, 200062, China
| | - Min Liu
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
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Liu X, Pan J, Liu Y, Li M, Gu JD. Diversity and distribution of Archaea in global estuarine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:349-358. [PMID: 29753224 DOI: 10.1016/j.scitotenv.2018.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 05/12/2023]
Abstract
Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.
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Affiliation(s)
- Xiaobo Liu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, People's Republic of China.
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5
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Wu YT, Yang CY, Chiang PW, Tseng CH, Chiu HH, Saeed I, Baatar B, Rogozin D, Halgamuge S, Degermendzhi A, Tang SL. Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia. Front Microbiol 2018; 9:1763. [PMID: 30177915 PMCID: PMC6109700 DOI: 10.3389/fmicb.2018.01763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2–5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.
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Affiliation(s)
- Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Neipu, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Hung Tseng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Germark Biotechnology Co., Ltd., Taichung, Taiwan
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Isaam Saeed
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Bayanmunkh Baatar
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Denis Rogozin
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia
| | - Saman Halgamuge
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrei Degermendzhi
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
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Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, Andersen GL. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. MICROBIOME 2018; 6:71. [PMID: 29661230 PMCID: PMC5902888 DOI: 10.1186/s40168-018-0453-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/28/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs. biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. RESULTS We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at - 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. CONCLUSIONS Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.
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Affiliation(s)
- Cinta Gomez-Silvan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Katherine A. Grue
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Current affiliation: Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, CA USA
| | - Randeep Kaur
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Gary L. Andersen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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Molina V, Dorador C, Fernández C, Bristow L, Eissler Y, Hengst M, Hernandez K, Olsen LM, Harrod C, Marchant F, Anguita C, Cornejo M. The activity of nitrifying microorganisms in a high-altitude Andean wetland. FEMS Microbiol Ecol 2018; 94:4969675. [DOI: 10.1093/femsec/fiy062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Verónica Molina
- Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Avenida Leopoldo Carvallo 270, Playa Ancha, Valparaíso, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
| | - Camila Fernández
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
- Interdisciplinary Center for Aquaculture Research (INCAR), COPAS SUR-AUSTRAL Program, Barrio Universitario s/n, Universidad de Concepción, Concepción, Chile
| | - Laura Bristow
- Nordic Center for Earth Evolution (NordCEE), Department of Biology, University of Southern Denmark, Campusvej 55-5230, Odense, Denmark
| | - Yoanna Eissler
- Centro de Investigación y Gestión de Recursos Naturales, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile
| | - Martha Hengst
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beaucheff 851 (Piso 7)
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte. Av Angamos 0610 Antofagasta, Chile
| | - Klaudia Hernandez
- Centro de Investigacion Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Avenida República 440, Santiago, Chile10
| | | | - Chris Harrod
- Fish and Stable Isotope Ecology Laboratory, Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisca Marchant
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta. Avenida Universidad de Antofagasta s/n, Antofagasta, Chile
| | - Cristobal Anguita
- Departamento de Ecologia y Biodiversidad, Facultad de Ecologia y Recursos Naturales, Universidad Andres Bello, Av. Republica 440, Santiago, Chile
| | - Marcela Cornejo
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía , Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile, Altamirano 1480, Valparaíso
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Lavergne C, Hugoni M, Hubas C, Debroas D, Dupuy C, Agogué H. Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study. MICROBIAL ECOLOGY 2018; 75:364-374. [PMID: 28779296 DOI: 10.1007/s00248-017-1048-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.
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Affiliation(s)
- C Lavergne
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France.
- School of Biochemical Engineering, Pontificia Universidad Católica Valparaíso, Avenida Brasil, 2085, Valparaíso, Chile.
| | - M Hugoni
- CNRS, UMR5557 Ecologie Microbienne, Université Lyon 1, INRA, UMR1418, 69220, Villeurbanne Cedex, France
| | - C Hubas
- Muséum National d'Histoire Naturelle, UMR BOREA, Sorbonne Universités, UPMC Univ Paris 6, CNRS 7208, IRD 207, UCN, UA, Station de Biologie Marine, 29900, Concarneau, France
| | - D Debroas
- Clermont Université, Université Blaise Pascal, LMGE, BP 10448, 63000, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, 63171, Aubière, France
| | - C Dupuy
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - H Agogué
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
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9
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Bertagnolli AD, Ulloa O. Hydrography shapes community composition and diversity of amoA-containing Thaumarchaeota in the coastal waters off central Chile. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:717-728. [PMID: 28836743 DOI: 10.1111/1758-2229.12579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Thaumarchaea are often abundant in low oxygen marine environments, and recent kinetic studies indicate a capacity for aerobic ammonia oxidation at vanishingly low oxygen levels (nM). However, molecular diversity surveys targeting this group to high sequencing coverage are limited, and how these populations are coupled to changes in dissolved oxygen remains unknown. In this study, the ammonia monooxygenase subunit A (amoA) gene was sequenced from samples collected in the Chilean coast (36.5 °S), a system prone to recurrent seasonal hypoxia and anoxia, at several depths over one year, to read depths that saturated coverage statistics. Temperature, salinity and depth displayed a stronger impact on community composition than chemical and biological variables, such as dissolved oxygen. The Nitrosopumilus water-column A clade (WCA) displayed high proportional representation in all samples (42%-100% of all amoA OTUs). The two dominant WCA OTUs displayed differences in their distributions that were inversely correlated with one another, providing the first evidence for intra-subgroup specific differences in the distributions among closely related WCA Thaumarcheota. Nitrosopumilus water-column B (WCB) representatives displayed increased proportional abundances (42%) at deeper depths during the spring and summer, were highly coupled to decreased dissolved oxygen conditions and were non-detectable during the austral winter. The depth of sequencing also enabled observation of lower abundance taxa that are typically not observed in marine environments, such as members of the genus Nitrosotalea amid austral winter surface waters. This study highlights a strong coupling between Thaumarchaeal community diversity and hydrographic variables, is the first to highlight intra-subclade depth specific shifts in community diversity amongst members of the WCA clade, and links the WCB clade to upwelling conditions associated with seasonal oxygen depletion.
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Affiliation(s)
- Anthony D Bertagnolli
- Department of Oceanography and Millennium Institute of Oceanography, Universidad de Concepción, Concepción, P.O. Box 160 C, Chile
| | - Osvaldo Ulloa
- Department of Oceanography and Millennium Institute of Oceanography, Universidad de Concepción, Concepción, P.O. Box 160 C, Chile
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Xia X, Guo W, Liu H. Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean. Front Microbiol 2017; 8:2057. [PMID: 29109713 PMCID: PMC5660102 DOI: 10.3389/fmicb.2017.02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/06/2017] [Indexed: 01/09/2023] Open
Abstract
The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.
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Affiliation(s)
| | | | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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11
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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12
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Long Y, Yi H, Chen S, Zhang Z, Cui K, Bing Y, Zhuo Q, Li B, Xie S, Guo Q. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19570-9. [PMID: 27392623 DOI: 10.1007/s11356-016-7166-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/28/2016] [Indexed: 05/12/2023]
Abstract
Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.
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Affiliation(s)
- Yan Long
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Hao Yi
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Kai Cui
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Yongxin Bing
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Qiongfang Zhuo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China.
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13
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Yang Y, Dai Y, Wu Z, Xie S, Liu Y. Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status. Front Microbiol 2016; 7:451. [PMID: 27065997 PMCID: PMC4814500 DOI: 10.3389/fmicb.2016.00451] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/21/2016] [Indexed: 11/20/2022] Open
Abstract
In either eutrophic Dianchi Lake or mesotrophic Erhai Lake, the abundance, diversity, and structure of archaeaplankton communities in spring were different from those in summer. In summer, archaeaplankton abundance generally decreased in Dianchi Lake but increased in Erhai Lake, while archaeaplankton diversity increased in both lakes. These two lakes had distinct archaeaplankton community structure. Archaeaplankton abundance was influenced by organic content, while trophic status determined archaeaplankton diversity and structure. Moreover, in summer, lake sediment archaeal abundance considerably decreased. Sediment archaeal abundance showed a remarkable spatial change in spring but only a slight one in summer. The evident spatial change of sediment archaeal diversity occurred in both seasons. In Dianchi Lake, sediment archaeal community structure in summer was remarkably different from that in spring. Compared to Erhai Lake, Dianchi Lake had relatively high sediment archaeal abundance but low diversity. These two lakes differed remarkably in sediment archaeal community structure. Trophic status determined sediment archaeal abundance, diversity and structure. Archaeal diversity in sediment was much higher than that in water. Water and sediment habitats differed greatly in archaeal community structure. Euryarchaeota predominated in water column, but showed much lower proportion in sediment. Bathyarchaeota was an important component of sediment archaeal community.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University Beijing, China
| | - Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University Beijing, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University Beijing, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University Beijing, China
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University Beijing, China
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14
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Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes. Appl Microbiol Biotechnol 2016; 100:4685-98. [PMID: 26810199 DOI: 10.1007/s00253-016-7318-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities.
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