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Brandani J, Peter H, Busi SB, Kohler TJ, Fodelianakis S, Ezzat L, Michoud G, Bourquin M, Pramateftaki P, Roncoroni M, Lane SN, Battin TJ. Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains. Front Microbiol 2022; 13:948165. [PMID: 36003939 PMCID: PMC9393633 DOI: 10.3389/fmicb.2022.948165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Glacier shrinkage opens new proglacial terrain with pronounced environmental gradients along longitudinal and lateral chronosequences. Despite the environmental harshness of the streams that drain glacier forelands, their benthic biofilms can harbor astonishing biodiversity spanning all domains of life. Here, we studied the spatial dynamics of prokaryotic and eukaryotic photoautotroph diversity within braided glacier-fed streams and tributaries draining lateral terraces predominantly fed by groundwater and snowmelt across three proglacial floodplains in the Swiss Alps. Along the lateral chronosequence, we found that benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams, and that their respective diversity and community composition differed markedly. We also found spatial turnover of bacterial communities in the glacier-fed streams along the longitudinal chronosequence. These patterns along the two chronosequences seem unexpected given the close spatial proximity and connectivity of the various streams, suggesting environmental filtering as an underlying mechanism. Furthermore, our results suggest that photoautotrophic communities shape bacterial communities across the various streams, which is understandable given that algae are the major source of organic matter in proglacial streams. Overall, our findings shed new light on benthic biofilms in proglacial streams now changing at rapid pace owing to climate-induced glacier shrinkage.
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Affiliation(s)
- Jade Brandani
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Hannes Peter
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tyler J. Kohler
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stilianos Fodelianakis
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Leila Ezzat
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Grégoire Michoud
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Massimo Bourquin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Paraskevi Pramateftaki
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Roncoroni
- Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Lausanne, Switzerland
| | - Stuart N. Lane
- Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Lausanne, Switzerland
| | - Tom J. Battin
- River Ecosystems Laboratory, Alpine and Polar Environmental Research Center, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- *Correspondence: Tom J. Battin,
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Wang C, Liu S, Wang P, Chen J, Wang X, Yuan Q, Ma J. How sediment bacterial community shifts along the urban river located in mining city. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42300-42312. [PMID: 33811632 DOI: 10.1007/s11356-020-12031-0] [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: 10/04/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China.
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Jingjie Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
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3
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Otte JM, Blackwell N, Soos V, Rughöft S, Maisch M, Kappler A, Kleindienst S, Schmidt C. Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples? FEMS Microbiol Ecol 2018; 94:5104375. [DOI: 10.1093/femsec/fiy189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Julia M Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Viktoria Soos
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Saskia Rughöft
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Markus Maisch
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
- Geomicrobiology, Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
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4
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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Kamjunke N, Herzsprung P, Neu TR. Quality of dissolved organic matter affects planktonic but not biofilm bacterial production in streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 506-507:353-360. [PMID: 25460970 DOI: 10.1016/j.scitotenv.2014.11.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/11/2014] [Accepted: 11/11/2014] [Indexed: 06/04/2023]
Abstract
Streams and rivers are important sites of organic carbon mineralization which is dependent on the land use within river catchments. Here we tested whether planktonic and epilithic biofilm bacteria differ in their response to the quality of dissolved organic carbon (DOC). Thus, planktonic and biofilm bacterial production was compared with patterns of DOC along a land-use gradient in the Bode catchment area (Germany). The freshness index of DOC was positively related to the proportion of agricultural area in the catchment. The humification index correlated with the proportion of forest area. Abundance and production of planktonic bacteria were lower in headwaters than at downstream sites. Planktonic production was weakly correlated to the total concentration of DOC but more strongly to quality-measures as revealed by spectra indexes, i.e. positively to the freshness index and negatively to the humification index. In contrast to planktonic bacteria, abundance and production of biofilm bacteria were independent of DOC quality. This finding may be explained by the association of biofilm bacteria with benthic algae and an extracellular matrix which represent additional substrate sources. The data show that planktonic bacteria seem to be regulated at a landscape scale controlled by land use, whereas biofilm bacteria are regulated at a biofilm matrix scale controlled by autochthonous production. Thus, the effects of catchment-scale land use changes on ecosystem processes are likely lower in small streams dominated by biofilm bacteria than in larger streams dominated by planktonic bacteria.
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Affiliation(s)
- Norbert Kamjunke
- Dept. of River Ecology, Helmholtz-Centre for Environmental Research UFZ, Brückstraße 3a, D-39114 Magdeburg, Germany; Dept. of Lake Research, Helmholtz-Centre for Environmental Research UFZ, Brückstraße 3a, D-39114 Magdeburg, Germany.
| | - Peter Herzsprung
- Dept. of Lake Research, Helmholtz-Centre for Environmental Research UFZ, Brückstraße 3a, D-39114 Magdeburg, Germany
| | - Thomas R Neu
- Dept. of River Ecology, Helmholtz-Centre for Environmental Research UFZ, Brückstraße 3a, D-39114 Magdeburg, Germany
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6
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Liu J, Li Z. Cascade Biotransformations via Enantioselective Reduction, Oxidation, and Hydrolysis: Preparation of (R)-δ-Lactones from 2-Alkylidenecyclopentanones. ACS Catal 2013. [DOI: 10.1021/cs400101v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ji Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive
4, Singapore 117576
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive
4, Singapore 117576
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7
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Coelho-Souza SA, Miranda MR, Salgado LT, Coutinho R, Guimaraes JRD. Adaptation of the 3H-leucine incorporation technique to measure heterotrophic activity associated with biofilm on the blades of the seaweed Sargassum spp. MICROBIAL ECOLOGY 2013; 65:424-36. [PMID: 22965803 DOI: 10.1007/s00248-012-0116-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 08/14/2012] [Indexed: 06/01/2023]
Abstract
The ecological interaction between microorganisms and seaweeds depends on the production of secondary compounds that can influence microbial diversity in the water column and the composition of reef environments. We adapted the (3)H-leucine incorporation technique to measure bacterial activity in biofilms associated with the blades of the macroalgae Sargassum spp. We evaluated (1) if the epiphytic bacteria on the blades were more active in detritus or in the biofilm, (2) substrate saturation and linearity of (3)H-leucine incorporation, (3) the influence of specific metabolic inhibitors during (3)H-leucine incorporation under the presence or absence of natural and artificial light, and (4) the efficiency of radiolabeled protein extraction. Scanning electron microscopy showed heterogeneous distribution of bacteria, diatoms, and polymeric extracellular secretions. Active bacteria were present in both biofilm and detritus on the blades. The highest (3)H-leucine incorporation was obtained when incubating blades not colonized by macroepibionts. Incubations done under field conditions reported higher (3)H-leucine incorporation than in the laboratory. Light quality and sampling manipulation seemed to be the main factors behind this difference. The use of specific metabolic inhibitors confirmed that bacteria are the main group incorporating (3)H-leucine but their association with primary production suggested a symbiotic relationship between bacteria, diatoms, and the seaweed.
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Affiliation(s)
- Sergio A Coelho-Souza
- Biotecnologia Marinha, Instituto de Ciências do Mar Almirante Paulo Moreira (IEAPM), Arraial do Cabo-RJ, Brazil.
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8
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Haglund AL, Lantz P, Törnblom E, Tranvik L. Depth distribution of active bacteria and bacterial activity in lake sediment. FEMS Microbiol Ecol 2012; 46:31-8. [PMID: 19719580 DOI: 10.1016/s0168-6496(03)00190-9] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Abstract The bacterial activity in sediments is often low considering the generally high bacterial abundance. Still, a large fraction of bacteria have been found active even in deep sediments. These findings suggest that sediment bacteria have comparatively low cell-specific production. We studied bacterial activity and the active fraction of bacteria in a lake sediment profile. Bacterial production and metabolism were measured by thymidine and leucine incorporation and by microcalorimetry. In addition to counts of total bacteria, we estimated the nucleoid-containing fraction of the bacteria by adding a destaining step to the DAPI staining method, and the live fraction using the Live/Dead Baclight bacterial viability kit. The bacterial activity and abundance decreased with sediment depth, while the proportion of active bacteria remained similar at all depths. Between 57 and 63% of the bacteria were scored viable, and 13-52% were scored as nucleoid-containing cells. Consequently, there was no accumulation of dead bacterial cells in deeper sediments. Cell-specific production of sediment bacteria may be severely underestimated if the active fraction of the sediment bacterial community is not considered during enumeration.
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Affiliation(s)
- Ann-Louise Haglund
- Department of Public Technology, Mälardalen University, Box 883, SE-721 23 Västerås, Sweden
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9
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Ask J, Karlsson J, Persson L, Ask P, Byström P, Jansson M. Whole-lake estimates of carbon flux through algae and bacteria in benthic and pelagic habitats of clear-water lakes. Ecology 2009; 90:1923-32. [DOI: 10.1890/07-1855.1] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Tietz A, Langergraber G, Watzinger A, Haberl R, Kirschner AKT. Bacterial carbon utilization in vertical subsurface flow constructed wetlands. WATER RESEARCH 2008; 42:1622-1634. [PMID: 17991505 DOI: 10.1016/j.watres.2007.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 10/04/2007] [Accepted: 10/09/2007] [Indexed: 05/25/2023]
Abstract
Subsurface vertical flow constructed wetlands with intermittent loading are considered as state of the art and can comply with stringent effluent requirements. It is usually assumed that microbial activity in the filter body of constructed wetlands, responsible for the removal of carbon and nitrogen, relies mainly on bacterially mediated transformations. However, little quantitative information is available on the distribution of bacterial biomass and production in the "black-box" constructed wetland. The spatial distribution of bacterial carbon utilization, based on bacterial (14)C-leucine incorporation measurements, was investigated for the filter body of planted and unplanted indoor pilot-scale constructed wetlands, as well as for a planted outdoor constructed wetland. A simple mass-balance approach was applied to explain the bacterially catalysed organic matter degradation in this system by comparing estimated bacterial carbon utilization rates with simultaneously measured carbon reduction values. The pilot-scale constructed wetlands proved to be a suitable model system for investigating microbial carbon utilization in constructed wetlands. Under an ideal operating mode, the bulk of bacterial productivity occurred within the first 10cm of the filter body. Plants seemed to have no significant influence on productivity and biomass of bacteria, as well as on wastewater total organic carbon removal.
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Affiliation(s)
- Alexandra Tietz
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Applied Life Sciences, Muthgasse, Vienna, Austria
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11
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Miranda MR, Guimarães JRD, Coelho-Souza AS. [3H]Leucine incorporation method as a tool to measure secondary production by periphytic bacteria associated to the roots of floating aquatic macrophyte. J Microbiol Methods 2007; 71:23-31. [PMID: 17765986 DOI: 10.1016/j.mimet.2007.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Revised: 06/29/2007] [Accepted: 06/30/2007] [Indexed: 10/23/2022]
Abstract
The present study assessed the application of [(3)H]Leucine incorporation into protein by periphytic bacteria associated with the roots of the floating aquatic macrophyte Eichornia crassipes. Basic assumptions underlying the method, such as linearity of leucine incorporation, saturation level of incorporation rates, incorporation into other macromolecules, specificity of incorporation for bacterial assemblages and [(3)H]Leucine degradation during samples storage were tested, and two procedures for extracting the incorporated leucine were compared. Both methods gave the same results, however, the hot TCA extraction method was less time consuming than the alkaline extraction method. Incorporation of [(3)H]Leucine was linear for up to 40 min. Saturation concentration of [(3)H]Leucine incorporation into protein was 1500 nM. An experiment with prokaryotic and eukaryotic inhibitors showed no significant [(3)H]Leucine incorporation into eukaryotes even in high leucine concentrations. No significant amounts of radiolabel were incorporated into other macromolecules. The maximum time of sample storage after the incubation is 15 days. The leucine incorporation method can be a reliable tool to measure bacterial production in the periphyton root-associated bacteria.
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Affiliation(s)
- M R Miranda
- Laboratório de Traçadores Wolfgang Christian Pfeiffer, Instituto de Biofísica Carlos Chagas Filho,Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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12
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Königs S, Cleven EJ. The bacterivory of interstitial ciliates in association with bacterial biomass and production in the hyporheic zone of a lowland stream. FEMS Microbiol Ecol 2007; 61:54-64. [PMID: 17506825 DOI: 10.1111/j.1574-6941.2007.00328.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Rates of bacteria ingestion by interstitial ciliates were estimated and compared to bacterial biomass and production. Investigation was carried out in the hyporheic zone of a lowland stream. FISH was applied to quantitatively determine bacteria within the ciliate's food vacuoles. To estimate bacteria ingestion rates using FISH, we had to strike a new path. When numbers of bacteria in the food vacuoles remains constant with time (bacterial digestion and ingestion are at equilibrium), ingestion rate can be estimated based on the digestion time and the average number of bacteria per cell. Ciliate community was predominantly composed of bacterivorous ciliates. FISH-signals deriving from ingested bacteria were detected in Cinetochilum margaritaceum, 'other small scuticociliates', Pleuronema spp., and Vorticella spp. Ingestion rates for these taxa were 78, 150, 86, and 38 bacteria ind(-1) h(-1), respectively. The grazing impacts on bacterial biomass and carbon production were calculated based on these ingestion rates. Ciliate grazing caused a decrease in bacterial biomass of 0.024% day(-1) and in bacterial carbon production of 1.60%. These findings suggest that interstitial ciliate grazing impact on bacteria biomass and production was too low to represent an important link in the carbon flow of the hyporheic zone under study.
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Affiliation(s)
- Sascha Königs
- Department of General Ecology and Limnology, Zoological Institute, University of Cologne, Köln, Germany
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13
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Guimarães JRD, Mauro JBN, Meili M, Sundbom M, Haglund AL, Coelho-Souza SA, Hylander LD. Simultaneous radioassays of bacterial production and mercury methylation in the periphyton of a tropical and a temperate wetland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2006; 81:95-100. [PMID: 16956711 DOI: 10.1016/j.jenvman.2005.09.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Revised: 03/03/2005] [Accepted: 09/30/2005] [Indexed: 05/04/2023]
Abstract
Laboratory radioassays were made to study mercury (Hg) methylation together with bacterial production in the periphyton of two aquatic macrophytes, the submerged Myriophyllum spicatum, from a constructed wetland in Sweden and the floating Eichhornia crassipes, from a eutrophied tropical lake in Brazil. Time course incubations were made by addition of (203)HgCl(2) and the methylmercury formed was extracted at pre-defined time intervals. Bacterial production ((14)C-leucine incorporation) was measured at the same time intervals, with plants removed from parallel incubations made with and without addition of cold HgCl(2). For E. crassipes, higher methylmercury production was observed at elevated bacterial production, whereas for M. spicatum, the bacterial production was significantly lower, and Hg methylation was below the detection limit. The combined results confirm the importance of microbial processes for Hg methylation, although other factors are known to influence this process in complex ways. The addition of Hg did not significantly influence bacterial production, while the incubation temperatures used (25 and 35 degrees C) resulted in different methylation rates. Radiotracer techniques for measurements of bacterial production such as (14)C-leucine uptake can provide useful insights into the Hg cycle in aquatic environments, and our data suggest that they may be used as a proxy of mercury methylation potentials.
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Affiliation(s)
- J R D Guimarães
- Laboratório de Radioisótopos EPF, IBCCF, UFRJ, Bloco G, CCS, CEP: 21949-900, Ilha do Fundão, Rio de Janeiro (RJ), Brazil.
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14
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Gillies JE, Kuehn KA, Francoeur SN, Neely RK. Application of the [3H]leucine incorporation technique for quantification of bacterial secondary production associated with decaying wetland plant litter. Appl Environ Microbiol 2006; 72:5948-56. [PMID: 16957215 PMCID: PMC1563605 DOI: 10.1128/aem.00696-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2006] [Accepted: 06/26/2006] [Indexed: 11/20/2022] Open
Abstract
The radiolabeled leucine incorporation technique for quantifying rates of bacterial production has increased in popularity since its original description for bacterioplankton communities. Prior studies addressing incorporation conditions (e.g., substrate saturation) for bacterial communities in other habitats, such as decaying plant litter, have reported a wide range of final leucine concentrations (400 nM to 50 microM) required to achieve saturation-level uptake. We assessed the application of the [(3)H]leucine incorporation procedure for measuring bacterial production on decaying wetland plant litter. Substrate saturation experiments (nine concentrations, 10 nM to 50 microM final leucine concentration) were conducted on three dates for microbial communities colonizing the submerged litter of three emergent plant species (Typha angustifolia, Schoenoplectus validus, and Phragmites australis). A modified [(3)H]leucine protocol was developed by coupling previously described incubation and alkaline extraction protocols with microdialysis (500 molecular weight cutoff membrane) of the final radiolabeled protein extract. The incorporation of [(3)H]leucine into protein exhibited a biphasic saturation curve, with lower apparent K(m) values ranging from 400 nM to 4.2 microM depending on the plant species studied. Upper apparent K(m) values ranged from 1.3 to 59 microM. These results suggest differential uptake by litter-associated microbial assemblages, with the lower apparent K(m) values possibly representing bacterial uptake and higher apparent K(m) values representing a combination of both bacterial and nonbacterial (e.g., eukaryotic) uptake.
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Affiliation(s)
- Jane E Gillies
- Department of Biological Sciences, 118 College Dr., #5018, The University of Southern Mississippi, Hattiesburg, MS 39406-0001, USA
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15
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Tao W, Hall KJ, Duff SJB. Heterotrophic bacterial activities and treatment performance of surface flow constructed wetlands receiving woodwaste leachate. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2006; 78:671-9. [PMID: 16929636 DOI: 10.2175/106143006x99821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Heterotrophic activities were investigated by measuring 3H-leucine incorporation to bacterial protein and 14C-glucose turnover in surface flow constructed wetlands receiving woodwaste leachate. No significant longitudinal variation was found in heterotrophic activities of bacterioplankton. An open wetland, a vegetated wetland, and a fertilized vegetated wetland were used to examine the effects of vegetation and ammonium nitrate amendment. There was not a significant difference in treatment performance among the three wetlands, except for a significant pH increase and more efficient volatile fatty acids removal in the fertilized wetland. The fertilized wetland had the highest leucine incorporation rate and shortest glucose turnover time accompanied by the lowest glucose mineralization percentage, followed by the open wetland, then the vegetated wetland. Planktonic and sedimentary bacteria contributed to the majority of the total heterotrophic activities; epiphytic bacteria played a minor role. Heterotrophic activities were influenced by the availability of nutrient, electron acceptor, and organic substrate.
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Affiliation(s)
- Wendong Tao
- Department of Civil Engineering, University of British Columbia, Vancouver, Canada.
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16
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Buesing N, Gessner MO. Benthic bacterial and fungal productivity and carbon turnover in a freshwater marsh. Appl Environ Microbiol 2006; 72:596-605. [PMID: 16391096 PMCID: PMC1352256 DOI: 10.1128/aem.72.1.596-605.2006] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterotrophic bacteria and fungi are widely recognized as crucial mediators of carbon, nutrient, and energy flow in ecosystems, yet information on their total annual production in benthic habitats is lacking. To assess the significance of annual microbial production in a structurally complex system, we measured production rates of bacteria and fungi over an annual cycle in four aerobic habitats of a littoral freshwater marsh. Production rates of fungi in plant litter were substantial (0.2 to 2.4 mg C g(-1) C) but were clearly outweighed by those of bacteria (2.6 to 18.8 mg C g(-1) C) throughout the year. This indicates that bacteria represent the most actively growing microorganisms on marsh plant litter in submerged conditions, a finding that contrasts strikingly with results from both standing dead shoots of marsh plants and submerged plant litter decaying in streams. Concomitant measurements of microbial respiration (1.5 to 15.3 mg C-CO2 g(-1) of plant litter C day(-1)) point to high microbial growth efficiencies on the plant litter, averaging 45.5%. The submerged plant litter layer together with the thin aerobic sediment layer underneath (average depth of 5 mm) contributed the bulk of microbial production per square meter of marsh surface (99%), whereas bacterial production in the marsh water column and epiphytic biofilms was negligible. The magnitude of the combined production in these compartments (approximately 1,490 g C m(-2) year(-1)) highlights the importance of carbon flows through microbial biomass, to the extent that even massive primary productivity of the marsh plants (603 g C m(-2) year(-1)) and subsidiary carbon sources (approximately 330 g C m(-2) year(-1)) were insufficient to meet the microbial carbon demand. These findings suggest that littoral freshwater marshes are genuine hot spots of aerobic microbial carbon transformations, which may act as net organic carbon importers from adjacent systems and, in turn, emit large amounts of CO2 (here, approximately 870 g C m(-2) year(-1)) into the atmosphere.
