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Root-associated bacteria play a vital role in the growth and adaptation of host plants to drought stress. These bacteria can be classified as rhizoplane and rhizosphere bacteria based on their distance from the root surface. Tomato plants are often exposed to periodic drought and nitrogen (N) addition throughout their life cycle, but the impacts of these factors on the plant and root-associated bacteria are not well understood. To gain insight into this relationship, we conducted an experiment to monitor the effects of periodic drought and N addition on rhizoplane and rhizosphere bacteria of tomato plants. Drought and N addition had interactive effects on plant and soil properties, which varied with the timing of drought. There were clear divergences in community traits such as alpha diversity, beta diversity, and network topological features between the two types of bacteria. The rhizoplane bacteria showed lower alpha diversity but higher beta diversity and were more sensitive to drought and N addition than the rhizosphere bacteria. Nitrogen addition could downsize the effects of drought on rhizoplane bacterial community compositions. The higher proximity to the root might induce a community to develop more cooperation between different members to cope with plant metabolites, as revealed by the more connected and modularized community network of the rhizoplane bacteria. Drought at the seedling stage had great legacy effects on plant and soil properties. It may enhance selection, cause the dominance of deterministic processes in the assembly of rhizoplane bacteria, and reduce bacterial community network complexity. In conclusion, N addition could interact with drought in affecting tomato plants and their root-associated bacteria, depending on the timing of drought and the fineness of root niches. The higher sensitivity of rhizoplane bacteria to drought and N addition calls for more research due to their higher proximity and importance to plants in future environmental changes.

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Fecal microbiota transplantation (FMT) is arguably the most effective treatment for recurrent Clostridioides difficileinfection (rCDI). Clinical reports on pediatric FMT have not systematically evaluated microbiome restoration in patients with co-morbidities. Here, we determined whether FMT recipient age and underlying co-morbidity influenced clinical outcomes and microbiome restoration when treated from shared fecal donor sources. Eighteen rCDI patients participating in a single-center, open-label prospective cohort study received fecal preparation from a self-designated (single case) or two universal donors. Twelve age-matched healthy children and four pediatric ulcerative colitis (UC) cases from an independent serial FMT trial, but with a shared fecal donor were examined as controls for microbiome restoration using 16S rRNAgene sequencing of longitudinal fecal specimens. FMT was significantly more effective in rCDI recipients without underlying chronic co-morbidities where fecal microbiome composition in post-transplant responders was restored to levels of healthy children. Microbiome reconstitution was not associated with symptomatic resolution in some rCDI patients who had co-morbidities. Significant elevation in Bacteroidaceae, Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceaewas consistently observed in pediatric rCDI responders, while Enterobacteriaceaedecreased, correlating with augmented complex carbohydrate degradation capacity. Recipient background disease was a significant risk factor influencing FMT outcomes. Special attention should be taken when considering FMT for pediatric rCDI patients with underlying co-morbidities.

16S ribosomal RNA-based analysis is the established standard for elucidating the composition of microbial communities. While short-read 16S rRNA analyses are largely confined to genus-level resolution at best, given that only a portion of the gene is sequenced, full-length 16S rRNA gene amplicon sequences have the potential to provide species-level accuracy. However, existing taxonomic identification algorithms are not optimized for the increased read length and error rate often observed in long-read data. Here we present Emu, an approach that uses an expectation–maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads. Results produced from simulated datasets and mock communities show that Emu is capable of accurate microbial community profiling while obtaining fewer false positives and false negatives than alternative methods. Additionally, we illustrate a real-world application of Emu by comparing clinical sample composition estimates generated by an established whole-genome shotgun sequencing workflow with those returned by full-length 16S rRNA gene sequences processed with Emu.

Shallow lakes, the most numerous waterbodies on Earth, are susceptible to climate warming and nutrient enrichment whose effects on the microbial functional potentials are not yet fully understood, however. Here, we applied a microarray‐based technology termed GeoChip 5.0 to investigate microbial functional genes at the beginning of April in shallow lake ecosystems simulated in mesocosms that have been undergoing nutrient enrichment and warming for 9 yr. Our results showed that warming exacerbated the impact of nutrient enrichment on microbial metabolic potentials and significantly elevated the microbial autotrophy potentials, carbon degradation potentials (e.g., starch, hemicellulose, cellulose, and chitin), and polyphosphate mobilization potentials. We also observed that warming enhanced the impacts of nutrient enrichment on microbial functional gene structure. The combination of warming and nutrient enrichment increased the deterministic effect from phytoplankton, causing higher interlinking of microbial functional genes involved in the carbon, nitrogen, phosphorus, and sulfur cycling in correlation‐based networks. Overall, we propose that the joint effect of warming and nutrient enrichment promoted the autotrophic carbon supply and the heterotrophic carbon demand and changed the carbon fluxes in the experimental mesocosms.

Ripened Pu-erh tea (RPT) has been shown to be an effective natural ingredient to defend against experimentally induced colitis. We hypothesized that RPT would alleviate dextran sulfate sodium (DSS) induced colitis via modulating intestinal microbiota. The effect of RPT on mice gut microbiota was evaluated using 16S rRNA gene amplicon sequencing, broad-spectrum antibiotic (ABX) treatment, and fecal microbiota transplantation (FMT). Pretreatment with RPT enhanced intestinal barrier function, reduced colonic and serum proinflammatory cytokine and macrophage infiltration, and preserved the resilience of gut microbiota in mice during a DSS challenge. Administration of either RPT-regulated or healthy control-derived gut microbiota showed similar protection against colitis, and such protection could not be recapitulated with fecal microbiota from ABX-treated mice, suggesting a key role of protective consortium in the disease protection. Mechanistically, cecal contents of short-chain fatty acids (SCFAs) and colonic peroxisome proliferator activated receptor-γ (PPAR-γ) expression in colitis mice increased significantly by RPT intervention. Collectively, RPT treatment improved DSS-induced colitis by partially reversing the dysbiosis state of gut microbiota, which might be associated with an increase in SCFA level and PPAR-γ expression.

Greenland and the Tibetan Plateau, also known as the third pole, are both cold environments where anthropogenic activities are relatively weak. There are multitudinous lakes in both regions, especially in Greenland, where small water bodies are continuously created as glaciers retreat. It is unclear whether the community structure and community assembly mechanisms of these water bodies are consistent with those of lakes in the Tibetan Plateau that were indirectly influenced by glaciers. In addition, due to different evolution times of the lakes, differences of microbial diversity, especially at the sub‐species level, are feasible but not yet reported. Microbial compositions in lake water and sediment were investigated based on high‐throughput sequencing of 16S rRNA genes. The oligotyping analysis revealed disproportionally distributed bacterial oligotypes in lakes between the two different areas. Moreover, microbial macrodiversity and intra‐operational taxonomic units microdiversity is significantly higher in Greenland lakes which experiencing early lake ontogeny. Microbial community composition and functionality significantly distinguished between the two regions and habitats. Multivariate analysis together with null model tests demonstrated that deterministic processes largely controlled the patterns of community structure in the sediment, while stochastic processes are more important for those in pelagic water in both regions. Microbes may be further subject to N and P co‐limitation in line with the evolution of lake ecosystems. The obtained results could help us understand evolution trajectory of these polar lakes under the future climate change scenario.

In warm monomictic lakes, the hypolimnion is important for accumulating and decomposing organic matter derived from surface production, and the regenerated nutrients will be supplied to the epilimnion through winter vertical mixing. So far, we know little about microbial community composition and function in the hypolimnion when the significant thermal stratification disappears. In this study, we investigated microbial community compositions and functional gene contents by means of metagenomics along a depth profile in the warm monomictic alpine Lake Fuxian during holomictic period. Overall, bacteria were the dominant microbial group at different water depths, while phages had their high relative abundance in the epilimnion. We observed slight thermal but strong chemical stratification even during this typical winter overturn. The anaerobic respiration with nitrate and sulfate as the terminal electron acceptors was accumulated at bottom of hypolimnionin as indicated through metabolic pathway reconstruction. We were able to get 440 metagenome‐assembled genomes (MAGs) and unraveled a high genomic diversity of freshwater pelagic microbiomes along this depth profile. We furthermore defined a new class of “Plancto_FXH1” of Planctomycetesfrom these MAGs, of which a distinct nitrate reduction operon was identified. Representatives of this phylum mainly thrive in the hypolimnion as previously suspected, but few lineages were detected in the epilimnion. In summary, metagenomics enabled us to find a new group of Planctomycetes, probably involved in denitrification in the hypolimnion in Lake Fuxian, which expand our knowledge on denitrifying bacterial diversity and their denitrification potential in deep freshwater lakes.

