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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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Phoma BS, Makhalanyane TP. Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands. MICROBIAL ECOLOGY 2021; 81:396-409. [PMID: 32935183 DOI: 10.1007/s00248-020-01589-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.
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Affiliation(s)
- Boitumelo Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
- Marine Microbiomics Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa.
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Fitch A, Orland C, Willer D, Emilson EJS, Tanentzap AJ. Feasting on terrestrial organic matter: Dining in a dark lake changes microbial decomposition. GLOBAL CHANGE BIOLOGY 2018; 24:5110-5122. [PMID: 29998600 PMCID: PMC6220883 DOI: 10.1111/gcb.14391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/30/2018] [Accepted: 06/22/2018] [Indexed: 06/08/2023]
Abstract
Boreal lakes are major components of the global carbon cycle, partly because of sediment-bound heterotrophic microorganisms that decompose within-lake and terrestrially derived organic matter (t-OM). The ability for sediment bacteria to break down and alter t-OM may depend on environmental characteristics and community composition. However, the connection between these two potential drivers of decomposition is poorly understood. We tested how bacterial activity changed along experimental gradients in the quality and quantity of t-OM inputs into littoral sediments of two small boreal lakes, a dark and a clear lake, and measured the abundance of operational taxonomic units and functional genes to identify mechanisms underlying bacterial responses. We found that bacterial production (BP) decreased across lakes with aromatic dissolved organic matter (DOM) in sediment pore water, but the process underlying this pattern differed between lakes. Bacteria in the dark lake invested in the energetically costly production of extracellular enzymes as aromatic DOM increased in availability in the sediments. By contrast, bacteria in the clear lake may have lacked the nutrients and/or genetic potential to degrade aromatic DOM and instead mineralized photo-degraded OM into CO2 . The two lakes differed in community composition, with concentrations of dissolved organic carbon and pH differentiating microbial assemblages. Furthermore, functional genes relating to t-OM degradation were relatively higher in the dark lake. Our results suggest that future changes in t-OM inputs to lake sediments will have different effects on carbon cycling depending on the potential for photo-degradation of OM and composition of resident bacterial communities.
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Affiliation(s)
- Amelia Fitch
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Chloe Orland
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - David Willer
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Erik J. S. Emilson
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
- Natural Resources Canada, Great Lakes Forestry CentreSault Ste. MarieOntario
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Kolmakova OV, Gladyshev MI, Fonvielle JA, Ganzert L, Hornick T, Grossart HP. Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling. Environ Microbiol 2018; 21:34-49. [PMID: 30246449 DOI: 10.1111/1462-2920.14418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 11/27/2022]
Abstract
Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh 13 C-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.
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Affiliation(s)
- Olesya V Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia.,Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michail I Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jérémy André Fonvielle
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Lars Ganzert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,GFZ German Research Centre for Geosciencess, Section 5.3 Geomicrobiology, Potsdam, Germany.,Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, Germany
| | - Thomas Hornick
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Biological early diagenesis and insolation-paced paleoproductivity signified in deep core sediment organic matter. Sci Rep 2017; 7:1581. [PMID: 28484263 PMCID: PMC5431472 DOI: 10.1038/s41598-017-01759-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/30/2017] [Indexed: 11/22/2022] Open
Abstract
The dynamics of a large stock of organic matter contained in deep sediments of marginal seas plays pivotal role in global carbon cycle, yet it is poorly constrained. Here, dissolved organic matter (DOM) in sediments was investigated for core sediment up to ~240 meters deep in the East/Japan Sea. The upper downcore profile (≤118 mbsf, or meters below seafloor) at a non-chimney site (U1) featured the exponential production of dissolved organic carbon (DOC) and optically active DOM with time in the pore water above sulfate-methane-transition-zone (SMTZ), concurrent with the increases of nutrients and alkalinity, and the reduction of sulfate. Such depth profiles signify a biological pathway of the DOM production during the early diagenesis of particulate organic matter presumably dominated by sulfate reduction. Below the SMTZ, an insolation-paced oscillation of DOM in a ~405-Kyr cycle of orbital eccentricity was observed at site U1, implying astronomically paced paleoproductivity stimulated by light availability. Furthermore, DOM dynamics of the deep sediments were likely governed by intensive humification as revealed by the less pronounced protein-like fluorescence and the lower H/C and O/C ratios below SMTZ among 15,281 formulas identified. Our findings here provide novel insights into organic matter dynamics in deep sediments.
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Teira E, Hernando-Morales V, Guerrero-Feijóo E, Varela MM. Leucine, starch and bicarbonate utilization by specific bacterial groups in surface shelf waters off Galicia (NW Spain). Environ Microbiol 2017; 19:2379-2390. [PMID: 28370995 DOI: 10.1111/1462-2920.13748] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 11/29/2022]
Abstract
The capability of different bacterial populations to degrade abundant polymers, such as algal-derived polysaccharides, or to utilize preferentially polymers over monomers, remains largely unknown. In this study, microautoradiography was combined with fluorescence in situ hybridization (MAR-FISH) to evaluate the ability of Bacteroidetes, SAR11, Roseobacter spp., Gammaproteobacteria and SAR86 cells to use bicarbonate, leucine and starch under natural light conditions at two locations in shelf surface waters off NW Spain. The percentage of cells incorporating bicarbonate was relatively high (mean 32% ± 4%) and was positively correlated with the intensity of solar radiation. The proportion of cells using starch (mean 56% ± 4%) or leucine (mean 47% ± 4%) was significantly higher than that using bicarbonate. On average, SAR11, Roseobacter spp. and Gammaproteobacteria showed a similarly high percentage of cells using leucine (47%-65% of hybridized cells) than using starch (51%-64% of hybridized cells), while Bacteroidetes and SAR86 cells preferentially used starch (53% of hybridized cells) over leucine (34%-40% of hybridized cells). We suggest that the great percentage of bacteria using starch is related to a high ambient availability of polymers associated to algal cell lysis, which, in turn, weakens the short-term coupling between phytoplankton release and bacterial production.
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Affiliation(s)
- E Teira
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.,Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - V Hernando-Morales
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.,Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - E Guerrero-Feijóo
- Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, IEO, Apdo. 130, Coruña, 15080- A, Spain
| | - M M Varela
- Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, IEO, Apdo. 130, Coruña, 15080- A, Spain
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