Microbial Ecosystem Research Articles

PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.

Profiling microbial communities at high resolution and with absolute quantification is essential to uncover hidden ecological interactions within microbial ecosystems. Nevertheless, achieving resolved and quantitative investigations has been elusive due to methodological limitations in distinguishing and quantifying highly related microbes. Here, we describe Phylogenetically Unique Primers in python (PUPpy), an automated computational pipeline to design taxon-specific primers within defined microbial communities. Taxon-specific primers can be used to selectively detect and quantify individual microbes and larger taxa within a microbial community. PUPpy achieves substrain-level specificity without the need for computationally intensive databases and prioritizes user-friendliness by enabling both terminal and graphical user interface applications. Altogether, PUPpy enables fast, inexpensive, and highly accurate perspectives into microbial ecosystems, supporting the characterization of bacterial communities in both in vitro and complex microbiota settings.

Metabolite Profiling of Urban and Forest Tree Rhizosphere Soil using Analytical Instruments

The rhizosphere is the area of the soil affected by plant roots and plays an important role in plant health, nutrient cycling, and soil structure. This study investigated differences in rhizosphere soil metabolites between trees in urban and forest environments using LC/MS-Q-TOF and GC/MS. Urban environments can cause soil pollution and ecosystem disturbance due to the accumulation of heavy metals and petrochemicals, while forest environments are rich in organic matter and fallen leaves, maintaining a nutrient-rich environment in which various microorganisms coexist. Rhizosphere soil samples were collected from Dankook University (city) and Taejo Mountain (forest) in Cheonan, South Korea, extracted using methanol and chloroform using the Soxhlet extraction method, and then analyzed by LC/MS-Q-TOF and GC/MS. N-Nitrosopyrrolidine, a possible carcinogen from automobile exhaust and industrial activities, has been found in the rhizosphere soil of urban trees. Forest rhizosphere samples showed high concentrations of momilactone A, which is important for plant defense mechanisms. 140 significant metabolites were identified through MPP analysis. Furthermore, GC/MS analysis confirmed that siloxanes and oleamides were predominantly detected in urban and forest samples, respectively. Overall, this study highlights the impact of environmental conditions on rhizosphere soil chemistry and microbial ecosystems and provides insights for urban greening and forest conservation strategies. Comprehensive profiling of rhizosphere metabolites will improve our understanding of plant-soil interactions and contribute to maintaining soil health and plant diversity in diverse ecosystems.

Microbial communities mediate the effect of cover cropping on soil ecosystem functions under precipitation reduction in an agroecosystem

Cover cropping is a sustainable agricultural practice that profoundly influences soil microbial communities and ecosystem functions. However, the responses of soil ecosystem functions and microbial communities to cover cropping under the projected changes in precipitation, remain largely unexplored. To address this gap, a field experiment with cover cropping (control, hairy vetch, ryegrass, and hairy vetch plus ryegrass) and precipitation reduction (ambient precipitation and 50 % reduction in ambient precipitation) treatments was conducted from 2018 to 2020 in an agroecosystem located in the Guanzhong Plain of China. Soil ecosystem functions related to nutrient storage, nutrient cycling, and organic matter decomposition were measured to assess the soil multifunctionality index and bacterial and fungal communities were determined by Illumina NovaSeq sequencing. The results indicated that cover cropping enhanced soil multifunctionality index, and reduced precipitation strengthened this effect. Microbial community composition, rather than microbial diversity, was significantly altered by cover cropping regardless of precipitation reduction. Cover cropping increased the microbial network complexity and stability, but this effect was dampened by reduced precipitation. The microbial community composition and network complexity significantly and positively correlated with soil multifunctionality index under ambient and reduced precipitation conditions. Linear regression analyses and structural equation models collectively demonstrated that the increase in soil multifunctionality index was attributed to cover cropping-induced changes in microbial community composition and network complexity, irrespective of precipitation reduction. This study highlights the crucial role of microbial communities in driving the response of soil multifunctionality to cover cropping in the context of reduced precipitation, which has important implications for agricultural management and sustainability under future climate change scenarios.

