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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA). BIOGEOCHEMISTRY 2023; 162:359-380. [PMID: 36873379 PMCID: PMC9971093 DOI: 10.1007/s10533-022-01008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Coastal wetlands are highly efficient 'blue carbon' sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments. GRAPHICAL ABSTRACT Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-01008-5.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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Wang Y, Liu Y, Wang J, Luo T, Zhang R, Sun J, Zheng Q, Jiao N. Seasonal dynamics of bacterial communities in the surface seawater around subtropical Xiamen Island, China, as determined by 16S rRNA gene profiling. MARINE POLLUTION BULLETIN 2019; 142:135-144. [PMID: 31232286 DOI: 10.1016/j.marpolbul.2019.03.035] [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: 05/12/2018] [Revised: 02/03/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the microbial structure in the surface seawater from five coastal sites around Xiamen Island, China, over four seasons to evaluate seasonal environmental fluctuations impact on them. This subtropical island is characterized by long, hot, humid summers, and short, mild, dry winters. All sites were dominated by Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes; microbial community composition was similar across four seasons. However, larger proportions of Gammaproteobacteria and Bacillus were observed during the summer than during any other season. The high ratio of Bacillus, Bacteroidetes, and Clostridia richness to Alphaproteobacteria richness in the summer, suggested that the sites we tested were heavily affected by waste water to other seasons. Correlation-based network analyses among the bacterial species and environmental variables indicated important connections between physiochemical variables and specific taxonomic groups. Collectively, our results suggested that seasonal shifts and wastewater pollution together shape the structures of the microbial communities around Xiamen Island.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People's Republic of China; Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, Fujian, People's Republic of China.
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Benaiges-Fernandez R, Urmeneta J. Use of specific PCR primers for the study of sulfate-reducing bacteria diversity in microbial mats of Ebro Delta, Spain. Int Microbiol 2018; 21:231-235. [PMID: 30810897 DOI: 10.1007/s10123-018-0020-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 11/27/2022]
Abstract
Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Sulfate-reducing bacteria (SRB) play a key role in sulfur and nutrient recycling in these ecosystems. In this work, specific primers for 16S rRNA encoding gene, previously described, were used to study the diversity of SRB in microbial mats of the Ebro Delta. We confirm that this method is reliable to identify the diversity of SRB in these ecosystems. However, some mismatches in obtained sequences had been observed in our system and must be taken under consideration. Various genera of SRB in Ebro Delta microbial mats were identified, such as Desulfonema, Desulfatitalea, Desulfosalsimonas, Desulfoccocus, and Desulfovibrio. The diversity observed in our samples is very similar to previously reported in other microbial mats communities.
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Affiliation(s)
- Robert Benaiges-Fernandez
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
- Institute of Environmental Assessment and Water Research (IDAEA, CSIC), 08034, Barcelona, Catalonia, Spain
| | - Jordi Urmeneta
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain.
- Biodiversity Research Institute (IRBio), Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain.
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Berlanga M, Palau M, Guerrero R. Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats. Front Microbiol 2017; 8:2619. [PMID: 29312277 PMCID: PMC5744480 DOI: 10.3389/fmicb.2017.02619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/15/2017] [Indexed: 01/11/2023] Open
Abstract
Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0–2, 2–4, and 4–6 mm). To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%), followed by Archaea (∼4%) and Eukarya (∼1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0–2 mm) than in the lower layers (2–4 and 4–6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat.
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Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Montserrat Palau
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona - Institut d'Investigació Biomédica de Bellvitge, Barcelona, Spain.,Academia Europaea-Barcelona Knowledge Hub, Barcelona, Spain
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5
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Sathiyanarayanan G, Saibaba G, Kiran GS, Yang YH, Selvin J. Marine sponge-associated bacteria as a potential source for polyhydroxyalkanoates. Crit Rev Microbiol 2016; 43:294-312. [DOI: 10.1080/1040841x.2016.1206060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ganesan Sathiyanarayanan
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Ganesan Saibaba
- Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Kalapet, India
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
- Microbial Carbohydrate Resource Bank, Konkuk University, Seoul, South Korea
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, India
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Hassard F, Gwyther CL, Farkas K, Andrews A, Jones V, Cox B, Brett H, Jones DL, McDonald JE, Malham SK. Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review. Front Microbiol 2016; 7:1692. [PMID: 27847499 PMCID: PMC5088438 DOI: 10.3389/fmicb.2016.01692] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/10/2016] [Indexed: 11/26/2022] Open
Abstract
The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.
