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Zhang H, Zheng J, Wang R, Liu Y, Gao Y, Wu F, Huo S. Response of lake phytoplankton to climate oscillation on the northeastern Tibetan Plateau: Evidence from a 1400-year-old sedimentary archive. Sci Bull (Beijing) 2024; 69:1208-1211. [PMID: 38423876 DOI: 10.1016/j.scib.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jianan Zheng
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Rong Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yong Liu
- Key Laboratory of Water and Sediment Science, Ministry of Education, College of Environmental Science and Engineering, Peking University, Beijing 100871, China
| | - Yang Gao
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Gu P, Jia J, Qi D, Gao Q, Zhang C, Yang X, Nie M, Liu D, Luo Y. Response of phytoplankton composition to environmental stressors under humidification in three alpine lakes on the Qinghai-Tibet Plateau, China. Front Microbiol 2024; 15:1370334. [PMID: 38686112 PMCID: PMC11057515 DOI: 10.3389/fmicb.2024.1370334] [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: 01/14/2024] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
Owning to their extreme environmental conditions, lakes on the Qinghai-Tibet Plateau have typically displayed a simplistic food web structure, rendering them more vulnerable to climate change compared to lakes in plains. Phytoplankton, undergoing a changing aquatic environment, play a crucial role in the material cycle and energy flow of the food chain, particularly important for the unique fish species of the Tibetan Plateau. To identify the changing environment indexes and determine the response of phytoplankton composition to the environment change in alpine lakes, three lakes-Lake Qinghai, Lake Keluke and Lake Tuosu-were selected as study areas. Seasonal sampling surveys were conducted in spring and summer annually from 2018 to 2020. Our findings revealed there were significant changes in physicochemical parameters and phytoplankton in the three lakes. Bacillariophyta was the predominant phytoplankton in Lake Qinghai from 2018 to 2020, with the genera Synedra sp., Navicula sp., Cymbella sp. and Achnanthidium sp. predominated alternately. Lake Keluke alternated between being dominated by Bacillariophyta and cyanobacteria during the same period. Dolichospermum sp., a cyanobacteria, was prevalent in the summer of 2018 and 2019 and in the spring of 2020. In Lake Tuosu, Bacillariophyta was the predominant phytoplankton from 2018 to 2020, except in the summer of 2019, which was dominated by cyanobacteria. Synedra sp., Oscillatoria sp., Pseudoanabaena sp., Chromulina sp. and Achnanthidium sp. appeared successively as the dominant genera. Analysis revealed that all three lakes exhibited higher phytoplankton abundance in 2018 that in 2019 and 2020. Concurrently, they experienced higher average temperatures in 2018 than in the subsequent years. The cyanobacteria, Bacillariophyta, Chlorophyta and overall phytoplankton increased with temperature and decreased with salinity and NH4-N. Besides, the ratios of cyanobacteria, and the ratios of Bacillariophyta accounted in total phytoplankton increased with temperature. These findings suggest that cyanobacteria and phytoplankton abundance, especially Bacillariophyta, may have an increase tendency in the three alpine lakes under warm and wet climate.
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Affiliation(s)
- Peiwen Gu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Junmei Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Xi Yang
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Dan Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yule Luo
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
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Huang H, Chen S, Xu Z, Wu Y, Mei L, Pan Y, Yan X, Zhou C. Comparative metabarcoding analysis of phytoplankton community composition and diversity in aquaculture water and the stomach contents of Tegillarca granosa during months of growth. MARINE POLLUTION BULLETIN 2023; 187:114556. [PMID: 36640496 DOI: 10.1016/j.marpolbul.2022.114556] [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: 07/03/2022] [Revised: 12/19/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Filter-feeder bivalves and phytoplankton are interdependent. Their interaction plays important role in estuarine and coastal ecosystem. The correlation between bivalve feeding and phytoplankton is highly species specificity and environment dependent. In the background of miniature and nondiatom trend of phytoplankton in coastal seawaters, how bivalve respond and how the response play roles in the phytoplankton community are poorly known. In the present study, by applying DNA metabarcoding approach based on plastid 23S rDNA, this question was addressed by comparing the phytoplankton composition in the seston and the stomach content of blood clam Tegillarca granosa sampled during the growth period from March to November 2020 in an experimental farm on tidal flat in Xiangshan Bay, East China Sea. The result showed that, a total of seven phyla, 55 genera and 73 species of phytoplankton were identified for all samples. Chlorophyta, Bacillariophyta, and Cyanobacteria were found to be three dominant phyla both in the stomach contents and seston. High diversity of pico-sized phytoplankton, which was easy overlooked by microscopy, was revealed both in seston and stomach contents. This result indicated that the clam was able to feed on the pico-sized algae. At the genus level, the most abundant genera were the pico-sized green alga Ostreococcus (6.12 %-67.88 %) in seston and Picochlorum (4.07 %-35.33 %) in the stomach contents. In addition, microalgae of high nutritional value showed trend of higher proportion in stomach contents than that in seston, especially in July and September when significant growth of T. granosa was observed during this period (the body size increased 155 %). Biodiversity of phytoplankton in the seston was totally higher than that in stomach content, however, the changes among the months showed respective trend. Especially in July when the biodiversity was the lowest in seston, that in the stomach content showed the highest. The results indicated that blood clam farming might influence the phytoplankton composition, including those of pico-sized level, although the particular species in seston were mainly correlating with the dominant environmental factors such as temperature, salinity, pH respectively. These results extend the understanding of roles that bivalve aquaculture may play in the changing of coastal phytoplankton community.
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Affiliation(s)
- Hailong Huang
- School of Marine Science, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Sentao Chen
- School of Marine Science, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Zhihui Xu
- School of Marine Science, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Yanhua Wu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Limin Mei
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Yuanbo Pan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Xiaojun Yan
- School of Marine Science, Ningbo University, Ningbo, Zhejiang 315211, China; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China.
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China.
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Li H, Zhang H, Chang F, Liu Q, Zhang Y, Liu F, Zhang X. Sedimentary DNA for tracking the long-term changes in biodiversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17039-17050. [PMID: 36622608 DOI: 10.1007/s11356-023-25130-5] [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: 05/25/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Yang Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
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Rampen SW, Friedl T, Rybalka N, Thiel V. The Long chain Diol Index: A marine palaeotemperature proxy based on eustigmatophyte lipids that records the warmest seasons. Proc Natl Acad Sci U S A 2022; 119:e2116812119. [PMID: 35412908 PMCID: PMC9169758 DOI: 10.1073/pnas.2116812119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/11/2022] [Indexed: 12/23/2022] Open
Abstract
Long chain 1,13- and 1,15-diols are lipids which are omnipresent in marine environments, and the Long chain Diol Index (LDI), based on their distributions, has previously been introduced as a proxy for sea surface temperature. The main biological sources for long chain 1,13- and 1,15-diols have remained unknown, but our combined lipid and 23S ribosomal RNA (23S rRNA) analyses on suspended particulate matter from the Mediterranean Sea demonstrate that these lipids are produced by a marine eustigmatophyte group that originated before the currently known eustigmatophytes diversified. The 18S rRNA data confirm the existence of early-branching marine eustigmatophytes, which occur at a global scale. Differences between LDI records and other paleotemperature proxies are generally attributed to differences between the seasons in which the proxy-related organisms occur. Our results, combined with available LDI data from surface sediments, indicate that the LDI primarily registers temperatures from the warmest month when mixed-layer depths, salinity, and nutrient concentrations are low. The LDI may not be applicable in areas where Proboscia diatoms contribute 1,13-diols, but this can be recognized by enhanced contributions of C28 1,12 diol. Freshwater input may also affect the correlation between temperature and the LDI, but relative C32 1,15-diol abundances help to identify and correct for these effects. When taking those factors into account, the calibration error of the LDI is 2.4 °C. As a well-defined proxy for temperatures of the warmest seasons, the LDI can unlock important and previously inaccessible paleoclimate information and will thereby substantially improve our understanding of past climate conditions.
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Affiliation(s)
- Sebastiaan W. Rampen
- Geobiology, Geoscience Centre, University of Göttingen, 37077 Göttingen, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, 37073 Germany
| | - Nataliya Rybalka
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, 37073 Germany
| | - Volker Thiel
- Geobiology, Geoscience Centre, University of Göttingen, 37077 Göttingen, Germany
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6
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Environmental palaeogenomic reconstruction of an Ice Age algal population. Commun Biol 2021; 4:220. [PMID: 33594237 PMCID: PMC7887274 DOI: 10.1038/s42003-021-01710-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA. Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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Capo E, Ninnes S, Domaizon I, Bertilsson S, Bigler C, Wang XR, Bindler R, Rydberg J. Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene. Microorganisms 2021; 9:microorganisms9020355. [PMID: 33670228 PMCID: PMC7916980 DOI: 10.3390/microorganisms9020355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/21/2022] Open
Abstract
On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes-where the oldest DNA samples are dated to only a few hundred years after the lake formation-certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.
