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At least 235 records · Page 13

Diverging drivers of fungal diversity: seasonal effects shape aboveground communities, while geographical patterns govern belowground communities in rubber tree ecosystems

Understanding the spatiotemporal dynamics of microbial communities is essential for predicting their ecological roles and interactions with host plants. In a recent study, Wei and colleagues (Microbiol Spectr 13:e02097-24, 2024) investigated fungal diversity across multiple plant and soil compartments in rubber trees over two seasons and two geographically distinct regions in China. Their findings revealed that alpha diversity was primarily influenced by seasonal changes and physicochemical factors, while beta diversity exhibited a strong geographical pattern, shaped by leaf phosphorus and soil available potassium. These results highlight the role of environmental drivers in shaping within-community diversity, while other factors contribute to the differences between fungal communities across the soil–plant continuum. By distinguishing the effects of temporal and spatial factors, this study provides detailed insights into plant-associated microbiomes and emphasizes the need for further research on the functional implications of microbial diversity in the context of changing environmental and agricultural conditions.

fungal diversity↗

Microbial metabolic dependency and its impacts on the soil carbon cycle (Final Technical Report, DE-SC0016364)

The terrestrial biosphere contains a large fraction of global carbon (C) and nearly 70% of the organic C in terrestrial systems is found in soils. Global changes in atmospheric CO 2 , temperature, precipitation, and ecosystem N inputs, will impact primary production and carbon inputs to soils, but it remains difficult to predict soil responses to these environmental conditions. Our ability to predict C-cycle responses to global change remains limited by unexplained variability within the terrestrial C-cycle. Our difficulty in predicting responses of the soil C-cycle to environmental change suggests a need for a greater understanding of the biotic mechanisms that govern soil C-transformations. Changes in microbial community structure and function have been proposed to impact soil processes, but mechanistic connections between microbial activity and C-cycle transformations remain poorly described. We assembled an interdisciplinary team to conduct cross-scale examination of microbial contributions to C-cycle dynamics and C-fate in soils. We investigated microbial contributions to soil C-transformations using a suite of complementary isotopic techniques including DNA-Stable Isotope Probing (DNA-SIP), metagenomic-SIP, metabolomic-SIP, proteomic-SIP, and microspatial analysis of soil organic C. These techniques were deployed in experiments that tested fundamental assumptions that underlie terrestrial C-cycle models. We characterized the functional characteristics of soil microorganisms responsible for major C-transformations in soil, evaluated the metabolic and ecological interactions that underlie soil C-cycle dynamics, and evaluated the degree to which these interactions impact rates of C mineralization and stabilization in soils.

54 ENVIRONMENTAL SCIENCES↗

Revisiting diffusion-based moisture functions: why do they fail?

Microbial activities in soil are controlled by the balance between physical and biological mechanisms that are currently implied by soil moisture-respiration relationships, but not explicitly represented. Diffusion based moisture functions focus on physical controls, while substrate kinetics based models primarily address biological drivers. How to harmonize these two types of models for robust predictions of soil respiration and other processes has not been addressed. Here we derived a generalizable analytical solution of diffusion-limited nonlinear microbial uptake kinetics, in which microbial metabolic rates were governed by both physical and biological drivers via substrate diffusion and microbial affinity. We proposed a soil trait concept to integrate both physical and biological perspectives into one unified function, and tested it using both laboratory and field based observations from a variety of soils. This approach provides a tractable and scalable approach that incorporates soil heterogeneity and functional complexity in macroscopic model descriptions.

59 BASIC BIOLOGICAL SCIENCES↗

Lipid production from non-sugar compounds in pretreated lignocellulose hydrolysates by Rhodococcus jostii RHA1

