Microbial Metabolic Potential Research Articles

Integrating biological knowledge for mechanistic inference in the host-associated microbiome.

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

Inflammatory Dietary Potential Is Associated with Vitamin Depletion and Gut Microbial Dysbiosis in Early Pregnancy.

Pregnancy alters many physiological systems, including the maternal gut microbiota. Diet is a key regulator of this system and can alter the host immune system to promote inflammation. Multiple perinatal disorders have been associated with inflammation, maternal metabolic alterations, and gut microbial dysbiosis, including gestational diabetes mellitus, pre-eclampsia, preterm birth, and mood disorders. However, the effects of high-inflammatory diets on the gut microbiota during pregnancy have yet to be fully explored. We aimed to address this gap using a system-based approach to characterize associations among dietary inflammatory potential, a measure of diet quality, and the gut microbiome during pregnancy. Forty-seven pregnant persons were recruited prior to 16 weeks of gestation. Participants completed a food frequency questionnaire (FFQ) and provided fecal samples. Dietary inflammatory potential was assessed using the Dietary Inflammatory Index (DII) from the FFQ data. Fecal samples were analyzed using 16S rRNA amplicon sequencing. Differential taxon abundances with respect to the DII score were identified, and the microbial metabolic potential was predicted using PICRUSt2. Inflammatory diets were associated with decreased vitamin and mineral intake and a dysbiotic gut microbiota structure and predicted metabolism. Gut microbial compositional differences revealed a decrease in short-chain fatty acid producers such as Faecalibacterium, and an increase in predicted vitamin B12 synthesis, methylglyoxal detoxification, galactose metabolism, and multidrug efflux systems in pregnant individuals with increased DII scores. Dietary inflammatory potential was associated with a reduction in the consumption of vitamins and minerals and predicted gut microbiota metabolic dysregulation.

Alleviation of cotton growth suppression caused by salinity through biochar is strongly linked to the microbial metabolic potential in saline-alkali soil

Biochar is a typical soil organic amendment; however, there is limited understanding of its impact on the metabolic characteristics of microorganisms in saline-alkaline soil microenvironment, as well as the advantages and disadvantages of plant-microorganism interactions. To elucidate the mechanisms underlying the impact of saline-alkali stress on cotton, a 6-month pot experiment was conducted, involving the sowing of cotton seedlings in saline-alkali soil. Three different biochar application levels were established: 0 % (C0), 1 % (C1), and 2 % (C2). Results indicated that biochar addition improved the biomass of cotton plants, especially under C2 treatment; the dry weight of cotton bolls were 8.15 times that of C0. Biochar application led to a rise in the accumulation of photosynthetic pigments by 8.30–51.89 % and carbohydrates by 7.4–10.7 times, respectively. Moreover, peroxidase (POD) activity, the content of glutathione (GSH), and ascorbic acid (ASA) were elevated by 23.97 %, 118.39 %, and 48.30 % under C2 treatment, respectively. Biochar caused a reduction in Na+ uptake by 8.21–39.47 %, relative electrical conductivity (REC) of plants, and improved K+/Na+ and Ca2+/Na+ ratio indicating that biochar alleviated salinity-caused growth reduction. Additionally, the application of biochar enhanced the absorption intensity of polysaccharide fingerprints in cotton leaves and roots. Two-factor co-occurrence analysis indicated that the key differential metabolites connected to several metabolic pathways were L-phenylalanine, piperidine, L-tryptophan, and allysine. Interestingly, biochar altered the metabolic characteristics of saline-alkali soil, especially related to the biosynthesis and metabolism of amino acids and purine metabolism. In conclusion, this study demonstrates that biochar may be advantageous in saline soil microenvironment; it has a favorable impact on how plants and soil microbial metabolism interact.

The Microbial Community Composition and Nitrogen Cycling Metabolic Potential of an Underground Reservoir in Rizhao, Shandong Province, China

Constructing underground reservoirs has emerged as a crucial strategy to address the shortage of fresh water in Rizhao, Shandong Province, China. However, the water quality, microbial community composition, and biogeochemical cycling of nutrients in underground reservoirs compared to raw water remain unknown. To unveil the characteristics of microbial community structures and their nitrogen cycling metabolic potential in coastal underground reservoirs, we utilized a functional gene array (GeoChip 5.0) in conjunction with high-throughput sequencing of 16S rRNA and 18S rRNA genes. Our findings indicate that the water quality in the underground reservoir exhibits a certain degree of eutrophication compared to raw water, with higher concentrations of TN, TP, NO3−N, NO2−-N, and Chl a, but lower concentrations of DO and NH4+-N. The alpha diversity of bacterial and microeukaryotic communities was significantly lower in the underground reservoir. The bacterial community presented a stronger correlation with environmental factors than the microeukaryotic community. Regarding the relative abundance of bacterial communities, Gammaproteobacteria dominated the bacterial community in raw water, while Gammaproteobacteria and Alphaproteobacteria dominated the bacterial community in underground reservoir water. Additionally, the relative abundance of Nitrospirae was noticeably higher in the underground reservoir water. Moreover, we found significantly higher sequence abundance of the archaea Thaumarchaeota in the underground reservoir. Furthermore, our analysis revealed that, except for the amoA functional gene, which significantly increased the metabolic potential of nitrification, the metabolic potential of other microbial nitrogen functional genes was significantly reduced. This reduction may contribute to the lower concentration of NH4+-N in the underground reservoir. This study provides a comprehensive understanding of the microbial community characteristics and their nitrogen cycling metabolic potential in underground reservoirs. It serves as a valuable reference for water source selection, the formulation of water quality assurance measures, and the construction and management of underground reservoirs for subsequent impounding.

Effects of increasing drip irrigation at different maize growth stages on soil microorganisms.

To investigate the effects of different drip irrigation periods on soil microbial communities and functions. Increasing drip irrigation amount at the seedling (S), jointing (J), bell (B), tasseling (T) and grain filling (G) stages of maize were studied using no increase in irrigation amount as control (CK). Principal component analysis was conducted to comprehensively evaluate soil microbial quality following the different drip irrigation treatments. In addition, the characteristics of the community structure and the potential functional composition of soil bacteria and fungi were comparatively analyzed by combining amplicon sequencing and functional prediction methods. The results indicated that MBNT15 was the most important genus for the classification of soil bacterial samples, Saitozyma was the most important genus for the classification of soil fungal samples, and fungi were more important than bacteria for the classification of soil microbial samples. Compared with fungal communities, bacterial communities exhibited high levels of functional diversity. The proportion of metabolism was the highest in the prediction of bacterial primary functions, and carbohydrate metabolism and amino acid metabolism were important functions in the prediction of bacterial secondary functions. BugBase phenotype prediction results showed that soil bacteria under B treatment had a higher number of aerobic bacteria and greater resistance to disease and stress. The J treatment had the highest number of bacteria with biofilm forms, and the J, S, and G treatments contained more potentially pathogenic bacteria but fewer stress-tolerant bacteria compared with the CK treatment. The number of Saprotroph was the largest and the number of Symbiotroph was the least. The relative abundances of Saprotroph, Pathotroph and Symbiotroph were 68.60%~74.33%, 15.76%~20.60% and 9.16%~11.13%, respectively. The findings provide a reference for conserving water resources, improving maize yield, and predicting soil microbial metabolic potential and function by reflecting the richness of the soil microbial community structure in maize fields.

Direct observations of microbial community succession on sinking marine particles.

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.

Expansive microbial metabolic versatility and spatial biodiversity of anammox coupling with denitrification granular sludge under different feeding strategies

Anammox coupling with denitrification has attracted increasing attention in low-strength wastewater treatment. However, its wide application in continuous-flow process is seriously restricted by insufficient anammox capacity due to the failed biomass retention. The functional capacities of communities inhabiting the fluctuating habitat has been little understood. This study developed a novel granular sludge-based partial denitrification coupling with anammox (PD/A) process with the feeding strategy shifting from sequencing to continuous flow in a Continuous Stirred Tank Reactor (CSTR), treating low-strength wastewater containing ammonia (NH4+-N) of 46.1 mg/L and nitrate (NO3−-N) of 60.7 mg/L. Significantly enhanced specific anammox activity was demonstrated, attributed to the robust nitrite (NO2−-N) generation with NO3−-N to NO2−-N transformation ratio (NTR) averaged 84.1 %. Remarkable total nitrogen (TN) removal of 95.4 % was thus achieved with anammox pathway contribution as high as 88.3 %. Interestingly, a dynamic and stratified microbial structure was obtained in CSTR, in which anammox migrated to outer layer together with Thauera capable of partial denitrification (PD) in big granules, resulting in more efficient cross-feeding and strengthening the cooperation between anammox and heterotrophic PD bacteria in CSTR. Metagenomic-based metabolic inferences provide first insight into the versatile microbial metabolic potential of anammox bacteria for reducing NO3−-N with acetate as electron donor in PD/A process. They were successfully enriched and retained with the relative abundance of 8.4 %, being attributed to the enhanced mass transfer efficiency. On the contrary, dominant denitrifier Thauera decreased sharply to 4.2 %. This study provides a new alternative of anammox coupling with heterotrophics granular sludge for efficient low-strength wastewater treatment under continuous feeding, and open up new perspectives for selecting distinctive communities that stand out by expansive metabolic versatility and excellent microbial collaboration.

Spatial and temporal variation of microbial populations and microbial metabolic potential in a tropical marine cage-culture sediment system

The ecological roles of benthic microbes and the effect of anthropogenic mariculture activities on sediment microbial communities remain largely unexplored. Here, sediment bacterial abundances and diversity and their response to the disturbance induced by marine cage-culture farming were investigated at the station of Maniao Bay, Hainan province, China, with a history of cage culture for approximately 20 years. We characterized the sediment-associated microbial populations taken at marine cage culture zones and non-mariculture zones across one year. However, no significant differences between the marine cage culture and the non-mariculture zone occurred in microbial community structure and diversity. Minor differences among microbial communities during the year were observed in the sampling sites, which may be driven by the content of organic matter and sulfide in the sediment. This fact indicated that the diverse sediment microbiome was resilient to the stress caused by a modest environmental change. On the other hand, the ecological roles of the benthic microbes were explored by metagenomics, and their response to the marine cage-culture farm biodeposition was investigated across three years. The biochemical function carried out by the sediment microbes showed no significant difference between the marine cage culture zone and the non-mariculture zone. A stable microbial community was revealed in the Maniao Bay mariculture area and its adjacent sea area, which might be promoted by the hydrodynamic characteristics of the aquaculture area and its adjacent sea area, aquaculture scale, and culture mode.

Geomicrobiology of the Rincon de Parangueo maar crater: Exploring the link between an evolving extreme environment and its potential metabolic diversity

Abstract Rincon de Parangueo (RP) is a Quaternary maar crater located in the Michoacan‐Guanajuato Volcanic Field in central Mexico. Like other volcanic craters in the region, the central part was occupied by an endorheic lacustrine system. As a consequence of extensive groundwater extraction, the perennial lake started a gradual desiccation process and now the remnant ponds host a highly saline–alkaline ecosystem. The stratigraphic record indicates an exceptional and long‐term sedimentation of carbonate microbialites. Previous studies based on the 16S rRNA gene have shown that microbial communities have a widespread presence in the crater at the microbialites, the remaining saline ponds, superficial soils and below the surface. To understand the possible role of the microbial communities that generate these biogeological structures, novel analytical methods to resolve the amplicon datasets and their microbial metabolic potential were used. We describe in detail the relationship between the microbial communities, the evolution of physicochemical parameters, and carbonate morphology, in four micro‐environments. A 16S rRNA gene sequencing dataset from previous publications was re‐analysed using an ASV‐based bioinformatic pipeline to identify new insights into the microbial assemblage. Finally, a taxon‐based metabolic profile was used to predict the potential metabolic contribution of the prokaryotic community. Results indicated a refinement in terms of community composition using the ASV‐based bioinformatic methods. Functional profiling through 16S rRNA gene‐based analysis suggested metabolisms associated with carbonate precipitation, indicating a broad potential for microbially mediated carbonate precipitation (e.g., carbon fixation and photosynthesis). The possibility of biogenic methane gas production by methanogenic microorganisms was recognised, supporting the estimated flow of methane on the surface soils. The lacustrine evolution over the last years and the extreme physicochemical characteristics of RP have an impact on the microbial community structure. Prokaryotic community and metabolic potential results from RP coincide with the diversity and abundance of microbial communities and functional metabolisms reported from other microbialite‐forming lakes along the Trans Mexican Volcanic Belt. The identification of important possible phylotypes involved in carbonate precipitation might be an important factor in considering RP microbialites as active calcifying entities. These findings provide novel insights into the potential key role of metabolic pathways driving the process of carbonate precipitation inside RP and evidence of its importance as a microbial biodiversity hotspot in Mexico.

Shotgun metagenomics from Monte Cristo cave (Brazil) reveals microbial metabolic potential related to iron and manganese biogeochemical cycles

Caves are among the most singular and understudied environments on Earth. Due to the harsh conditions observed in many caves, including scarcity of nutrients and low levels of light, these ecosystems are considered extreme environments (Gabriel and Northup 2012). Therefore, it may be worth paying special attention to the microbial communities existing in these unique systems. Previously, it has been suggested that the high levels of Manganese (Mn) and Iron (Fe) at Lechuguilla and Spider Caves in the United States may influence their microbial community structure in different ways (Northup et al. 2003, Carmichael and Bräuer 2015). In this context, caves are promising environments for investigating microbial functional capabilities in relation to these elements and the ecological interactions that allow these microbes to thrive. Monte Cristo cave (MCC) - in Diamantina, Brazil - was chosen for this study. The cave is located in a region known for historic mining activity and occurrences of Mn and Fe-rich rocks (Costa et al. 2003). With that in mind, our main goal is to investigate if within the microbial community of MCC there is evidence of taxa and genes associated with Fe and Mn metabolism. The samples were collected in 2018 from walls and saprolite deposits within MCC. Community DNA from three samples, P1b, P3 and P7, were independently sequenced using Illumina shotgun sequencing, and the data were analysed using conventional metagenomic pipelines and in-house python scripts. Taxonomic classification was assessed using Kraken2; Fe related genes with FeGenie; and Mn related genes were predicted using BlastP against a collection of manually curated Mn-oxidizing proteins. Environmental Mn and Fe concentrations were measured using ICP-OES. Our results suggest the presence of a microbial community potentially able to change Fe and Mn redox states. In sites P1b and P7, genes associated to Fe and Mn oxidation were identified, Fig. 1. Taxonomic evidence for these metabolisms includes the presence of the taxa Comamonadaceae and Hyphomicrobiaceae, both families that were previously reported to harbour species able to oxidize Mn and Fe (Spring and Kämpfer 2015, Carmichael and Bräuer 2015). Our analysis also assigned contigs to the archaeal phyla Crenarchaeota, Euryarchaeota and Thaumarchaeota, whose presence has been associated with oligotrophic caves where archaea play a role in primary production (Ortiz et al. 2013) (Fig. 2). Moreover, the phylum Euryarchaeota harbours members that use Fe or Mn as electron acceptors during methane oxidation (Ettwig et al. 2016). Our results therefore contribute to understanding how microbial communities of MCC may be playing a role in the biogeochemical cycles of Fe and Mn under the conditions imposed by the subterranean environment, which might reflect similar processes in other caves yet to be explored by a metagenomics approach.

