51
|
Molybdenum-Based Diazotrophy in a Sphagnum Peatland in Northern Minnesota. Appl Environ Microbiol 2017; 83:AEM.01174-17. [PMID: 28667112 DOI: 10.1128/aem.01174-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microbial N2 fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2 and are susceptible to the changing climate. The objectives of this study were (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in an ombrotrophic Sphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, and CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and 15N2 incorporation. A molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated by Alphaproteobacteria (Bradyrhizobiaceae and Beijerinckiaceae). Despite higher concentrations of dissolved vanadium ([V] 11 nM) than molybdenum ([Mo] 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing, and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water contents. Incorporation of 15N2 was suppressed 90% by O2 and 55% by C2H2 and was unaffected by CH4 and CO2 amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2-sensitive and C2H2-insensitive microbes that are more active at low concentrations of O2 and show similar activity at high and low concentrations of CH4 IMPORTANCE Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy in Sphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process, remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy and that members of the Alphaproteobacteria (Rhizobiales) catalyze this process at the bog surface using the molybdenum-based form of the nitrogenase enzyme.
Collapse
|
52
|
Turner S, Mikutta R, Meyer-Stüve S, Guggenberger G, Schaarschmidt F, Lazar CS, Dohrmann R, Schippers A. Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development. Front Microbiol 2017; 8:874. [PMID: 28579976 PMCID: PMC5437693 DOI: 10.3389/fmicb.2017.00874] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 05/01/2017] [Indexed: 11/13/2022] Open
Abstract
Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils.
Collapse
Affiliation(s)
- Stephanie Turner
- Geomicrobiology, Federal Institute for Geosciences and Natural ResourcesHanover, Germany
| | - Robert Mikutta
- Soil Science and Soil Protection, Martin Luther University Halle-WittenbergHalle, Germany
| | | | | | | | - Cassandre S Lazar
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Reiner Dohrmann
- Technical Mineralogy and Clay Mineralogy, Federal Institute for Geosciences and Natural ResourcesHanover, Germany
| | - Axel Schippers
- Geomicrobiology, Federal Institute for Geosciences and Natural ResourcesHanover, Germany
| |
Collapse
|
53
|
Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
Collapse
|
54
|
Wilson RM, Hopple AM, Tfaily MM, Sebestyen SD, Schadt CW, Pfeifer-Meister L, Medvedeff C, McFarlane KJ, Kostka JE, Kolton M, Kolka R, Kluber LA, Keller JK, Guilderson TP, Griffiths NA, Chanton JP, Bridgham SD, Hanson PJ. Stability of peatland carbon to rising temperatures. Nat Commun 2016; 7:13723. [PMID: 27958276 PMCID: PMC5159855 DOI: 10.1038/ncomms13723] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/27/2016] [Indexed: 01/22/2023] Open
Abstract
Peatlands contain one-third of soil carbon (C), mostly buried in deep, saturated anoxic zones (catotelm). The response of catotelm C to climate forcing is uncertain, because prior experiments have focused on surface warming. We show that deep peat heating of a 2 m-thick peat column results in an exponential increase in CH4 emissions. However, this response is due solely to surface processes and not degradation of catotelm peat. Incubations show that only the top 20-30 cm of peat from experimental plots have higher CH4 production rates at elevated temperatures. Radiocarbon analyses demonstrate that CH4 and CO2 are produced primarily from decomposition of surface-derived modern photosynthate, not catotelm C. There are no differences in microbial abundances, dissolved organic matter concentrations or degradative enzyme activities among treatments. These results suggest that although surface peat will respond to increasing temperature, the large reservoir of catotelm C is stable under current anoxic conditions.
Collapse
Affiliation(s)
- R. M. Wilson
- Earth, Ocean and Atmospheric Sciences, Florida State University, 117 N Woodward Avenue, Tallahassee, Florida 32306, USA
| | - A. M. Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - M. M. Tfaily
- Environmental Molecular Sciences Laboratory—Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - S. D. Sebestyen
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota 55744, USA
| | - C. W. Schadt
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - L. Pfeifer-Meister
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - C. Medvedeff
- Schmid College of Science and Technology, Chapman University, Orange, California 92866, USA
| | - K. J. McFarlane
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - J. E. Kostka
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M. Kolton
- School of Biological Sciences and School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R.K. Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota 55744, USA
| | - L. A. Kluber
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J. K. Keller
- Schmid College of Science and Technology, Chapman University, Orange, California 92866, USA
| | - T. P. Guilderson
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - N. A. Griffiths
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J. P. Chanton
- Earth, Ocean and Atmospheric Sciences, Florida State University, 117 N Woodward Avenue, Tallahassee, Florida 32306, USA
| | - S. D. Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - P. J. Hanson
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| |
Collapse
|
55
|
Ivanova AA, Wegner CE, Kim Y, Liesack W, Dedysh SN. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol Ecol 2016; 25:4818-35. [DOI: 10.1111/mec.13806] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 06/12/2016] [Accepted: 08/11/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
| | - Carl-Eric Wegner
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Yongkyu Kim
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
| |
Collapse
|
56
|
Kostka JE, Weston DJ, Glass JB, Lilleskov EA, Shaw AJ, Turetsky MR. The Sphagnum microbiome: new insights from an ancient plant lineage. THE NEW PHYTOLOGIST 2016; 211:57-64. [PMID: 27173909 DOI: 10.1111/nph.13993] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/15/2016] [Indexed: 05/03/2023]
Abstract
57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63 SUMMARY: Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20-30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum-microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant-microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.
Collapse
Affiliation(s)
- Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN, 37831, USA
| | - Jennifer B Glass
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Erik A Lilleskov
- Northern Research Station, USDA Forest Service, Houghton, MI, 49931, USA
| | | | - Merritt R Turetsky
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
57
|
Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog. Appl Environ Microbiol 2016; 82:2363-2371. [PMID: 26873322 DOI: 10.1128/aem.03640-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
Collapse
|
58
|
de Gannes V, Eudoxie G, Bekele I, Hickey WJ. Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad. Front Microbiol 2015; 6:1045. [PMID: 26483772 PMCID: PMC4588118 DOI: 10.3389/fmicb.2015.01045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/14/2015] [Indexed: 11/15/2022] Open
Abstract
Understanding how community structure of Bacteria, Archaea, and Fungi varies as a function of edaphic characteristics is key to elucidating associations between soil ecosystem function and the microbiome that sustains it. In this study, non-managed tropical soils were examined that represented a range of edaphic characteristics, and a comprehensive soil microbiome analysis was done by Illumina sequencing of amplicon libraries that targeted Bacteria (universal prokaryotic 16S rRNA gene primers), Archaea (primers selective for archaeal 16S rRNA genes), or Fungi (internal transcribed spacer region). Microbiome diversity decreased in the order: Bacteria > Archaea > Fungi. Bacterial community composition had a strong relationship to edaphic factors while that of Archaea and Fungi was comparatively weak. Bacterial communities were 70–80% alike, while communities of Fungi and Archaea had 40–50% similarity. While each of the three component communities differed in species turnover patterns, soils having relatively similar bacterial communities also housed similar archaeal communities. In contrast, the composition of fungal communities had no correlation to bacterial or archaeal communities. Bacterial and archaeal diversity had significant (negative) correlations to pH, whereas fungal diversity was not correlated to pH. Edaphic characteristics that best explained variation between soils in bacterial community structure were: total carbon, sodium, magnesium, and zinc. For fungi, the best variables were: sodium, magnesium, phosphorus, boron, and C/N. Archaeal communities had two sets of edaphic factors of equal strength, one contained sulfur, sodium, and ammonium-N and the other was composed of clay, potassium, ammonium-N, and nitrate-N. Collectively, the data indicate that Bacteria, Archaea, and Fungi did not closely parallel one another in community structure development, and thus microbiomes in each soil acquired unique identities. This divergence could in part reflect the finding that unknown factor(s) were stronger than edaphic characteristics in shaping fungal and archaeal communities.
Collapse
Affiliation(s)
- Vidya de Gannes
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - Gaius Eudoxie
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - Isaac Bekele
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison Madison, WI, USA
| |
Collapse
|
59
|
Lin X, Handley KM, Gilbert JA, Kostka JE. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME JOURNAL 2015; 9:2740-4. [PMID: 26000553 DOI: 10.1038/ismej.2015.77] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/28/2015] [Accepted: 04/01/2015] [Indexed: 01/08/2023]
Abstract
To probe the metabolic potential of abundant Archaea in boreal peats, we reconstructed two near-complete archaeal genomes, affiliated with Thaumarchaeota group 1.1c (bin Fn1, 8% abundance), which was a genomically unrepresented group, and Thermoplasmata (bin Bg1, 26% abundance), from metagenomic data acquired from deep anoxic peat layers. Each of the near-complete genomes encodes the potential to degrade long-chain fatty acids (LCFA) via β-oxidation. Fn1 has the potential to oxidize LCFA either by syntrophic interaction with methanogens or by coupling oxidation with anaerobic respiration using fumarate as a terminal electron acceptor (TEA). Fn1 is the first Thaumarchaeota genome without an identifiable carbon fixation pathway, indicating that this mesophilic phylum encompasses more diverse metabolisms than previously thought. Furthermore, we report genetic evidence suggestive of sulfite and/or organosulfonate reduction by Thermoplasmata Bg1. In deep peat, inorganic TEAs are often depleted to extremely low levels, yet the anaerobic respiration predicted for two abundant archaeal members suggests organic electron acceptors such as fumarate and organosulfonate (enriched in humic substances) may be important for respiration and C mineralization in peatlands.
