1
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White IS, Canniffe DP, Hitchcock A. The diversity of physiology and metabolism in chlorophototrophic bacteria. Adv Microb Physiol 2025; 86:1-98. [PMID: 40404267 DOI: 10.1016/bs.ampbs.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2025]
Abstract
Photosynthesis by (bacterio)chlorophyll-producing organisms ("chlorophototrophy") sustains virtually all life on Earth, providing the biosphere with food and energy. The oxygenic process carried out by plants, algae and cyanobacteria also generates the oxygen we breathe, and ancient cyanobacteria were responsible for oxygenating the atmosphere, creating the conditions that allowed the evolution of complex life. Cyanobacteria were also the endosymbiotic progenitors of chloroplasts, play major roles in biogeochemical cycles and as primary producers in aquatic ecosystems, and act as genetically tractable model organisms for studying oxygenic photosynthesis. In addition to the Cyanobacteriota, eight other bacterial phyla, namely Proteobacteria/Pseudomonadota, Chlorobiota, Chloroflexota, Bacillota, Acidobacteriota, Gemmatimonadota, Vulcanimicrobiota and Myxococcota contain at least one putative chlorophototrophic species, all of which perform a variant of anoxygenic photosynthesis, which does not yield oxygen as a by-product. These chlorophototrophic organisms display incredible diversity in the habitats that they colonise, and in their biochemistry, physiology and metabolism, with variation in the light-harvesting complexes and pigments they produce to utilise solar energy. Whilst some are very well understood, such as the proteobacterial 'purple bacteria', others have only been identified in the last few years and therefore relatively little is known about them - especially those that have not yet been isolated and cultured. In this chapter, we aim to summarise and compare the photosynthetic physiology and central metabolic processes of chlorophototrophic members from the nine phyla in which they are found, giving both a short historical perspective and highlighting gaps in our understanding.
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Affiliation(s)
- Isaac S White
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Daniel P Canniffe
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom; Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom.
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2
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Liu C, Hu J, Zhen G, Chen J, Chen H, Huang S, Liu Y. Droplet Interactions with Hot Surfaces: Boiling Modes, Leidenfrost Temperature, Dynamics, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025:e2501592. [PMID: 40317884 DOI: 10.1002/smll.202501592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 04/14/2025] [Indexed: 05/07/2025]
Abstract
The interaction of droplets with high-temperature solid surfaces is critical in processes like machining cooling and internal combustion engine operations. As surface temperature rises, droplets transition through distinct boiling regimes: film evaporation, contact boiling, transition boiling, and film boiling. In the film boiling regime, droplets are suspended on a vapor layer formed by their evaporation, known as the Leidenfrost effect, which occurs above the Leidenfrost point-the minimum temperature for this phenomenon. While the vapors layer impairs heat transfer by acting as an insulator, it also facilitates droplet mobility, enabling applications in fluid motion control and driving research interest in this area. This review provides a comprehensive overview of droplet interactions with heated surfaces. It begins with a classification of boiling regimes and the criteria defining them, followed by an analysis of factors influencing the Leidenfrost point, including surface properties, liquid characteristics, and external conditions. The motion behaviors of droplets on high-temperature structured surfaces such as horizontal transport, vertical detachment, and rotation are then explored. Finally, potential applications for controlling droplet behavior on hot surfaces are discussed, including enhanced heat transfer, self-cleaning, drag reduction, and energy conversion, while highlighting emerging directions for future research.
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Affiliation(s)
- Cong Liu
- School of Mechanical Engineering, Yanshan University, Qinhuangdao, 066000, China
| | - Jinming Hu
- School of Mechanical Engineering, Yanshan University, Qinhuangdao, 066000, China
| | - Guangwei Zhen
- School of Mechanical Engineering, Yanshan University, Qinhuangdao, 066000, China
| | - Jigang Chen
- School of Mechanical Engineering, Yanshan University, Qinhuangdao, 066000, China
| | - Hao Chen
- School of Mechanical Engineering, Yanshan University, Qinhuangdao, 066000, China
| | - Shuiquan Huang
- School of Mechanical Engineering, Yanshan University, Qinhuangdao, 066000, China
| | - Yahua Liu
- State Key Laboratory of High-performance Precision Manufacturing, Dalian University of Technology, Department of Anaesthesiology, Central Hospital of Dalian University of Technology, Dalian, 116033, China
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3
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Nikeleit V, Maisch M, Straub D, Eroglu S, Lopez-Rivoldi JC, Strauss H, Ring-Hrubesh F, Byrne JM, Kappler A, Bryce C. Cryptic iron cycling influenced by organic carbon availability in a seasonally stratified lake. FEMS Microbiol Ecol 2025; 101:fiaf029. [PMID: 40113245 PMCID: PMC11974394 DOI: 10.1093/femsec/fiaf029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 02/19/2025] [Accepted: 03/19/2025] [Indexed: 03/22/2025] Open
Abstract
Iron cycling including phototrophic Fe(II) oxidation has been observed in multiple permanently stratified meromictic lakes, yet less focus has been on dimictic lakes, which seasonally overturn and are vastly more common. Here, we investigated iron cycling in a dimictic lake, Großes Heiliges Meer in northwest Germany, using 16S rRNA amplicon sequencing, as well as in-situ and lab-based experiments. Bacterial community composition in the lake follows geochemical gradients and differs markedly between oxic and anoxic conditions. Potential iron-metabolizing bacteria were found mostly in anoxic conditions at 7 and 8 m depth and were comprised of taxa from the genera Chlorobium, Thiodictyon, Sideroxydans, Geobacter, and Rhodoferrax. We were able to recreate active iron cycling (1) with an ex-situ microbial community from 8 m depth and (2) with a successful microbial enrichment culture from 7 m depth. Varying the light and organic carbon availability in lab-based experiments showed that Fe(III) reduction overshadows Fe(II) oxidation leading to a cryptic iron cycle. Overall, we could demonstrate that microbial iron cycling can be a key biogeochemical process in dimictic lakes despite regular disturbance, and that complex environmental factors such as organic substrates control the balance between Fe(II) oxidation and Fe(III) reduction.
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Affiliation(s)
- Verena Nikeleit
- Department of Geoscience, University of Tübingen, 72076 Tübingen, Germany
- now: NORCE Norwegian Research Center AS, 5008 Bergen, Norway
| | - Markus Maisch
- Department of Geoscience, University of Tübingen, 72076 Tübingen, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
| | - Sümeyya Eroglu
- Institute for Geology and Paleontology, University of Münster, 48149 Münster, Germany
| | | | - Harald Strauss
- Institute for Geology and Paleontology, University of Münster, 48149 Münster, Germany
| | - Fin Ring-Hrubesh
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
| | - James M Byrne
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
| | - Andreas Kappler
- Department of Geoscience, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
| | - Casey Bryce
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
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4
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Martin G, Rissanen AJ, Garcia SL, Peura S. Dark carbon fixation is a common process in the water column of stratified boreal lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 958:177433. [PMID: 39522777 DOI: 10.1016/j.scitotenv.2024.177433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 10/21/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]
Abstract
CO2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water.
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Affiliation(s)
- Gaëtan Martin
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Tropical Plant and Soil Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, United States of America.
| | - Antti J Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Finland; Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden; Swedish Nuclear Fuel and Waste Management Co. (SKB), Solna, Sweden
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5
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Kamyshny A, Klein R, Eckert W, Avetisyan K. Influence of environmental settings, including vegetation, on speciation of the redox-sensitive elements in the sediments of monomictic Lake Kinneret. LIMNOLOGY 2024; 26:1-18. [PMID: 39840382 PMCID: PMC11743360 DOI: 10.1007/s10201-024-00756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/16/2024] [Indexed: 01/23/2025]
Abstract
The redox conditions in the littoral limnic sediments may be affected by the penetration of plant roots which provide channels for oxygen transport into the sediment while decomposition of the dead roots results in consumption of oxygen. The goal of this work was to study the impact of environmental parameters including penetration of roots of Cyperus articulatus L. into the sediments on cycling of the redox-sensitive elements in Lake Kinneret. We measured roots content, porosity, and chemical parameters including pH, sulfur, iron and manganese speciation in the sediments from the shore, littoral and sublittoral zones with and without vegetation. Our results show that at ≥ 12 m water depth, the upper 10 cm of the sediments are affected by the active sulfur cycling with concentrations of hydrogen sulfide > 70 μM near the sediment-water interface. Speciation of sulfur, iron, and manganese in the upper 10 cm of littoral sediments, which are covered by < 20 cm of water, are affected by their permeability and, to a lesser extent, by roots penetration. In the case when sediments are not covered by water, oxygen penetration to the sediments by desiccation is an additional important control of the redox zonation in the surface sediments. In the shore sediments, despite relatively high concentrations of sulfate in the pore-waters, sulfur cycling may be described as "cryptic" as expressed by very low concentrations of hydrogen sulfide in the pore-waters. This is most likely a result of its fast reoxidation by the abundant highly reactive Fe(III) and Mn(IV) phases. Supplementary Information The online version contains supplementary material available at 10.1007/s10201-024-00756-7.