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Affiliation(s)
- Nanna Buesing
- Department of Limnology, Swiss Federal Institute of Aquatic Science and Technology (Eawag/ETH), 6047 Kastanienbaum, Switzerland.
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17
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Mueller DR, Vincent WF, Bonilla S, Laurion I. Extremotrophs, extremophiles and broadband pigmentation strategies in a high arctic ice shelf ecosystem. FEMS Microbiol Ecol 2004; 53:73-87. [PMID: 16329931 DOI: 10.1016/j.femsec.2004.11.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Revised: 11/05/2004] [Accepted: 11/05/2004] [Indexed: 10/26/2022] Open
Abstract
Remnant ice shelves along the northern coast of Ellesmere Island, Nunavut, Canada ( approximately 83 degrees N) provide a habitat for cryo-tolerant microbial mat communities. Bioassays of bacterial and primary production were undertaken to quantify the short-term physiological response of the mats to changes in key variables that characterize this cryo-ecosystem (salinity, irradiance and temperature). The heterotrophic versus autotrophic community responses to these stressors differed markedly. The heterotrophic bacteria were extremophilic and specifically adapted to ambient conditions on the ice shelf, whereas the autotrophic community had broader tolerance ranges and optima outside the ambient range. This latter, extremotrophic response may be partly due to a diverse suite of pigments including oligosaccharide mycosporine-like amino acids, scytonemins, carotenoids, phycobiliproteins and chlorophylls that absorb from the near UV-B to red wavelengths. These pigments provide a comprehensive broadband strategy for coping with the multiple stressors of high irradiance, variable salinity and low temperatures in this extreme cryo-environment.
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Affiliation(s)
- Derek R Mueller
- Centre d'études nordiques et Département de biologie, Université Laval, Pavillon Vachon, Quebec City, QC, Canada G1K 7P4.
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18
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Eiler A, Farnleitner AH, Zechmeister TC, Herzig A, Hurban C, Wesner W, Krachler R, Velimirov B, Kirschner AKT. Factors controlling extremely productive heterotrophic bacterial communities in shallow soda pools. MICROBIAL ECOLOGY 2003; 46:43-54. [PMID: 12739080 DOI: 10.1007/s00248-002-2041-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2002] [Accepted: 12/23/2002] [Indexed: 05/24/2023]
Abstract
Dilute soda lakes are among the world's most productive environments and are usually dominated by dense blooms of cyanobacteria. Up to now, there has been little information available on heterotrophic bacterial abundance, production, and their controlling factors in these ecosystems. In the present study the main environmental factors responsible for the control of the heterotrophic bacterial community in five shallow soda pools in Eastern Austria were investigated during an annual cycle. Extremely high cyanobacterial numbers and heterotrophic bacterial numbers up to 307 x 10(9) L(-1) and 268 x 10(9) L(-1) were found, respectively. Bacterial secondary production rates up to 738 micro g C L(-1) h(-1) and specific growth rates up to 1.65 h(-1) were recorded in summer and represent the highest reported values for natural aquatic ecosystems. The combination of dense phytoplankton blooms, high temperature, high turbidity, and nutrient concentration due to evaporation is supposed to enable the development of such extremely productive microbial populations. By principal component analysis containing the data set of all five investigated pools, two factors were extracted which explained 62.5% of the total variation of the systems. The first factor could be interpreted as a turbidity factor; the second was assigned to as concentration factor. From this it was deduced that bacterial and cyanobacterial abundance were mainly controlled by wind-induced sediment resuspension and turbidity stabilized by the high pH and salinity and less by evaporative concentration of salinity and dissolved organic carbon. Bacterial production was clustered with temperature in factor 3, showing that bacterial growth was mainly controlled by temperature. The concept of describing the turbid water columns of the shallow soda pools as "fluid sediment" is discussed.
