Temporal and spatial dynamics of peat microbiomes in drained and rewetted soils of three temperate peatlands

AbstractBackgroundDrainage of high-organic peatlands for agricultural purposes has led to increased greenhouse gas emissions and loss of biodiversity. In the last decades, rewetting of peatlands is on the rise worldwide, to mitigate these negative impacts. However, it remains still questionable how rewetting would influence peat microbiota as important drivers of nutrient cycles and ecosystem restoration. Here, we investigate the spatial and temporal dynamics of the diversity, community composition and network interactions of prokaryotes and eukaryotes, and the influence of rewetting on these microbial features in formerly long-term drained and agriculturally used fens. Peat-soils were sampled seasonally from three drained and three rewetted sites representing the dominating fen peatland types of glacial landscapes in Northern Germany, namely alder forest, costal fen and percolation fen.ResultsCostal fens as salt-water impacted systems showed a lower microbial diversity and their microbial community composition showed the strongest distinction from the other two peatland types. Prokaryotic and eukaryotic community compositions showed a congruent pattern which was mostly driven by peatland type and rewetting. Rewetting decreased the abundances of fungi and prokaryotic decomposers, while the abundance of potential methanogens was significantly higher in the rewetted sites. Rewetting also influenced the abundance of ecological clusters in the microbial communities identified from the co-occurrence network. The microbial communities changed only slightly with depth and over time. According to structural equation models rewetted conditions affected the microbial communities through different mechanisms across the three studied peatland types.ConclusionsOur results suggest that rewetting strongly impacts the structure of microbial communities and, thus, important biogeochemical processes, which may explain the high variation in greenhouse gas emissions upon rewetting of peatlands. The improved understanding of functional mechanisms of rewetting in different peatland types lays the foundation for securing best practices to fulfil multiple restoration goals including those targeting on climate, water, and species protection.

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Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities

10.1101/197855 ◽

2017 ◽

Author(s):

Eric R Hester ◽

Sarah F. Harpenslager ◽

Josepha MH van Diggelen ◽

Leon L Lamers ◽

Mike SM Jetten ◽

...

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Amplicon Sequencing ◽

N Fertilization ◽

Wetland Soil ◽

N Availability ◽

Gas Emissions ◽

16S Rrna Amplicon Sequencing ◽

N Input

AbstractWetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning such as control of greenhouse gas emissions. Therefore it is important to understand how increased N input into pristine wetlands affects the composition and activity of micro-organisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangle the effects of N fertilization on the microbial community in bulk soil and the rhizosphere ofJuncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations withJ. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA amplicon sequencing and metagenomics, we determined that the bacterial orders Opitutales, Subgroup-6 Acidobacteria and Sphingobacteriales significantly responded to high N availability and we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, severely altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

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Climate Effects on Greenhouse Gas Emissions and Microbial Communities in Wetlands

Korean Journal of Agricultural and Forest Meteorology ◽

10.5532/kjafm.2007.9.3.161 ◽

2007 ◽

Vol 9 (3) ◽

pp. 161-169

Author(s):

Seon-Young Kim ◽

Ho-Jeong Kang

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Gas Emissions ◽

Climate Effects

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NITROGEN-REMOVING WASTEWATER TREATMENT SYSTEMS: MICROBIAL COMMUNITIES AND GREENHOUSE GAS EMISSIONS

10.23860/diss-wigginton-sara-2020 ◽

2020 ◽

Author(s):

◽

Sara Wigginton

Keyword(s):

Wastewater Treatment ◽

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Gas Emissions ◽

Wastewater Treatment Systems

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0932 - Smart residue amendments to modulate microbial communities to reduce greenhouse gas emissions from agricultural soils

10.26226/morressier.5b5199c1b1b87b000ecee765 ◽

2018 ◽

Author(s):

Kristof Brenzinger

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Agricultural Soils ◽

Gas Emissions

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Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities

10.1101/265132 ◽

2018 ◽

Cited By ~ 3

Author(s):

Eric M. Bottos ◽

David W. Kennedy ◽

Elvira B. Romero ◽

Sarah J. Fansler ◽

Joseph M. Brown ◽

...

Keyword(s):

Microbial Community ◽

Variable Selection ◽

Microbial Communities ◽

Community Composition ◽

Structural Equation ◽

Microbial Community Composition ◽

Dispersal Limitation ◽

Equation Modeling ◽

Permafrost Soil ◽

Total Selection

AbstractUnderstanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.

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Microbial trait-based approaches for agroecosystems

10.31219/osf.io/tw56v ◽

2021 ◽

Author(s):

Sascha M.B. Krause ◽

Stefan Bertilsson ◽

Hans-Peter Grossart ◽

Paul L.E. Bodelier ◽

Peter van Bodegom ◽

...

