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Microorganisms
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Wetland Soil Microbiology
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Wetland Soil Microbiology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (15 February 2020) | Viewed by 24411

Special Issue Editors

Prof. Dr. Bruce H. Bleakley

E-Mail Website
Guest Editor
Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
Interests: soil microbiology; environmental microbiology; use of microorganisms as biocontrol agents
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Rebecca Lee Phillips

E-Mail Website
Guest Editor
Ecological Insights Corporation, 130 69th Street SE; Hazelton, ND 58544, USA
Interests: carbon and nitrogen biogeochemistry; prairie pothole wetlands; terrestrial microbiomes; ecosystem ecology

Special Issue Information

Dear Colleagues,

As research in disciplines including soil and water quality, and sustainability of soil and water resources advances, the contribution of wetland soils and their microorganisms to these research areas should not be overlooked. Microorganisms of wetland soils impact ecosystem services; water quality; biogeochemical cycling of C, N, and P; and greenhouse gas emissions in many terrestrial environments. There is a need for more information about wetland soil microorganisms, their attendant biogeochemical and other activities, and their relationships to the plants and animals they associate with, to help us better understand wetland soil biology/microbiology, to conserve wetland resources, and to better plan and implement agricultural and other practices for a sustainable healthy environment. 

For this Special Issue of Microorganisms, we invite you to send contributions concerning any aspect of wetland soil microbiology and attendant biogeochemistry.

Prof. Dr. Bruce H. Bleakley
Prof. Dr. Rebecca Lee Phillips
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • wetland soil
  • wetland soil microorganism
  • wetland soil biogeochemistry
  • wetland soil nitrogen
  • wetland soil sulfur
  • wetland soil carbon
  • wetland soil methane
  • wetland greenhouse gas

Published Papers (7 papers)