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Affiliation(s)
| | - Ceri L. Gwyther
- Department of Engineering and Innovation, Open UniversityMilton Keynes, UK
| | - Kata Farkas
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
| | | | | | | | | | - Davey L. Jones
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
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Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism. Appl Environ Microbiol 2016; 82:4126-4132. [PMID: 27129963 DOI: 10.1128/aem.00493-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCE Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem.
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8
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Elling FJ, Becker KW, Könneke M, Schröder JM, Kellermann MY, Thomm M, Hinrichs KU. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environ Microbiol 2015; 18:692-707. [PMID: 26472620 DOI: 10.1111/1462-2920.13086] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/28/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022]
Abstract
The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Jan M Schröder
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, 93053, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
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10
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Discovery of bacterial polyhydroxyalkanoate synthase (PhaC)-encoding genes from seasonal Baltic Sea ice and cold estuarine waters. Extremophiles 2014; 19:197-206. [DOI: 10.1007/s00792-014-0699-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/20/2014] [Indexed: 10/24/2022]
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11
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Kunihiro T, Veuger B, Vasquez-Cardenas D, Pozzato L, Le Guitton M, Moriya K, Kuwae M, Omori K, Boschker HTS, van Oevelen D. Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments. PLoS One 2014; 9:e96219. [PMID: 24769853 PMCID: PMC4000199 DOI: 10.1371/journal.pone.0096219] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022] Open
Abstract
Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.
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Affiliation(s)
- Tadao Kunihiro
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- * E-mail:
| | - Bart Veuger
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Diana Vasquez-Cardenas
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Lara Pozzato
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Marie Le Guitton
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Kazuyoshi Moriya
- School of Natural Science & Technology, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Michinobu Kuwae
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
| | - Koji Omori
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime, Japan
| | - Henricus T. S. Boschker
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
| | - Dick van Oevelen
- Department of Ecosystem Studies, Royal Netherlands Institute of Sea Research (NIOZ), Yerseke, The Netherlands
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Armitage DW, Gallagher KL, Youngblut ND, Buckley DH, Zinder SH. Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. Front Microbiol 2012; 3:293. [PMID: 22908010 PMCID: PMC3415947 DOI: 10.3389/fmicb.2012.00293] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/24/2012] [Indexed: 01/01/2023] Open
Abstract
Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.
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Affiliation(s)
- David W Armitage
- Department of Integrative Biology, University of California Berkeley Berkeley, CA, USA
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13
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Long RA, Eveillard D, Franco SLM, Reeves E, Pinckney JL. Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats. FEMS Microbiol Ecol 2012; 83:74-81. [PMID: 22809069 DOI: 10.1111/j.1574-6941.2012.01457.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 07/02/2012] [Accepted: 07/08/2012] [Indexed: 11/28/2022] Open
Abstract
Microbial mats are laminae of self-sustaining microbial communities with a high level of competition for resources. We tested the hypothesis that chemically mediated antagonism is a potential mechanism for structuring the bacterial community. In the co-culturing assay, 57% of the isolates expressed antagonistic behavior toward one or more isolates and 5% of the isolates inhibited more than 80% of the isolates. We observed greater levels of antagonism between isolates from adjacent laminae than within. The bacterial isolate library derived from the mat was predominately Gram-positive, and inhibition within this group was greater than against the few Gram-negative isolates. Microdiversity of 16S rRNA gene was observed for Bacillus marisflavi isolates, which represented 23 of the 75 isolates in the library. Within this and other groups, the patterns of inhibition and sensitivity varied greatly, suggesting rapid gain and loss of the ability to produce antagonistic secondary metabolites and resistance toward such molecules. Our observations are consistent with the hypothesis that antagonistic interactions are a potential mechanism in addition to physiochemical properties that regulate the vertical distribution of aerobic heterotrophic bacteria in hypersaline microbial mats.
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Affiliation(s)
- Richard A Long
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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14
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Xiao N, Jiao N. Formation of polyhydroxyalkanoate in aerobic anoxygenic phototrophic bacteria and its relationship to carbon source and light availability. Appl Environ Microbiol 2011; 77:7445-50. [PMID: 21908634 PMCID: PMC3209146 DOI: 10.1128/aem.05955-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 08/30/2011] [Indexed: 11/20/2022] Open
Abstract
Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (Dinoroseobacter sp. JL1447, Roseobacter denitrificans OCh 114, Roseobacter litoralis OCh 149, Dinoroseobacter shibae DFL 12(T), Labrenzia alexandrii DFL 11(T), and Erythrobacter longus DSMZ 6997) were examined, and all of them demonstrated the ability to form the carbon polymer polyhydroxyalkanoate (PHA) in the cell. The PHA in Dinoroseobacter sp. JL1447 was identified as poly-beta-hydroxybutyrate (PHB) according to evidence from Fourier transform infrared spectroscopy, differential scanning calorimetry, and (1)H nuclear magnetic resonance spectroscopy examinations. Carbon sources turned out to be critical for PHA production in AAPB. Among the eight media tested with Dinoroseobacter sp. JL1447, sodium acetate, giving a PHA production rate of 72%, was the most productive carbon source, followed by glucose, with a 68% PHA production rate. Such PHA production rates are among the highest recorded for all bacteria. The C/N ratio of substrates was verified by the experiments as another key factor in PHA production. In the case of R. denitrificans OCh 114, PHA was not detected when the organism was cultured at C/N ratios of <2 but became apparent at C/N ratios of >3. Light is also important for the formation of PHA in AAPB. In the case of Dinoroseobacter sp. JL1447, up to a one-quarter increase in PHB production was observed when the culture underwent growth in a light-dark cycle compared to growth completely in the dark.
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Affiliation(s)
- Na Xiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, People's Republic of China
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Koller M, Gasser I, Schmid F, Berg G. Linking ecology with economy: Insights into polyhydroxyalkanoate-producing microorganisms. Eng Life Sci 2011. [DOI: 10.1002/elsc.201000190] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Villanueva L, del Campo J, Guerrero R, Geyer R. Intact phospholipid and quinone biomarkers to assess microbial diversity and redox state in microbial mats. MICROBIAL ECOLOGY 2010; 60:226-238. [PMID: 20237775 DOI: 10.1007/s00248-010-9645-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Accepted: 02/10/2010] [Indexed: 05/28/2023]
Abstract
Microbial mats are stratified microbial communities composed by highly inter-related populations and therefore are frequently chosen as model systems to study diversity and ecophysiological strategies. The present study describes an integrated approach to analyze microbial quinones and intact polar lipids (IPLs) in microbial mats within layers as thin as 500 microm by liquid chromatography-tandem mass spectrometry. Quinone profiles revealed important depth-related differences in community composition in two mat systems. The higher abundance of ubiquinones, compared to menaquinones, reflected the clear predominance of microorganisms belonging to aerobic alpha-, beta-, and gamma-Proteobacteria in Ebro delta estuarine mats. Hypersaline photosynthetic Camargue mats (France) showed a predominance of menaquinone-9 at the top of the mat, which is consistent with an important contribution of facultative aerobic or anaerobic bacteria in its photic zone. Quinone indices also indicated a higher diversity of non-phototrophs and a more anaerobic character in the hypersaline mats. Besides, the dissimilarity index suggested that the samples were greatly influenced by a depth-related redox state gradient. In the analysis of IPLs, there was a predominance of phosphatidylglycerols and sulfoquinovosyldiacylglycerols, the latter being an abundant biomarker of Cyanobacteria. This combined approach based on quinone and IPL analysis has proven to be a useful method to establish differences in the microbial diversity and redox state of highly structure microbial mat systems at a fine-scale level.
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Affiliation(s)
- Laura Villanueva
- Department of Microbiology, University of Barcelona, Barcelona, Spain.
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Pruett ST, Bushnev A, Hagedorn K, Adiga M, Haynes CA, Sullards MC, Liotta DC, Merrill AH. Biodiversity of sphingoid bases ("sphingosines") and related amino alcohols. J Lipid Res 2008; 49:1621-39. [PMID: 18499644 PMCID: PMC2444003 DOI: 10.1194/jlr.r800012-jlr200] [Citation(s) in RCA: 315] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
"Sphingosin" was first described by J. L. W. Thudichum in 1884 and structurally characterized as 2S,3R,4E-2-aminooctadec-4-ene-1,3-diol in 1947 by Herb Carter, who also proposed the designation of "lipides derived from sphingosine as sphingolipides." This category of amino alcohols is now known to encompass hundreds of compounds that are referred to as sphingoid bases and sphingoid base-like compounds, which vary in chain length, number, position, and stereochemistry of double bonds, hydroxyl groups, and other functionalities. Some have especially intriguing features, such as the tail-to-tail combination of two sphingoid bases in the alpha,omega-sphingoids produced by sponges. Most of these compounds participate in cell structure and regulation, and some (such as the fumonisins) disrupt normal sphingolipid metabolism and cause plant and animal disease. Many of the naturally occurring and synthetic sphingoid bases are cytotoxic for cancer cells and pathogenic microorganisms or have other potentially useful bioactivities; hence, they offer promise as pharmaceutical leads. This thematic review gives an overview of the biodiversity of the backbones of sphingolipids and the broader field of naturally occurring and synthetic sphingoid base-like compounds.
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Affiliation(s)
- Sarah T Pruett
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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