Microbial transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions.

Background: In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites.

Metatranscriptomics of microbial biofilm succession on HDPE foil: uncovering plastic-degrading potential in soil communities.

Background: Although plastic pollution is increasing worldwide, very little is known about the microbial processes that take place once plastic debris is incorporated into the soil matrix. In this study, we conducted the first metatranscriptome analysis of polyethylene (PE)-associated biofilm communities in highly polluted landfill soil and compared their gene expression to that of a forest soil community within a 53-day period.

Results: Our findings indicate that the microbial population present in soil contaminated with plastic debris is predisposed to both inhabit and degrade plastic surfaces.

Microbial assemblages in Arctic coastal thermokarst lakes and lagoons.

Several studies have investigated changes in microbial community composition in thawing permafrost landscapes, but microbial assemblages in the transient ecosystems of the Arctic coastline remain poorly understood. Thermokarst lakes, abrupt permafrost thaw features, are widespread along the pan-Arctic coast and transform into thermokarst lagoons upon coastal erosion and sea-level rise. This study looks at the effect of marine water inundation (imposing a sulfate-rich, saline environment on top of former thermokarst lake sediments) on microbial community composition and the processes potentially driving microbial community assembly.

Microbial impact on initial soil formation in arid and semiarid environments under simulated climate change.

The microbiota is attributed to be important for initial soil formation under extreme climate conditions, but experimental evidence for its relevance is scarce. To fill this gap, we investigated the impact of microbial communities and their interrelationship with biocrust and plants compared to abiotic controls on soil formation in initial arid and semiarid soils. Additionally, we assessed the response of bacterial communities to climate change.

Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.

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.

Microbial methane cycling in sediments of Arctic thermokarst lagoons.

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH ) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate-rich marine water, altered the microbial methane-cycling community.

A globally relevant stock of soil nitrogen in the Yedoma permafrost domain.

Nitrogen regulates multiple aspects of the permafrost climate feedback, including plant growth, organic matter decomposition, and the production of the potent greenhouse gas nitrous oxide. Despite its importance, current estimates of permafrost nitrogen are highly uncertain. Here, we compiled a dataset of >2000 samples to quantify nitrogen stocks in the Yedoma domain, a region with organic-rich permafrost that contains ~25% of all permafrost carbon.

The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis.

Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable.

Microbiome assembly in thawing permafrost and its feedbacks to climate.

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks.

sp. nov., a novel hexadecane-degrading species isolated from plastic waste.

Strain NGK65, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65 hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0-1% NaCl and at pH 7.

sp. nov., a novel species of the family isolated from plastic waste.

Strain NGK35 is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 µm long and 0.

Species-Level Spatio-Temporal Dynamics of Cyanobacteria in a Hard-Water Temperate Lake in the Southern Baltics.

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.

Methylomonas albis sp. nov. and Methylomonas fluvii sp. nov.: Two cold-adapted methanotrophs from the river Elbe and emended description of the species Methylovulum psychrotolerans.

Three strains of methanotrophic bacteria (EbA, EbB and Eb1) were isolated from the River Elbe, Germany. These Gram-negative, rod-shaped or coccoid cells contain intracytoplasmic membranes perpendicular to the cell surface. Colonies and liquid cultures appeared bright-pink.

The Terrestrial Plastisphere: Diversity and Polymer-Colonizing Potential of Plastic-Associated Microbial Communities in Soil.

The concept of a 'plastisphere microbial community' arose from research on aquatic plastic debris, while the effect of plastics on microbial communities in soils remains poorly understood. Therefore, we examined the inhabiting microbial communities of two plastic debris ecosystems with regard to their diversity and composition relative to plastic-free soils from the same area using 16S rRNA amplicon sequencing. Furthermore, we studied the plastic-colonizing potential of bacteria originating from both study sites as a measure of surface adhesion to UV-weathered polyethylene (PE) using high-magnification field emission scanning electron microscopy (FESEM).

From Water into Sediment-Tracing Freshwater via DNA Analyses.

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 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.

Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming.

Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH and CO production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516).

Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils.

Plasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil-an environment with a relatively low biomass and seasonal freeze-thaw cycles that is strongly affected by global warming.

Greenhouse gas production and lipid biomarker distribution in Yedoma and Alas thermokarst lake sediments in Eastern Siberia.

Permafrost thaw leads to thermokarst lake formation and talik growth tens of meters deep, enabling microbial decomposition of formerly frozen organic matter (OM). We analyzed two 17-m-long thermokarst lake sediment cores taken in Central Yakutia, Russia. One core was from an Alas lake in a Holocene thermokarst basin that underwent multiple lake generations, and the second core from a young Yedoma upland lake (formed ~70 years ago) whose sediments have thawed for the first time since deposition.

Environmental patterns of brown moss- and Sphagnum-associated microbial communities.

Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables.

Roles of Thermokarst Lakes in a Warming World.

Permafrost covers a quarter of the northern hemisphere land surface and contains twice the amount of carbon that is currently present in the atmosphere. Future climate change is expected to reduce its near-surface cover by over 90% by the end of the 21st century, leading to thermokarst lake formation. Thermokarst lakes are point sources of carbon dioxide and methane which release long-term carbon stocks into the atmosphere, thereby initiating a positive climate feedback potentially contributing up to a 0.

Methanogenic response to long-term permafrost thaw is determined by paleoenvironment.

Methane production in thawing permafrost can be substantial, yet often evolves after long lag phases or is even lacking. A central question is to which extent the production of methane after permafrost thaw is determined by the initial methanogenic community. We quantified the production of methane relative to carbon dioxide (CO2) and enumerated methanogenic (mcrA) gene copies in long-term (2-7 years) anoxic incubations at 4 °C using interglacial and glacial permafrost samples of Holocene and Pleistocene, including Eemian, origin.

Anaerobic methanotrophic communities thrive in deep submarine permafrost.

Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments.

Community structure of rare methanogenic archaea: insight from a single functional group.

The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures.

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments.

Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public gene datasets.