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Affiliation(s)
- Alexey Kamyshny
- Department of Geological and Environmental Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105 Beer Sheva, Israel
| | - Rotem Klein
- Department of Geological and Environmental Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105 Beer Sheva, Israel
| | - Werner Eckert
- Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic & Limnological Research Ltd, P.O. Box 447, 14950 Migdal, Israel
| | - Khoren Avetisyan
- Department of Geological and Environmental Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105 Beer Sheva, Israel
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4 Canada
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6
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Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, Watanabe T, Fukui M, Hanada S, Tank M, Neufeld JD. Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 2024; 627:915-922. [PMID: 38480893 PMCID: PMC10972752 DOI: 10.1038/s41586-024-07180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/08/2024] [Indexed: 04/01/2024]
Abstract
Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, Waterloo, Ontario, Canada.
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.
| | - N A Shaw
- University of Waterloo, Waterloo, Ontario, Canada
| | - S Nagashima
- Tokyo Metropolitan University, Tokyo, Japan
- Kanagawa University, Yokohama, Japan
| | - J J Venkiteswaran
- University of Waterloo, Waterloo, Ontario, Canada
- Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - S L Schiff
- University of Waterloo, Waterloo, Ontario, Canada
| | - T Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - M Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - S Hanada
- Tokyo Metropolitan University, Tokyo, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Tank
- Tokyo Metropolitan University, Tokyo, Japan
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - J D Neufeld
- University of Waterloo, Waterloo, Ontario, Canada.
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7
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Lau MP, Hutchins RHS, Tank SE, A Del Giorgio P. The chemical succession in anoxic lake waters as source of molecular diversity of organic matter. Sci Rep 2024; 14:3831. [PMID: 38360896 PMCID: PMC10869704 DOI: 10.1038/s41598-024-54387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 02/17/2024] Open
Abstract
The aquatic networks that connect soils with oceans receive each year 5.1 Pg of terrestrial carbon to transport, bury and process. Stagnant sections of aquatic networks often become anoxic. Mineral surfaces attract specific components of organic carbon, which are released under anoxic conditions to the pool of dissolved organic matter (DOM). The impact of the anoxic release on DOM molecular composition and reactivity in inland waters is unknown. Here, we report concurrent release of iron and DOM in anoxic bottom waters of northern lakes, removing DOM from the protection of iron oxides and remobilizing previously buried carbon to the water column. The deprotected DOM appears to be highly reactive, terrestrially derived and molecularly distinct, generating an ambient DOM pool that relieves energetic constraints that are often assumed to limit carbon turnover in anoxic waters. The Fe-to-C stoichiometry during anoxic mobilization differs from that after oxic precipitation, suggesting that up to 21% of buried OM escapes a lake-internal release-precipitation cycle, and can instead be exported downstream. Although anoxic habitats are transient and comprise relatively small volumes of water on the landscape scale, our results show that they may play a major role in structuring the reactivity and molecular composition of DOM transiting through aquatic networks and reaching the oceans.
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Affiliation(s)
- Maximilian P Lau
- Interdisciplinary Environmental Research Centre, Technische Universität Bergakademie Freiberg, Brennhausgasse 14, 09599, Freiberg, Germany.
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montreal, QC, H2X 1Y4, Canada.
| | - Ryan H S Hutchins
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, M5B 2K3, Canada
| | - Suzanne E Tank
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Paul A Del Giorgio
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montreal, QC, H2X 1Y4, Canada
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Reis PCJ, Tsuji JM, Weiblen C, Schiff SL, Scott M, Stein LY, Neufeld JD. Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. THE ISME JOURNAL 2024; 18:wrae041. [PMID: 38470309 PMCID: PMC11008690 DOI: 10.1093/ismejo/wrae041] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 03/13/2024]
Abstract
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence on dioxygen (O2) for CH4 oxidation, abundant populations of putatively aerobic methanotrophs have been detected within microoxic and anoxic waters and sediments of lakes. Experimental work has demonstrated active aerobic methanotrophs under those conditions, but how they are able to persist and oxidize CH4 under O2 deficiency remains enigmatic. In this review, we discuss possible mechanisms that underpin the persistence and activity of aerobic methanotrophs under O2-limiting conditions in freshwater habitats, particularly lakes, summarize experimental evidence for microbial oxidation of CH4 by aerobic bacteria under low or no O2, and suggest future research directions to further explore the ecology and metabolism of aerobic methanotrophs in O2-limiting environments.
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Affiliation(s)
- Paula C J Reis
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jackson M Tsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Cerrise Weiblen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sherry L Schiff
- Department of Earth & Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Matthew Scott
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Intestinal Microbiota of Anser fabalis Wintering in Two Lakes in the Middle and Lower Yangtze River Floodplain. Animals (Basel) 2023; 13:ani13040707. [PMID: 36830494 PMCID: PMC9952484 DOI: 10.3390/ani13040707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The intestinal microbiota of migratory birds participate in the life activities of the host and are affected by external environmental factors. The difference in habitat environment provides diversity in external environmental selection pressure for the same overwintering waterfowl, which may be reflected in their intestinal microbiota. Caizi lake and Shengjin Lake in the Middle and Lower Yangtze River Floodplain are the main habitats for migratory waterfowl in winter, especially the Anser fabalis (A. fabalis). It is important to explore the changes in intestinal microbiota composition and function of A. fabalis in the early overwintering period to clarify the effect of habitat size and protection status on intestinal microbiota. In this study, the composition and structural characteristics of the intestinal microbiota of A. fabalis in Shengjin Lake (SL) and Caizi Lake (CL) were preliminarily explored in order to obtain data for the migratory birds. In both SL and CL groups, 16S rRNA amplicon sequencing analysis showed that Firmicutes was the dominant bacterial phylum, but the relative abundance showed significant differences. Lactobacillus was the most abundant genus in both SL and CL groups. At the species level, the abundance of L. aviaries was the highest, with a relative abundance in both SL and CL groups of more than 34%. When comparing the average relative abundance of the 15 most abundant genera, it was found that Subdoligranulum, Exiguobacterium, and Terrisporobacter had higher abundances in the intestinal microbiota of CL A. fabalis, while Streptococcus and Rothia had higher abundances in the intestinal microbiota of SL A. fabalis. There was only a positive correlation between Bacteroidota and Proteobacteria in the intestinal microbiota flora of SL A. fabalis, and the species were closely related. At the same time, there were positive and negative correlations between Firmicutes and Actinomycetes. However, CL is mainly associated with a positive correlation between Firmicutes and Actinomycetes, and there are also a small number of connections between Firmicutes. PICRUSt1 prediction analysis revealed that the Clusters of Orthologous Groups (COG) functions of SL and CL involve energy production and transformation, amino acid transport and metabolism, carbohydrate transport and metabolism, and transcription. Understanding the changes in intestinal microbiota in Aves during the overwintering period is of great importance to explore the adaptation mechanism of migratory Aves to the overwintering environment. This work provides basic data for an A. fabalis intestinal microbiota study.
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10
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Liu K, Schiff SL, Wu L, Molot LA, Venkiteswaran JJ, Paterson MJ, Elgood RJ, Tsuji JM, Neufeld JD. Large Fractionation in Iron Isotopes Implicates Metabolic Pathways for Iron Cycling in Boreal Shield Lakes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14840-14851. [PMID: 36162065 DOI: 10.1021/acs.est.2c04247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Stable Fe isotopes have only recently been measured in freshwater systems, mainly in meromictic lakes. Here we report the δ56Fe of dissolved, particulate, and sediment Fe in two small dimictic boreal shield headwater lakes: manipulated eutrophic Lake 227, with annual cyanobacterial blooms, and unmanipulated oligotrophic Lake 442. Within the lakes, the range in δ56Fe is large (ca. -0.9 to +1.8‰), spanning more than half the entire range of natural Earth surface samples. Two layers in the water column with distinctive δ56Fe of dissolved (dis) and particulate (spm) Fe were observed, despite differences in trophic states. In the epilimnia of both lakes, a large Δ56Fedis-spm fractionation of 0.4-1‰ between dissolved and particulate Fe was only observed during cyanobacterial blooms in Lake 227, possibly regulated by selective biological uptake of isotopically light Fe by cyanobacteria. In the anoxic layers in both lakes, upward flux from sediments dominates the dissolved Fe pool with an apparent Δ56Fedis-spm fractionation of -2.2 to -0.6‰. Large Δ56Fedis-spm and previously published metagenome sequence data suggest active Fe cycling processes in anoxic layers, such as microaerophilic Fe(II) oxidation or photoferrotrophy, could regulate biogeochemical cycling. Large fractionation of stable Fe isotopes in these lakes provides a potential tool to probe Fe cycling and the acquisition of Fe by cyanobacteria, with relevance for understanding biogeochemical cycling of Earth's early ferruginous oceans.
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Affiliation(s)
- Kai Liu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Sherry L Schiff
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lingling Wu
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lewis A Molot
- Faculty of Environmental and Urban Change, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jason J Venkiteswaran
- Department of Geography and Environmental Studies, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada
| | | | - Richard J Elgood
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Josh D Neufeld
- Water Institute, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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11
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Swanner ED, Wüstner M, Leung T, Pust J, Fatka M, Lambrecht N, Chmiel HE, Strauss H. Seasonal phytoplankton and geochemical shifts in the subsurface chlorophyll maximum layer of a dimictic ferruginous lake. Microbiologyopen 2022; 11:e1287. [PMID: 35765183 PMCID: PMC9108440 DOI: 10.1002/mbo3.1287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
Subsurface chlorophyll maxima layers (SCML) are ubiquitous features of stratified aquatic systems. Availability of the micronutrient iron is known to influence marine SCML, but iron has not been explored in detail as a factor in the development of freshwater SCML. This study investigates the relationship between dissolved iron and the SCML within the dimictic, ferruginous lake Grosses Heiliges Meer in northern Germany. The occurrence of the SCML under nonferruginous conditions in the spring and ferruginous conditions in the fall are context to explore temporal changes in the phytoplankton community and indicators of primary productivity. Results indicate that despite more abundant chlorophyll in the spring, the SCML sits below a likely primary productivity maximum within the epilimnion, inferred based on colocated dissolved oxygen, δ13 CDIC , and pH maxima. The peak amount of chlorophyll in the SCML is lower in the fall than in the spring, but in the fall the SCML is colocated with elevated dissolved iron concentrations and a local δ13 CDIC maximum. Cyanobacteria and Chlorophyta have elevated abundances within the SCML in the fall. Further investigation of the relationship of iron to primary productivity within ferruginous SCML may help to understand the environmental controls on primary productivity in past ferruginous oceans.
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Affiliation(s)
| | - Marina Wüstner
- Center for Applied GeoscienceUniversity of TübingenTübingenGermany
| | - Tania Leung
- Department of Geological & Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Jürgen Pust
- Naturschutzgebietes Heiliges MeerLandschaftsverband Westfalen‐Lippe (LWL) Museum für NaturkundeReckeGermany
| | - Micah Fatka
- Department of Geological & Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Nick Lambrecht
- Department of Geological & Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Hannah E. Chmiel
- Environmental Engineering InstituteÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Harald Strauss
- Institute for Geology and PaleontologyUniversity of MünsterMünsterGermany
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12
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Gorbunov MY, Khlopko YA, Kataev VY, Umanskaya MV. Bacterial Diversity in Attached Communities of a Cold High-Sulfide Water Body in European Russia. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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Han G, Yang K, Zeng J, Zhao Y. Dissolved iron and isotopic geochemical characteristics in a typical tropical river across the floodplain: The potential environmental implication. ENVIRONMENTAL RESEARCH 2021; 200:111452. [PMID: 34111438 DOI: 10.1016/j.envres.2021.111452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/23/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Iron (Fe) is an essential element for bio-physiological functioning terrestrial organisms, in particular of aquatic organisms. It is therefore crucial to understand the aquatic iron cycle and geochemical characteristics, which is also significant to obtain the key information on earth-surface evolution. The stable iron isotopic composition (δ56Fe) of the dissolved fraction is determined in the Mun River (main tributary of Mekong River), northeast Thailand to distinguish the human and nature influenced riverine iron geochemical behavior. The results show that dissolved Fe concentration ranges from 8.04 to 135.27 μg/L, and the δ56Fe ranges from -1.34‰ to 0.48‰, with an average of 0.23‰, 0.14‰ and -0.15‰ in the upper, middle and lower reaches, respectively. The δ56Fe values of river water are close to that of the bulk continental crust and other tropical rivers. The correlations between δ56Fe and Fe, Al, and physicochemical parameters show mixing processes of different Fe end-members, including the rock weathering end-member (low Fe/Al ratio and high δ56Fe), the urban activities end-member (high Fe/Al ratio and moderate δ56Fe), and a third end-member with probable sources from the Chi River and reservoir. For the most river water samples, the primary contribution is attributed to rock weathering, and the second is urban activities (only a few samples are from the upper and middle reaches). Thus, Fe isotopes could be employed as a proxy to identify and quantify the natural and anthropogenic contributions, respectively. These findings also provide data support for the scientific management of water resources in the Mun River catchment and other large tropical rivers.
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Affiliation(s)
- Guilin Han
- Institute of Earth Sciences, China University of Geosciences, Beijing, China.
| | - Kunhua Yang
- Institute of Earth Sciences, China University of Geosciences, Beijing, China
| | - Jie Zeng
- Institute of Earth Sciences, China University of Geosciences, Beijing, China
| | - Ye Zhao
- Nu Instruments, 74 Clywedog Road South, Wrexham Industrial Estate, Wrexham, LL13 9XS, United Kingdom
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14
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Rojas CA, De Santiago Torio A, Park S, Bosak T, Klepac-Ceraj V. Organic Electron Donors and Terminal Electron Acceptors Structure Anaerobic Microbial Communities and Interactions in a Permanently Stratified Sulfidic Lake. Front Microbiol 2021; 12:620424. [PMID: 33967973 PMCID: PMC8103211 DOI: 10.3389/fmicb.2021.620424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, United States, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (∼52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin's index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose far below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities via interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
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Affiliation(s)
- Connie A. Rojas
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
- Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI, United States
| | - Ana De Santiago Torio
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Serry Park
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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15
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Tsuji JM, Tran N, Schiff SL, Venkiteswaran JJ, Molot LA, Tank M, Hanada S, Neufeld JD. Anoxygenic photosynthesis and iron-sulfur metabolic potential of Chlorobia populations from seasonally anoxic Boreal Shield lakes. THE ISME JOURNAL 2020; 14:2732-2747. [PMID: 32747714 PMCID: PMC7784702 DOI: 10.1038/s41396-020-0725-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/02/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022]
Abstract
Aquatic environments with high levels of dissolved ferrous iron and low levels of sulfate serve as an important systems for exploring biogeochemical processes relevant to the early Earth. Boreal Shield lakes, which number in the tens of millions globally, commonly develop seasonally anoxic waters that become iron rich and sulfate poor, yet the iron-sulfur microbiology of these systems has been poorly examined. Here we use genome-resolved metagenomics and enrichment cultivation to explore the metabolic diversity and ecology of anoxygenic photosynthesis and iron/sulfur cycling in the anoxic water columns of three Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel "Candidatus Chlorobium canadense", encoded the cyc2 gene that is associated with photoferrotrophy among cultured Chlorobia members, along with genes for phototrophic sulfide oxidation. One environmental genome bin also encoded cyc2. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in "Ca. Chlorobium canadense". Genomic potential for phototrophic sulfide oxidation was more commonly detected than cyc2 among environmental genome bins of Chlorobia, and metagenome and cultivation data suggested the potential for cryptic sulfur cycling to fuel sulfide-based growth. Overall, our results provide an important basis for further probing the functional role of cyc2 and indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have underexplored photophysiology pertinent to understanding Earth's early microbial communities.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - N Tran
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - S L Schiff
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - J J Venkiteswaran
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, N2L 3C5, Canada
| | - L A Molot
- York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - M Tank
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7B, 38124, Braunschweig, Germany
- Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - S Hanada
- Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, 192-0397, Japan
| | - J D Neufeld
- University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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16
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Microbial Residents of the Atlantis Massif's Shallow Serpentinite Subsurface. Appl Environ Microbiol 2020; 86:AEM.00356-20. [PMID: 32220840 PMCID: PMC7237769 DOI: 10.1128/aem.00356-20] [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: 02/13/2020] [Accepted: 03/21/2020] [Indexed: 12/25/2022] Open
Abstract
The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites. The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s lower crust and upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H2), methane (CH4), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 m below seafloor) marine serpentinites and mafic assemblages. Here, we report the census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence and relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobia, and Chloroflexi. IMPORTANCE The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.
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17
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Lau MP, Del Giorgio P. Reactivity, fate and functional roles of dissolved organic matter in anoxic inland waters. Biol Lett 2020; 16:20190694. [PMID: 32097596 DOI: 10.1098/rsbl.2019.0694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The transit of organic matter (OM) through the aquatic compartment of its global cycle has been intensively studied, traditionally with a focus on the processing and degradation of its dissolved fraction (dissolved organic matter, DOM). Because this is so intimately related to oxidation, the notion tenaciously persists that where oxygen is absent, DOM turnover is markedly slowed. In this Opinion Piece, we outline how diverse processes shape, transform and degrade DOM also in anoxic aquatic environments, and we focus here on inland waters as a particular case study. A suite of biogeochemical DOM functions that have received comparatively little attention may only be expressed in anoxic conditions and may result in enhanced biogeochemical roles of these deoxygenated habitats on a network scale.
