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Surveying bacterial and archaeal microbial communities in host and environmental studies requires the collection and storage of samples. Many studies are conducted in distant locations challenging these prerequisites. The use of preserving buffers is an important alternative when lacking access to cryopreservation, however, its effectivity for samples with challenging chemistry or samples that provide opportunities for fast bacterial or archaeal growth upon exposure to an aerobic environment, like peat samples, requires methodological assessment. Here, in combination with an identified optimal DNA extraction kit for peat soil samples, we test the application of several commercial and a homemade preservation buffer and make recommendations on the method that can most effectively preserve a microbiome reflective of the original state. In treatments with a non-optimal buffer or in the absence, we observed notable community shifts beginning as early as three days post-preservation lowering diversity and community evenness, with growth-driven artifacts from a few specific phyla. However other buffers retain a very close composition relative to the original state, and we described several metrics to understand some variation across them. Due to the chemical effects of preservation buffers, it is critical to test their compatibility and reliability to preserve the original bacterial and archaeal community in different environments. 

Northern forest soils are vital for climate change mitigation since upland sandy soils favor the net consumption/oxidation of atmospheric methane (CH4). We are studying biogeochemical CH4 cycle processes in a Northern Forest (Howland Research Forest, Maine), where upland soils are interspersed with wetland (Sphagnum bog), and upland-wetland transition soils along with hummock-hollow microtopography. This complex mosaic of microsites with sources and sinks of CH4 is subjected to change under future wet climates projected for this region, with a potential for these forests to shift from a net CH4 sink to a net CH4 source. Net CH4 emissions in a wet climate can increase either by inhibiting methanotrophs or favoring methanogens, or both. Thus, quantifying underlying processes of gross CH4 production and consumption can reduce the uncertainty of CH4 sink/source estimation in this critical ecosystem. We have collected baseline soil data across the forest's landscape including Total Carbon and Total Nitrogen with the Elemental Analyzer, Gravimetric Soil Moisture, and pH. Furthermore, stable isotope dilution method will serve as a proxy for methanogenic and methanotrophic activities to quantify gross rates of CH4 production and consumption from a flooding (wet-up) experiment in Howland Forest. We will differentiate between CH4 consumption and production by measuring both the change in the amount of CH4 and the ratio between labeled and unlabeled CH4 in a closed system. We will analyze the stable C isotope in 13CH4 to determine gross rates of CH4 production and oxidation in situ and within laboratory incubations. The in situ stable isotope dilution technique will be compared with the gas push-pull method, to test the suitability of a simple, low cost method to quantify gross CH4 oxidation rates. Novel data obtained in this study will constrain CH4 cycle processes in a biogeochemical model to quantify CH4 source-sink potential in Northern Forests under current and future climatic conditions. 

ABSTRACT The decomposition of soil organic carbon within tropical peatlands is influenced by the functional composition of the microbial community. In this study, building upon our previous work, we recovered a total of 28 metagenome-assembled genomes (MAGs) classified as Bathyarchaeia from the tropical peatlands of the Pastaza-Marañón Foreland Basin (PMFB) in the Amazon. Using phylogenomic analyses, we identified nine genus-level clades to have representatives from the PMFB, with four forming a putative novel family (“CandidatusPaludivitaceae”) endemic to peatlands. We focus on theCa. Paludivitaceae MAGs due to the novelty of this group and the limited understanding of their role within tropical peatlands. Functional analysis of these MAGs reveals that this putative family comprises facultative anaerobes, possessing the genetic potential for oxygen, sulfide, or nitrogen oxidation. This metabolic versatility can be coupled to the fermentation of acetoin, propanol, or proline. The other clades outsideCa. Paludivitaceae are putatively capable of acetogenesis andde novoamino acid biosynthesis and encode a high amount of Fe³⁺transporters. Crucially, theCa. Paludivitaceae are predicted to be carboxydotrophic, capable of utilizing CO for energy generation or biomass production. Through this metabolism, they could detoxify the environment from CO, a byproduct of methanogenesis, or produce methanogenic substrates like CO₂and H₂. Overall, our results show the complex metabolism and various lineages of Bathyarchaeia within tropical peatlands pointing to the need to further evaluate their role in these ecosystems. IMPORTANCEWith the expansion of theCandidatusPaludivitaceae family by the assembly of 28 new metagenome assembled genomes, this study provides novel insights into their metabolic diversity and ecological significance in peatland ecosystems. From a comprehensive phylogenic and functional analysis, we have elucidated their putative unique facultative anaerobic capabilities and CO detoxification potential. This research highlights their crucial role in carbon cycling and greenhouse gas regulation. These findings are essential for resolving the microbial processes affecting peat soil stability, offering new perspectives on the ecological roles of previously underexplored and underrepresented archaeal populations. 

