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Besaury L, Bocquart M, Rémond C. Isolation of Saccharibacillus WB17 strain from wheat bran phyllosphere and genomic insight into the cellulolytic and hemicellulolytic complex of the Saccharibacillus genus. Braz J Microbiol 2022; 53:1829-1842. [PMID: 36040685 PMCID: PMC9679120 DOI: 10.1007/s42770-022-00819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/23/2022] [Indexed: 01/13/2023] Open
Abstract
The microorganisms living on the phyllosphere (the aerial part of the plants) are in contact with the lignocellulosic plant cell wall and might have a lignocellulolytic potential. We isolated a Saccharibacillus strain (Saccharibacillus WB17) from wheat bran phyllosphere and its cellulolytic and hemicellulolytic potential was investigated during growth onto wheat bran. Five other type strains from that genus selected from databases were also cultivated onto wheat bran and glucose. Studying the chemical composition of wheat bran residues by FTIR after growth of the six strains showed an important attack of the stretching C-O vibrations assigned to polysaccharides for all the strains, whereas the C = O bond/esterified carboxyl groups were not impacted. The genomic content of the strains showed that they harbored several CAZymes (comprised between 196 and 276) and possessed four of the fifth modules reflecting the presence of a high diversity of enzymes families. Xylanase and amylase activities were the most active enzymes with values reaching more than 4746 ± 1400 mIU/mg protein for the xylanase activity in case of Saccharibacillus deserti KCTC 33693 T and 452 ± 110 mIU/mg protein for the amylase activity of Saccharibacillus WB17. The total enzymatic activities obtained was not correlated to the total abundance of CAZyme along that genus. The Saccharibacillus strains harbor also some promising proteins in the GH30 and GH109 modules with potential arabinofuranosidase and oxidoreductase activities. Overall, the genus Saccharibacillus and more specifically the Saccharibacillus WB17 strain represent biological tools of interest for further biotechnological applications.
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Affiliation(s)
- Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
| | - Mathilde Bocquart
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Caroline Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
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2
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Barroso GC, Abril G, Machado W, Abuchacra RC, Peixoto RB, Bernardes M, Marques GS, Sanders CJ, Oliveira GB, Oliveira Filho SR, Amora-Nogueira L, Marotta H. Linking eutrophication to carbon dioxide and methane emissions from exposed mangrove soils along an urban gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157988. [PMID: 35963403 DOI: 10.1016/j.scitotenv.2022.157988] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 07/22/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Mangroves are one of the most important but threatened blue carbon ecosystems globally. Rapid urban growth has resulted in nutrient inputs and subsequent coastal eutrophication, associated with an enrichment in organic matter (OM) from algal and sewage sources and substantial changes in greenhouse gas (GHG) emissions. However, the effects of nitrogen (N) and phosphorus (P) enrichment on mangrove soil OM composition and GHG emissions, such as methane (CH4) and carbon dioxide (CO2), are still poorly understood. Here, we aim to evaluate the relationships between CO2 and CH4 efflux with OM composition in exposed soils from three mangrove areas along watersheds with different urbanization levels (Rio de Janeiro State, Brazil). To assess spatial (lower vs. upper intertidal zones) and seasonal (summer vs. winter) variability, we measured soil-air CO2 and CH4 fluxes at low spring tide, analyzing elementary (C, N, and P), isotopic (δ13C and δ15N), and the molecular (n-alkanes and sterols) composition of surface soil OM. A general trend of OM composition was found with increasing urban influence, with higher δ15N (proxy of anthropogenic N enrichment), less negative δ13C, more short-chain n-alkanes, lower C:N ratio (proxies of algal biomass), and higher epicoprostanol content (proxies of sewage-derived OM). The CO2 efflux from exposed soils increased greatly in median (25/75 % interquartile range) from 4.6 (2.9/8.3) to 24.0 (21.5/32.7) mmol m-2 h-1 from more pristine to more urbanized watersheds, independent of intertidal zone and seasonality. The CO2 fluxes at the most eutrophicated site were among the highest reported worldwide for mangrove soils. Conversely, CH4 emissions were relatively low (three orders of magnitude lower than CO2 fluxes), with high peaks in the lower intertidal zone during the rainy summer. Thus, our findings demonstrate the influence of coastal eutrophication on global warming potentials related to enhanced heterotrophic remineralization of blue carbon within mangrove soils.
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Affiliation(s)
- Glenda C Barroso
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil
| | - Gwenaël Abril
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), FRE 2020, Muséum National d'Histoire Naturelle, CNRS, IRD, SU, UCN, UA, Paris, France
| | - Wilson Machado
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil
| | - Rodrigo C Abuchacra
- Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil; Department of Geography, Graduate Program in Geography, State University of Rio de Janeiro (UERJ/FFP), Rua Dr. Francisco Portela, 1470 São Gonçalo, 24435-005 Rio de Janeiro, Brazil
| | - Roberta B Peixoto
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil
| | - Marcelo Bernardes
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil
| | - Gabriela S Marques
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil
| | - Christian J Sanders
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2540, Australia
| | - Gabriela B Oliveira
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil
| | - Silvio R Oliveira Filho
- Physical Geography Laboratory (LAGEF-UFF), Department of Geography, Graduate Program in Geography, Fluminense Federal University (UFF), Av. Gal. Milton Tavares de Souza, s/n°, Niterói, RJ 24210-346, Brazil
| | - Leonardo Amora-Nogueira
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil; Physical Geography Laboratory (LAGEF-UFF), Department of Geography, Graduate Program in Geography, Fluminense Federal University (UFF), Av. Gal. Milton Tavares de Souza, s/n°, Niterói, RJ 24210-346, Brazil
| | - Humberto Marotta
- Graduate Program in Geosciences (Environmental Geochemistry), Fluminense Federal University (UFF), Outeiro São João Baptista, s/n, 24020-007 Niterói, Brazil; Ecosystems and Global Change Laboratory (LEMG-UFF)/Brazilian Ocean Acidification Network (BrOA), International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NAB-UFF), Fluminense Federal University (UFF), Av. Edmundo March, s/n°, Niterói, RJ 24210-310, Brazil; Physical Geography Laboratory (LAGEF-UFF), Department of Geography, Graduate Program in Geography, Fluminense Federal University (UFF), Av. Gal. Milton Tavares de Souza, s/n°, Niterói, RJ 24210-346, Brazil.
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3
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Salmeán AA, Willats WGT, Ribeiro S, Andersen TJ, Ellegaard M. Over 100-Year Preservation and Temporal Fluctuations of Cell Wall Polysaccharides in Marine Sediments. FRONTIERS IN PLANT SCIENCE 2022; 13:785902. [PMID: 35519816 PMCID: PMC9062592 DOI: 10.3389/fpls.2022.785902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/28/2022] [Indexed: 05/16/2023]
Abstract
Polysaccharides constitute an important carbon pool in marine systems, but much is still unknown about the fate and degradation of these compounds. They are derived partly from production in situ, and in coastal areas, they are partly terrestrially derived, originating from freshwater runoff from land. The aim of this study was to test the applicability of high-throughput polysaccharide profiling for plant and algal cell-wall compounds in dated sediment cores from a coastal marine environment, to examine the preservation of cell-wall polysaccharides and explore their potential as proxies for temporal environmental changes. Preserved compounds and remains of organisms are routinely used as paleoenvironmental proxies as the amount and composition of different compounds that can provide insight into past environmental conditions, and novel means for reporting environmental changes are highly sought.
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Affiliation(s)
- Armando A. Salmeán
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Department of Technology, University College Copenhagen, Copenhagen, Denmark
| | - William George Tycho Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sofia Ribeiro
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Thorbjørn Joest Andersen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Ellegaard
- Department of Technology, University College Copenhagen, Copenhagen, Denmark
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4
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Riekenberg PM, Oakes JM, Eyre BD. Shining Light on Priming in Euphotic Sediments: Nutrient Enrichment Stimulates Export of Stored Organic Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11165-11172. [PMID: 32786559 DOI: 10.1021/acs.est.0c01914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Estuarine sediments are important sites for the interception, processing, and retention of organic matter, prior to its export to the coastal oceans. Stimulated microbial co-metabolism (priming) potentially increases export of refractory organic matter through increased production of hydrolytic enzymes. Using the microphytobenthos community to directly introduce a pulse of labile carbon into sediment, we traced a priming effect and assessed the decomposition and export of preexisting organic matter. We show enhanced efflux of preexisting carbon from intertidal sediments enriched with water column nutrients. Nutrient enrichment increased production of labile microphytobenthos carbon, which stimulated degradation of previously unavailable organic matter and led to increased liberation of "old" (6855 ± 120 years BP) refractory carbon as dissolved organic carbon (DOC). These enhanced DOC effluxes occurred at a scale that decreases estimates for global organic carbon burial in coastal systems and should be considered as an impact of eutrophication on estuarine carbon budgets.
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Affiliation(s)
- Philip M Riekenberg
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research and Utrecht University, P.O. Box 59, Den Hoorn 1790AB, The Netherlands
- Centre for Coastal Biogeochemistry, School of Environment, Science and Engineering, Southern Cross University, P.O. Box 157, Lismore, NSW 2480, Australia
| | - Joanne M Oakes
- Centre for Coastal Biogeochemistry, School of Environment, Science and Engineering, Southern Cross University, P.O. Box 157, Lismore, NSW 2480, Australia
| | - Bradley D Eyre
- Centre for Coastal Biogeochemistry, School of Environment, Science and Engineering, Southern Cross University, P.O. Box 157, Lismore, NSW 2480, Australia
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5
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Casado-Coy N, Sánchez-Jerez P, Holmer M, Sanz-Lazaro C. Bioturbation may not always enhance the metabolic capacity of organic polluted sediments. MARINE ENVIRONMENTAL RESEARCH 2020; 155:104882. [PMID: 32072982 DOI: 10.1016/j.marenvres.2020.104882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/14/2020] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Marine sediments are a major sink of organic matter, playing a crucial role in the global cycling of major elements. Macrofauna, through the reworking of particles and movement of solutes (bioturbation), enhances oxic conditions and the sediment metabolic capacity. Increases in the inputs of organic matter can lead to profound changes in the seabed and impact benthic ecological functions. Through a microcosm experiment, the effect of bioturbation of the polychaete Lumbrineris latreilli on biogeochemical fluxes under scenarios of increasing loads of organic matter was quantified. We found that bioturbation can buffer the negative consequences of anoxic conditions produced by organic enrichment, preventing the build-up of toxic by-products derived from anaerobic metabolic pathways by maintaining oxic conditions. However, the maintenance of oxic conditions by bioturbation is at the expense of limiting the sediment metabolic capacity. The maintenance of oxic conditions may limit anaerobic metabolic pathways, and consequently, the metabolic capacity of sediment. Thus, under organic matter pollution conditions, bioturbation may lessen the metabolic capacity of the sediment.
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Affiliation(s)
- Nuria Casado-Coy
- Department of Marine Science and Applied Biology, University of Alicante, PO Box 99, E-03080, Alicante, Spain.
| | - Pablo Sánchez-Jerez
- Department of Marine Science and Applied Biology, University of Alicante, PO Box 99, E-03080, Alicante, Spain; Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, E-03080, Alicante, Spain
| | - Marianne Holmer
- Institute of Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Carlos Sanz-Lazaro
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, E-03080, Alicante, Spain; Department of Ecology, University of Alicante, PO Box 99, E-03080, Alicante, Spain
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6
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Quigley LNM, Edwards A, Steen AD, Buchan A. Characterization of the Interactive Effects of Labile and Recalcitrant Organic Matter on Microbial Growth and Metabolism. Front Microbiol 2019; 10:493. [PMID: 30941109 PMCID: PMC6433851 DOI: 10.3389/fmicb.2019.00493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/26/2019] [Indexed: 11/23/2022] Open
Abstract
Geochemical models typically represent organic matter (OM) as consisting of multiple, independent pools of compounds, each accessed by microorganisms at different rates. However, recent findings indicate that organic compounds can interact within microbial metabolisms. The relevance of interactive effects within marine systems is debated and a mechanistic understanding of its complexities, including microbe-substrate relationships, is lacking. As a first step toward uncovering mediating processes, the interactive effects of distinct pools of OM on the growth and respiration of marine bacteria, individual strains and a simple, constructed community of Roseobacter lineage members were tested. Isolates were provided with natural organic matter (NOM) and different concentrations (1, 4, 40, 400 μM-C) and forms of labile OM (acetate, casamino acids, tryptone, coumarate). The microbial response to the mixed substrate regimes was assessed using viable counts and respiration in two separate experiments. Two marine bacteria and a six-member constructed community were assayed with these experiments. Both synergistic and antagonistic growth responses were evident for all strains, but all were transient. The specific substrate conditions promoting a response, and the direction of that response, varied amongst species. These findings indicate that the substrate conditions that result in OM interactive effects are both transient and species-specific and thus influenced by both the composition and metabolic potential of a microbial community.
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Affiliation(s)
- Lauren N M Quigley
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Abigail Edwards
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Andrew D Steen
- Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Alison Buchan
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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7
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Ortega-Arbulú AS, Pichler M, Vuillemin A, Orsi WD. Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. Environ Microbiol 2018; 21:374-388. [PMID: 30411473 PMCID: PMC7379666 DOI: 10.1111/1462-2920.14469] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 11/30/2022]
Abstract
Fungi living in sediments (‘mycobenthos’) are hypothesized to play a role in the degradation of organic matter deposited at the land‐sea interface, but the environmental factors influencing the mycobenthos are poorly understood. We used mock community calibrated Illumina sequencing to show that the mycobenthos community structure in a coastal lagoon was significantly changed after exposure to a lignocellulose extract and subsequent development of benthic anoxia over a relatively short (10 h) incubation. Saprotrophic taxa dominated and were selected for under benthic anoxia, specifically Aquamyces (Chytridiomycota) and Orbilia (Ascomycota), implicating these genera as important benthic saprotrophs. Protein encoding genes involved in energy and biomass production from Fungi and the fungal‐analogue group Labyrinthulomycetes had the highest increase in expression with the added organic matter compared with all other groups, indicating that lignocellulose stimulates metabolic activity in the mycobenthos. Flavobacteria dominated the active bacterial community that grew rapidly with the lignocellulose extract and crashed sharply upon O2 depletion. Our findings indicate that the diversity, activity and trophic potential of the mycobenthos changes rapidly in response to organic matter and decreasing O2 concentrations, which together with heterotrophic Flavobacteria, undergo ‘boom and bust’ dynamics during lignocellulose degradation in estuarine ecosystems.
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Affiliation(s)
- Ana-Sofia Ortega-Arbulú
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Monica Pichler
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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8
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Kolmakova OV, Gladyshev MI, Fonvielle JA, Ganzert L, Hornick T, Grossart HP. Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling. Environ Microbiol 2018; 21:34-49. [PMID: 30246449 DOI: 10.1111/1462-2920.14418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 11/27/2022]
Abstract
Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh 13 C-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.
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Affiliation(s)
- Olesya V Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia.,Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michail I Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jérémy André Fonvielle
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Lars Ganzert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,GFZ German Research Centre for Geosciencess, Section 5.3 Geomicrobiology, Potsdam, Germany.,Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, Germany
| | - Thomas Hornick
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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9
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Woo HL, Hazen TC. Enrichment of Bacteria From Eastern Mediterranean Sea Involved in Lignin Degradation via the Phenylacetyl-CoA Pathway. Front Microbiol 2018; 9:922. [PMID: 29867833 PMCID: PMC5954211 DOI: 10.3389/fmicb.2018.00922] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/20/2018] [Indexed: 02/01/2023] Open
Abstract
The degradation of allochthonous terrestrial organic matter, such as recalcitrant lignin and hemicellulose from plants, occurs in the ocean. We hypothesize that bacteria instead of white-rot fungi, the model organisms of aerobic lignin degradation within terrestrial environments, are responsible for lignin degradation in the ocean due to the ocean's oligotrophy and hypersalinity. Warm oxic seawater from the Eastern Mediterranean Sea was enriched on lignin in laboratory microcosms. Lignin mineralization rates by the lignin-adapted consortia improved after two sequential incubations. Shotgun metagenomic sequencing detected a higher abundance of aromatic compound degradation genes in response to lignin, particularly phenylacetyl-CoA, which may be an effective strategy for marine microbes in fluctuating oxygen concentrations. 16S rRNA gene amplicon sequencing detected a higher abundance of Gammaproteobacteria and Alphaproteobacteria bacteria such as taxonomic families Idiomarinaceae, Alcanivoraceae, and Alteromonadaceae in response to lignin. Meanwhile, fungal Ascomycetes and Basidiomycetes remained at very low abundance. Our findings demonstrate the significant potential of bacteria and microbes utilizing the phenylacetyl-CoA pathway to contribute to lignin degradation in the Eastern Mediterranean where environmental conditions are unfavorable for fungi. Exploring the diversity of bacterial lignin degraders may provide important enzymes for lignin conversion in industry. Enzymes may be key in breaking down high molecular weight lignin and enabling industry to use it as a low-cost and sustainable feedstock for biofuels or other higher-value products.
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Affiliation(s)
- Hannah L Woo
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Science, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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10
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Pérez A, Machado W, Gutiérrez D, Borges AC, Patchineelam SR, Sanders CJ. Carbon accumulation and storage capacity in mangrove sediments three decades after deforestation within a eutrophic bay. MARINE POLLUTION BULLETIN 2018; 126:275-280. [PMID: 29421098 DOI: 10.1016/j.marpolbul.2017.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/08/2017] [Accepted: 11/13/2017] [Indexed: 06/08/2023]
Abstract
A dated sediment core from an eutrophic mangrove area presented non-significant differences in carbon accumulation rates before (55.7±10.2gm-2yr-1) and after three decades of deforestation (59.7±7.2gm-2yr-1). Although eutrophication effects appear to compensate the loss of mangrove organic matter input, the results in this work show a threefold lower carbon accumulation than the global averages estimated for mangrove sediments. The effects of increasing eutrophication and enhanced sediment dry bulk density observed after deforestation (~30% higher) did not result in higher carbon stocks. Moreover, the lower TOC:OP (<400) and C:N (~20) molar ratios, as well as increased nutrient accumulation, reflect the dominance of phytoplankton-derived organic matter after deforestation, resulting in less-efficient sedimentary carbon sinks. These results indicate that the organic material deposited from eutrophication may not compensate mangrove deforestation losses on carbon accumulation in mangrove ecosystems.
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Affiliation(s)
- A Pérez
- Programa de Pós-Graduação em Geoquímica, Universidade Federal Fluminense, Departamento de Geoquímica, Rua Outeiro São João Baptista s/n, Niteroi, RJ, Brazil.
| | - W Machado
- Programa de Pós-Graduação em Geoquímica, Universidade Federal Fluminense, Departamento de Geoquímica, Rua Outeiro São João Baptista s/n, Niteroi, RJ, Brazil
| | - D Gutiérrez
- Dirección General de Investigaciones en Oceanografía y Cambio Climático, Instituto del Mar del Perú, Av. Gamarra y General Valle, s/n, Chucuito, Callao, Peru
| | - A C Borges
- Programa de Pós-Graduação em Geoquímica, Universidade Federal Fluminense, Departamento de Geoquímica, Rua Outeiro São João Baptista s/n, Niteroi, RJ, Brazil
| | - S R Patchineelam
- Programa de Pós-Graduação em Geoquímica, Universidade Federal Fluminense, Departamento de Geoquímica, Rua Outeiro São João Baptista s/n, Niteroi, RJ, Brazil
| | - C J Sanders
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
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11
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Sekar R, Shin HD, DiChristina TJ. Direct conversion of cellulose and hemicellulose to fermentable sugars by a microbially-driven Fenton reaction. BIORESOURCE TECHNOLOGY 2016; 218:1133-1139. [PMID: 27469094 DOI: 10.1016/j.biortech.2016.07.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 06/06/2023]
Abstract
The aim of this work was to develop a microbially-driven Fenton reaction that fragments cellulose and hemicellulose, degrades cellodextrins and xylodextrins, and produces short-chain oligosaccharides and monomeric sugars in a single bioreactor. The lignocellulose degradation system operates at neutral pH and does not require addition of conventional lignocellulose-degrading enzymes, thus avoiding problems associated with enzyme accessibility and specificity. The ability to produce useful bioproducts was demonstrated by production of the bioplastic polyhydroxybutyrate with the xylan degradation products as starting substrate.
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Affiliation(s)
- Ramanan Sekar
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyun Dong Shin
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Thomas J DiChristina
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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12
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Correction: Occurrence of Priming in the Degradation of Lignocellulose in Marine Sediments. PLoS One 2016; 11:e0154365. [PMID: 27100652 PMCID: PMC4839761 DOI: 10.1371/journal.pone.0154365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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