Recovery of fen peatland microbiomes and predicted functional profiles after rewetting.
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ABSTRACT:
SUBMITTER: Emsens WJ
PROVIDER: S-EPMC7305128 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Peatlands have been drained for land use for a long time and on a large scale, turning them from carbon and nutrient sinks into respective sources, diminishing water regulation capacity, causing surface height loss and destroying biodiversity. Over the last decades, drained peatlands have been rewetted for biodiversity restoration and, as it strongly decreases greenhouse gas emissions, also for climate protection. We quantify restoration success by comparing 320 rewetted fen peatland sites to 243 near-natural peatland sites of similar origin across temperate Europe, all set into perspective by 10k additional European fen vegetation plots. Results imply that rewetting of drained fen peatlands induces the establishment of tall, graminoid wetland plants (helophytisation) and long-lasting differences to pre-drainage biodiversity (vegetation), ecosystem functioning (geochemistry, hydrology), and land cover characteristics (spectral temporal metrics). The Paris Agreement entails the rewetting of 500,000 km2 of drained peatlands worldwide until 2050-2070. A better understanding of the resulting locally novel ecosystems is required to improve planning and implementation of peatland rewetting and subsequent management.
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Project description:In recent years, many peatlands in Europe have been rewetted for nature conservation and global warming mitigation. However, the effects on emissions of the greenhouse gas nitrous oxide (N2O) have been found to be highly variable and driving factors are poorly understood. Therefore, we measured N2O fluxes every two weeks over three years on pairs of sites (one drained, one rewetted) of three important peatland types in North-Eastern Germany, namely, percolation fen, alder forest and coastal fen. Additionally, every three months, sources of N2O were determined using a stable isotope mapping approach. Overall, fluxes were under the very dry conditions of the study years usually small with large temporal and spatial variations. Ammonium concentrations consistently and significantly correlated positively with N2O fluxes for all sites. Cumulative fluxes were often not significantly different from zero and apart from the rewetted alder forest, which was always a source of N2O, sites showed varying cumulative emission behavior (insignificant, source, potentially sink in one case) among years. Precipitation was positively correlated with cumulative fluxes on all drained sites and the rewetted alder forest. Isotope mapping indicated that N2O was always produced by more than one process simultaneously, with the estimated contribution of denitrification varying between 20 and 80%. N2O reduction played a potentially large role, with 5 to 50% of total emissions, showing large variations among sites and over time. Overall, neither the effect of rewetting, water level nor seasonality was clearly reflected in the fluxes or sources. Emissions were concentrated in hotspots and hot moments. A better understanding of the driving factors of N2O production and reduction in (rewetted) fens is essential and stable isotope methods including measurements of 15N and 18O as well as site preferences can help foster the necessary comprehension of the underlying mechanisms. Supplementary Information The online version contains supplementary material available at 10.1007/s10705-022-10244-y.
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Project description:Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities v max were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting mitigation of N2O emissions by increased N2O-reduction rates after flooding. N2O was consumed to subatmospheric levels in all microcosms after flooding. The collective data indicate that water table manipulations had only minor effects on in situ N2O fluxes, denitrifier abundance, and denitrifier community composition of the acidic fen, while active subpopulations of denitrifiers changed in response to water table manipulations, suggesting functionally redundant subpopulations occupying distinct ecological niches in the fen.
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Project description:The Indonesian government committed to restoring over 2 million ha of degraded peatland by the end of 2020, mainly to reduce peat fires and greenhouse gas emissions. Although it is unlikely the government will meet this target, restoration projects are still underway. One restoration strategy involves blocking peatland drainage canals, but the consequences of this for smallholder farmers whose livelihoods are dependent on agriculture are unclear. This paper investigates perceived impacts of canal blocks on smallholder farmers and identifies factors that affect their willingness to accept canal blocks on their land. We use data from 181 household questionnaires collected in 2018 across three villages in Jambi province, Sumatra. We found that the majority of respondents would accept canal blocks on their farms, perceiving that the blocks would have no impact on yields or farm access, and would decrease fire risk. Respondents who would not accept blocks on their farms were more likely to use canals to access their farms and perceive that canal blocks would decrease yields. The majority of farmers unwilling to accept canal blocks did not change their mind when provided with an option of a block that would allow boat travel. Our results improve understanding of why some smallholders may be unwilling to engage with peatland restoration. Further research is needed to understand the impact of canal blocks on smallholders' yields. Engaging with stakeholders from the outset to understand farmers' concerns, and perceptions is key if the government is to succeed in meeting its peatland restoration target and to ensure that the costs and benefits of restoration are evenly shared between local stakeholders and other actors.Supplementary informationThe online version contains supplementary material available at 10.1007/s10113-020-01737-z.
| S-EPMC7749744 | biostudies-literature
Project description:Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C(T), a methanogen isolated from a minerotrophic fen. This is the first genome report of the Methanosphaerula genus, within the Methanoregulaceae family, in the Methanomicrobiales order. E1-9C(T) relatives are found in a wide range of ecological and geographical settings.
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Project description:Ticks transmit the most diverse array of disease agents and harbor one of the most diverse microbial communities. Major progress has been made in the characterization of the taxonomic profiles of tick microbiota. However, the functional profiles of tick microbiome have been comparatively less studied. In this proof of concept we used state-of-the-art functional metagenomics analytical tools to explore previously reported datasets of bacteria found in male and female Ixodes ovatus, Ixodes persulcatus, and Amblyomma variegatum. Results showed that both taxonomic and functional profiles have differences between sexes of the same species. KEGG pathway analysis revealed that male and female of the same species had major differences in the abundance of genes involved in different metabolic pathways including vitamin B, amino acids, carbohydrates, nucleotides, and antibiotics among others. Partial reconstruction of metabolic pathways using KEGG enzymes suggests that tick microbiome form a complex metabolic network that may increase microbial community resilience and adaptability. Linkage analysis between taxonomic and functional profiles showed that among the KEGG enzymes with differential abundance in male and female ticks only 12% were present in single bacterial genera. The rest of these enzymes were found in more than two bacterial genera, and 27% of them were found in five up to ten bacterial genera. Comparison of bacterial genera contributing to the differences in the taxonomic and functional profiles of males and females revealed that while a small group of bacteria has a dual-role, most of the bacteria contribute only to functional or taxonomic differentiation between sexes. Results suggest that the different life styles of male and female ticks exert sex-specific evolutionary pressures that act independently on the phenomes (set of phenotypes) and genomes of bacteria in tick gut microbiota. We conclude that functional redundancy is a fundamental property of male and female tick microbiota and propose that functional metagenomics should be combined with taxonomic profiling of microbiota because both analyses are complementary.
| S-EPMC6702836 | biostudies-literature
Project description:Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.
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Project description:The understanding of the effects of compounds on the gut microbiome is limited and in particular we don’t know whether structurally similar compounds have similar or distinct effects on the gut microbiome. Here we selected berberine (BBR), an isoquinoline quaternary alkaloid, and sixteen structural analogues, and evaluated their effects on in vitro cultured individual gut microbiomes. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. BBR and eight analogues led to changes in proteins involved in microbial defense and stress responses, and enrichment of proteins from Verrumicrobia, Proteobacteria and Bacteroides phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, Sanguinarine, Chelerythrine and Ethoxysanguinarine activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogues can have distinct effects on the microbiome.
2020-07-21 | PXD015934 | Pride
Project description:The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.
| S-EPMC3457479 | biostudies-literature
Project description:Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ?1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted.
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