Exploring spatial segregation induced by competition avoidance as driving mechanism for emergent coexistence in microbial communities.

This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge the sufficiency of mean-field pairwise interaction models, and we consider the impact of spatial dynamics. We developed an individual-based spatial simulation depicting bacterial movement through a pattern of random walks influenced by competition avoidance, leading to the formation of spatially segregated clusters. This model was integrated with a Lotka-Volterra metapopulation framework focused on competitive interactions. Our findings reveal that spatial segregation combined with low diffusion rates and high compositional heterogeneity among patches can lead to emergent coexistence in microbial communities. This reveals a novel mechanism underpinning the formation of stable, coexisting microbe clusters, which is nonetheless incapable of promoting coexistence in the case of isolated pairs of species. This study underscores the importance of considering spatial factors in understanding the dynamics of microbial ecosystems.

Exploring the interactions of JAK inhibitor and S1P receptor modulator drugs with the human gut microbiome: Implications for colonic drug delivery and inflammatory bowel disease

The gut microbiota is a complex ecosystem, home to hundreds of bacterial species and a vast repository of enzymes capable of metabolising a wide range of pharmaceuticals. Several drugs have been shown to affect negatively the composition and function of the gut microbial ecosystem. Janus Kinase (JAK) inhibitors and Sphingosine-1-phosphate (S1P) receptor modulators are drugs recently approved for inflammatory bowel disease through an immediate release formulation and would potentially benefit from colonic targeted delivery to enhance the local drug concentration at the diseased site. However, their impact on the human gut microbiota and susceptibility to bacterial metabolism remain unexplored. With the use of calorimetric, optical density measurements, and metagenomics next-generation sequencing, we show that JAK inhibitors (tofacitinib citrate, baricitinib, filgotinib) have a minor impact on the composition of the human gut microbiota, while ozanimod exerts a significant antimicrobial effect, leading to a prevalence of the Enterococcus genus and a markedly different metabolic landscape when compared to the untreated microbiota. Moreover, ozanimod, unlike the JAK inhibitors, is the only drug subject to enzymatic degradation by the human gut microbiota sourced from six healthy donors. Overall, given the crucial role of the gut microbiome in health, screening assays to investigate the interaction of drugs with the microbiota should be encouraged for the pharmaceutical industry as a standard in the drug discovery and development process.

Estimating the global root exudate carbon flux

Root exudation, the export of low-molecular weight organic carbon (C) from living plant roots to soil, influences microbial activity, nutrient availability, and ecosystem feedbacks to climate change, but the magnitude of this C flux at ecosystem and global scales is largely unknown. Here, we synthesize in situ measurements of root exudation rates and couple those to estimates of fine root biomass to estimate global and biome-level root exudate C fluxes. We estimate a global root exudate flux of 13.4 (10.1–20.2) Pg C y−1, or about 9% (7–14%) of global annual gross primary productivity. We did not find differences in root mass-specific exudation rates among biomes, though total exudate fluxes are estimated to be greatest in grasslands owing to their high density of absorptive root biomass. Our synthesis highlights the global importance of root exudates in the terrestrial C cycle and identifies regions where more in situ measurements are needed to improve future estimates of root exudate C fluxes.

Phaseolus vulgaris Extract Combined With a Low-Calorie Diet Positively Modulates Gut Microbial Ecosystem in Subjects With Severe Obesity: A Randomized Controlled Trial

Phaseolus vulgaris Extract Combined With a Low-Calorie Diet Positively Modulates Gut Microbial Ecosystem in Subjects With Severe Obesity: A Randomized Controlled Trial

A randomized cross-over trial of prebiotics and probiotics in multiple sclerosis: Trial feasibility, supplement tolerability and symptom abatement