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Affiliation(s)
- Maximilian P Lau
- Département des sciences biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montréal, Quebec, Canada H2X 1Y4
| | - Paul Del Giorgio
- Département des sciences biologiques, Université du Québec à Montréal (UQAM), 141 Avenue du Président-Kennedy, Montréal, Quebec, Canada H2X 1Y4
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18
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Rissanen AJ, Peura S, Mpamah PA, Taipale S, Tiirola M, Biasi C, Mäki A, Nykänen H. Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake. FEMS Microbiol Lett 2019; 366:5365400. [PMID: 30806656 PMCID: PMC6476745 DOI: 10.1093/femsle/fnz044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 02/23/2019] [Indexed: 01/22/2023] Open
Abstract
Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.
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Affiliation(s)
- Antti J Rissanen
- Tampere University, Faculty of Engineering and Natural Sciences, Korkeakoulunkatu 10, FI-33720, Tampere, Finland.,University of Jyväskylä, Department of Biological and Environmental Science, PO Box 35, FI-40014, Jyväskylä, Finland
| | - Sari Peura
- University of Jyväskylä, Department of Biological and Environmental Science, PO Box 35, FI-40014, Jyväskylä, Finland
| | - Promise A Mpamah
- University of Jyväskylä, Department of Biological and Environmental Science, PO Box 35, FI-40014, Jyväskylä, Finland
| | - Sami Taipale
- University of Jyväskylä, Department of Biological and Environmental Science, PO Box 35, FI-40014, Jyväskylä, Finland
| | - Marja Tiirola
- University of Jyväskylä, Department of Biological and Environmental Science, PO Box 35, FI-40014, Jyväskylä, Finland
| | - Christina Biasi
- University of Eastern Finland, Department of Environmental and Biological Sciences, PO Box 1627, FI-70211, Kuopio, Finland
| | - Anita Mäki
- University of Jyväskylä, Department of Biological and Environmental Science, PO Box 35, FI-40014, Jyväskylä, Finland
| | - Hannu Nykänen
- University of Eastern Finland, Department of Environmental and Biological Sciences, PO Box 1627, FI-70211, Kuopio, Finland
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19
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Crevecoeur S, Ruiz-González C, Prairie YT, Del Giorgio PA. Large-scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters. Mol Ecol 2019; 28:4181-4196. [PMID: 31479544 DOI: 10.1111/mec.15223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023]
Abstract
Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial-aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation.
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Affiliation(s)
- Sophie Crevecoeur
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
| | - Paul A Del Giorgio
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
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20
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Thomas SP, Shanmuganathan B, Jaiswal MK, Kumaresan A, Sadasivam SK. Legacy of a Pleistocene bacterial community: Patterns in community dynamics through changing ecosystems. Microbiol Res 2019; 226:65-73. [PMID: 31284946 DOI: 10.1016/j.micres.2019.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/01/2019] [Accepted: 06/02/2019] [Indexed: 12/01/2022]
Abstract
Bacterial communities are resilient to the environmental changes, yet the effect of long term ecological changes on bacterial communities remain poorly explored. To study the effect of prolonged environmental changes, a 25 m long sediment core was excavated from a paleo beach ridge located on the Cauvery delta, south east coast of India. Geological evidences suggested that the site has experienced multiple marine transgressions and regressions. The three paleosols from Vettaikaraniruppu (VKI) beach ridge, VKI-2 (2.8 m bgl; 3 kybp), VKI-5 (7.2 m bgl; 6 kybp) and VKI-14 (24.5 m bgl; 146 kybp) was chosen for bacterial community analysis based on their formation period. Bacterial community structure of paleosols was reconstructed using V3 hypervariable region of bacterial 16S rDNA targeted Illumina sequencing. The VKI-5 sediment layer which formed under marine environment contained highest bacterial diversity, and the community was a mix up of terrestrial and marine bacterial population. The final community VKI-2 exhibited an approximate structural pattern witnessed in the native bacterial community VKI-14 which formed during marine regression. Furthermore, marine transgression and regression experienced in VKI resulted in the formation of distinct biogeographic patterns.
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Affiliation(s)
- Shan P Thomas
- Geobiotechnology Laboratory, National College (Autonomous), Tiruchirappalli, 620 001, Tamil Nadu, India
| | | | - Manoj Kumar Jaiswal
- Department of Earth Sciences, Indian Institute of Science Education and Research (IISER), Kolkata, India
| | - Anbarasu Kumaresan
- PG and Research Department of Geology, National College (Autonomous), Tiruchirappalli, 620 001, Tamil Nadu, India
| | - Senthil Kumar Sadasivam
- Geobiotechnology Laboratory, National College (Autonomous), Tiruchirappalli, 620 001, Tamil Nadu, India; PG and Research Department of Botany, National College (Autonomous), Tiruchirappalli, 620 001, Tamil Nadu, India.
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21
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Song Y, Wang Y, Mao G, Gao G, Wang Y. Impact of planktonic low nucleic acid-content bacteria to bacterial community structure and associated ecological functions in a shallow lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 658:868-878. [PMID: 30678021 DOI: 10.1016/j.scitotenv.2018.12.274] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
In this study, 0.45 μm filtration, flow cytometric fingerprint, 16S rRNA amplicon sequencing, and bioinformation tools were adopted to analyze the structural diversity and potential functions of planktonic low nucleic acid (LNA)- content bacteria in a shallow lake. Three bacterial groups, namely, "LNA," "high nucleic acid (HNA)-Small," and "HNA-Large," were classified through flow cytometric fingerprint, among which the "HNA-Small" group was possibly in the proliferation stage of the "LNA" group. Total nitrogen and phosphate were the key factors that influence the growth of LNA bacteria. Results of 16S rRNA amplicon sequencing showed that LNA bacteria were phylogenetically less diverse than HNA bacteria, and Actinobacteria and Proteobacteria (especially Gamma-Proteobacteria) were the dominant phyla in LNA bacterial operational taxonomic units (OTUs). Accordingly, hgcI_clade and Pseudomonas were the most abundant bacterial genera in LNA bacterial OTUs. The fraction of low-abundance LNA bacteria was sensitive to several environmental factors, indicating that environmental factors only determined the fraction distribution of low-abundance bacteria. The prediction of metabolic and ecological functions showed that LNA and HNA bacteria had distinct metabolic and ecological functions, which were mainly attributed to the dominant and exclusive bacterial groups.
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Affiliation(s)
- Yuhao Song
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yufeng Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Guannan Mao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Guanghai Gao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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22
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Camacho A, Walter XA, Picazo A, Zopfi J. Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments. Front Microbiol 2017; 8:323. [PMID: 28377745 PMCID: PMC5359306 DOI: 10.3389/fmicb.2017.00323] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most of the Archean, the ancient ocean evolved toward euxinic (anoxic and sulfide rich) conditions and, finally, much after the advent of oxygenic photosynthesis, to a predominantly oxic environment. Under these new conditions photoferrotrophs lost importance as primary producers, and now photoferrotrophy remains as a vestige of a formerly relevant photosynthetic process. Apart from the geological record and other biogeochemical markers, modern environments resembling the redox conditions of these ancient oceans can offer insights into the past significance of photoferrotrophy and help to explain how this metabolism operated as an important source of organic carbon for the early biosphere. Iron-rich meromictic (permanently stratified) lakes can be considered as modern analogs of the ancient Archean ocean, as they present anoxic ferruginous water columns where light can still be available at the chemocline, thus offering suitable niches for photoferrotrophs. A few bacterial strains of purple bacteria as well as of green sulfur bacteria have been shown to possess photoferrotrophic capacities, and hence, could thrive in these modern Archean ocean analogs. Studies addressing the occurrence and the biogeochemical significance of photoferrotrophy in ferruginous environments have been conducted so far in lakes Matano, Pavin, La Cruz, and the Kabuno Bay of Lake Kivu. To date, only in the latter two lakes a biogeochemical role of photoferrotrophs has been confirmed. In this review we critically summarize the current knowledge on iron-driven photosynthesis, as a remains of ancient Earth biogeochemistry.
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Affiliation(s)
- Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of ValenciaBurjassot, Spain
| | - Xavier A. Walter
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of EnglandBristol, UK
| | - Antonio Picazo
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of ValenciaBurjassot, Spain
| | - Jakob Zopfi
- Aquatic and Stable Isotope Biogeochemistry, Department of Environmental Sciences, University of BaselBasel, Switzerland
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