1
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Taylor AE, Mellbye BL. Differential Responses of the Catalytic Efficiency of Ammonia and Nitrite Oxidation to Changes in Temperature. Front Microbiol 2022; 13:817986. [PMID: 35620102 PMCID: PMC9127996 DOI: 10.3389/fmicb.2022.817986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated nitrification plays an important role in the nitrogen (N) cycle, and rates of activity have been shown to change significantly with temperature. Despite this, the substrate affinities of nitrifying bacteria and archaea have not been comprehensively measured and are often assumed to be static in mathematical models of environmental systems. In this study, we measured the oxidation kinetics of ammonia- (NH3) oxidizing archaea (AOA), NH3-oxidizing bacteria (AOB), and two distinct groups of nitrite (NO2 -)-oxidizing bacteria (NOB), of the genera Nitrobacter and Nitrospira, by measuring the maximum rates of apparent activity (V max(app)), the apparent half-saturation constant (K m(app)), and the overall catalytic efficiency (V max(app) /K m(app)) over a range of temperatures. Changes in V max(app) and K m(app) with temperature were different between groups, with V max(app) and catalytic efficiency increasing with temperature in AOA, while V max(app) , K m(app), and catalytic efficiency increased in AOB. In Nitrobacter NOB, V max(app) and K m(app) increased, but catalytic efficiency decreased significantly with temperature. Nitrospira NOB were variable, but V max(app) increased while catalytic efficiency and K m(app) remained relatively unchanged. Michaelis-Menten (MM) and Haldane (H) kinetic models of NH3 oxidation and NO2 - oxidation based on the collected data correctly predict nitrification potential in some soil incubation experiments, but not others. Despite previous observations of coupled nitrification in many natural systems, our results demonstrate significant differences in response to temperature strategies between the different groups of nitrifiers; and indicate the need to further investigate the response of nitrifiers to environmental changes.
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Affiliation(s)
- Anne E. Taylor
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Brett L. Mellbye
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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2
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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3
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Reddington K, Eccles D, O'Grady J, Drown DM, Hansen LH, Nielsen TK, Ducluzeau AL, Leggett RM, Heavens D, Peel N, Snutch TP, Bayega A, Oikonomopoulos S, Ragoussis I, Barry T, van der Helm E, Jolic D, Richardson H, Jansen H, Tyson JR, Jain M, Brown BL. Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function. Gigascience 2020; 9:5855463. [PMID: 32520351 PMCID: PMC7285869 DOI: 10.1093/gigascience/giaa053] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/23/2020] [Accepted: 04/27/2020] [Indexed: 12/02/2022] Open
Abstract
Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad “aquascape” scale, and few if any have applied the newest nanopore technology. Results We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5–1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers. Conclusions Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.
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Affiliation(s)
- Kate Reddington
- Microbial Diagnostics Research Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, University Road, Galway, Ireland H91 TK33, Ireland
| | - David Eccles
- Malaghan Institute of Medical Research, Gate 7, Victoria University Kelburn Parade, Wellington 6140, Wellington 6242, New Zealand
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, James Watson Rd, Norwich NR4 7TJ, UK
| | - Devin M Drown
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Fairbanks, 2140 Koyukuk Drive, Fairbanks, AK 9975-7000, USA
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Aarhus University, PO Box 358, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.,Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Environmental Science, Aarhus University, PO Box 358, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.,Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Anne-Lise Ducluzeau
- Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving 1 Building P.O. Box 757000 2140 Koyukuk Drive Fairbanks, AK 99775-7000, USA
| | | | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Ned Peel
- Earlham Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Terrance P Snutch
- Michael Smith Laboratories and Department of Zoology, University of British Columbia, #301-2185 East Mall Vancouver, BC V6T 1Z4, Canada
| | - Anthony Bayega
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 3640 rue University, Montreal, Quebec H3A 0C7, Canada
| | - Spyridon Oikonomopoulos
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 3640 rue University, Montreal, Quebec H3A 0C7, Canada
| | - Ioannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 3640 rue University, Montreal, Quebec H3A 0C7, Canada
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory, Microbiology, School of Natural Sciences, National University of Ireland, University Road, Galway, Ireland H91 TK33, Ireland
| | - Eric van der Helm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Dino Jolic
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5 72076 Tübingen, Germany
| | - Hollian Richardson
- Norwich Medical School, University of East Anglia, James Watson Rd, Norwich NR4 7TJ, UK
| | - Hans Jansen
- Future Genomics Technologies B.V., Nucleus building, Sylviusweg 74, 2333 BE Leiden, The Netherlands
| | - John R Tyson
- Michael Smith Laboratories and Department of Zoology, University of British Columbia, #301-2185 East Mall Vancouver, BC V6T 1Z4, Canada
| | - Miten Jain
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Bonnie L Brown
- Department of Biological Sciences, University of New Hampshire, 38 Academic Way, Durham, NH 03824, USA
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4
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Song W, Song W, Gu H, Li F. Progress in the Remote Sensing Monitoring of the Ecological Environment in Mining Areas. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E1846. [PMID: 32178376 PMCID: PMC7142410 DOI: 10.3390/ijerph17061846] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 11/20/2022]
Abstract
Based on the results of an extensive literature research, we summarize the research progress of remote sensing monitoring in terms of identifying mining area boundaries and monitoring land use or land cover changes of mining areas. We also analyze the application of remote sensing in monitoring the biodiversity, landscape structure, vegetation change, soil environment, surface runoff conditions, and the atmospheric environment in mining areas and predict the prospects of remote sensing in monitoring the ecological environment in mining areas. Based on the results, the accurate classification of land use or land cover and the accurate extraction of environmental factors are the basis for remote sensing monitoring of the ecological environment in mining areas. In terms of the extraction of ecological factors, vegetation extraction is relatively advanced in contrast to the extraction of animal and microbial data. For the monitoring of environmental conditions of mining areas, sophisticated methods are available to identify pollution levels of vegetation and to accurately monitor soil quality. However, the methods for water and air pollution monitoring in mining areas still need to be improved. These limitations considerably impede the application of remote sensing monitoring in mining areas. The solving of these problems depends on the progress of multi-source remote sensing data and stereoscopic monitoring techniques.
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Affiliation(s)
- Wen Song
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
- College of Mining Engineering, North China University of Science and Technology, Tangshan 063210, China; (H.G.); (F.L.)
| | - Wei Song
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
| | - Haihong Gu
- College of Mining Engineering, North China University of Science and Technology, Tangshan 063210, China; (H.G.); (F.L.)
- Hebei Key Laboratory of Mining Development and Security Technology, Tangshan 063210, China
- Hebei Industrial Technology Institute of Mine Ecological Remediation, Tangshan 063210, China
| | - Fuping Li
- College of Mining Engineering, North China University of Science and Technology, Tangshan 063210, China; (H.G.); (F.L.)
- Hebei Key Laboratory of Mining Development and Security Technology, Tangshan 063210, China
- Hebei Industrial Technology Institute of Mine Ecological Remediation, Tangshan 063210, China
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5
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Abstract
Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel. However, this is labor intensive, especially when measuring biogas production. Commercial solutions for multiplying reactors performing continuous anaerobic digestion exist but are expensive and use comparably large reactor volumes, requiring the preparation of substantial amounts of media. Here, a flexible system of Lab-scale Automated and Multiplexed Anaerobic Chemostat system (LAMACs) with a working volume of 200 mL is introduced. Sterile feeding, biomass wasting and pressure monitoring are automated. One module containing six reactors fits the typical dimensions of a lab bench. Thanks to automation, time required for reactor operation and maintenance are reduced compared to traditional lab-scale systems. Several modules can be used together, and so far the parallel operation of 30 reactors was demonstrated. The chemostats are autoclavable. Parameters like reactor volume, flow rates and operating temperature can be freely set. The robustness of the system was tested in a two-month long experiment in which three inocula in four replicates, i.e., twelve continuous digesters were monitored. Statistically significant differences in the biogas production between inocula were observed. In anaerobic digestion, biogas production and consequently pressure development in a closed environment is a proxy for ecosystem performance. The precision of the pressure measurement is thus crucial. The measured maximum and minimum rates of gas production could be determined at the same precision. The LAMACs is a tool that enables us to put in practice the often-demanded need for replication and rigorous testing in microbial ecology as well as bioprocess engineering.