BackgroundDietary supplements can modulate the gut microbial ecosystem and affect the immune system. This has potential implications for autoimmune diseases, including multiple sclerosis (MS). Prior studies explored tolerability, symptomatic improvement, and immunologic effects of probiotics in people with MS (pwMS), but no study has examined prebiotics in this population or compared prebiotics with probiotics. MethodsThis is a randomized, open-label trial of participants with relapsing-remitting MS on B-cell depletion therapy from two MS centers. 22 participants enrolled in the original cross-over study in which probiotic (Visbiome, containing Lactobacillus, Bifidobacterium and Streptococcus species) or prebiotic (Prebiotin, containing oligofructose enriched inulin) supplementation for 6 weeks was randomized, each followed by a washout period. Due to pandemic-related interruptions and expiration of the study supply of probiotics, another 15 participants enrolled in a single-arm study to receive prebiotic supplementation for 6 weeks followed by a washout period. We assessed supplement tolerability and patient-reported outcomes (PRO) relevant to MS (disability, fatigue, mood, and bowel symptoms) before and after each supplement administration period and each washout period. We bio-archived plasma, serum, peripheral blood mononuclear cells and stool samples at each timepoint for future multi-omic assessment. ResultsPrebiotics and probiotics had comparable adherence rates and both supplements were well tolerated in pwMS. Participants on either supplement reported minor adverse events, most of which were mild and self-limited. There was a subjective preference for prebiotics over probiotics. Comparing supplement-associated changes in PRO scores from baseline to 6 weeks post-supplementation, there were significant difference between prebiotics and probiotics for the change in patient-reported global symptom burden (MSRS-R Total) and bowel control (BWCS), but only probiotics statistically improved bowel control from baseline to post-supplementation. ConclusionSupplementation with either prebiotics or probiotics is reasonably well-tolerated and safe. Probiotics improved bowel control, but did not improve other PROs in a 6-week time frame. These data regarding feasibility, tolerability, adherence, and adverse events of supplements will inform future clinical trial designs to definitively compare the efficacy and safety of prebiotics and probiotics. The biological data that will be generated from this study in the future will provide mechanistic insights into the effects of these dietary supplements on MS pathophysiology.

Pyritic stromatolites from the Paleoarchean Dresser Formation, Pilbara Craton: Resolving biogenicity and hydrothermally influenced ecosystem dynamics.

This study investigates the paleobiological significance of pyritic stromatolites from the 3.48 billion-year-old Dresser Formation, Pilbara Craton. By combining paleoenvironmental analyses with observations from well-preserved stromatolites in newly obtained drill cores, the research reveals stratiform and columnar to domal pyritic structures with wavy to wrinkly laminations and crest thickening, hosted within facies variably influenced by syn-depositional hydrothermal activity. The columnar and domal stromatolites occur in strata with clearly distinguishable primary depositional textures. Mineralogical variability and fine-scale interference textures between the microbialites and the enclosing sediment highlight interplays between microbial and depositional processes. The stromatolites consist of organomineralization - nanoporous pyrite and microspherulitic barite - hosting significant thermally mature organic matter (OM). This includes filamentous organic microstructures encased within nanoporous pyrite, resembling the extracellular polymeric substance (EPS) of microbes. These findings imply biogenicity and support the activity of microbial life in a volcano-sedimentary environment with hydrothermal activity and evaporative cycles. Coupled changes in stromatolite morphology and host facies suggest growth in diverse niches, from dynamic, hydrothermally influenced shallow-water environments to restricted brine pools strongly enriched in from seawater and hydrothermal activity. These observations, along with S stable isotope data indicating influence by S metabolisms, and accumulations of biologically significant metals and metalloids (Ni and As) within the microbialites, help constrain microbial processes. Columnar to domal stromatolites in dynamic, hydrothermally influenced shallow water deposits likely formed by microbial communities dominated by phototrophs. Stratiform pyritic structures within barite-rich strata may reflect the prevalence of chemotrophs near hydrothermal venting, where hydrothermal activity and microbial processes influenced barite precipitation. Rapid pyrite precipitation, a putative taphonomic process for preserving microbial remnants, is attributed to microbial sulfate reduction and reduced S sourced from hydrothermal activity. In conclusion, this research underscores the biogenicity of the Dresser stromatolites and advances our understanding of microbial ecosystems in Earth's early history.

Controls of Atmospheric Methane on Early Earth and Inhabited Earth-like Terrestrial Exoplanets

Methane (CH4) is a primarily biogenic greenhouse gas. As such, it represents an essential biosignature to search for life on exoplanets. Atmospheric CH4 abundance on Earth-like inhabited exoplanets is likely controlled by marine biogenic production and atmospheric photochemical consumption. Such interactions have been previously examined for the case of the early Earth where primitive marine ecosystems supplied CH4 to the atmosphere, showing that the atmospheric CH4 response to biogenic CH4 flux variations is nonlinear, a critical property when assessing CH4 reliability as a biosignature. However, the contributions of atmospheric photochemistry, metabolic reactions, or solar irradiance to this nonlinear response are not well understood. Using an atmospheric photochemical model and a marine microbial ecosystem model, we show that the production of hydroxyl radicals from water vapor photodissociation is a critical factor controlling the atmospheric CH4 abundance. Consequently, atmospheric CH4 partial pressure (pCH4) on inhabited Earth-like exoplanets orbiting Sun-like stars (F-, G-, and K-type stars) would be controlled primarily by stellar irradiance. Specifically, irradiance at wavelengths of approximately 200–210 nm is a major controlling factor for atmospheric pCH4 when the carbon dioxide partial pressure is sufficiently high to absorb most stellar irradiance at 170–200 nm. Finally, we also demonstrated that inhabited exoplanets orbiting near the outer edge of K-type stars’ habitable zones are better suited for atmospheric pCH4 buildup. Such properties will provide valuable support for future detection of life signatures.

Prebiotic and probiotic potential of fermented milk with cashew (Anacardium occidentale) by-products evaluated in microbiome model

This study aimed to assess the functional attributes of the cashew by-product (CB) in fermented milk with the probiotic strain Lacticaseibacillus paracasei subsp. paracasei F19® (F19®) and the starter Streptococcus thermophilus ST-M6® (ST-M6®) using the Simulator of Human Intestinal Microbial Ecosystem (SHIME®). Two formulations of the fermented milk were assayed, in duplicates: Treatment 1 (T1, without CB) and Treatment 2 (T2, with CB). The strains behavior in the formulations and other bacterial groups of interest were assessed in SHIME®. The populations of the microbiota microorganisms and of the starter and probiotic strains were determined by PMA-qPCR. Metabolites produced in SHIME® reactors fermentation associated with nitrogen balance, antioxidant and phenolic compounds, and short-chain fatty acids (SCFA) were also measured. In SHIME®, both formulations had positive effects on the microbiota (an increase in Bifidobacterium spp. and Lactobacillus spp. and a decrease in Clostridium and Gamma Proteobacteria phyla). Considering these findings, probiotic fermented milk with F19®and ST-M6®, with or without cashew by-product, appears promising for a novel food product with enhanced nutrition, potentially classified as a synergistic synbiotic or at least a probiotic product.

INFLUENCE OF ULTRAFINE PARTICLES OF SILICON IV OXIDE (SiO2) AND OAK BARK EXTRACT ON BACTERIAL LUMINESCENCE

Background. Phytobiotic additives and ultrafine particles (UFP), especially of metallic nature, are increasingly used in agriculture as fertilizers and components of feed additives. However, there is very little data about the effect of non-metallic UFP. In particular, silicon-containing UFP have shown high efficiency as plant growth stimulators under stress conditions, but whether they can act as antibacterial agents or as protective agents in microbial ecosystems is unknown. Therefore, the aim of the presented work is to evaluate positive and negative reactions of the model luminescent microorganism Escherichia coli K12 TG1 when exposed to suspensions of silicon IV oxide (SiO2) in various concentrations both in pure form and in combination with phytobiotic additive – oak bark extract. Materials and methods. The luminescence intensity of the recombinant strain of Echerichia coli of the natural marine microorganism Photobacterium leiongnathi with cloned luxCDABE-genes under the influence of concentrations (0.5-0.00024 M) of UFP SiO2 and aqueous extract of oak bark (2-1024 multiples) was studied. Results. It was found that UFP in pure form stimulate bacterial luminescence by 252.2 % with respect to the control in the stationary phase of growth at 0.5 mol/L. They also act as protectors of intracellular metabolism, reducing the inhibitory effect of oak bark extract. The latter in pure form suppresses more than 50 % of bacterial luminescence up to 4-fold dilution (12.5 mg/mL), which determines the possibility of its use as an alternative to antibiotic drugs. Conclusion. UFP SiO2 have pronounced protective properties with respect to microbial community.