Collapse
Affiliation(s)
- Xueju Lin
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kim M Handley
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, Biosciences Division,Argonne National Laboratory, Lemont, IL, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.,Institute for Genomics and Systems Biology, Biosciences Division,Argonne National Laboratory, Lemont, IL, USA.,Marine Biological Laboratory, Woods Hole, MA, USA.,College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Joel E Kostka
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| |
Collapse
|
60
|
Elliott DR, Caporn SJM, Nwaishi F, Nilsson RH, Sen R. Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation. PLoS One 2015; 10:e0124726. [PMID: 25969988 PMCID: PMC4430338 DOI: 10.1371/journal.pone.0124726] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/04/2015] [Indexed: 02/01/2023] Open
Abstract
The UK hosts 15–19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration.
Collapse
Affiliation(s)
- David R. Elliott
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
- * E-mail:
| | - Simon J. M. Caporn
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
| | - Felix Nwaishi
- Cold Regions Research Centre, Wilfrid Laurier University, Waterloo, Ontario, 2NL 3C5, Canada
| | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30. Gothenburg, Sweden
| | - Robin Sen
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
| |
Collapse
|
61
|
Hunger S, Gößner AS, Drake HL. Anaerobic trophic interactions of contrasting methane-emitting mire soils: processes versus taxa. FEMS Microbiol Ecol 2015; 91:fiv045. [PMID: 25877342 DOI: 10.1093/femsec/fiv045] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2015] [Indexed: 11/13/2022] Open
Abstract
Natural wetlands such as mires contribute up to 33% to the global emission of methane. The emission of methane is driven by trophic interactions of anaerobes that collectively degrade biopolymers. The hypothesis of this study was that these interactions in contrasting methane-emitting mire soils are functionally similar but linked to dissimilar taxa. This hypothesis was addressed by evaluating anaerobic processes and microbial taxa of eutrophic, mesotrophic and oligotrophic mire soils. Glucose was fermented to various products (e.g. H2, CO2, butyrate, acetate). Acetoclastic methanogenesis occurred, and acetogenesis and methanogenesis transformed H2-CO2 to acetate and methane, respectively. Although product profiles, cultivable cell numbers and gene copy numbers [mcrA (encodes alpha-subunit of methyl-CoM reductase) and 16S rRNA genes] were similar for all mire soils, only approximately 15% of detected family-level bacteria and species-level methanogens were shared by all mire soils. Approximately, 40% of the detected family-level taxa of each mire soil have no cultured isolates. Acidic conditions appeared to restrict the number of dominant phylotypes. The results indicated (a) that microbial processes which drive methanogenesis are similar but facilitated by dissimilar microbial communities in contrasting mire soils and (b) that mire soils harbor a large number of taxa with no cultured isolates.
Collapse
Affiliation(s)
- Sindy Hunger
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Anita S Gößner
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Harold L Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| |
Collapse
|
62
|
Next-generation pyrosequencing analysis of microbial biofilm communities on granular activated carbon in treatment of oil sands process-affected water. Appl Environ Microbiol 2015; 81:4037-48. [PMID: 25841014 DOI: 10.1128/aem.04258-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10(9) gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds.
Collapse
|
63
|
Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland. Appl Environ Microbiol 2014; 80:3531-40. [PMID: 24682299 DOI: 10.1128/aem.00206-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and oligosaccharide degradation at MEF relative to other wetland and soil environments, consistent with the nutrient-poor and carbohydrate-rich conditions found in this Sphagnum-dominated boreal peatland.
Collapse
|
64
|
Tsitko I, Lusa M, Lehto J, Parviainen L, Ikonen ATK, Lahdenperä AM, Bomberg M. The Variation of Microbial Communities in a Depth Profile of an Acidic, Nutrient-Poor Boreal Bog in Southwestern Finland. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/oje.2014.413071] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|