Description: Strain NGK35T is a motile, Gram-stain- negative,rod-shaped (1.0–2.1 μm long and 0.6–0.8 μm wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 °C (optimum, 28 °C), in 0–10 % NaCl (optimum, 1 %) and at pH 6.0–9.5 (optimum, pH 7.5–8.5). It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C16 : 1 cis9 and C16 : 0, followed by C17 : 0 cyclo and C18 : 1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35T belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761AT (96.90 %) and Paenalcaligenes suwonensis ABC02-12T (96.94 %). The genomic DNA G+C content of strain NGK35T was 52.1 mol %. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes. Based on phenotypic and molecular characterization, strain NGK35T can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed. The type strain is NGK35T (=DSM 113270T=NCCB 100854T).

Description: Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25–50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

Description: Soils in the permafrost region have acted as carbon sinks for thousands of years. As a result of global warming, permafrost soils are thawing and will potentially release greenhouse gases (GHGs) such as methane (CH4) and carbon dioxide (CO2). However, small-scale spatial heterogeneities of GHG production have been neglected in previous incubation studies. Here, we used an anaerobic incubation experiment to simulate permafrost thaw along a transect from upland Yedoma to the floodplain on Kurungnakh Island. Potential CO2 and CH4 production was measured during incubation of the active layer and permafrost soils at 4 and 20 ∘C, first for 60 d (approximate length of the growing season) and then continuing for 1 year. An assessment of methanogen abundance was performed in parallel for the first 60 d. Yedoma samples from upland and slope cores remained in a lag phase during the growing season simulation, while those located in the floodplain showed high production of CH4 (6.5×103 µg CH4-C g−1 C) and CO2 (6.9×103 µg CO2-C g−1 C) at 20 ∘C. The Yedoma samples from the permafrost layer started producing CH4 after 6 months of incubation. We conclude that landscape position is a key factor triggering CH4 production during the growing season time on Kurungnakh Island.

Description: The rewetting of peatlands is a promising measure to mitigate greenhouse gas (GHG) emissions by preventing the further mineralization of the peat soil through aeration. In coastal peatland, the rewetting with brackish water can increase the GHG mitigation potential by the introduction of sulfate, a terminal electron acceptor (TEA). Sulfate is known to lower the CH4 production and thus, its emission by favoring the growth of sulfate-reducers, which outcompete methanogens for substrate. The data contain porewater variables such as pH, electrical conductivity (EC) and sulfate, chloride, dissolved CO2 and CH4 concentrations, as well as absolute abundances of methane- and sulfate-cycling microbial communities. The data were collected in spring and autumn 2019 after a storm surge with brackish water inflow in January 2019. Field sampling was conducted in the nature reserve Heiligensee and Hütelmoor in North-East Germany, close to the Southern Baltic Sea coast. We took peat cores using a Russian peat corer in addition to pore water diffusion samplers and plastic liners (length: 60cm; inner diameter 10 cm) at four locations along a transect from further inland towards the Baltic Sea. We wanted to compare the soil and pore water geochemistry as well as the microbial communities after the brackish water inflow to the common freshwater rewetting state. Pore water was extracted using pore water suction samplers in the lab and environmental variables were quantified with an ICP. Microbial samples were sampled from the peat core using sterile equipment. We used quantitative polymerase chain reaction (qPCR) to characterize pools of DNA and cDNA targeting total and putatively active bacteria and archaea. qPCR was performed on key functional genes of methane production (mcrA), aerobic methane oxidation (pmoA) and sulfate reduction (dsrB) in addition to the 16S rRNA gene for the absolute abundance of total prokaryotes. Furthermore, we retrieved soil plugs to determine the concentrations and isotopic signatures of dissolved trace gases (CO2/DIC and CH4) in the pore water.

Description: Rewetted peatlands can be a significant source of methane (CH4), but in coastal ecosystems, input of sulfate-rich seawater could potentially mitigate these emissions. The presence of sulfate as an electron acceptor during organic matter decomposition is known to suppress methanogenesis by favoring the growth of sulfate reducers, which outcompete methanogens for substrate. We investigated the effects of a brackish water inflow on the microbial communities relative to CH4 production–consumption dynamics in a freshwater rewetted fen at the southern Baltic Sea coast after a storm surge in January 2019 and analyzed our data in context with the previous freshwater rewetted state (2014 serves as our baseline) and the conditions after a severe drought in 2018 (Fig. 1). We took peat cores at four previously sampled locations along a brackishness gradient to compare soil and pore water geochemistry as well as the microbial methane- and sulfate-cycling communities with the previous conditions. We used high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to characterize pools of DNA and RNA targeting total and putatively active bacteria and archaea. Furthermore, we measured CH4 fluxes along the gradient and determined the concentrations and isotopic signatures of trace gases in the peat. We found that both the inflow effect of brackish water and the preceding drought increased the sulfate availability in the surface and pore water. Nevertheless, peat soil CH4 concentrations and the 13C compositions of CH4 and total dissolved inorganic carbon (DIC) indicated ongoing methanogenesis and little methane oxidation. Accordingly, we did not observe a decrease in absolute methanogenic archaea abundance or a substantial change in methanogenic community composition following the inflow but found that the methanogenic community had mainly changed during the preceding drought. In contrast, absolute abundances of aerobic methanotrophic bacteria decreased back to their pre-drought level after the inflow, while they had increased during the drought year. In line with the higher sulfate concentrations, the absolute abundances of sulfate-reducing bacteria (SRB) increased – as expected – by almost 3 orders of magnitude compared to the freshwater state and also exceeded abundances recorded during the drought by over 2 orders of magnitude. Against our expectations, methanotrophic archaea (ANME), capable of sulfate-mediated anaerobic methane oxidation, did not increase in abundance after the brackish water inflow. Altogether, we could find no microbial evidence for hampered methane production or increased methane consumption in the peat soil after the brackish water inflow. Because Koebsch et al. (2020) reported a new minimum in CH4 fluxes at this site since rewetting of the site in 2009, methane oxidation may, however, take place in the water column above the peat soil or in the loose organic litter on the ground. This highlights the importance of considering all compartments across the peat–water–atmosphere continuum to develop an in-depth understanding of inflow events in rewetted peatlands. We propose that the changes in microbial communities and greenhouse gas (GHG) fluxes relative to the previous freshwater rewetting state cannot be explained with the brackish water inflow alone but were potentially reinforced by a biogeochemical legacy effect of the preceding drought.