Explaining nitrogen turnover in sediments and water through variations in microbial community composition and potential function

Anthropogenic activities greatly impact nitrogen (N) biogeochemical cycling in aquatic ecosystems. High N concentrations in coastal aquaculture waters threaten fishery production and aquaculture ecosystems and have become an urgent problem to be solved. Existing microbial flora and metabolic potential significantly regulate N turnover in aquatic ecosystems. To clarify the contribution of microorganisms to N turnover in sediment and water, we investigated three types of aquaculture ecosystems in coastal areas of Guangdong, China. Nitrate nitrogen (NO3−-N) was the dominant component of total nitrogen in the sediment (interstitial water, 90.4%) and water (61.6%). This finding indicates that NO3−-N (1.67–2.86 mg/L and 2.98–7.89 mg/L in the sediment and water) is a major pollutant in aquaculture ecosystems. In water, the relative abundances of assimilation nitrogen reduction and aerobic denitrifying bacteria, as well as the metabolic potentials of nitrogen fixation and dissimilated nitrogen in fish monoculture, were only 61.0%, 31.5%, 47.5%, and 27.2% of fish and shrimp polyculture, respectively. In addition, fish-shrimp polyculture reduced NO3−-N content (2.86 mg/L) compared to fish monoculture (7.89 mg/L), which was consistent with changes in aerobic denitrification and nitrate assimilation, suggesting that polyculture could reduce TN concentrations in water bodies and alleviate nitrogen pollution risks. Further analysis via structural equation modeling (SEM) revealed that functional pathways (36% and 31%) explained TN changes better than microbial groups in sediment and water (13% and 11%), suggesting that microbial functional capabilities explain TN better than microbial community composition and other factors (pH, O2, and aquaculture type). This study enhances our understanding of nitrogen pollution characteristics and microbial community and functional capabilities related to sediment-water nitrogen turnover in three types of aquaculture ecosystems, which can contribute to the preservation of healthy coastal ecosystems.

Infants exposed in utero to Hurricane Maria have gut microbiomes with reduced diversity and altered metabolic capacity.

The gut microbiome is a potentially important mechanism that links prenatal disaster exposures with increased disease risks. However, whether prenatal disaster exposures are associated with alterations in the infant's gut microbiome remains unknown. We established a birth cohort study named Hurricane as the Origin of Later Alterations in Microbiome (HOLA) after Hurricane Maria struck Puerto Rico in 2017. We enrolled vaginally born Latino term infants aged 2 to 6 months, including n = 29 infants who were exposed in utero to Hurricane Maria in Puerto Rico and n = 34 infants who were conceived at least 5 months after the hurricane as controls. Shotgun metagenomic sequencing was performed on infant stool swabs. Infants exposed in utero to Hurricane Maria had a reduced diversity in their gut microbiome compared to the control infants, which was mainly seen in the exclusively formula-fed group (P = 0.02). Four bacterial species, including Bacteroides vulgatus, Clostridium innocuum, Bifidobacterium pseudocatenulatum, and Clostridium neonatale, were depleted in the exposure group compared to the control group. Compositional differences in the microbial community and metabolic genes between the exposure and control groups were significant, which were driven by the formula feeding group (P = 0.02 for the microbial community and P = 0.008 for the metabolic genes). Metabolic modules involved in carbohydrate metabolism were reduced in the exposure group. Prenatal maternal exposure to Hurricane Maria was associated with a reduced gut commensal and an altered microbial composition and metabolic potential in the offspring's gut. Breastfeeding can adjust the composition of the gut microbiomes of exposed infants. IMPORTANCE Climate change is a serious issue that is affecting human health. With more frequent and intense weather disasters due to climate change, there is an urgent need to evaluate and understand the impacts of prenatal disaster exposures on the offspring. The prenatal stage is a particularly vulnerable stage for disease origination. However, the impact of prenatal weather disaster exposures on the offspring's gut microbiome has not been evaluated. Our HOLA study starts to fill this knowledge gap and provides novel insights into the microbiome as a mechanism that links prenatal disaster exposures with elevated disease risks. Our major finding that reduced microbial diversity and altered metabolic capacity are associated with prenatal hurricane exposures warrants further studies to evaluate the impact of weather disasters on the unborn.

Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity.

The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.

Metagenomic analysis reveals microbial metabolic potentials alterations under antibiotic stress during sludge anaerobic digestion

The presence of antibiotics in sludge is considered to have a detrimental effect on methane production and microbial community. However, the underlying mechanism of how antibiotic impact the metabolic potentials is still unclear. This study investigated the long-term effects of antibiotics on different stages of sludge anaerobic digestion and on the metabolic potentials of key functional microorganism, revealed the response mechanism of dominant microbiome on antibiotic stress through metagenomic sequencing and binning strategy. Experimental results demonstrated that the abundance of many functional genes associated with glycolysis, protein hydrolysis and acidification increased by 3 %–200 % under the antibiotics stress. While functional genes related to acetate and acetyl-coA conversion were reduced. Besides, the major methanogenic metabolic pathways had also been altered under antibiotic stress, from acetoclastic methanogenesis to methanogenesis of methylamine. The metabolic potentials of ten typical metagenome-assembled genomes (MAGs) associated with hydrolysis, acidogenesis and methanogenesis were also investigated through the metagenomic binning strategy. The dominant MAGs under antibiotic stress contained abundant functional genes associated with EPS biosynthesis, secondary metabolite biosynthesis and bacterial chemotaxis, which may contribute to their dominance. This study shed light on complex metabolic potentials of microorganisms under the antibiotic stress, and provide novel insights into the underlying mechanism of antibiotic inhibition on anaerobic digestion.

Pollutants removal and connections among sludge properties, metabolism potential and microbial characteristics in aerobic granular sequencing batch reactor for petrochemical wastewater treatment

Petrochemical wastewater contains inhibitory compounds such as aromatics that are toxic to microorganisms during biological treatment. The compact and layered structure and the high amount of extracellular polymeric substances (EPS) in aerobic granular sludge (AGS) can contribute to protecting microorganisms from the harsh environment. This study evaluated the changes in the granule properties, pollutants removal, microbial metabolic potential and molecular microbial characteristics of the AGS process for petrochemical wastewater treatment. Granules treating petrochemical wastewater had a higher SVI30/SVI5 value (0.94) than that treating synthetic wastewater. An increase in bioactivity and EPS secretion with higher bio-polymer composition, specifically the functional groups such as hydroxyl, alkoxy and amino in protein, was observed, which promoted biomass aggregation. The granules also had more than 2-fold higher specific oxygen utilization rate. The AGS-SBR process obtained an average COD removal of 93% during petrochemical wastewater treatment and an effluent bCOD of below 1 mg L−1. No obvious inhibition of nitrification and denitrification activity was observed in the processes attributed to the layered structure of AGS. The average effluent NH4+-N of 5.0 mg L−1 was obtained and TN removal efficiencies of over 80.0% was achieved. Molecular microbial analysis showed that abundant functional genera Stenotrophomonas and Pseudoxanthomonas contributed to the degradation of aromatics and other petroleum organic pollutants. They were enriched with the variation of group behavior while metabolisms of amino acids and carboxylic acids by the relevant functional genera (e.g., Cytophagia) were significantly inhibited. The enrichment of Flavobacterium and Thermomonas promoted nitrification and denitrification, respectively. This research revealed the rapid start-up, enhanced granule structural strength, high inhibition resistance and considerable performance of AGS-SBR for petrochemical wastewater treatment.

Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.

Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.

Fecal matters: Microbial signatures distinguish clinically relevant subtypes of precancerous colorectal polyps

Colorectal cancer (CRC) can arise from adenomatous or serrated polyps, which differ in their detection rate and risk of cancer progression. In this issue, Lee etal. report that these polyp subtypes demonstrate distinct fecal microbial species composition and metabolic potential that associate with diet and medications.

Microbial community composition and metabolic potential during a succession of algal blooms from Skeletonema sp. to Phaeocystis sp.

Elucidating the interactions between algal and microbial communities is essential for understanding the dynamic mechanisms regulating algal blooms in the marine environment. Shifts in bacterial communities when a single species dominates algal blooms have been extensively investigated. However, bacterioplankton community dynamics during bloom succession when one algal species shift to another is still poorly understood. In this study, we used metagenomic analysis to investigate the bacterial community composition and function during algal bloom succession from Skeletonema sp. to Phaeocystis sp. The results revealed that bacterial community structure and function shifted with bloom succession. The dominant group in the Skeletonema bloom was Alphaproteobacteria, while Bacteroidia and Gammaproteobacteria dominated the Phaeocystis bloom. The most noticeable feature during the successions was the change from Rhodobacteraceae to Flavobacteriaceae in the bacterial communities. The Shannon diversity indices were significantly higher in the transitional phase of the two blooms. Metabolic reconstruction of the metagenome-assembled genomes (MAGs) showed that dominant bacteria exhibited some environmental adaptability in both blooms, capable of metabolizing the main organic compounds, and possibly providing inorganic sulfur to the host algae. Moreover, we identified specific metabolic capabilities of cofactor biosynthesis (e.g., B vitamins) in MAGs in the two algal blooms. In the Skeletonema bloom, Rhodobacteraceae family members might participate in synthesizing vitamin B1 and B12 to the host, whereas in the Phaeocystis bloom, Flavobacteriaceae was the potential contributor for synthesizing vitamin B7 to the host. In addition, signal communication (quorum sensing and indole-3-acetic acid molecules) might have also participated in the bacterial response to bloom succession. Bloom-associated microorganisms showed a noticeable response in composition and function to algal succession. The changes in bacterial community structure and function might be an internal driving factor for the bloom succession.

Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.

Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.

Buried wood effects on macronutrient supply and microbial activity and metabolic potential in different oil sands reclamation soils in northern Alberta

Buried wood is an important yet understudied component of natural and anthropogenic soils. Nutrient immobilization as a response to wood addition during oil sands' reclamation may be a concern since surface wood is salvaged with the soil, thereby becoming buried wood in reclamation cover soils. This project investigated the impact of buried wood on macronutrient supply and microbial communities in different reclamation soils. A 60-day incubation was performed with different rates and types of wood (0%–50%, aspen and pine) and four different soils: fine and coarse forest floor-mineral mix (fFFMM and cFFMM), peat-mineral mix (PMM), and peat. Analysis of macronutrient supply rates using Plant Root Simulator (PRS™) probes and a community-level physiological profiling (CLPP) to assess metabolic potential was performed at the end of the incubation period; microbial activity was measured through soil respiration during the incubation. Responses varied by soil type; however, buried wood caused nitrogen immobilization in three soils due to an increase in the C:N ratio. Soils with lower C:N ratios like fFFMM and PMM were more susceptible to immobilization with a decrease in available nitrogen by up to 95% at a 10% of wood addition. Phosphorus immobilization was observed in cFFMM, and potassium supply increased at 20% of wood and above. Soil microbial activity and metabolic potential increased but no significant changes in the soil profiles were observed. The findings of this study demonstrate that buried wood increases the soil C:N ratio and can potentially cause nitrogen immobilization when added by 10% of volume or more.