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6
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The Global Lake Ecological Observatory Network. ECOL INFORM 2018. [DOI: 10.1007/978-3-319-59928-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Fontana S, Thomas MK, Moldoveanu M, Spaak P, Pomati F. Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness. ISME JOURNAL 2017; 12:356-366. [PMID: 28972571 PMCID: PMC5776449 DOI: 10.1038/ismej.2017.160] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/15/2017] [Accepted: 08/21/2017] [Indexed: 11/09/2022]
Abstract
Understanding how microbial diversity influences ecosystem properties is of paramount importance. Cellular traits-which determine responses to the abiotic and biotic environment-may help us rigorously link them. However, our capacity to measure traits in natural communities has thus far been limited. Here we compared the predictive power of trait richness (trait space coverage), evenness (regularity in trait distribution) and divergence (prevalence of extreme phenotypes) derived from individual-based measurements with two species-level metrics (taxonomic richness and evenness) when modelling the productivity of natural phytoplankton communities. Using phytoplankton data obtained from 28 lakes sampled at different spatial and temporal scales, we found that the diversity in individual-level morphophysiological traits strongly improved our ability to predict community resource-use and biomass yield. Trait evenness-the regularity in distribution of individual cells/colonies within the trait space-was the strongest predictor, exhibiting a robust negative relationship across scales. Our study suggests that quantifying individual microbial phenotypes in trait space may help us understand how to link physiology to ecosystem-scale processes. Elucidating the mechanisms scaling individual-level trait variation to microbial community dynamics could there improve our ability to forecast changes in ecosystem properties across environmental gradients.
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Affiliation(s)
- Simone Fontana
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Mridul Kanianthara Thomas
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Mirela Moldoveanu
- Department of Ecology, Taxonomy and Nature Conservation, Institute of Biology Bucharest, Romanian Academy, Bucharest, Romania
| | - Piet Spaak
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland
| | - Francesco Pomati
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland
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8
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Schierenbeck TM, Smith MC. Path to Impact for Autonomous Field Deployable Chemical Sensors: A Case Study of in Situ Nitrite Sensors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4755-4771. [PMID: 28332819 DOI: 10.1021/acs.est.6b06171] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Natural freshwater systems have been severely affected by excess loading of macronutrients (e.g., nitrogen and phosphorus) from fertilizers, fossil fuels, and human and livestock waste. In the USA, impacts to drinking water quality, biogeochemical cycles, and aquatic ecosystems are estimated to cost US$210 billion annually. Field-deployable nutrient sensors (FDS) offer potential to support research and resource management efforts by acquiring higher resolution data than are currently supported by expensive conventional sampling methods. Following nearly 40 years of research and development, FDS instruments are now starting to penetrate commercial markets. However, instrument uncertainty factors (high cost, reliability, accuracy, and precision) are key drivers impeding the uptake of FDS by the majority of users. Using nitrite sensors as a case study, we review the trends, opportunities, and challenges in producing and implementing FDS from a perspective of innovation and impact. We characterize the user community and consumer needs, identify trends in research approaches, tabulate state-of-the-art examples and specifications, and discuss data life cycle considerations. With further development of FDS through prototyping and testing in real-world applications, these tools can deliver information for protecting and restoring natural waters, enhancing process control for industrial operations and water treatment, and providing novel research insights.
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Affiliation(s)
- Tim M Schierenbeck
- School of Freshwater Sciences, University of Wisconsin-Milwaukee , 600 E. Greenfield Avenue, Milwaukee, Wisconsin 53204, United States
| | - Matthew C Smith
- School of Freshwater Sciences, University of Wisconsin-Milwaukee , 600 E. Greenfield Avenue, Milwaukee, Wisconsin 53204, United States
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9
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Besmer MD, Epting J, Page RM, Sigrist JA, Huggenberger P, Hammes F. Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment. Sci Rep 2016; 6:38462. [PMID: 27924920 PMCID: PMC5141442 DOI: 10.1038/srep38462] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/09/2016] [Indexed: 01/21/2023] Open
Abstract
Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL−1. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.