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Research

17 pages, 3396 KiB  
Article
Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai–Tibetan Plateau
by Wen Zhou, Xiaoliang Jiang, Jian Ouyang, Bei Lu, Wenzhi Liu and Guihua Liu
Microorganisms 2020, 8(6), 933; https://doi.org/10.3390/microorganisms8060933 - 21 Jun 2020
Cited by 13 | Viewed by 2809
Abstract
In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities [...] Read more.
In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai–Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g−1 and 9.73 × 103 copies g−1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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20 pages, 3651 KiB  
Article
Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering
by Micha Weil, Haitao Wang, Mia Bengtsson, Daniel Köhn, Anke Günther, Gerald Jurasinski, John Couwenberg, Wakene Negassa, Dominik Zak and Tim Urich
Microorganisms 2020, 8(4), 550; https://doi.org/10.3390/microorganisms8040550 - 10 Apr 2020
Cited by 23 | Viewed by 3820
Abstract
Drained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy used to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers [...] Read more.
Drained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy used to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are the biotic and abiotic factors that control community composition. We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent long-term rewetting. Abiotic soil properties including moisture, dissolved organic matter, methane fluxes, and ecosystem respiration rates were also determined. The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundances of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses, we identified soil moisture as a major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than 10-fold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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19 pages, 3111 KiB  
Article
The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration
by Eric A. Weingarten, Lauren A. Lawson and Colin R. Jackson
Microorganisms 2020, 8(4), 538; https://doi.org/10.3390/microorganisms8040538 - 8 Apr 2020
Cited by 8 | Viewed by 3318
Abstract
Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm [...] Read more.
Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple halophiles, both observed in greater proportions in surface sediment. Functional inference of metagenomic data showed that saltpan sediments in the inundated state had greater potential for microbial activity and that several energetic and degradation pathways were more prevalent in saltpan sediment than in nearby tidal marsh sediment. Microbial communities within saltpan sediments differed in composition from those in adjacent freshwater and brackish marshes. These findings indicate that the bacterial and archaeal microbiomes of saltpans are highly stratified by sediment depth and are only minimally influenced by changes in hydration. The surface sediment community is likely isolated from the shallow subsurface community by compaction, with the microbial community dominated by marine and terrestrial halophiles. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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17 pages, 5748 KiB  
Article
Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens
by Anastasia A. Ivanova, Alexey V. Beletsky, Andrey L. Rakitin, Vitaly V. Kadnikov, Dmitriy A. Philippov, Andrey V. Mardanov, Nikolai V. Ravin and Svetlana N. Dedysh
Microorganisms 2020, 8(4), 484; https://doi.org/10.3390/microorganisms8040484 - 29 Mar 2020
Cited by 24 | Viewed by 3391
Abstract
Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat [...] Read more.
Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%–40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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17 pages, 1924 KiB  
Article
Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters
by Mingyue Li, Tiezhu Mi, Zhigang Yu, Manman Ma and Yu Zhen
Microorganisms 2020, 8(2), 198; https://doi.org/10.3390/microorganisms8020198 - 31 Jan 2020
Cited by 6 | Viewed by 2638
Abstract
Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain [...] Read more.
Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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21 pages, 6210 KiB  
Article
Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence
by Igor Y. Oshkin, Kirill K. Miroshnikov, Olga V. Danilova, Anna Hakobyan, Werner Liesack and Svetlana N. Dedysh
Microorganisms 2019, 7(12), 683; https://doi.org/10.3390/microorganisms7120683 - 11 Dec 2019
Cited by 12 | Viewed by 3415
Abstract
Candidatus Methylospira mobilis is a recently described spiral-shaped, micro-aerobic methanotroph, which inhabits northern freshwater wetlands and sediments. Due to difficulties of cultivation, it could not be obtained in a pure culture for a long time. Here, we report on the successful isolation of [...] Read more.
Candidatus Methylospira mobilis is a recently described spiral-shaped, micro-aerobic methanotroph, which inhabits northern freshwater wetlands and sediments. Due to difficulties of cultivation, it could not be obtained in a pure culture for a long time. Here, we report on the successful isolation of strain Shm1, the first axenic culture of this unique methanotroph. The complete genome sequence obtained for strain Shm1 was 4.7 Mb in size and contained over 4800 potential protein-coding genes. The array of genes encoding C1 metabolic capabilities in strain Shm1 was highly similar to that in the closely related non-motile, moderately thermophilic methanotroph Methylococcus capsulatus Bath. The genomes of both methanotrophs encoded both low- and high-affinity oxidases, which allow their survival in a wide range of oxygen concentrations. The repertoire of signal transduction systems encoded in the genome of strain Shm1, however, by far exceeded that in Methylococcus capsulatus Bath but was comparable to those in other motile gammaproteobacterial methanotrophs. The complete set of motility genes, the presence of both the molybdenum–iron and vanadium-iron nitrogenases, as well as a large number of insertion sequences were also among the features, which define environmental adaptation of Methylospira mobilis to water-saturated, micro-oxic, heterogeneous habitats depleted in available nitrogen. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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18 pages, 30174 KiB  
Article
Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina
by Martina Gonzalez Mateu, Cedric Evan Park, Cullen Patrick McAskill, Andrew H. Baldwin and Stephanie A. Yarwood
Microorganisms 2019, 7(3), 72; https://doi.org/10.3390/microorganisms7030072 - 6 Mar 2019
Cited by 2 | Viewed by 3842
Abstract
Urban expansion causes coastal wetland loss, and environmental stressors associated with development can lead to wetland degradation and loss of ecosystem services. This study investigated the effect of urbanization on prokaryotic community composition in tidal freshwater wetlands. Sites in an urban, suburban, and [...] Read more.
Urban expansion causes coastal wetland loss, and environmental stressors associated with development can lead to wetland degradation and loss of ecosystem services. This study investigated the effect of urbanization on prokaryotic community composition in tidal freshwater wetlands. Sites in an urban, suburban, and rural setting were located near Buenos Aires, Argentina, and Washington D.C., USA. We sampled soil associated with two pairs of functionally similar plant species, and used Illumina sequencing of the 16S rRNA gene to examine changes in prokaryotic communities. Urban stressors included raw sewage inputs, nutrient pollution, and polycyclic aromatic hydrocarbons. Prokaryotic communities changed along the gradient (nested PerMANOVA, Buenos Aires: p = 0.005; Washington D.C.: p = 0.001), but did not differ between plant species within sites. Indicator taxa included Methanobacteria in rural sites, and nitrifying bacteria in urban sites, and we observed a decrease in methanogens and an increase in ammonia-oxidizers from rural to urban sites. Functional profiles in the Buenos Aires communities showed higher abundance of pathways related to nitrification and xenobiotic degradation in the urban site. These results suggest that changes in prokaryotic taxa across the gradient were due to surrounding stressors, and communities in urban and rural wetlands are likely carrying out different functions. Full article
(This article belongs to the Special Issue Wetland Soil Microbiology)
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