Valorization of all carbon sources from biorefinery wastes to biofuels and bioproducts is an attractive but challenging strategy to improve the carbon efficiency of the entire biorefinery process for economic competitiveness. Rhodococcus jostii RHA1 is considered as a promising candidate for conversion of non-sugar compounds in pretreated lignocellulose hydrolysate, which contain aromatic monomers, furans and acids derived from biomass. However, the insufficient understanding of the strain’s complex metabolism network limits its application. In this study, furans (furfural, 5-hydroxymethylfurfural), phenols (vanillin, vanillate), and organic acids (acetic acid), which mimic the complex components of the non-sugar compounds in pretreated biomass hydrolysate, were mixed with benzoate or used individually as carbon sources to investigate the growth and lipid accumulation of R. jostii RHA1. Fermentation kinetics, specific growth rates (h-1) and lipid yield (g(g) -1, g(mmol)-1), for each selected biomass-derived compound were compared for lipid production. The order of the specific growth rates (h-1) was benzoate > acetic acid > vanillate > vanillin. Higher consumption rate of benzoate than that of vanillate, as well as different lipid yield from them, suggested the preference of strain employing two branches of ß-ketoadipate pathway and plausibly distinct carbon routing to lipid biosynthesis. And acetic acid showed the lowest lipid yield (g(mmol)-1) indicating less carbon contributed to lipid production. The highest lipid content (0.46 g lipid/g CDW) was achieved using benzoate as a main carbon source in the presence of 5-hydroxymethylfurfural (5-HMF). The generated lipids predominantly contained C16:0 and C17:0 fatty acids. The concentration of furfural and 5-HMF in fermentation broth decreased individually or simultaneously with benzoate catabolism. NMR results revealed the oxidation of furfural and 5-HMF by R. jostii RHA1. This study provides new insights into the catabolism and metabolism of non-sugar compounds derived from biomass by Rhodococcus in terms of growth and lipid production, facilitating its application to 2nd generation biofuel production.

Li, Xiaolu↗

Divergent responses of soil microorganisms to throughfall exclusion across tropical forest soils driven by soil fertility and climate history

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how throughfall exclusion might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in Mean Annual Precipitation (MAP: 2335–3421 mm). We expected microbial communities at sites with lower MAP to be less sensitive to throughfall exclusion than sites with higher MAP and fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 × 10 m plots to reduce direct precipitation input. After short-term (~3–9 months) throughfall exclusion, prokaryotic communities showed no change in composition. However, prolonged (12–18 months) throughfall exclusion resulted in divergent prokaryotic community responses, reflecting MAP and soil fertility. We observed the emergence of a “drought microbiome” within infertile sites, whereby the community structure of the experimental throughfall exclusion plots at the lower MAP sites diverged from their respective control sites and converged towards overlapping assemblages. Furthermore, under throughfall exclusion, taxa increasing in relative abundance at the wettest site reflected that endemic to control plots at the lowest MAP site, suggesting a shift toward communities with lifehistory traits selected for under a lower MAP. By contrast, fungal community composition across sites was resilient to throughfall exclusion; however, biomass diverged in response to throughfall exclusion, increasing at two sites while decreasing in the other two. Broadly, our results suggest that microbial communities’ sensitivity to frequent drying and rewetting periods in tropical forest soils will depend on climate history and soil fertility, with infertile sites likely to respond readily to changes in precipitation.

54 ENVIRONMENTAL SCIENCES↗

Manganese effects on plant residue decomposition and carbon distribution in soil fractions depend on soil nitrogen availability

Recent studies have highlighted the critical role of manganese (Mn) in plant litter decomposition and soil organic carbon (C) cycling in forest ecosystems. Long term nitrogen (N) deposition and N fertilization can increase soil acidity and mobilize bioavailable Mn (Mn 2+ ) in soil. However, no studies have examined the interactive effect of N and Mn fertilization on litter decomposition and carbon distribution in agricultural soils, despite agroecosystems being subject to both N and Mn management. We hypothesized that increased soil N and Mn availability would accelerate plant residue decomposition and transfer of its C to mineral-associated organic matter (MAOM), and that the combined effect of Mn and N enrichment would be greater than the individual effect. Here, we conducted a laboratory incubation experiment by adding 13 C-labeled residue of perennial grass Glyceria striata (Lam.) to agricultural soils that had received 225 kg N ha –1 yr –1 for 27 years (N 1 ) and comparable soils that received no N (N 0 ). Before the experiment, these soils also received three levels of dissolved Mn 2+ , designated M 0 (no additional Mn), M 1 (50 mg kg –1 ), or M 2 (250 mg kg –1 ). We measured total CO 2 production as well as distribution of 13 C from the residue into CO 2 , particulate organic matter (POM), MAOM, and dissolved organic carbon (DOC) over a 1-year period. Manganese amendments significantly increased CO 2 production from residue decomposition in the N 1 soil, but no such effect was observed in the N 0 soil. Manganese also accelerated the loss of residue-derived C from POM and DOC, but increased its recovery in MAOM. However, the positive effect of added Mn in decomposition and recovery in MAOM in the presence of N fertilization occurred only during the initial 30-day decomposition period, where M 2 showed a 12% increase in cumulative CO 2 production from residue, 8% increase in POM loss, and 43% increase in recovery of residue C in MAOM compared to M 0 . For M 1 , only CO 2 emission from residue was significantly higher than Mo during this period. At 365 days M 2 showed 8% increase in CO 2 production, 1% increase in POM loss, and 16% increase in recovery of residue C in MAOM compared to M 0 , but none of these were statistically significant (p < 0.05). This study adds to the growing evidence that increasing Mn availability enhances plant litter decomposition. However, the occurrence and magnitude of Mn-induced stimulation of decomposition is context specific. Further investigation with greater temporal resolution, involving a multitude of litter and soil types and including microbial compositional and functional characterization, is recommended to fully elucidate the interactive role of Mn and N on C cycling.

59 BASIC BIOLOGICAL SCIENCES↗

A genomic catalog of Earth’s microbiomes

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

MOTIVATION: High-throughput sequencing (HTS) is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragments from the microorganisms within a given sample. This technology presents a unique opportunity for artificial intelligence to comprehend the underlying functional relationships of microbial communities. However, due to the unstructured nature of HTS data, nearly all computational models are limited to processing DNA sequences individually. This limitation causes them to miss out on key interactions between microorganisms, significantly hindering our understanding of how these interactions influence the microbial communities as a whole. Furthermore, most computational methods rely on post-processing of samples which could inadvertently introduce unintentional protocol-specific bias. RESULTS: Addressing these concerns, we present SetBERT, a robust pre-training methodology for creating generalized deep learning models for processing HTS data to produce contextualized embeddings and be fine-tuned for downstream tasks with explainable predictions. By leveraging sequence interactions, we show that SetBERT significantly outperforms other models in taxonomic classification with genus-level classification accuracy of 95%. Furthermore, we demonstrate that SetBERT is able to accurately explain its predictions autonomously by confirming the biological-relevance of taxa identified by the model. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/DLii-Research/setbert. SetBERT may be used through the q2-deepdna QIIME 2 plugin whose source code is available at https://github.com/DLii-Research/q2-deepdna.

Ludwig, David W↗

Functional team selection as a framework for local adaptation in plants and their belowground microbiomes

Abstract Multicellular organisms are hosts to diverse communities of smaller organisms known as microbiomes. Plants have distinctive microbiomes that can provide important functions related to nutrition, defense, and stress tolerance. Empirical studies provide convincing evidence that in some—but not all—circumstances, belowground microbiomes help plants adapt to their local environment. The purpose of this review is to develop functional team selection (FTS) as a framework to help predict the conditions necessary for root microbiomes to generate local adaptation for their plant hosts. FTS envisions plants and their microbiomes as complex adaptive systems, and plant adaptations as emergent properties of these systems. If plants have the capacity to recognize and cultivate beneficial microbes and suppress pathogens, then it is possible for plants to evolve the capacity to gain adaptations by curating their microbiome. In resource-limited and stressful environments, the emergent functions of complex microbial systems may contribute to positive feedback linked to plant vigor, and ultimately, local adaptation. The key factors in this process are: (i) selective force, (ii) host constitution, (iii) microbial diversity, and (iv) time. There is increasing interest in harnessing beneficial microbial interactions in agriculture and many microbial growth-promoting products are commercially available, but their use is controversial because a large proportion of these products fail to consistently enhance plant growth. The FTS framework may help direct the development of durable plant-microbiome systems that enhance crop production and diminish pathogens. It may also provide valuable insights for understanding and managing other kinds of host-microbe systems.

Environmental Sciences & Ecology↗

Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes

Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants.

59 BASIC BIOLOGICAL SCIENCES↗

The need for an integrated multi-OMICs approach in microbiome science in the food system

Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop “Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research” gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.

60 APPLIED LIFE SCIENCES↗

Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction

ABSTRACT Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a “top 10” list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.

Microbiology↗

The need for standardization and improved open (meta)data practices in metaproteomics

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices.

Armengaud, Jean [Universite Paris-Saclay, France]↗

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage–host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.