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Affiliation(s)
- Michael D Besmer
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Jannis Epting
- Applied and Environmental Geology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Rebecca M Page
- Applied and Environmental Geology, Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Endress+Hauser (Schweiz) AG, Kägenstrasse 2, 4153 Reinach, Switzerland
| | - Jürg A Sigrist
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Peter Huggenberger
- Applied and Environmental Geology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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10
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Willers C, Jansen van Rensburg P, Claassens S. Microbial signature lipid biomarker analysis - an approach that is still preferred, even amid various method modifications. J Appl Microbiol 2015; 118:1251-63. [PMID: 25765073 DOI: 10.1111/jam.12798] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 11/26/2022]
Affiliation(s)
- C. Willers
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
| | | | - S. Claassens
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom South Africa
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11
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Brown MV, Ostrowski M, Grzymski JJ, Lauro FM. A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades. Mar Genomics 2014; 15:17-28. [PMID: 24662471 DOI: 10.1016/j.margen.2014.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/08/2014] [Accepted: 03/08/2014] [Indexed: 11/26/2022]
Abstract
Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa.
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Affiliation(s)
- Mark V Brown
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Evolution and Ecology Research Center, University of New South Wales, Sydney, Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Joseph J Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Federico M Lauro
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
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12
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Robidart J, Callister SJ, Song P, Nicora CD, Wheat CG, Girguis PR. Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:4399-4407. [PMID: 23495803 DOI: 10.1021/es3037302] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Microbes play a key role in mediating aquatic biogeochemical cycles. However, our understanding of the relationships between microbial phylogenetic/physiological diversity and habitat physicochemical characteristics is restrained by our limited capacity to concurrently collect microbial and geochemical samples at appropriate spatial and temporal scales. Accordingly, we have developed a low-cost, continuous fluid sampling system (the Biological OsmoSampling System, or BOSS) to address this limitation. The BOSS does not use electricity, can be deployed in harsh/remote environments, and collects/preserves samples with daily resolution for >1 year. Here, we present data on the efficacy of DNA and protein preservation during a 1.5 year laboratory study as well as the results of two field deployments at deep-sea hydrothermal vents, wherein we examined changes in microbial diversity, protein expression, and geochemistry over time. Our data reveal marked changes in microbial composition co-occurring with changes in hydrothermal fluid composition as well as the temporal dynamics of an enigmatic sulfide-oxidizing symbiont in its free-living state. We also present the first data on in situ protein preservation and expression dynamics highlighting the BOSS's potential utility in meta-proteomic studies. These data illustrate the value of using BOSS to study relationships among microbial and geochemical phenomena and environmental conditions.
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Affiliation(s)
- Julie Robidart
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
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13
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Staying afloat in the sensor data deluge. Trends Ecol Evol 2012; 27:121-9. [DOI: 10.1016/j.tree.2011.11.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/24/2011] [Accepted: 11/24/2011] [Indexed: 11/22/2022]
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14
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Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation. ISME JOURNAL 2011; 6:513-23. [PMID: 21975596 DOI: 10.1038/ismej.2011.127] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales.
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Shade A, Chiu CY, McMahon KD. Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics. MICROBIAL ECOLOGY 2010; 59:546-554. [PMID: 19760448 DOI: 10.1007/s00248-009-9589-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 09/01/2009] [Indexed: 05/28/2023]
Abstract
Yuan Yang Lake (YYL), Taiwan, experiences both winter and typhoon-initiated mixing, and each type of mixing event is characterized by contrasting environmental conditions. Previous work suggested that after typhoon mixing, bacterial communities in YYL reset to a pioneer composition and then follow a predictable trajectory of change until the next typhoon. Our goal was to continue this investigation by observing bacterial community change after a range of mixing intensities, including seasonal winter mixing. We fingerprinted aquatic bacterial communities in the epilimnion and hypolimnion using automated ribosomal intergenic spacer analysis and then assessed community response using multivariate statistics. We found a significant linear relationship between water column stability and the epilimnion to hypolimnion divergences. In comparison to the summer, we found the winter community had a distinct composition and less variation. We divided the bacterial community into population subsets according to abundance (rare, common, or dominant) and occurrence (transient or persistent) and further explored the contribution of these subsets to the overall community patterns. We found that transient taxa did not drive bacterial community patterns following weak typhoon mixing events, but contributed substantially to patterns observed following strong events. Common taxa generally did not follow the community trajectory after weak or strong events. Our results suggest intensity, frequency, and seasonality jointly contribute to aquatic bacterial response to mixing disturbance.
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Affiliation(s)
- Ashley Shade
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA.
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