Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.

A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors.

Microenvironments on individual sand grains enhance nitrogen loss in coastal sediments.

The permeable silicate sediments which cover more than 50% of the continental shelves are a major, but poorly constrained sink for the vast amount of anthropogenic nitrogen (N) that enters the ocean. Surface-attached microbial communities on sand grains remove fixed-N via denitrification, a process generally restricted to anoxic or low oxygen (O) environments. Yet, in sands, denitrification also occurs in the centimeters thick well-oxygenated surface layer, which leads to additional and substantial N-loss.

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126.

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources.

Global mapping of flux and microbial sources for oceanic NO.

The ocean is the largest source of NO emissions from global aquatic ecosystems. However, the NO production-consumption mechanism and microbial spatial distribution are still unclear. Our study established a bottom-up model based on the source‒sink boundary and the microbial sources of NO.

Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.

Motivation: Gene function annotation in microbial genomes and metagenomes is a fundamental first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.

Biochar application using recycled annual self straw reduces long-term greenhouse gas emissions from paddy fields with economic benefits.

Paddy fields are major contributors to agricultural greenhouse gas emissions. Applying ~1% biochar by topsoil weight (high single, HS) effectively reduces greenhouse gas emissions from paddy fields, but long-term impacts are unclear. Here we present 8-year field experiments showing HS reduces CO equivalent per hectare by 59% and yields a net benefit of US$1,810 per hectare.

Key role of in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.

Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol C year. This remarkable activity is largely attributable to the deltaproteobacterial family of complete oxidizers (to CO), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown.

sp. nov., a marine methylotrophic methanogen isolated from an anaerobic methane-oxidizing enrichment culture.

Enrichment cultures of archaea and bacteria performing the anaerobic oxidation of methane (AOM) regularly contain persistent methanogens. Here, we isolated the marine methanogen sp. nov.

Single-cell imaging reveals efficient nutrient uptake and growth of microalgae darkening the Greenland Ice Sheet.

Blooms of dark pigmented microalgae accelerate glacier and ice sheet melting by reducing the surface albedo. However, the role of nutrient availability in regulating algal growth on the ice remains poorly understood. Here, we investigate glacier ice algae on the Greenland Ice Sheet, providing single-cell measurements of carbon:nitrogen:phosphorus (C:N:P) ratios and assimilation rates of dissolved inorganic carbon (DIC), ammonium and nitrate following nutrient amendments.

Comparison of cable bacteria genera reveals details of their conduction machinery.

Cable bacteria are centimeter-long multicellular bacteria conducting electricity through periplasmic conductive fibers (PCFs). Using single-strain enrichments of the genera Electrothrix and Electronema we systematically investigate variations and similarities in morphology and electrical properties across both genera. Electrical conductivity of different PCFs spans three orders of magnitude warranting further investigations of the plasticity of their conduction machinery.

Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla.

Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes.

Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.

Members of Methylotenera are signature denitrifiers and methylotrophs commonly found together with methanotrophic bacteria in lakes and freshwater sediments. Here, we show that three distinct Methylotenera ecotypes were abundant in methane-rich groundwaters recharged during the Pleistocene. Just like in surface water biomes, groundwater Methylotenera often co-occurred with methane-oxidizing bacteria, even though they were generally unable to denitrify.

Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.

Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding.

Conformational dynamics of a multienzyme complex in anaerobic carbon fixation.

In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates.

Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo.

The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases.

Influences of fluctuating nutrient loadings on nitrate-reducing microorganisms in rivers.

Rivers serve important functions for human society and are significantly impacted by anthropogenic nutrient inputs (e.g. organic and sulfur compounds).

Sustainable management of riverine NO emission baselines.

The riverine NO fluxes are assumed to linearly increase with nitrate loading. However, this linear relationship with a uniform EF is poorly constrained, which impedes the NO estimation and mitigation. Our meta-analysis discovered a universal NO emission baseline (EF = k/[NO ], k = 0.

Universal, untargeted detection of bacteria in tissues using metabolomics workflows.

Fast and reliable identification of bacteria directly in clinical samples is a critical factor in clinical microbiological diagnostics. Current approaches require time-consuming bacterial isolation and enrichment procedures, delaying stratified treatment. Here, we describe a biomarker-based strategy that utilises bacterial small molecular metabolites and lipids for direct detection of bacteria in complex samples using mass spectrometry (MS).

Defective in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.

Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease.

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.

Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e.

Ubiquitous genome streamlined in freshwater environments.

are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia.