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Liu J, Huang X, Jiang X, Qing C, Li Y, Xia P. Loss of submerged macrophytes in shallow lakes alters bacterial and archaeal community structures, and reduces their co-occurrence networks connectivity and complexity. Front Microbiol 2024; 15:1380805. [PMID: 38601927 PMCID: PMC11004660 DOI: 10.3389/fmicb.2024.1380805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Bacteria and archaea are important components in shallow lake ecosystems and are crucial for biogeochemical cycling. While the submerged macrophyte loss is widespread in shallow lakes, the effect on the bacteria and archaea in the sediment and water is not yet widely understood. Methods In this study, 16S rRNA gene sequencing was used to explore the bacteria and archaea in samples taken from the sediment and water in the submerged macrophyte abundant (MA) and submerged macrophyte loss (ML) areas of Caohai Lake, Guizhou, China. Results The results showed that the dominant bacterial phyla were Proteobacteria and Chloroflexi in the sediment; the dominant phyla were Proteobacteria, Actinobacteriota, and Bacteroidota in the water. The dominant archaea in sediment and water were the same, in the order of Crenarchaeota, Thermoplasmatota, and Halobacterota. Non-metric multidimensional scaling (NMDS) analyses showed that bacterial and archaeal community structures in the water were significantly affected by the loss of submerged macrophytes, but not by significant changes in the sediment. This suggests that the loss of submerged macrophytes has a stronger effect on the bacterial and archaeal community structures in water than in sediment. Furthermore, plant biomass (PB) was the key factor significantly influencing the bacterial community structure in water, while total nitrogen (TN) was the main factor significantly influencing the archaeal community structure in water. The loss of submerged macrophytes did not significantly affect the alpha diversity of the bacterial and archaeal communities in either the sediment or water. Based on network analyses, we found that the loss of submerged macrophytes reduced the connectivity and complexity of bacterial patterns in sediment and water. For archaea, network associations were stronger for MA network than for ML network in sediment, but network complexity for archaea in water was not significantly different between the two areas. Discussion This study assesses the impacts of submerged macrophyte loss on bacteria and archaea in lakes from microbial perspective, which can help to provide further theoretical basis for microbiological research and submerged macrophytes restoration in shallow lakes.
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Affiliation(s)
- Jiahui Liu
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
| | - Xianfei Huang
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
| | - Xin Jiang
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
| | - Chun Qing
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
| | - Yue Li
- Guizhou Caohai National Nature Reserve Management Committee, Bijie, Guizhou, China
| | - Pinhua Xia
- Guizhou Province Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment, Guizhou Normal University, Guiyang, China
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2
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Acetoclastic archaea adaptation under increasing temperature in lake sediments and wetland soils from Alaska. Polar Biol 2023. [DOI: 10.1007/s00300-023-03120-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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3
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Noyer M, Bernard M, Verneau O, Palacios C. Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49685-49702. [PMID: 36780079 DOI: 10.1007/s11356-023-25637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/14/2023]
Abstract
Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.
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Affiliation(s)
- Mégane Noyer
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France
| | - Maria Bernard
- Univ. Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Olivier Verneau
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.,Unit. for Environmental Sciences and Management, North-West University, Potchefstroom, ZA-2520, South Africa
| | - Carmen Palacios
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France. .,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.
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Xiang X, Wang H, Man B, Xu Y, Gong L, Tian W, Yang H. Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China. MICROBIAL ECOLOGY 2023; 85:557-571. [PMID: 35332366 DOI: 10.1007/s00248-022-01990-1] [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: 06/04/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.
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Affiliation(s)
- Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Linfeng Gong
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
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5
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Zou D, Li H, Du P, Wang B, Lin H, Liu H, Chen J, Li M. Distinct Features of Sedimentary Archaeal Communities in Hypoxia and Non-Hypoxia Regions off the Changjiang River Estuary. Microbiol Spectr 2022; 10:e0194722. [PMID: 36066619 PMCID: PMC9602602 DOI: 10.1128/spectrum.01947-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
Water hypoxia (DO < 2 mg/L) is a growing global environmental concern that has the potential to significantly influence not only the aquatic ecosystem but also the benthic sedimentary ecosystem. The Changjiang River Estuary hypoxia, classified as one of the world's largest seasonal hypoxic water basins, has been reported to be expanding rapidly in recent decades. However, the microbial community dynamics and responses to this water hypoxia are still unclear. In this study, we examined the abundance, community composition, and distribution of sedimentary archaea, one important component of microbial communities in the Changjiang River Estuary and the East China Sea (ECS). Our results indicated that Thaumarchaeota and Bathyarchaeota were predominant archaeal groups in these research areas, with their 16S rRNA gene abundance ranged from 8.55 × 106 to 7.51 × 108 and 3.18 × 105 to 1.11 × 108 copies/g, respectively. The sedimentary archaeal community was mainly influenced by DO, together with the concentration of ammonium, nitrate, and sulfide. In addition, distinct differences in the archaeal community's composition, abundance, and driving factors were discovered between samples from hypoxia and non-hypoxia stations. Furtherly, microbial networks suggest various microbes leading the different activities in hypoxic and normoxic environments. Bathyarchaeota and Thermoprofundales were "key stone" archaeal members of the low-DO network, whereas Thaumarchaeota constituted a significant component of the high-DO network. Our results provide a clear picture of the sedimentary archaeal community in coastal hypoxia zones and indicates potential distinctions of archaea in hypoxia and non-hypoxia environments, including ecological niches and metabolic functions. IMPORTANCE In this study, the sedimentary archaeal community composition and abundance were detailed revealed and quantified based on 16S rRNA genes off the Changjiang River Estuary. We found that the community composition was distinct between hypoxia and non-hypoxia regions, while Thaumarchaeota and Bathyarchaeota dominated in non-hypoxia and hypoxia samples, respectively. In hypoxia regions, the sedimentary archaea were mainly affected by salinity, ammonium, and nitrate, whereas total organic carbon, total nitrogen, and sulfide were major influencing factors in non-hypoxia regions. The distinct microbial network may suggest the niche difference of archaeal community under various oxygen level.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Hongliang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Ping Du
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Bin Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hua Lin
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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6
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Wang L, Liang Z, Guo Z, Cong W, Song M, Wang Y, Jiang Z. Response mechanism of microbial community to seasonal hypoxia in marine ranching. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152387. [PMID: 34915008 DOI: 10.1016/j.scitotenv.2021.152387] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/05/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Seasonal hypoxia, as an increasingly recognized environmental issue, frequently occurred in marine ranching from northern Yellow Sea, China. Although microorganisms play an important ecological role in marine ecosystems, but little is known on the response mechanism of microbial community to seasonal hypoxia in marine ranching. A total of 132 seawater samples and 47 sediment samples were collected from the marine ranching, both in the death disaster zone of sea cucumbers and the non-disaster zone, and in different months. 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors. The results showed that the stratification in community composition and dissolved oxygen content appeared in August. The Alpha diversity in seawater was higher in summer than in winter, and significant differences in Beta diversity appeared between the death disaster zone of sea cucumbers and the non-disaster zone in sediments. In addition, environmental effects explained more of the variation in bacterial community composition in seawater as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. The present results could provide fundamental data for understanding the response mechanism of the microbial community to seasonal hypoxia in marine ranching and are of great significance for the management and protection of marine ranching.
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Affiliation(s)
- Lu Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhansheng Guo
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Wei Cong
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Minpeng Song
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Yuxin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhaoyang Jiang
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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Seasonal Dynamics of Bathyarchaeota-Dominated Benthic Archaeal Communities Associated with Seagrass (Zostera japonica) Meadows. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9111304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Little is known about the seasonal dynamic of archaeal communities and their potential ecological functions in temperate seagrass ecosystems. In this study, seasonal changes in diversity, community structure, and potential metabolic functions of benthic archaea in surface sediments of two seagrass meadows along the northern Bohai Sea in China were investigated using Miseq sequencing of the 16S rRNA gene and Tax4Fun2 functional prediction. Overall, Crenarchaeota (mainly Bathy-15, Bathy-8, and Bathy-6) dominated, followed by Thermoplasmatota, Asgardarchaeota, and Halobacterota, in terms of alpha diversities and relative abundance. Significant seasonal changes in the entire archaeal community structure were observed. The major phyla Methanobacteria, Nitrosopumilales, and genus Methanolobus had higher proportions in spring, while MBG-D and Bathyarchaeota were more abundant in summer and autumn, respectively. Alpha diversities (Shannon and Simpson) were the highest in summer and the lowest in autumn (ANOVA test, p < 0.05). Salinity, total organic carbon, and total organic nitrogen were the most significant factors influencing the entire archaeal community. Higher cellulose and hemicellulose degradation potentials occurred in summer, while methane metabolism potentials were higher in winter. This study indicated that season had strong effects in modulating benthic archaeal diversity and functional potentials in the temperate seagrass ecosystems.