Description: Rewetted peatlands can be a significant source of methane (CH4), but in coastal ecosystems, input of sulfate-rich seawater could potentially mitigate these emissions. The presence of sulfate as electron acceptor during organic matter decomposition is known to suppress methanogenesis, by favoring the growth of sulfate-reducers, which outcompete methanogens for substrate. We investigated the effects of a brackish water inflow on the microbial communities relative to CH4 production-consumption dynamics in a freshwater rewetted fen at the southern Baltic Sea coast after a storm surge in January 2019 and analyzed our data in context with the previous freshwater rewetted state (2014 serves as our baseline) and the conditions after a severe drought in 2018. We took peat cores at four previously sampled locations along a brackishness gradient to compare soil and pore water geochemistry as well as the microbial methane and sulfate cycling communities with the previous conditions. We used high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to characterize pools of DNA and cDNA targeting total and putatively active bacteria and archaea. Furthermore, we measured CH4 fluxes along the gradient and determined the concentrations and isotopic signatures of trace gases in the peat. We found that both, the inflow effect of brackish water and in parts also the preceding drought increased the sulfate availability in the surface and pore water. Still, peat soil CH4 concentrations and the 13C compositions of CH4 and total dissolved inorganic carbon (DIC) indicated ongoing methanogenesis and little methane oxidation. Accordingly, we did not observe a decrease of absolute methanogenic archaea abundance or a substantial change in methanogenic community composition following the inflow, but found that the methanogenic community had mainly changed during the precedent drought. In contrast, absolute abundances of aerobic methanotrophic bacteria decreased back to their pre-drought level after the inflow while they had increased during the drought year. In line with the higher sulfate concentrations, the absolute abundances of sulfate reducing bacteria (SRB) increased – as expected – by almost three orders of magnitude compared to the freshwater state and also exceeded abundances recorded during the drought by over two orders of magnitude. Against our expectations, methanotrophic archaea (ANME), capable of sulfate-mediated anaerobic methane oxidation, did not increase in abundance after the brackish water inflow. Altogether, we could find no microbial evidence for hampered methane production or increased methane consumption in the peat soil after the brackish water inflow. Because Koebsch et al. (2020) reported a new minimum in CH4 fluxes at this site since rewetting of the site in 2009, methane oxidation may, however, take place in the water column above the peat soil or in the lose organic litter on the ground. This highlights the importance to consider all compartments across the peat-water-atmosphere continuum to develop an in-depth understanding of inflow events in rewetted peatlands. We propose that the changes in microbial communities and GHG fluxes relative to the previous freshwater rewetting state cannot be explained with the brackish water inflow alone, but was potentially reinforced by a biogeochemical legacy effect of the precedent drought.

Description: Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, δ13C data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.

Description: Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p 〉 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May–October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations. View Full-Text

Description: Both the frequency and intensity of drought events are expected to increase, with unresolved alterations to peatland methane cycling and the involved microbial communities. While existing studies have assessed drought effects via experimental approaches under controlled conditions, to our knowledge, no studies have examined the in-situ effects of natural drought in restored temperate fens. In this study, we used quantitative polymerase chain reaction (qPCR) and high throughput 16S rRNA gene amplicon sequencing of DNA and complementary DNA (cDNA) to determine the abundances and community structure of total and putatively active microbial communities following the 2018 European summer drought. Together with geochemical and methane flux data, we compared these results to a non-drought reference dataset. During drought, water level and methane flux rates decreased to a new recent minimum in both fens. This corresponded with pronounced shifts in porewater geochemistry. Microbial community composition in the drought year differed markedly, and was characterized by a greater relative and total abundance of aerobic methanotrophs, and, in one of the two sites, by a decrease in total methanogen abundance. In contrast to the non-drought reference years, type I methanotrophs were clearly more dominant than type II methanotrophs in both fens. cDNA sequencing confirmed the activity of type I methanotrophs during drought, with Methylomonaceae having the highest average relative abundance of bacterial cDNA transcripts. We show that changes in microbial community dynamics, porewater geochemistry, and ecosystem methane fluxes can be substantial following natural drought in restored fens, and provide the first in-situ evidence from a natural drought which suggests type I methanotroph populations are more active than type II methanotrophs in response to drought effects. Type I methanotrophs may represent a key microbial control over methane emissions in restored temperate fens subject to natural drought.

Description: Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p 〈0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter—when the water column is mixed—picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes.