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The fate of tropical peatland carbon cycling under environmental change is highly uncertain. We found that a palm swamp peatland in the Peruvian Amazon that was a strong annual sink for 2 years switched to carbon neutral in the absence of a major anthropogenic disturbance. We attributed the change in carbon sink strength to (a) photoinhibition of canopy photosynthesis when skies were clearer and thus solar irradiance higher and (b) increased ecosystem respiration when the water table position was below the peat surface, and heterotrophic respiration was amplified. These mechanisms were not, however, synchronous in time. The importance of photoinhibition as a driver of changes in peatland carbon budgets is a novel finding, and an understudied mechanism of canopy photosynthetic impairment. Shifts in climate that increase periods with sustained high solar irradiance and/or low water table are thus likely to amplify interannual variability in the carbon sink strength. Plain Language Summary Peatlands store about one third of global soil carbon despite occupying less than 5% of the land area. Recent estimates show that tropical peatlands store much more carbon than previously thought. There are considerable gaps in knowledge regarding the interannual variability of carbon budgets in tropical peatlands and the way that changing environmental conditions influence the carbon cycling in these ecosystems. We show that a palm swamp peatland in the Peruvian Amazon is sensitive to changes in environmental conditions and can flip from a large carbon sink to carbon neutral when there are prolonged periods with (a) clear skies and higher light intensities that impair canopy photosynthesis and (b) a lower water table that increases peat decomposition. These findings show that the carbon budgets of these ecosystems are highly sensitive to environmental variability. Key Points Clear skies and low water tables caused an Amazonian peatland to switch from a large carbon sink to being carbon neutral Canopy photosynthesis was subject to photoinhibition when there were prolonged periods with clear skies and higher solar irradiance When the water table dropped below the surface, ecosystem respiration increased

Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats) are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations. We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population. The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population.

Amazonian peatlands store a large amount of soil organic carbon (SOC), and its fate under a future changing climate is unknown. Here, we use a process-based peatland biogeochemistry model to quantify the carbon accumulation for peatland and nonpeatland ecosystems in the Pastaza-Marañon foreland basin (PMFB) in the Peruvian Amazon from 12,000 y before present to AD 2100. Model simulations indicate that warming accelerates peat SOC loss, while increasing precipitation accelerates peat SOC accumulation at millennial time scales. The uncertain parameters and spatial variation of climate are significant sources of uncertainty to modeled peat carbon accumulation. Under warmer and presumably wetter conditions over the 21st century, SOC accumulation rate in the PMFB slows down to 7.9 (4.3–12.2) g·C·m−2·y−1 from the current rate of 16.1 (9.1–23.7) g·C·m−2·y−1, and the region may turn into a carbon source to the atmosphere at −53.3 (−66.8 to −41.2) g·C·m−2·y−1 (negative indicates source), depending on the level of warming. Peatland ecosystems show a higher vulnerability than nonpeatland ecosystems, as indicated by the ratio of their soil carbon density changes (ranging from 3.9 to 5.8). This is primarily due to larger peatlands carbon stocks and more dramatic responses of their aerobic and anaerobic decompositions in comparison with nonpeatland ecosystems under future climate conditions. Peatland and nonpeatland soils in the PMFB may lose up to 0.4 (0.32–0.52) Pg·C by AD 2100 with the largest loss from palm swamp. The carbon-dense Amazonian peatland may switch from a current carbon sink into a source in the 21st century.

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity. Production and consumption of metabolites by soil microorganisms are important for nutrient cycling and maintenance of microbial diversity. Here, Baran et al . study metabolite uptake and release by desert soil microorganisms, showing that coexisting microbes can have divergent substrate preferences.

Background Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX , free, online software for the processing and analysis of T-RFLP data. Results Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX . With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model. Conclusion T-REX provides a free, platform-independent tool to the research community that allows for an integrated, rapid, and more robust analysis of T-RFLP data.

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 higher T max than 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. Loss of peat through increased burning will have major impacts on the global carbon cycle. Here, the authors 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.

Effective environmental policies for the tropics depend on accurate, representative scientific data. However, there is strong evidence from particular disciplines and regions that existing research is patchily distributed. Here, we show that poor representation of sampling and citation in some biomes and across key environmental gradients from all disciplines for the entire tropics may lead to flawed scientific paradigms and inappropriate policy prescriptions. We map sampling locations and citations from 2 738 published studies in natural terrestrial tropical environments across all disciplines to identify gaps in field sampling effort and research attention. Five ecoregions – all in moist broadleaf forests – generate 22% of the total citations but cover only 3% of the tropical land area. By contrast, drier biomes with low tree cover account collectively for 57% of the tropical area but generate only 20% of total citations. Locations that are drier, colder, with greater plant species richness, lower tree cover and facing greater climate change extremes are under-sampled and under-cited. Our results will help to correct these imbalances to improve the scientific basis for environmental policies across the tropics. Research in the tropics is unevenly distributed across regions and biomes. Here, the authors find that moist broadleaf forests account for 73% of all tropical citations but cover 29% of the land area, while drier, climate-vulnerable areas with fewer trees remain under-sampled and under-cited.

Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic \"continents,\" indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.

Background Exploring 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. Results We 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. Conclusions BinaRena 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 at https://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. 85aKgQNhGdzniqM56hYkLt Video Abstract

Deforestation from artisanal, small-scale gold mining is transforming large regions of the tropics, from lush rainforest to barren collections of tailings and ponds. Natural forest regeneration is slow due to dramatic soil changes, and existing reforestation strategies are failing. Here we combine remote sensing, electrical resistivity imaging, and measurements of soil properties to characterize post-mining areas in the Madre de Dios region, Peru. We find that the post-mining landscape has dramatically changed water infiltration dynamics, driving decreases in subsurface water availability and presenting a major barrier to revegetation. Mining tailings are extremely hydraulically conductive, allowing for 14.76 m day −1 infiltration relative to 0.074 m day −1 in primary forest soils, leading to lower average soil moisture and extreme temperatures (60 °C). Electrical resistivity imaging reveals a highly resistive, 1.5–2 m deep layer of dry sand across the mining landscape. Areas close to the water table (e.g., pond edges) show higher soil moisture, lower temperatures, and greater natural regeneration compared to topographically elevated tailings. Our results suggest that access to water should be prioritized when targeting reforestation sites, potentially requiring large-scale geomorphological reconfiguration. As gold mining is expected to expand, responsible practices and remediation strategies must account for the critical yet often overlooked role of water. Post-mining areas in the Madre de Dios region of Peru exhibit altered water infiltration dynamics that hinder revegetation, according to remote sensing, electrical resistivity imaging, and soil property measurements.