Archaea oxidizing alkanes through alkyl-coenzyme M reductases.

This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.

Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.

The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.

Artificial light at night causes community instability of bacterial community in urban soils.

Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.

Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist.

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO2 via beta oxidation and the oxidative Wood-Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps. Etymology: Desulfosarcina aeriophaga, aério (Greek): gas; phágos (Greek): eater; D. aeriophaga: a gas eating or gas feeding Desulfosarcina.

High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.

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.

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses.

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used 13C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein-stable isotope probing. The detection of 13C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling.

The rise of oxygen on the early Earth about 2.4 billion years ago reorganized the redox cycle of harmful metal(loids), including that of arsenic, which doubtlessly imposed substantial barriers to the physiology and diversification of life. Evaluating the adaptive biological responses to these environmental challenges is inherently difficult because of the paucity of fossil records. Here we applied molecular clock analyses to 13 gene families participating in principal pathways of arsenic resistance and cycling, to explore the nature of early arsenic biogeocycles and decipher feedbacks associated with planetary oxygenation. Our results reveal the advent of nascent arsenic resistance systems under the anoxic environment predating the Great Oxidation Event (GOE), with the primary function of detoxifying reduced arsenic compounds that were abundant in Archean environments. To cope with the increased toxicity of oxidized arsenic species that occurred as oxygen built up in Earth's atmosphere, we found that parts of preexisting detoxification systems for trivalent arsenicals were merged with newly emerged pathways that originated via convergent evolution. Further expansion of arsenic resistance systems was made feasible by incorporation of oxygen-dependent enzymatic pathways into the detoxification network. These genetic innovations, together with adaptive responses to other redox-sensitive metals, provided organisms with novel mechanisms for adaption to changes in global biogeocycles that emerged as a consequence of the GOE.

Bioavailable arsenic and amorphous iron oxides provide reliable predictions for arsenic transfer in soil-wheat system.

The application of current soil quality standards based on total arsenic (As) fails to assess the ecological risks of soil arsenic or to ensure the safety of crops and foods. In this study, bioavailable arsenic instead of total arsenic was applied to improve predictive models for arsenic transfer from soil to wheat (Triticum turgidum L.). The stepwise multiple-linear regression analysis showed that bioavailable arsenic and amorphous iron oxides (FeOX) were the two most important factors contributing to arsenic accumulation in wheat grain, with the explained percentage of variation being up to 82%. Compared with the bioavailable arsenic extracted by NH4H2PO4, bioavailable arsenic extracted by HNO3 from soils generated better predictions of the amount of arsenic in grain. The best reliable model was log[Asgrain] = 0.917 log[HNO3-As] - 0.452 log[FeOX] - 1.507 (R2 = 0.82, P <  0.001). Consistently, bioavailable arsenic and FeOX were also the key factors to predict arsenic accumulation in wheat straw, leaves and spikes. Our prediction models was successfully verified for three independent soils. Our results highlight the role of soil bioavailable heavy metals in predicting their transfer in soil-plant systems and can be used to improve existing Chinese soil quality standards.

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.

Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps1-3, and through ethane-dependent sulfate reduction in slurries4-7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown8. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'9. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps10-12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.

Organic Carbon Amendments Affect the Chemodiversity of Soil Dissolved Organic Matter and Its Associations with Soil Microbial Communities.

The "4 per mil" initiative recognizes the pivotal role of soil in carbon resequestration. The need for evidence to substantiate the influence of agricultural practices on chemical nature of soil carbon and microbial biodiversity has become a priority. However, owing to the molecular complexity of soil dissolved organic matter (DOM), specific linkages to microbial biodiversity have eluded researchers. Here, we characterized the chemodiversity of soil DOM, assessed the variation of soil bacterial community composition (BCC), and identified specific linkages between DOM traits and BCC. Sustained organic carbon amendment significantly ( P < 0.05) increased total organic matter reservoirs, resulted in higher chemodiversity of DOM and emergence of recalcitrant moieties (H/C < 1.5). In the meantime, sustained organic carbon amendment shaped the BCC to a more eutrophic state while long-term chemical fertilization directed the BCC toward an oligotrophic state. Meanwhile, higher connectivity and complexity were observed in organic carbon amendment by DOM-BCC network analysis, indicating that soil microbes tended to have more interaction with DOM molecules after organic matter inputs. These results highlight the potential for organic carbon amendments to not only build soil carbon stocks and increase their resilience but also mediate the functional state of soil bacterial communities.

DNA stable-isotope probing identifies uncultivated members of Pseudonocardia associated with biodegradation of pyrene in agricultural soil.

Identifying functional microorganisms involved in the degradation of high-molecular-mass polycyclic aromatic hydrocarbons (HMM-PAHs) in agricultural soil environments could assist in developing bioremediation strategies for soil PAH contamination. Active populations of HMM-PAH degraders in agricultural soils are currently poorly understood. In this study, we identified aerobic pyrene-degrading bacteria in agricultural and industrial soils by [13C]pyrene incubations followed by DNA stable-isotope probing and high-throughput sequencing. More than 80% of pyrene was degraded during an incubation time of 35 days in both soils, with slower mineralization rates observed in agricultural soil compared with industrial soil. Members of the Pseudonocardia genus, not previously implicated in pyrene degradation, were the dominant pyrene-degrading population in agricultural soil; their relative abundance increased by three orders of magnitude. In industrial soil, Arthrobacter sp. appeared as the major pyrene degraders, while Pseudonocardia was not detectable. Mycobacterium, a group of well-known pyrene degraders, was found to be active in pyrene degradation in both soils. These results highlight the role of uncultivated members of Pseudonocardia in natural PAH biodegradation processes and expand our understanding of the metabolic potential of uncultivated microorganisms for bioremediation applications in agricultural soils.

Molecular Chemodiversity of Dissolved Organic Matter in Paddy Soils.

Organic matter (OM), and dissolved organic matter (DOM), have a major influence upon biogeochemical processes; most significantly, the carbon cycle. To date, very few studies have examined the spatial heterogeneity of DOM in paddy soils. Thus, very little is known about the DOM molecular profiles and the key environmental factors that underpin DOM molecular chemodiversity in paddy soils. Here, Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry was applied to unambiguously resolve 11 361 molecular formulas in 16 paddy soils; thereby elucidating the molecular characteristics of paddy soil DOM. Soil pH, iron complexing index (Fep/FeR) and C/N ratio were established to be key factors controlling DOM profiles. Polycyclic aromatics (derived from combustion) and polyphenols (derived from plants) increased with increasing pH, while polyphenols molecules, pyrogenic aromatics, and carboxylic compounds decreased with increasing iron complexing index. Patterns in molecular profiles indicated DOM in paddy soils to become more recalcitrant at higher soil C/N ratio and higher pH. Furthermore, plant-derived polyphenols and pyrogenic DOM were retained favorably by iron and the chemodiversity of DOM in paddy soil increased with increasing soil C/N ratios. This study provides critical information about DOM characteristics at a molecular level and will inform better global management of soil carbon in paddy soil ecosystems.

Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic.

The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic. To elucidate the history of arsenic adaptation across the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-adenosylmethionine (SAM) methyltransferase. Our results suggest that life successfully moved into arsenic-rich environments in the late Archean Eon and Proterozoic Eon, respectively, by the spread of arsM genes. The arsM genes of bacterial origin have been transferred to other kingdoms of life on at least six occasions, and the resulting domesticated arsM genes promoted adaptation to environmental arsenic. These results allow us to peer into the history of arsenic adaptation of life on our planet and imply that dissemination of genes encoding diverse adaptive functions to toxic chemicals permit adaptation to changes in concentrations of environmental toxins over evolutionary history.

Distribution of soil selenium in China is potentially controlled by deposition and volatilization?

Elucidating the environmental drivers of selenium (Se) spatial distribution in soils at a continental scale is essential to better understand it's biogeochemical cycling to improve Se transfer into diets. Through modelling Se biogeochemistry in China we found that deposition and volatilization are key factors controlling distribution in surface soil, rather than bedrock-derived Se (<0.1 mg/kg). Wet deposition associated with the East Asian summer monsoon, and dry deposition associated with the East Asian winter monsoon, are responsible for dominant Se inputs into northwest and southeast China, respectively. In Central China the rate of soil Se volatilization is similar to that of Se deposition, suggesting that Se volatilization offsets it's deposition, resulting in negligible net Se input in soil. Selenium in surface soil at Central China is roughly equal to low petrogenic Se, which is the main reason for the presence of the Se poor belt. We suggest that both deposition and volatilization of Se could play a key role in Se balance in other terrestrial environments worldwide.

Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils.

Desulfitobacterium hafniense strain DH is a sulfate-reducing species. Here, we report the draft genome sequence of strain DH, with a size of 5,368,588 bp, average G+C content of 47.48%, and 5,296 predicted protein-coding sequences.

Dynamic equilibrium of endogenous selenium nanoparticles in selenite-exposed cancer cells: a deep insight into the interaction between endogenous SeNPs and proteins.

Elemental selenium (Se) was recently found to exist as endogenous nanoparticles (i.e., SeNPs) in selenite-exposed cancer cells. By sequestrating critical intracellular proteins, SeNPs appear capable of giving rise to multiple cytotoxicity mechanisms including inhibition of glycolysis, glycolysis-dependent mitochondrial dysfunction, microtubule depolymerization and inhibition of autophagy. In this work, we reveal a dynamic equilibrium of endogenous SeNP assembly and disassembly in selenite-exposed H157 cells. Endogenous SeNPs are observed both in the cytoplasm and in organelles. There is an increase in endogenous SeNPs between 24 h and 36 h, and a decrease between 36 h and 72 h according to transmission electron microscopy results and UV-Vis measurements. These observations imply that elemental Se in SeNPs could be oxidized back into selenite by scavenging superoxide radicals and ultimately re-reduced into selenide; then the assembly and disassembly of SeNPs proceed simultaneously with the sequestration and release of SeNP high-affinity proteins. There is also a possibility that the reduction of elemental Se to selenide pathway may lie in selenite-exposed cancer cells, which results in the assembly and disassembly of endogenous SeNPs. Genome-wide expression analysis results show that endogenous SeNPs significantly altered the expression of 504 genes, compared to the control. The endogenous SeNPs induced mitochondrial impairment and decreasing of the annexin A2 level can lead to inhibition of cancer cell invasion and migration. This dynamic flux of endogenous SeNPs amplifies their cytotoxic potential in cancer cells, thus provide a starting point to design more efficient intracellular self-assembling systems for overcoming multidrug resistance.

A novel kernelized fuzzy C-means algorithm with application in medical image segmentation.

Image segmentation plays a crucial role in many medical imaging applications. In this paper, we present a novel algorithm for fuzzy segmentation of magnetic resonance imaging (MRI) data. The algorithm is realized by modifying the objective function in the conventional fuzzy C-means (FCM) algorithm using a kernel-induced distance metric and a spatial penalty on the membership functions. Firstly, the original Euclidean distance in the FCM is replaced by a kernel-induced distance, and thus the corresponding algorithm is derived and called as the kernelized fuzzy C-means (KFCM) algorithm, which is shown to be more robust than FCM. Then a spatial penalty is added to the objective function in KFCM to compensate for the intensity inhomogeneities of MR image and to allow the labeling of a pixel to be influenced by its neighbors in the image. The penalty term acts as a regularizer and has a coefficient ranging from zero to one. Experimental results on both synthetic and real MR images show that the proposed algorithms have better performance when noise and other artifacts are present than the standard algorithms.