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Zhu QZ, Elvert M, Meador TB, Schröder JM, Doeana KD, Becker KW, Elling FJ, Lipp JS, Heuer VB, Zabel M, Hinrichs KU. Comprehensive molecular-isotopic characterization of archaeal lipids in the Black Sea water column and underlying sediments. GEOBIOLOGY 2024; 22:e12589. [PMID: 38465505 DOI: 10.1111/gbi.12589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The Black Sea is a permanently anoxic, marine basin serving as model system for the deposition of organic-rich sediments in a highly stratified ocean. In such systems, archaeal lipids are widely used as paleoceanographic and biogeochemical proxies; however, the diverse planktonic and benthic sources as well as their potentially distinct diagenetic fate may complicate their application. To track the flux of archaeal lipids and to constrain their sources and turnover, we quantitatively examined the distributions and stable carbon isotopic compositions (δ13 C) of intact polar lipids (IPLs) and core lipids (CLs) from the upper oxic water column into the underlying sediments, reaching deposits from the last glacial. The distribution of IPLs responded more sensitively to the geochemical zonation than the CLs, with the latter being governed by the deposition from the chemocline. The isotopic composition of archaeal lipids indicates CLs and IPLs in the deep anoxic water column have negligible influence on the sedimentary pool. Archaeol substitutes tetraether lipids as the most abundant IPL in the deep anoxic water column and the lacustrine methanic zone. Its elevated IPL/CL ratios and negative δ13 C values indicate active methane metabolism. Sedimentary CL- and IPL-crenarchaeol were exclusively derived from the water column, as indicated by non-variable δ13 C values that are identical to those in the chemocline and by the low BIT (branched isoprenoid tetraether index). By contrast, in situ production accounts on average for 22% of the sedimentary IPL-GDGT-0 (glycerol dibiphytanyl glycerol tetraether) based on isotopic mass balance using the fermentation product lactate as an endmember for the dissolved substrate pool. Despite the structural similarity, glycosidic crenarchaeol appears to be more recalcitrant in comparison to its non-cycloalkylated counterpart GDGT-0, as indicated by its consistently higher IPL/CL ratio in sediments. The higher TEX86 , CCaT, and GDGT-2/-3 values in glacial sediments could plausibly result from selective turnover of archaeal lipids and/or an archaeal ecology shift during the transition from the glacial lacustrine to the Holocene marine setting. Our in-depth molecular-isotopic examination of archaeal core and intact polar lipids provided new constraints on the sources and fate of archaeal lipids and their applicability in paleoceanographic and biogeochemical studies.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Travis B Meador
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Biology Centre CAS, Soil and Water Research Infrastructure, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan M Schröder
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Katiana D Doeana
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kevin W Becker
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Felix J Elling
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Matthias Zabel
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
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2
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Pavlovska M, Prekrasna I, Dykyi E, Zotov A, Dzhulai A, Frolova A, Slobodnik J, Stoica E. Niche partitioning of bacterial communities along the stratified water column in the Black Sea. Microbiologyopen 2021; 10:e1195. [PMID: 34180601 PMCID: PMC8217838 DOI: 10.1002/mbo3.1195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine.,National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine
| | - Andrii Zotov
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,State Institution Institute of Marine Biology of the NAS of Ukraine, Odesa, Ukraine
| | - Artem Dzhulai
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania
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Zhang Y, Pavlovska M, Stoica E, Prekrasna I, Yang J, Slobodnik J, Zhang X, Dykyi E. Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach: From bacteria to marine mammals. ENVIRONMENT INTERNATIONAL 2020; 135:105307. [PMID: 31881429 DOI: 10.1016/j.envint.2019.105307] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
As the largest semi-closed marine ecosystem in the world, the Black Sea has been heavily affected by human activities for a long time. Describing the biodiversity of multi-trophic biota in pelagic zone of the Black Sea and identifying the dominant environmental factors are prerequisites for protecting the sustainability of ecosystems. However, up to now, the taxonomic and distributional information about the Black Sea biota is not clear. Here, we employed a Tree-of-Life metabarcoding to analyze the biodiversity of eight communities in the Black Sea, investigated their biogeographical distribution, and further analyzed the influence of biological and abiotic factors on biota on large scales. We found that, (1) Over 8900 OTUs were detected in the Black Sea, of which 630 species were identified, covering the holistic biota from single-celled (bacteria 5620 OTUs 141 species; algae 1096 OTUs 185 species; protozoa 546 OTUs 146 species) to multicellular organisms (invertebrate metazoans 150 OTUs 34 species; fishes 1369 OTUs 76 species; large marine mammals 39 OTUs 5 species). (2) Higher trophic organisms (fishes and large mammals) distributed more evenly in space than the lower (microorganisms, protozoa and invertebrates). For lower trophic organisms, the vertical stratification was more obvious than the horizontal stratification (vertical p < 0.02, horizontal p < 0.05). (3) The bottom trophic organisms (bacteria and algae) of the food web significantly affected the distribution and composition of the others through biological interactions (Mantel p < 0.05). (4) At the level of abiotic factors, the effect of local species sorting on the composition of communities was 15% higher than that of mass dispersal effect. For the first time, this study monitored and profiled the holistic biodiversity in the pelagic zone of the Black Sea, and provided technological advances and preliminary knowledge for the ongoing Black Sea ecosystem protection efforts.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mariia Pavlovska
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odesa, Ukraine; State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Blvd. Mamaia no. 300, RO-900581 Constanţa 3, Romania
| | - Ievgeniia Prekrasna
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odesa, Ukraine; State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | | | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Evgen Dykyi