Metagenomics: Advances in Environmental Microbiology, Human Health, and Agriculture

Metagenomics, as a revolutionary technology, plays an important role in the study of environmental microbial ecosystems. Metagenomics has revolutionized our understanding of microbial communities by enabling the comprehensive analysis of genetic material directly from environmental samples. This paper reviews recent advances in metagenomics and its applications in environmental microbiology, human health, and agriculture. We highlight key methodologies, significant findings, and the potential of metagenomics to drive innovations across various scientific and practical domains.

Synthetic microbial ecology: engineering habitats for modular consortia.

Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.

Microbial dynamics in rapidly transforming Arctic proglacial landscapes

Arctic glacial environments are rapidly changing, as the Arctic warms at a rate three to four times faster than the global average (the phenomenon known as Arctic amplification). Microorganisms are uniquely adapted to extreme glacial environments and studying how ecological and climatic feedback loops affect the diversity of these communities is crucial to the characterisation of vulnerable Arctic habitats. Glacial landscapes span a wide range of habitats, from glacier ice to marine waters, and encompass terrestrial, aquatic, and interzonal systems. While glacier shrinkage has been the focus of scientific attention, auxiliary habitats are also impacted by rapid glacier retreat. Auxiliary habitats include terrestrial systems, such as outwash plains, vegetated periglacial environments, and aquatic systems, such as glacier-fed streams, lakes, and glacier-adjacent marine environments. Glacier recession drives high-impact changes in glacier-associated habitats: rising temperatures, increased light penetration of glacial streams, changes in nitrogen-to-phosphate ratios, and increases in availability of glacier-derived organic compounds. In turn, microbial systems in these habitats may experience changes in nutrient dynamics and shifts in community structures. The exposure of new lands by retreating glaciers may also result in increased dust and microbial dispersal into the atmosphere. Here, we discuss the effects of climate change on glacial microbiomes and the feedback loops between microbial community dynamics and the large-scale climatic processes in the Arctic. We characterise aspects of vulnerable microbial ecosystems and highlight the importance of preserving unseen microbial biodiversity. We then outline current capacities for microbial conservation, focusing on cryopreservation and biobanking. Lastly, we suggest future research directions and steps that academic and governmental institutions may take to foster research and collaboration with Indigenous communities.

Difference in the Intestinal Microbiota between Breastfeed Infants and Infants Fed with Artificial Milk: A Systematic Review.

The gut microbiota (GM) plays a crucial role in human health, particularly during the first years of life. Differences in GM between breastfed and formula (F)-fed infants may influence long-term health outcomes. This systematic review aims to compare the gut microbiota of breastfed infants with that of F-fed infants and to evaluate the clinical implications of these differences. We searched databases on Scopus, Web of Science, and Pubmed with the following keywords: "gut microbiota", "gut microbiome", and "neonatal milk". The inclusion criteria were articles relating to the analysis of the intestinal microbiome of newborns in relation to the type of nutrition, clinical studies or case series, excluding reviews, meta-analyses, animal models, and in vitro studies. The screening phase ended with the selection of 13 publications for this work. Breastfed infants showed higher levels of beneficial bacteria such as Bifidobacterium and Lactobacillus, while F-fed infants had a higher prevalence of potentially pathogenic bacteria, including Clostridium difficile and Enterobacteriaceae. Infant feeding type influences the composition of oral GM significantly. Breastfeeding promotes a healthier and more diverse microbial ecosystem, which may offer protective health benefits. Future research should explore strategies to improve the GM of F-fed infants and understand the long-term health implications.

A concise review of the nutritional profiles, microbial dynamics, and health impacts of fermented mushrooms.

