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  1. Abstract

    Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.

     
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  2. Free, publicly-accessible full text available August 1, 2024
  3. null (Ed.)
    Over 300 species of naturally occurring-organoarsenicals have been identified with the development of modern analytical techniques. Why there so many environmental organoarsenicals exist is a real enigma. Are they protective or harmful? Or are they simply by-products of existing pathways for non-arsenical compounds? Fundamental unanswered questions exist about their occurrence, prevalence and fate in the environment, metabolisms, toxicology and biological functions. This review focuses on possible answers. As a beginning, we classified them into two categories: water-soluble and lipid-soluble organoarsenicals (arsenolipids). Continual improvements in analytical techniques will lead to identification of additional organoarsenicals. In this review, we enumerate identified environmental organoarsenicals and speculate about their pathways of synthesis and degradation based on structural data and previous studies. Organoarsenicals are frequently considered to be nontoxic, yet trivalent methylarsenicals, synthetic aromatic arsenicals and some pentavalent arsenic-containing compounds have been shown to be highly toxic. The biological functions of some organoarsenicals have been defined. For example, arsenobetaine acts as an osmolyte, and membrane arsenolipids have a phosphate-sparing role under phosphate-limited conditions. However, the toxicological properties and biological functions of most organoarsenicals are largely unknown. The objective of this review is to summarize the toxicological and physiological properties and to provide novel insights into future studies. 
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  4. Cann, Isaac (Ed.)
    ABSTRACT Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes ( ars ) including arsR , acr3 , arsB , arsC , arsM , arsI , arsP , and arsH as well as energy-generating As respiratory oxidation ( aioA ) and reduction ( arrA ) genes. Somewhat unexpectedly, the relative DNA abundances and diversities of ars , aioA , and arrA genes were not significantly different between low and high (∼10 versus ∼100 mg kg −1 ) As soils. Compared to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars gene abundance only when its concentration was higher than 410 mg kg −1 . In contrast, metatranscriptomics revealed that relative to low-As soils, high-As soils showed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community wide as opposed to taxon specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil or other environments should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level; thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems. 
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