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odesa, Ukraine; State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
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Gavrilov SN, Korzhenkov AA, Kublanov IV, Bargiela R, Zamana LV, Popova AA, Toshchakov SV, Golyshin PN, Golyshina OV. Microbial Communities of Polymetallic Deposits' Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts. Front Microbiol 2019; 10:1573. [PMID: 31379766 PMCID: PMC6650587 DOI: 10.3389/fmicb.2019.01573] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/24/2019] [Indexed: 12/26/2022] Open
Abstract
Acid mine drainage (AMD) systems are globally widespread and are an important source of metal pollution in riverine and coastal systems. Microbial AMD communities have been extensively studied for their ability to thrive under extremely acidic conditions and for their immense contribution to the dissolution of metal ores. However, little is known on microbial inhabitants of AMD systems subjected to extremely contrasting continental seasonal temperature patterns as opposed to maritime climate zones, experiencing much weaker annual temperature variations. Here, we investigated three types of AMD sites in Eastern Transbaikalia (Russia). In this region, all surface water bodies undergo a deep and long (up to 6 months) freezing, with seasonal temperatures varying between -33 and +24°C, which starkly contrasts the common well-studied AMD environments. We sampled acidic pit lake (Sherlovaya Gora site) located in the area of a polymetallic deposit, acidic drainage water from Bugdaya gold-molybdenum-tungsten deposit and Ulan-Bulak natural acidic spring. These systems showed the abundance of bacteria-derived reads mostly affiliated with Actinobacteria, Acidobacteria, Alpha- and Gammaproteobacteria, chloroplasts, Chloroflexi, Bacteroidetes, and Firmicutes. Furthermore, candidate taxa "Ca. Saccharibacteria" (previously known as TM7), "Ca. Parcubacteria" (OD1) and WPS-2 were represented in substantial quantities (10-20%). Heterotrophy and iron redox cycling can be considered as central processes of carbon and energy flow for majority of detected bacterial taxa. Archaea were detected in low numbers, with Terrestrial Miscellaneous Euryarchaeal Group (TMEG), to be most abundant (3%) in acidic spring Ulan-Bulak. Composition of these communities was found to be typical in comparison to other AMD sites; however, certain groups (as Ignavibacteriae) could be specifically associated with this area. This study provides insight into the microbial diversity patterns in acidic ecosystems formed in areas of polymetallic deposits in extreme continental climate zone with contrasting temperature parameters.
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Affiliation(s)
- Sergey N. Gavrilov
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Aleksei A. Korzhenkov
- Laboratory of Bioinformatics, Genomics and Genome Editing, NRC Kurchatov Institute, Moscow, Russia
| | - Ilya V. Kublanov
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Leonid V. Zamana
- Laboratory of Geoecology and Hydrogeochemistry, Institute of Natural Resources, Ecology and Cryology, SB RAS, Chita, Russia
| | - Alexandra A. Popova
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Stepan V. Toshchakov
- Laboratory of Metabolism of Extremophiles, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Moscow, Russia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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Salmaso N, Albanese D, Capelli C, Boscaini A, Pindo M, Donati C. Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake. MICROBIAL ECOLOGY 2018; 76:125-143. [PMID: 29192335 DOI: 10.1007/s00248-017-1120-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy.
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Camilla Capelli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
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Long Y, Yi H, Chen S, Zhang Z, Cui K, Bing Y, Zhuo Q, Li B, Xie S, Guo Q. Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19570-9. [PMID: 27392623 DOI: 10.1007/s11356-016-7166-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/28/2016] [Indexed: 05/12/2023]
Abstract
Both bacteria and archaeal communities can play important roles in biogeochemical processes in constructed wetland (CW) system. However, the influence of plant type on microbial community in surface water CW remains unclear. The present study investigated bacterial and archaeal communities in five surface water CW systems with different plant species. The abundance, richness, and diversity of both bacterial and archaeal communities considerably differed in these five CW systems. Compared with the other three CW systems, the CW systems planted with Vetiveria zizanioides or Juncus effusus L. showed much higher bacterial abundance but lower archaeal abundance. Bacteria outnumbered archaea in each CW system. Moreover, the CW systems planted with V. zizanioides or J. effusus L. had relatively lower archaeal but higher bacterial richness and diversity. In each CW system, bacterial community displayed much higher richness and diversity than archaeal community. In addition, a remarkable difference of both bacterial and archaeal community structures was observed in the five studied CW systems. Proteobacteria was the most abundant bacterial group (accounting for 33-60 %). Thaumarchaeota organisms (57 %) predominated in archaeal communities in CW systems planted with V. zizanioides or J. effusus L., while Woesearchaeota (23 or 24 %) and Euryarchaeota (23 or 15 %) were the major archaeal groups in CW systems planted with Cyperus papyrus or Canna indica L. Archaeal community in CW planted with Typha orientalis Presl was mainly composed of unclassified archaea. Therefore, plant type exerted a considerable influence on microbial community in surface water CW system.
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Affiliation(s)
- Yan Long
- Key Laboratory of Water/Soil Toxic Pollutants Control and Bioremediation of Guangdong Higher Education Institutes, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Hao Yi
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Zhengke Zhang
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Kai Cui
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Yongxin Bing
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Qiongfang Zhuo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Bingxin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Environment Protection (MEP), Guangzhou, 510655, China.
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Merkel AY, Podosokorskaya OA, Sokolova TG, Bonch-Osmolovskaya EA. Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka). Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716030073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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