Mushrooms have garnered significant attention for their nutritional composition and potential health benefits, including antioxidant, antihypertensive, and cholesterol-lowering properties. This review explores the nutritional composition of edible mushrooms, including their high protein content, essential amino acids, low fat, cholesterol levels, and bioactive compounds with medicinal value. Moreover, the study analyzes the microbiology of mushroom fermentation, focusing on the diverse microbial ecosystem involved in the transformation of raw mushrooms and the preservation methods employed to extend their shelf life. Special emphasis is placed on lactic acid fermentation as a cost-effective and efficient preservation technique. It involves controlling the growth of lactic acid bacteria to enhance the microbial stability and nutritional quality of mushrooms. Furthermore, the bioactivities of fermented mushrooms are elucidated, which are antioxidant, antimicrobial, anticancer, anti-glycemic, immune modulatory, and other biological activities. The mechanisms underlying these bioactivities are explored, emphasizing the role of fermented mushrooms in suppressing free radicals, enhancing antioxidant defenses, and modulating immune responses. Overall, this review provides comprehensive insights into the nutritional composition, microbiology, bioactivities, and underlying mechanisms of fermented mushrooms, highlighting their potential as functional foods with significant health-promoting properties.

Oxygenation of Earth's atmosphere induced metabolic and ecologic transformations recorded in the Lomagundi-Jatuli carbon isotopic excursion.

The oxygenation of Earth's atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves 13C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of 12C into organic carbon and CH4. Extreme and variable 13C enrichments in carbonates were caused by 13C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly 13C enriched. Thus, the loss of extreme 13C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earth's atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earth's atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earth's surface chemistry through time.

Unveiling soil bacterial diversity in the Andes-Amazon transition zone: Impacts of forest conversion to pasture

Soil microorganisms play a crucial role in the functioning of ecosystems by performing several essential functions. However, their resilience is tested by disturbances, primarily driven by land use changes. The Andes-Amazon transition zone, renowned for its ecological importance, is experiencing a growing pressure of removing native forests to establish pastures. In the last decades, efforts to characterize biodiversity in this region have been increasing; however, our comprehension of soil microbial communities and their responses to land use changes remains limited. Here, we used a shotgun DNA metagenomic sequencing approach to investigate the composition, diversity, and functions of soil bacterial communities in the litter and topsoil (0–10 cm) of a forest localized in an Andes-Amazon transition zone in Colombia and evaluate how they are affected by pasture establishments. Our findings unveiled the forest litter as a distinct microbial ecosystem, characterized by the highest bacterial richness and diversity. This layer was positively associated with increased availability of carbon (C), nitrogen (N), and phosphorus (P), and enzymatic activity linked to the mineralization of these elements. The transition from forest to pasture altered the microbial community structure, which was accompanied by a reduction of soil acidity. We observed that Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant phyla in all environments, with a predominance of Proteobacteria and Bacteroidetes in forest litter, while forest-pasture conversion increased the abundance of Verrucomicrobia and Firmicutes in the soil. Functional profiles were over-represented in the litter, followed by pasture and forest soils. These results provide a foundational framework for comprehending the microbiome in the Andes-Amazon transition zone and its role in ecosystem functioning. Furthermore, this study sheds light on the far-reaching consequences of land use changes on microbial communities.

Mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics.

Time series studies of microbiome interventions provide valuable data about microbial ecosystem structure. Unfortunately, existing models of microbial community dynamics have limited temporal memory and expressivity, relying on Markov or linearity assumptions. To address this, we introduce a new class of models based on transfer functions. These models learn impulse responses, capturing the potentially delayed effects of environmental changes on the microbial community. This allows us to simulate trajectories under hypothetical interventions and select significantly perturbed taxa with False Discovery Rate guarantees. Through simulations, we show that our approach effectively reduces forecasting errors compared to strong baselines and accurately pinpoints taxa of interest. Our case studies highlight the interpretability of the resulting differential response trajectories. An R package, mbtransfer, and notebooks to replicate the simulation and case studies are provided.