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Affiliation(s)
- A Eiler
- Institute of Medical Biology, Vienna University, Waehringerstr. 10, A-1090 Vienna, Austria.
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Bastviken D, Olsson M, Tranvik L. Simultaneous measurements of organic carbon mineralization and bacterial production in oxic and anoxic lake sediments. MICROBIAL ECOLOGY 2003; 46:73-82. [PMID: 12739075 DOI: 10.1007/s00248-002-1061-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2002] [Accepted: 12/02/2002] [Indexed: 05/21/2023]
Abstract
Based on work in marine sediments it can be hypothesized that (i) overall OM mineralization depends on the enzymatic capacity and is largely independent from the energy yield, (ii) similar oxic and anoxic rates are expected for fresh OM, while oxic rates should be faster for old OM that is partially degraded or adsorbed to particles, and (iii) that the thermodynamic energy yield does not regulate mineralization, but primarily determines the energy fraction allocated to bacterial production (BP). We addressed these hypotheses by simultaneous measurements of mineralization rates (MR) and BP in sediments from a eutrophic lake, along with MR measurements in sediments of a dystrophic lake. Anoxic MR were 44 and 78% of oxic MR in the eutrophic and dystrophic lake, respectively, which was always higher than expected given the theoretical energy yields. The BP:MR ratio was 0.94 and 0.24 in the oxic and anoxic treatments, respectively, in accordance with the expected energy yields. Thus, the results support all three hypotheses above. We also critically discuss BP measurements in sediments and suggest that bacterial growth efficiency values from simultaneous MR and BP measurements can be used to evaluate the reliability of BP estimates.
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Affiliation(s)
- D Bastviken
- Environmental Science Programme, Department of Thematic Studies, Linköping University, 581 83 Linköping, Sweden.
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20
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Bastviken D, Tranvik L. The leucine incorporation method estimates bacterial growth equally well in both oxic and anoxic lake waters. Appl Environ Microbiol 2001; 67:2916-21. [PMID: 11425702 PMCID: PMC92961 DOI: 10.1128/aem.67.7.2916-2921.2001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial biomass production is often estimated from incorporation of radioactively labeled leucine into protein, in both oxic and anoxic waters and sediments. However, the validity of the method in anoxic environments has so far not been tested. We compared the leucine incorporation of bacterial assemblages growing in oxic and anoxic waters from three lakes differing in nutrient and humic contents. The method was modified to avoid O(2) contamination by performing the incubation in syringes. Isotope saturation levels in oxic and anoxic waters were determined, and leucine incorporation rates were compared to microscopically observed bacterial growth. Finally, we evaluated the effects of O(2) contamination during incubation with leucine, as well as the potential effects of a headspace in the incubation vessel. Isotope saturation occurred at a leucine concentration of above about 50 nM in both oxic and anoxic waters from all three lakes. Leucine incorporation rates were linearly correlated to observed growth, and there was no significant difference between oxic and anoxic conditions. O(2) contamination of anoxic water during 1-h incubations with leucine had no detectable impact on the incorporation rate, while a headspace in the incubation vessel caused leucine incorporation to increase in both anoxic and O(2)-contaminated samples. The results indicate that the leucine incorporation method relates equally to bacterial growth rates under oxic and anoxic conditions and that incubation should be performed without a headspace.
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Affiliation(s)
- D Bastviken
- Department of Water and Environmental Studies, Linköping University, SE 581 83 Linköping, Sweden.
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