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Affiliation(s)
- Eric Capo
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
- Correspondence:
| | - Sofia Ninnes
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Isabelle Domaizon
- UMR CARRTEL, INRAE, Université Savoie Mont Blanc, 74200 Thonon les Bains, France;
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, SLU, 75007 Uppsala, Sweden;
| | - Christian Bigler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Richard Bindler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Johan Rydberg
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
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Helama S, Stoffel M, Hall RJ, Jones PD, Arppe L, Matskovsky VV, Timonen M, Nöjd P, Mielikäinen K, Oinonen M. Recurrent transitions to Little Ice Age-like climatic regimes over the Holocene. CLIMATE DYNAMICS 2021; 56:3817-3833. [PMID: 34776646 PMCID: PMC8550666 DOI: 10.1007/s00382-021-05669-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/20/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Holocene climate variability is punctuated by episodic climatic events such as the Little Ice Age (LIA) predating the industrial-era warming. Their dating and forcing mechanisms have however remained controversial. Even more crucially, it is uncertain whether earlier events represent climatic regimes similar to the LIA. Here we produce and analyse a new 7500-year long palaeoclimate record tailored to detect LIA-like climatic regimes from northern European tree-ring data. In addition to the actual LIA, we identify LIA-like ca. 100-800 year periods with cold temperatures combined with clear sky conditions from 540 CE, 1670 BCE, 3240 BCE and 5450 BCE onwards, these LIA-like regimes covering 20% of the study period. Consistent with climate modelling, the LIA-like regimes originate from a coupled atmosphere-ocean-sea ice North Atlantic-Arctic system and were amplified by volcanic activity (multiple eruptions closely spaced in time), tree-ring evidence pointing to similarly enhanced LIA-like regimes starting after the eruptions recorded in 1627 BCE, 536/540 CE and 1809/1815 CE. Conversely, the ongoing decline in Arctic sea-ice extent is mirrored in our data which shows reversal of the LIA-like conditions since the late nineteenth century, our record also correlating highly with the instrumentally recorded Northern Hemisphere and global temperatures over the same period. Our results bridge the gaps between low- and high-resolution, precisely dated proxies and demonstrate the efficacy of slow and fast components of the climate system to generate LIA-like climate regimes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00382-021-05669-0.
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Affiliation(s)
- Samuli Helama
- Natural Resources Institute Finland, Ounasjoentie 6, 96200 Rovaniemi, Finland
| | - Markus Stoffel
- Climate Change Impacts and Risks in the Anthropocene (C-CIA), Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
- dendrolab.Ch, Department of Earth Sciences, University of Geneva, Geneva, Switzerland
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva, Switzerland
| | - Richard J. Hall
- School of Geography and Lincoln Centre for Water and Planetary Health, University of Lincoln, Lincoln, UK
| | - Phil D. Jones
- Climatic Research Unit, School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Laura Arppe
- Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Gustaf Hällströmin Katu 2, 00014 Helsinki, Finland
| | | | - Mauri Timonen
- Natural Resources Institute Finland, Ounasjoentie 6, 96200 Rovaniemi, Finland
| | - Pekka Nöjd
- Natural Resources Institute Finland, Tietotie 2, 02150 Espoo, Finland
| | - Kari Mielikäinen
- Natural Resources Institute Finland, Tietotie 2, 02150 Espoo, Finland
| | - Markku Oinonen
- Laboratory of Chronology, Finnish Museum of Natural History, University of Helsinki, Gustaf Hällströmin Katu 2, 00014 Helsinki, Finland
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Optimal Growth Temperature and Intergenic Distances in Bacteria, Archaea, and Plastids of Rhodophytic Branch. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3465380. [PMID: 32025518 PMCID: PMC6991167 DOI: 10.1155/2020/3465380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 10/19/2019] [Accepted: 12/23/2019] [Indexed: 01/07/2023]
Abstract
The lengths of intergenic regions between neighboring genes that are convergent, divergent, or unidirectional were calculated for plastids of the rhodophytic branch and complete archaeal and bacterial genomes. Statistically significant linear relationships between any pair of the medians of these three length types have been revealed in each genomic group. Exponential relationships between the optimal growth temperature and each of the three medians have been revealed as well. The leading coefficients of the regression equations relating all pairs of the medians as well as temperature and any of the medians have the same sign and order of magnitude. The results obtained for plastids, archaea, and bacteria are also similar at the qualitative level. For instance, the medians are always low at high temperatures. At low temperatures, the medians tend to statistically significant greater values and scattering. The original model was used to test our hypothesis that the intergenic distances are optimized in particular to decrease the competition of RNA polymerases within the locus that results in transcribing shortened RNAs. Overall, this points to an effect of temperature for both remote and close genomes.
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Cegłowska M, Toruńska-Sitarz A, Kowalewska G, Mazur-Marzec H. Specific Chemical and Genetic Markers Revealed a Thousands-Year Presence of Toxic Nodularia spumigena in the Baltic Sea. Mar Drugs 2018; 16:md16040116. [PMID: 29617355 PMCID: PMC5923403 DOI: 10.3390/md16040116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 01/07/2023] Open
Abstract
In the Baltic Sea, diazotrophic cyanobacteria have been present for thousands of years, over the whole brackish water phase of the ecosystem. However, our knowledge about the species composition of the cyanobacterial community is limited to the last several decades. In the current study, the presence of species-specific chemical and genetic markers in deep sediments were analyzed to increase the existing knowledge on the history of toxic Nodularia spumigena blooms in the Baltic Sea. As chemical markers, three cyclic nonribosomal peptides were applied: the hepatotoxic nodularin, which in the sea was detected solely in N. spumigena, and two anabaenopeptins (AP827 and AP883a) characteristic of two different chemotypes of this species. From the same sediment samples, DNA was isolated and the gene involved in biosynthesis of nodularin, as well as the phycocyanin intergenic spacer region (PC-IGS), were amplified. The results of chemical and genetic analyses proved for the first time the thousands-year presence of toxic N. spumigena in the Baltic Sea. They also indicated that through all this time, the same two sub-populations of the species co-existed.
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Affiliation(s)
- Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81-727 Sopot, Poland.
| | - Anna Toruńska-Sitarz
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Płisudskiego 46, PL-81-378 Gdynia, Poland.
| | - Grażyna Kowalewska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81-727 Sopot, Poland.
| | - Hanna Mazur-Marzec
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81-727 Sopot, Poland.
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Płisudskiego 46, PL-81-378 Gdynia, Poland.
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Purification of Dye-stuff Contained Wastewater by a Hybrid Adsorption-Periphyton Reactor (HAPR): Performance and Mechanisms. Sci Rep 2017; 7:9635. [PMID: 28852105 PMCID: PMC5574932 DOI: 10.1038/s41598-017-10255-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to develop an environmental-benign bio-measure that could be used to purify dye-contaminated wastewater. Herein, a hybrid adsorption-periphyton reactor (HAPR), combining a bioadsorbent based adsorption unit and a periphyton-based photo-bioreactor (PPBR), was built and applied for the first time. Firstly, an efficient bioadsorbent, i.e, microwave-activated swede rape hull (MSRH), was produced, characterized and applied in an adsorption column, to pretreat methylene blue (MB) wastewater with high concentration (~100 mg L−1 or higher). Thereafter, the effluent of adsorption column, with lower dye concentration (~0.5 mg L−1), was collected and further purified by PPBR. Results showed that dye removal efficiency by HAPR was 99.95% (from 200 mg L−1 to 0.1 mg L−1 or lower). Decolorization mechanisms by PPBR, included adsorption process by extracellular polymeric substances (EPS) on the surface of periphyton and degradation process. The study showed that HAPR was a novel, environmental friendly, efficient and promising dye-purification method and deserved further attention in future investigation.
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Parducci L, Bennett KD, Ficetola GF, Alsos IG, Suyama Y, Wood JR, Pedersen MW. Ancient plant DNA in lake sediments. THE NEW PHYTOLOGIST 2017; 214:924-942. [PMID: 28370025 DOI: 10.1111/nph.14470] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/07/2016] [Indexed: 05/14/2023]
Abstract
Contents 924 I. 925 II. 925 III. 927 IV. 929 V. 930 VI. 930 VII. 931 VIII. 933 IX. 935 X. 936 XI. 938 938 References 938 SUMMARY: Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
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Affiliation(s)
- Laura Parducci
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Keith D Bennett
- Department of Geography & Sustainable Development, School of Geography & Geosciences, University of St Andrews, St Andrews, Fife, KY16 9AL, UK
- Marine Laboratory, Queen's University Belfast, Portaferry, BT22 1LS, UK
| | - Gentile Francesco Ficetola
- CNRS, Université Grenoble-Alpes, Laboratoire d'Ecologie Alpine (LECA), Grenoble, F-38000, France
- Department of Biosciences, Università degli Studi di Milano, Milan, 20133, Italy
| | - Inger Greve Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
| | - Jamie R Wood
- Long-term Ecology Lab, Landcare Research, PO Box 69040, Lincoln Canterbury, 7640, New Zealand
| | - Mikkel Winther Pedersen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
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