Loss of peat through increased burning will have major impacts on the global carbon cycle. In a normal hydrological state, the risk of fire propagation is largely controlled by peat bulk density and moisture content. However, where humans have interfered with the moisture status of peat either via drainage, or indirectly via climate change, we hypothesise that its botanical composition will become important to flammability, such that peats from different latitudes might have different compositionally-driven susceptibility to ignition. We use pyrolysis combustion flow calorimetry to determine the temperature of maximum thermal decomposition (T_max) of peats from different latitudes, and couple this to a botanical composition analysis. We find that tropical peat has higherT_maxthan other regions, likely on account of its higher wood content which appears to convey a greater resistance to ignition. This resistance also increases with depth, which means that loss of surface peat in tropical regions may lead to a reduction in the subsequent ignitability of deeper peat layers as they are exposed, potentially resulting in a negative feedback on increased fire occurrence and severity. 

Tropical peatlands are highly vulnerable to anthropogenic alterations. In Costa Rica, riverine peatlands are understudied, and most are not included in protected areas. This study aims to generating information useful to assess the anthropogenic pressure in a riverine peatland in Los Robles Sector (LRS) of Medio Queso Wetland (MQW) complex. Evaluations of impacts of fires on vegetation and surface peat chemistry, and the post-2021 fire, makeup of dominant vegetation changes with the Cyperaceae species Scleria melaleuca replacing Eleocharis interstincta as the dominant species are presented. The topsoil (0–20 cm) total C content was quantified as lower than 300 g kg−1 with no significant statistical differences in total C and N content between soil shortly after the fires or two years later. The species E. interstincta is observed to promote higher C stability during the dry season, and has a more recalcitrant composition of the root system compared to the post 2021-fire dominant S. melaleuca. To reduce the impact on C accumulation, measures to prevent grazing-originated fires, especially when the water table is low, are urgent. Hence, this work aims at proving information that can be a baseline for impacts assessment and to inform conservation measures and policies. 

Abstract BackgroundExploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. ResultsWe present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time.In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. ConclusionsBinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted athttps://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. 

Abstract. Peatlands store large amounts of soil carbon and freshwater, constituting an important component of the global carbon and hydrologic cycles. Accurate information on the global extent and distribution of peatlands is presently lacking but is needed by Earth system models (ESMs) to simulate the effects of climate change on the global carbon and hydrologic balance. Here, we present Peat-ML, a spatially continuous global map of peatland fractional coverage generated using machine learning (ML) techniques suitable for use as a prescribed geophysical field in an ESM. Inputs to our statistical model follow drivers of peatland formation and include spatially distributed climate, geomorphological and soil data, and remotely sensed vegetation indices. Available maps of peatland fractional coverage for 14 relatively extensive regions were used along with mapped ecoregions of non-peatland areas to train the statistical model. In addition to qualitative comparisons to other maps in the literature, we estimated model error in two ways. The first estimate used the training data in a blocked leave-one-out cross-validation strategy designed to minimize the influence of spatial autocorrelation. That approach yielded an average r2 of 0.73 with a root-mean-square error and mean bias error of 9.11 % and −0.36 %, respectively. Our second error estimate was generated by comparing Peat-ML against a high-quality, extensively ground-truthed map generated by Ducks Unlimited Canada for the Canadian Boreal Plains region. This comparison suggests our map to be of comparable quality to mapping products generated through more traditional approaches, at least for boreal peatlands. 

Abstract Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.