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8
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Chen Y, Qiu K, Zhong Z, Zhou T. Influence of Environmental Factors on the Variability of Archaeal Communities in a Karst Wetland. Front Microbiol 2021; 12:675665. [PMID: 34539596 PMCID: PMC8448418 DOI: 10.3389/fmicb.2021.675665] [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: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Archaea are ubiquitous and play an important role in elemental cycles in Earth’s biosphere; but little is known about their diversity, distribution, abundance, and impact in karst environments. The present study investigated the effect of environmental factors on the variability of archaeal communities in the sediment of the Huixian karst wetland, the largest karst wetland in South China. Sediment cores were obtained from four sampling sites with different water depths and macrophyte inhabitants in both the winter of 2016 and the summer of 2018. The community analysis was based on PacBio sequencing and quantitative PCR of the archaeal 16S rRNA gene. The results showed that Euryarchaeota (57.4%) and Bathyarchaeota (38.7%) were dominant in all the samples. Methanogenic Methanosarcinales (25.1%) and Methanomicrobiales (13.7%), and methanotrophic archaea ANME-2d (9.0%) were the dominant Euryarchaeota; MCG-11 (16.5%), MCG-6 (9.1%), and MCG-5b (5.5%) were the dominant Bathyarchaeota. The community composition remained stable between summer and winter, and the vertical distributions of the archaeal phyla conformed to two patterns among the four sampling sites. In the winter samples, the archaeal 16S rRNA gene abundance was approximately 1.0E+10 copies/g of wet sediment and the Shannon index was 7.3±5, which were significantly higher than in the summer samples and in other karst environments. A correlation analysis showed that the moisture content and pH were the factors that mostly affected the archaeal communities. The prevalence of nitrate in the summer may be a key factor causing a significant decrease in archaeal abundance and diversity. Two features specific to karst environments, calcium-richness and weak alkalescence of the water supplies, may benefit the prevalence of bathyarchaeotal subgroups MCG-11, MCG-5b, and MCG-6. These results suggest that in karst wetlands, most of the archaea belong to clades that have significant roles in carbon turnover; their composition remains stable, but their abundance and diversity vary significantly from season to season.
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Affiliation(s)
- Ying Chen
- School of Biotechnology, Guilin Medical University, Guilin, China
| | - Kairui Qiu
- School of Biotechnology, Guilin Medical University, Guilin, China
| | - Ziyuan Zhong
- School of Biotechnology, Guilin Medical University, Guilin, China
| | - Tao Zhou
- School of Biotechnology, Guilin Medical University, Guilin, China
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9
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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11
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Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir. Sci Rep 2020; 10:11288. [PMID: 32647153 PMCID: PMC7347578 DOI: 10.1038/s41598-020-67774-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/22/2020] [Indexed: 02/01/2023] Open
Abstract
Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.
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12
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Compte-Port S, Fillol M, Gich F, Borrego CM. Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. PLoS One 2020; 15:e0231238. [PMID: 32267873 PMCID: PMC7141681 DOI: 10.1371/journal.pone.0231238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.
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Affiliation(s)
- Sergi Compte-Port
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Frederic Gich
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M. Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
- * E-mail:
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13
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Pan J, Zhou Z, Béjà O, Cai M, Yang Y, Liu Y, Gu JD, Li M. Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota. MICROBIOME 2020; 8:43. [PMID: 32234071 PMCID: PMC7110647 DOI: 10.1186/s40168-020-00820-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. RESULTS In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup. CONCLUSIONS The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. Video abstract.
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Affiliation(s)
- Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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14
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Zou D, Pan J, Liu Z, Zhang C, Liu H, Li M. The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient. Front Microbiol 2020; 11:285. [PMID: 32174899 PMCID: PMC7056671 DOI: 10.3389/fmicb.2020.00285] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/07/2020] [Indexed: 01/05/2023] Open
Abstract
Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Metabolic pathways of the Bathyarchaeota members are diverse and, hence, this phylum has been proposed to play an important role in global biogeochemical cycles. Bathyarchaeota members are distributed in the estuarine environments. However, limited information is available about their detailed community structure, abundance, and functions in the Pearl River estuary (PRE). In the current study, we performed a comprehensive investigation of the archaeal community in the PRE surface sediments along a salinity gradient, with a focus on Bathyarchaeota. Bathyarchaeota was the dominant archaeal phylum, with the abundance of the bathyarchaeotal 16S rRNA gene ranging from 1.43 × 108 to 1.22 × 109 copies/g sediment dry weight (d.w.), and Bathy-8 was the dominant subgroup. Thaumarchaeota, Lokiarchaeota, and Euryarchaeota, including Thermoprofundales (MBG-D archaea), were the other major archaeal groups in the PRE. The differences of community distributions in the high- and low-salinity sediments were hence investigated. Statistical analysis revealed that besides salinity, ammonium, and total organic carbon were the most important environmental factors influencing the archaea community structure, including that of Bathyarchaeota, in the PRE. The archaeal network indicated the cooccurrence among Bathyarchaeota, Lokiarchaeota, and Euryarchaeota, while Bathy-6 presented unique correlations compared with other bathyarchaeotal subgroups. These observations indicate that Bathyarchaeota may play a role in ecosystem function through microbe-microbe interactions, revealing a possible different lifestyle for Bathy-6 in eutrophic estuarine sediments.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zongbao Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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15
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Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:5108012. [PMID: 31827386 PMCID: PMC6885780 DOI: 10.1155/2019/5108012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/29/2019] [Accepted: 10/10/2019] [Indexed: 01/31/2023]
Abstract
Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.
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16
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Mania I, Gorra R, Colombo N, Freppaz M, Martin M, Anesio AM. Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. MICROBIAL ECOLOGY 2019; 78:70-84. [PMID: 30317429 DOI: 10.1007/s00248-018-1272-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4+) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.
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Affiliation(s)
- I Mania
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK.
| | - R Gorra
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - N Colombo
- Department of Earth Sciences, University of Turin, Via Valperga Caluso 35, 10125, Torino, Italy
- Department of Geography and Environmental Studies, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - M Freppaz
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - M Martin
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - A M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Department of Environmental Sciences, Aarhus University, 4000, Roskilde, Denmark
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17
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Pan J, Chen Y, Wang Y, Zhou Z, Li M. Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6. MICROBIAL ECOLOGY 2019; 77:417-428. [PMID: 30612184 DOI: 10.1007/s00248-018-1309-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.
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Affiliation(s)
- Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yulian Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yongming Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Zhichao Zhou
- 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.
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18
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Sollai M, Villanueva L, Hopmans EC, Reichart G, Sinninghe Damsté JS. A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. GEOBIOLOGY 2019; 17:91-109. [PMID: 30281902 PMCID: PMC6586073 DOI: 10.1111/gbi.12316] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.
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Affiliation(s)
- Martina Sollai
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Laura Villanueva
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Ellen C. Hopmans
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Gert‐Jan Reichart
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
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19
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Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev 2018; 42:639-655. [PMID: 29790926 DOI: 10.1093/femsre/fuy023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.
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Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.,Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
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20
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von Gunten K, Hamilton SM, Zhong C, Nesbø C, Li J, Muehlenbachs K, Konhauser KO, Alessi DS. Electron donor-driven bacterial and archaeal community patterns along forest ring edges in Ontario, Canada. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:663-672. [PMID: 30014579 DOI: 10.1111/1758-2229.12678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/08/2018] [Indexed: 06/08/2023]
Abstract
Forest rings are 50-1600 m diameter circular structures found in boreal forests around the globe. They are believed to be chemically reducing chimney features, having an accumulation of reduced species in the middle of the ring and oxidation processes occurring at the ring's edges. It has been suggested that microorganisms could be responsible for charge transfer from the inside to the outside of the ring. To explore this, we focused on the changes in bacterial and archaeal communities in the ring edges of two forest rings, the 'Bean' and the 'Thorn North' ring, in proximity to each other in Ontario, Canada. The drier samples from the methane-sourced Bean ring were characterized by the abundance of bacteria from the classes Deltaproteobacteria and Gemmatimonadetes. Geobacter spp. and methanotrophs, such as Candidatus Methylomirabilis and Methylobacter, were highly abundant in these samples. The Thorn North ring, centred on an H2 S accumulation in groundwater, had wetter samples and its communities were dominated by the classes Alphaproteobacteria and Anaerolineae. This ring's microbial communities showed an overall higher microbial diversity supported by higher available free energy. For both rings, the species diversity was highest near the borders of the 20-30 m broad ring edges.
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Affiliation(s)
- Konstantin von Gunten
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Stewart M Hamilton
- Ministry of Northern Development and Mines, Sudbury Office, 159 Cedar Street, Sudbury, Ontario, P3E 6A5, Canada
| | - Cheng Zhong
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Camilla Nesbø
- University of Alberta, Biological Sciences, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Jiaying Li
- University of Alberta, Biological Sciences, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Karlis Muehlenbachs
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Kurt O Konhauser
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Daniel S Alessi
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
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21
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Rinta-Kanto J, Pehkonen K, Sinkko H, Tamminen M, Timonen S. Archaeaare prominent members of the prokaryotic communities colonizing common forest mushrooms. Can J Microbiol 2018; 64:716-726. [DOI: 10.1139/cjm-2018-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.
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Affiliation(s)
- J.M. Rinta-Kanto
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
| | - K. Pehkonen
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
| | - H. Sinkko
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
| | - M.V. Tamminen
- Department of Biology, University Hill, 20014 University of Turku, Finland
| | - S. Timonen
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
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22
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Successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota from the Pearl River estuary to the northern South China Sea. Appl Microbiol Biotechnol 2018; 102:8035-8048. [PMID: 29946932 DOI: 10.1007/s00253-018-9147-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/05/2018] [Accepted: 05/23/2018] [Indexed: 01/09/2023]
Abstract
Thaumarchaeota and Bathyarchaeota (formerly named Miscellaneous Crenarchaeotal Group, MCG) are globally occurring archaea playing potential roles in nitrogen and carbon cycling, especially in marine benthic biogeochemical cycle. Information on their distributional and compositional patterns could provide critical clues to further delineate their physiological and biochemical characteristics. Profiles of thaumarchaeotal and the total archaeal community in the northern South China Sea surface sediments revealed a successively transitional pattern of Thaumarchaeota composition using MiSeq sequencing. Shallow-sea sediment enriched phylotypes decreased gradually along the slope from estuarine and coastal marine region to the deep-sea, while deep-sea sediment enriched phylotypes showed a trend of increasing. Proportion of Thaumarchaeota within the total archaea increased with seawater depth. Phylotypes enriched in shallow- and deep-sea sediments were affiliated to OTUs originated from similar niches, suggesting that physiological adaption not geographical distance shaped the distribution of Thaumarchaeota lineages. Quantitative PCR also depicted a successive decrease of thaumarchaeotal 16S rRNA gene abundance from the highest at shallow-sea sites E708S and E709S (2.57 × 106 and 2.73 × 106 gene copies/g of dry sediment) to the lowest at deep-sea sites E525S and E407S (1.97 × 106 and 2.14 × 106 gene copies/g of dry sediment). Both of the abundance fractions of Bathyarchaeota subgroups (including subgroups 1, 6, 8, 10, 13, 15, 17, and ungrouped Bathyarchaeota) and the total Bathyarchaeota in the total archaea showed a negative distribution to seawater depth. Partitioned distribution of Bathyarchaeota fraction in the total archaea is documented for the first time in this study, and the shallow- and deep-sea Bathyarchaeota could account for 17.8 and 0.8%, respectively, on average. Subgroups 6 and 8, enriched subgroups in shallow-sea sediments, largely explained this partitioned distribution pattern according to seawater depth. Their prevalence in shallow-sea and suboxic estuarine sediments rather than deep-sea sediments hints that their metabolic properties of carbon metabolism are adapted to carbon substrates in these environments.
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23
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Compte-Port S, Borrego CM, Moussard H, Jeanbille M, Restrepo-Ortiz CX, de Diego A, Rodriguez-Iruretagoiena A, Gredilla A, Fdez-Ortiz de Vallejuelo S, Galand PE, Kalenitchenko D, Rols JL, Pokrovsky OS, Gonzalez AG, Camarero L, Muñiz S, Navarro-Navarro E, Auguet JC. Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes. Environ Microbiol 2018; 20:2422-2437. [PMID: 29687572 DOI: 10.1111/1462-2920.14252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 12/22/2022]
Abstract
Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (105 to 109 copies g-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.
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Affiliation(s)
- Sergi Compte-Port
- Group of Quality and Microbial Diversity, Catalan Institute for Water research (ICRA), Girona, Spain
| | - Carles M Borrego
- Group of Quality and Microbial Diversity, Catalan Institute for Water research (ICRA), Girona, Spain.,Group of Molecular Microbial Ecology (gEMM), Institute of Aquatic Ecology, University of Girona (UdG), Girona, Spain
| | - Hélène Moussard
- Equipe Environnement et Microbiologie (IPREM-EEM), UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Mathilde Jeanbille
- Department of plant pathology and forest mycology Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
| | | | - Alberto de Diego
- Department of analytical chemistry, Faculty of science and technology, University of Basque Country, Bilbao, Spain
| | | | - Ainara Gredilla
- Department of analytical chemistry, Faculty of science and technology, University of Basque Country, Bilbao, Spain
| | | | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls/Mer, F-66650, France
| | - Dimitri Kalenitchenko
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls/Mer, F-66650, France
| | - Jean-Luc Rols
- EcoLab, UMR CNRS 5245, Observatory of Midi-Pyrénées, University Paul Sabatier, Toulouse, France
| | - Oleg S Pokrovsky
- Geosciences and Environment Toulouse, UMR 5563 CNRS, 14 Avenue Edouard Belin 31400, Toulouse, France.,BIO-GEO-CLIM Laboratory, Tomsk State University, Tomsk, Russia
| | - Aridane G Gonzalez
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Lluis Camarero
- Group of integrative freshwater ecology, Department of continental ecology, Center of advanced studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Selene Muñiz
- Pyrenean institute of ecology (IPE-CSIC), Zaragoza, Spain
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24
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Tassi F, Fazi S, Rossetti S, Pratesi P, Ceccotti M, Cabassi J, Capecchiacci F, Venturi S, Vaselli O. The biogeochemical vertical structure renders a meromictic volcanic lake a trap for geogenic CO2 (Lake Averno, Italy). PLoS One 2018; 13:e0193914. [PMID: 29509779 PMCID: PMC5839588 DOI: 10.1371/journal.pone.0193914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/07/2018] [Indexed: 11/18/2022] Open
Abstract
Volcanic lakes are characterized by physicochemical favorable conditions for the development of reservoirs of C-bearing greenhouse gases that can be dispersed to air during occasional rollover events. By combining a microbiological and geochemical approach, we showed that the chemistry of the CO2- and CH4-rich gas reservoir hosted within the meromictic Lake Averno (Campi Flegrei, southern Italy) are related to the microbial niche differentiation along the vertical water column. The simultaneous occurrence of diverse functional groups of microbes operating under different conditions suggests that these habitats harbor complex microbial consortia that impact on the production and consumption of greenhouse gases. In the epilimnion, the activity of aerobic methanotrophic bacteria and photosynthetic biota, together with CO2 dissolution at relatively high pH, enhanced CO2- and CH4 consumption, which also occurred in the hypolimnion. Moreover, results from computations carried out to evaluate the dependence of the lake stability on the CO2/CH4 ratios, suggested that the water density vertical gradient was mainly controlled by salinity and temperature, whereas the effect of dissolved gases was minor, excepting if extremely high increases of CH4 are admitted. Therefore, biological processes, controlling the composition of CO2 and CH4, contributed to stabilize the lake stratification of the lake. Overall, Lake Averno, and supposedly the numerous worldwide distributed volcanic lakes having similar features (namely bio-activity lakes), acts as a sink for the CO2 supplied from the hydrothermal/magmatic system, displaying a significant influence on the local carbon budget.