59 BASIC BIOLOGICAL SCIENCES↗

WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Surface Water FTICR-MS, NPOC, TN, Anions, Stable Isotopes, Bacterial Abundance, and Dissolved Inorganic Carbon (v8)

The WHONDRS Summer 2019 Sampling (S19S) Campaign collected samples in 97 globally distributed river corridor systems between July and September 2019. Surficial streambed sediments were collected at three locations within each site (upstream, midstream, and downstream). Surface water was collected at the downstream site. This dataset includes a portion of the data types produced from the surface water samples and does not include any results from the sediment. Sediment data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1729719. The S19S campaign was designed with the science community to ask questions associated with links among core/transient metabolomes, microbial metabolism, biogeochemical function, and physical properties of watershed and river corridor systems. This data package was originally published in March 2020. It was updated in October 2020 (v2, new and modified files), July 2021 (v3, new and modified files), January 2023 (v4, new and modified files), February 2023 (v5, new and modified files), August 2023 (v6, new and modified files), July 2025 (v7,new and modified files), and August 2026 (v8, new and modified files). Version 8 includes major restructuring of the files and their formats. See the change history section in readme for more details. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset contains (1) readme, (2) data dictionary, (3) file level metadata, (4) sampling protocol, (5) a data checks report, (6) field metadata, (7) international generic sample number (IGSN) mapping file, (8) joint genome institute (JGI) mapping file, and (9) a folder of sample data. The sample data folder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) and FTICR methods, (2) dissolved inorganic carbon (DIC), (3) stable water isotopes (O and H), (4) specific conductivity, (5) total dissolved nitrogen (TN), (6) anions, (7) flow cytometry bacterial abundance data, (8) laboratory methods, and (9) a folder containing unaligned, peak-picked high resolution characterization of dissolved organic matter from sediment via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL, https://www.pnnl.gov/environmental-molecular-sciences-laboratory), and (12) a folder containing processed FTICR-MS data. All files are .msa, .txt, .spx, .xml, .csv, .pdf, .txt, .html, .jpg, or .jpeg.

18-O↗

WHONDRS Summer 2019 Sampling Campaign: Global River Corridor Sediment FTICR-MS, Dissolved Organic Carbon, Aerobic Respiration, Elemental Composition, Grain Size, Total Nitrogen and Organic Carbon Content, Bacterial Abundance, and Stable Isotopes (v10)

The WHONDRS Summer 2019 Sampling (S19S) Campaign collected samples in 97 globally distributed river corridor systems between July and September 2019. Surficial streambed sediments were collected at three locations within each site (upstream, midstream, and downstream). Surface water was collected at the downstream site. This dataset includes a portion of the data types produced from the sediment samples and does not include any results from the surface water. Surface water data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1603775. The S19S campaign was designed with the science community to ask questions associated with links among core/transient metabolomes, microbial metabolism, biogeochemical function, and physical properties of watershed and river corridor systems. This data package was originally published in December 2020. It was updated in April 2021 (v2; modified files), May 2022 (v3; new and modified files), November 2022 (v4; new and modified files), January 2023 (v5 and v6; new and modified files), February 2023 (v7; new and modified files), August 2023 (v8; new and modified files), July 2025 (v9; new and modified files), and June 2026 (v10; new and modified files). Version 10 includes major restructuring of the files and their formats. See the change history in the readme for details. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset contains (1) readme, (2) data dictionary, (3) file level metadata, (4) sampling protocol, (5) a data checks report, (6) field metadata, (7) international generic sample number (IGSN) mapping file, (8) joint genome institute (JGI) mapping file, (9) a folder of site photos, and (10) a folder of sample data. The sample data folder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) and FTICR methods; (2) respiration rates and normalized respiration rates calculated from laboratory sediment incubations, (3) X-ray fluorescence (XRF) elemental composition, (4) grain size distribution from the < 2 millimeter fraction of sediment, (5) total organic carbon and total nitrogen content, (6) bacterial abundance flow cytometry data, (7) sediment stable isotopes (C and N), (8) laboratory methods, (9) water and sediment mass and volume used in incubations, (10) a folder with code, inputs, and plots for the respiration rates, (11) a folder containing XRF data, (12) a folder containing unaligned, peak-picked high resolution characterization of dissolved organic matter from sediment via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory), (12) and a folder containing processed FTICR-MS data. All files are .msa, .txt, .spx, .xml, .csv, .pdf, .txt, .jpg, or .jpeg.

13C↗