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Critical Role ◽

Agricultural Practices ◽

Plant Performance ◽

Strong Interactions ◽

Adaptation To Climate Change ◽

Soil Biodiversity ◽

Gas Emissions

Conventional agricultural practices negatively impact soil biodiversity, carbon stocks, and greenhouse gas emissions in ways that make them unsustainable for supporting future supply of food and fiber. Better management of agrobiodiversity will likely play a critical role in transitioning towards more sustainable practices. In particular, innovation and developments targeting the aboveground and belowground components of agroecosystems should be informed by frameworks and approaches that harness the –in particular functional– diversity of complex microbial communities. Here, we review and discuss microbial trait-based approaches that will help us understand and steer agroecosystem functioning in the face of global change. We highlight how trait-based approaches can improve agricultural practices related to soil functioning (e.g. soil fertility and aggregation); climate regulation (e.g. carbon storage and greenhouse gas emissions) and adaptation to climate change; plant health; and reduction of contaminant-related hazards for human health. We also consider how microbial trait-based approaches can be used as a tool to improve cultivated plant performance through artificial selection and microbiome engineering. Last, we discuss the inherent obstacles associated with the development and implementation of trait-based approaches owing to strong interactions within microbial communities and linkages between plants and the soil environment. Despite these obstacles, microbial trait-based approaches hold promise for the sustainable management of agricultural ecosystems needed to feed and nourish a rapidly growing human population.

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How do tropical peatland greenhouse gas emissions respond in the immediate aftermath of a fire?

10.5194/egusphere-egu2020-12567 ◽

2020 ◽

Author(s):

Thomas Smith ◽

Stephanie Evers ◽

Massimo Lupascu ◽

Hayli Chiu

Keyword(s):

Microbial Communities ◽

Greenhouse Gas Emissions ◽

Greenhouse Gas ◽

Fire Disturbance ◽

Gas Emissions ◽

Ongoing Research ◽

Tropical Peatland ◽

Fire Emissions ◽

Fire Effect ◽

Forest Clearance

Southeast Asia is a region where forest clearance, drainage of peatlands for agriculture, and ongoing use of fire to &#8216;manage&#8217; land leads to extensive emissions of greenhouse gases to the atmosphere, and significant disturbance to peatland soils. While recent campaigns investigating tropical peatland fire emissions have improved our knowledge and understanding of &#8216;direct&#8217; greenhouse gas emissions during fires, there remains a significant gap in our knowledge of the immediate post-fire impacts on peat respiration and methanogenesis. Ongoing research shows that peatland microbial communities (responsible for respiration), including methanogens and methanotrophs (responsible for controlling net methane emissions), are considerably altered following fire disturbance. As such, we hypothesise that peatland fires will lead to significant alterations to GHG emissions, compared to sites that have not burned. Further, we also hypothesise that the magnitude of this post-fire effect will be predictably interrelated to different forms of peatland degradation and land-use history.Here we present results from seven fire locations (recently burnt) and their corresponding neighbouring control sites (not recently burnt), three of our fire locations were associated with forest clearance fires, while the other four locations were slash fires on oil palm plantations. We characterize the post-fire disturbance emissions of carbon dioxide (CO2) and methane (CH4) in situ, in the immediate aftermath of a fire (within days or weeks), and in the subsequent months following a fire at our burn sites. For comparison, we also measure CO2 and CH4 emissions from neighbouring control sites that remained unburnt. We find substantial, significant differences in CH4 emissions between the burn sites and control sites for all seven of our measurement locations. We suggest a number of mechanisms responsible for this post-fire effect, including disturbance to the methanotroph microbial communities at the burn sites, as well as reduced elevation at the burn sites, leading to higher water tables.

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Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions

mBio ◽

10.1128/mbio.00066-15 ◽

2015 ◽

Vol 6 (3) ◽

Cited By ~ 44

Author(s):

Shaomei He ◽

Stephanie A. Malfatti ◽

Jack W. McFarland ◽

Frank E. Anderson ◽

Amrita Pati ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Greenhouse Gas ◽

Community Composition ◽

Electron Acceptor ◽

Methane Production ◽

Microbial Community Composition ◽

Restored Wetland ◽

Reducing Bacteria ◽

Metal Reducing Bacteria

ABSTRACTWetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest.IMPORTANCEWetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities that mediate carbon cycling in wetlands is critical to accurately predicting their responses to changes in land management and climate. Here, we studied a restored wetland and revealed substantial spatial heterogeneity in biogeochemistry, methane production, and microbial communities, largely associated with the wetland hydraulic design. We observed patterns in microbial community composition and functions correlated with biogeochemistry and methane production, including diverse microorganisms involved in methane production and consumption. We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem. These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.

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