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Affiliation(s)
- Franco Tassi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, Florence, Italy
- IGG-CNR Institute of Geosciences and Earth Resources, National Research Council of Italy, Via La Pira 4, Florence, Italy
- * E-mail:
| | - Stefano Fazi
- IRSA-CNR Water Research Institute, National Research Council of Italy, Via Salaria, Monterotondo, Rome, Italy
| | - Simona Rossetti
- IRSA-CNR Water Research Institute, National Research Council of Italy, Via Salaria, Monterotondo, Rome, Italy
| | - Paolo Pratesi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, Florence, Italy
| | - Marco Ceccotti
- IRSA-CNR Water Research Institute, National Research Council of Italy, Via Salaria, Monterotondo, Rome, Italy
| | - Jacopo Cabassi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, Florence, Italy
- IGG-CNR Institute of Geosciences and Earth Resources, National Research Council of Italy, Via La Pira 4, Florence, Italy
| | | | - Stefania Venturi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, Florence, Italy
- IGG-CNR Institute of Geosciences and Earth Resources, National Research Council of Italy, Via La Pira 4, Florence, Italy
| | - Orlando Vaselli
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, Florence, Italy
- IGG-CNR Institute of Geosciences and Earth Resources, National Research Council of Italy, Via La Pira 4, Florence, Italy
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25
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Xie W, Luo H, Murugapiran SK, Dodsworth JA, Chen S, Sun Y, Hedlund BP, Wang P, Fang H, Deng M, Zhang CL. Localized high abundance of Marine Group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environ Microbiol 2017; 20:734-754. [PMID: 29235710 DOI: 10.1111/1462-2920.14004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 11/29/2022]
Abstract
Marine Group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/l), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments. 10‰ salinity appeared to be a threshold value for these MGII because MGII abundance decreased sharply below it. Above 10‰ salinity, the abundance of MGII on the particles was positively correlated with phototrophs and MGII in the surface water was negatively correlated with irradiance. However, the abundances of those free-living MGII showed positive correlations with salinity and temperature, suggesting the different physiological characteristics between particle-attached and free-living MGIIs. A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binning methods. Compared with the other two MGII genomes from surface ocean, MGIIa_P contained higher proportions of glycoside hydrolases, indicating the ability of MGIIa_P to hydrolyse glycosidic bonds in complex sugars in PRE. MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be involved in scavenging reactive oxygen species generated by the abundant phototrophs in the eutrophic PRE. Our study presented the widespread and high abundance of MGII in the water columns of PRE, and characterized the determinant abiotic factors affecting their distribution. Their association with heterotrophs, preference for particles and resourceful metabolic traits indicate MGII might play a significant role in metabolising organic matters in the PRE and other temperate estuarine systems.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA.,MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Songze Chen
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Huaying Fang
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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26
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Suter EA, Pachiadaki M, Taylor GT, Astor Y, Edgcomb VP. Free‐living chemoautotrophic and particle‐attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Environ Microbiol 2017; 20:693-712. [DOI: 10.1111/1462-2920.13997] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Elizabeth A. Suter
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
- Department of Biological SciencesWagner CollegeStaten Island NY 10301 USA
| | - Maria Pachiadaki
- Woods Hole Oceanographic InstitutionWoods Hole MA USA
- Bigelow Laboratory for Ocean SciencesEast Boothbay ME USA
| | - Gordon T. Taylor
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
| | - Yrene Astor
- Fundación La Salle de Ciencias Naturales, EDIMARPorlamar Nueva Esparta Venezuela
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27
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Compte-Port S, Subirats J, Fillol M, Sànchez-Melsió A, Marcé R, Rivas-Ruiz P, Rosell-Melé A, Borrego CM. Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula. MICROBIAL ECOLOGY 2017; 74:776-787. [PMID: 28508926 DOI: 10.1007/s00248-017-0989-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/23/2017] [Indexed: 06/07/2023]
Abstract
Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.
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Affiliation(s)
- Sergi Compte-Port
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Rafael Marcé
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Pedro Rivas-Ruiz
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Rosell-Melé
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010, Barcelona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain.
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28
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Ma KL, Li XK, Wang K, Meng LW, Liu GG, Zhang J. Establishment of thermophilic anaerobic terephthalic acid degradation system through one-step temperature increase startup strategy - Revealed by Illumina Miseq Sequencing. CHEMOSPHERE 2017; 184:951-959. [PMID: 28655114 DOI: 10.1016/j.chemosphere.2017.06.090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/16/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition.
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Affiliation(s)
- Kai-Li Ma
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China.
| | - Xiang-Kun Li
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China.
| | - Ke Wang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China.
| | - Ling-Wei Meng
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China
| | - Gai-Ge Liu
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China
| | - Jie Zhang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China
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29
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Yu T, Liang Q, Niu M, Wang F. High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:374-382. [PMID: 28419783 DOI: 10.1111/1758-2229.12539] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep-sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy-2, Bathy-8 and Bathy-10 were dominant bathyarchaeotal members of the deep-sea sediments in the SCS. Bathy-8 was found predominantly within the reducing and deeper sediment layers, while Bathy-10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well-understood sedimentary archaeal group.
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Affiliation(s)
- Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qianyong Liang
- Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510070, China
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
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30
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Louca S, Jacques SMS, Pires APF, Leal JS, González AL, Doebeli M, Farjalla VF. Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions. Environ Microbiol 2017; 19:3132-3151. [PMID: 28488752 DOI: 10.1111/1462-2920.13788] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/24/2017] [Indexed: 11/27/2022]
Abstract
Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Saulo M S Jacques
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Ecologia e Evolução, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aliny P F Pires
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S Leal
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Angélica L González
- Biology Department & Center for Computational & Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Vinicius F Farjalla
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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31
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Fan X, Xing P. Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu. Front Microbiol 2016; 7:1510. [PMID: 27708641 PMCID: PMC5030832 DOI: 10.3389/fmicb.2016.01510] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/09/2016] [Indexed: 11/13/2022] Open
Abstract
In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats.
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Affiliation(s)
- Xianfang Fan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology (CAS)Nanjing, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science (CAS)Nanjing, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology (CAS) Nanjing, China
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Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary. Appl Microbiol Biotechnol 2016; 100:9683-9697. [PMID: 27557722 DOI: 10.1007/s00253-016-7802-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/09/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
There are close exchanges between sediment and water in estuaries; however, the patterns of prokaryotic community assembly in these two habitat types are still unclear. This study investigated the bacterial and archaeal abundance, diversity, and community composition in the sediment and the overlying water of the Yellow River estuary. Notably higher prokaryotic abundance and diversity were detected in the sediment than in the water, and bacterial abundance and diversity were remarkably higher than those of archaea. Furthermore, the ratio of bacterial to archaeal 16S rRNA gene abundance was significantly lower in the sediment than in the water. Bacterial communities at different taxonomic levels were apparently distinct between the sediment and water, but archaeal communities were not. The most dominant bacteria were affiliated with Deltaproteobacteria and Gammaproteobacteria in sediment and with Alphaproteobacteria and Betaproteobacteria in water. Euryarchaeota and Thaumarchaeota were the most abundant archaea in both habitats. Although distinct prokaryotic distribution patterns were observed, most of the dominant bacteria and archaea present were related to carbon, nitrogen, and sulfur cycling processes, such as methanogenesis, ammonia oxidation, and sulfate reduction. Unexpectedly, prokaryotes from the water showed a higher sensitivity to environmental factors, while only a few factors affected sediment communities. Additionally, some potential co-occurrence relationships between prokaryotes were also found in this study. These results suggested distinct distribution patterns of bacterial and archaeal communities between sediment and overlying water in this important temperate estuary, which may serve as a useful community model for the further ecological and evolutionary study of prokaryotes in estuarine ecosystems.
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The Vertical Distribution of Sediment Archaeal Community in the "Black Bloom" Disturbing Zhushan Bay of Lake Taihu. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:8232135. [PMID: 26884723 PMCID: PMC4738990 DOI: 10.1155/2016/8232135] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/27/2015] [Accepted: 12/20/2015] [Indexed: 11/18/2022]
Abstract
Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3–6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus (TP). And loss on ignition (LOI) was an important environmental factor for Methanobacterium. As the typical archaeal taxa in the surface layer sediment, DHVEG-6 and Methanobacterium might be more adapted to abundant substrate supply from cyanobacterial blooms and take active part in the biomass transformation. We propose that DHVEG-6 and Methanobacterium could be the key archaeal taxa correlated with the “black bloom” formation in Zhushan Bay.
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Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage. ISME JOURNAL 2015; 10:665-77. [PMID: 26284443 DOI: 10.1038/ismej.2015.143] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/26/2015] [Accepted: 07/01/2015] [Indexed: 11/08/2022]
Abstract
Members of the archaeal Miscellaneous Crenarchaeotic Group (MCG) are among the most successful microorganisms on the planet. During its evolutionary diversification, this very diverse group has managed to cross the saline-freshwater boundary, one of the most important evolutionary barriers structuring microbial communities. However, the current understanding on the ecological significance of MCG in freshwater habitats is scarce and the evolutionary relationships between freshwater and saline MCG remains poorly known. Here, we carried out molecular phylogenies using publicly available 16S rRNA gene sequences from various geographic locations to investigate the distribution of MCG in freshwater and saline sediments and to evaluate the implications of saline-freshwater transitions during the diversification events. Our approach provided a robust ecological framework in which MCG archaea appeared as a core generalist group in the sediment realm. However, the analysis of the complex intragroup phylogeny of the 21 subgroups currently forming the MCG lineage revealed that distinct evolutionary MCG subgroups have arisen in marine and freshwater sediments suggesting the occurrence of adaptive evolution specific to each habitat. The ancestral state reconstruction analysis indicated that this segregation was mainly due to the occurrence of a few saline-freshwater transition events during the MCG diversification. In addition, a network analysis showed that both saline and freshwater MCG recurrently co-occur with archaea of the class Thermoplasmata in sediment ecosystems, suggesting a potentially relevant trophic connection between the two clades.
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