Shallow lakes often exhibit a macrophyte‐dominated (MD) clear state or a phytoplankton‐dominated (PD) turbid state, each of which has profound impacts on biological communities, including bacterioplankton community composition (BCC). However, the response of microbial functional gene structure (FGS) to regime shift has not been thoroughly elucidated to date. In this study, we used a functional gene array (GeoChip 5.0) in combination with high‐throughput sequencing of the bacterial 16S rRNA gene to investigate the FGS and BCC between the two regimes in Lake Taihu, a large shallow freshwater lake in China. A simultaneous change in the BCC and FGS was observed between the two different regimes. We observed higher numbers of bacterial operational taxonomic units and functional genes detected by the GeoChip 5.0 in the MD samples than in the PD samples. By performing network analyses, we observed stronger microbe‐microbe interactions but weaker functional gene interactions involved in nutrient metabolism in the MD community than in the PD community. We speculate that at higher concentrations of phosphorus, the domination of Microcystisbloom may weaken the interactions among microbial species by releasing more labile dissolved organic carbon, but enhance the selection and interactions of functional genes involved in carbon cycling in the PD community. In contrast, the lower levels of phosphorus may enhance microbe‐microbe interactions but weaken the interactions between the primary nutrients and particular genes. Overall, this study demonstrated contrasting patterns in the BCC and FGS between the MD and PD communities in a large shallow freshwater lake.

Objective:Laser acupuncture has become increasingly attractive in clinical practice, especially for patients with needle phobias well as elderly people and children. However, literature concerning the safety of laser acupuncture has been limited. This systematic review synthesizes the current available literature on the safety of laser acupuncture.Methods:Ovid MEDLINE,®Epub Ahead of Print, In-Process & Other Non-Indexed Citations Daily, Ovid Embase, Scopus, and EBM Reviews—Cochrane Central Register of Controlled Trials databases were searched for available randomized controlled trials (RCTs) on laser acupuncture. Safety data were extracted from the included studies. Adverse events (AEs) data were extracted and assessed in terms of severity and causality.Results:Of 737 articles, 21 RCTs were included. The majority of these RCTs reported that laser acupuncture was safe, without AEs; 6 trials reported AEs (including tingling, pain flare-ups, and transient fatigue). All AEs were mild and resolved spontaneously within 24 hours. The causal relationship between AEs and laser acupuncture was felt to be “certain” in 4 studies, “probable” in 1 study, and “possible” in 1 study. AEs were collected and monitored by evaluation methods in 7 trials: 5 with AE questionnaires, 1 with a checklist, and 1 with oral reports.Conclusions:Laser acupuncture appears to be a safe therapy associated with few mild and transient AEs. However, given the heterogeneity of current studies, large, well-designed placebo-controlled RCTs with rigorous evaluation methods are needed to assess the safety of laser acupuncture more completely.

The carbon burial and greenhouse gas emissions of lakes are pivotal in the global carbon cycle to offset or accelerate global warming. However, their balance or the magnitude of anthropogenic increase of carbon burial remains uncertain in global lakes. Here, we quantified the carbon sink dynamics and the sink-source balance in global lakes with effect-size metrics, that is, the log-response ratio of organic carbon burial between post-1950 and pre-1900 periods and the carbon balance ratio between carbon burial and greenhouse gas emissions, respectively. The organic carbon burial ratios revealed an average increase of 2.45 times in carbon burial rates during the Anthropocene, while the carbon balance ratios were negative in 82.68% of lakes, indicating that most lakes had lower burial rates than emission rates and acted as carbon sources rather than carbon sinks. The organic carbon burial ratios exhibited a significantly decreasing latitudinal trend and were mainly influenced by lake’s trophic state with the explained variation of 44.79%. They were also indirectly influenced by climate, lake morphometry, and catchment properties through their interactions with the lake’s trophic state. The carbon balance ratios, however, showed a nonsignificant latitudinal trend. They were primarily affected by lake catchment properties with the explained variation of 26.21% and were also indirectly affected by climate variables via the interactions with catchment properties. Overall, our study highlights that human activities such as lake eutrophication and catchment changes have altered the carbon sink and source in global lakes during the Anthropocene, and are essential drivers for future evaluations of lake carbon budgets.

The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata(the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis(AOA), and Nitrosomonas nitrosaNm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinatawas supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinatawas likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

Acidic coal mining lakes (AMLs) are characterized by low pH, low biodiversity, and high concentrations of sulfate and metals. However, to date, knowledge is inadequate on the involvement of the aquatic microbial functions in biogeochemical processes of an AML. Here, we use a natural weakly alkaline lake (WAL) as a reference to investigate the functional gene structure of microbial communities in the aerobic surface waters of an AML by using a metagenomic approach with GeoChip‐based functional gene arrays (GeoChip 5.0). We found significant differences in the compositions of the microbial functional genes between the two lake types. The AML had significantly lower gene diversity than the WAL, and the functional genes detected in the AML were almost a subset of those in the WAL. We also found significant differences in the microbial metabolic potentials between the two lake types. In the AML, the microbial communities had higher functional capacities in phosphorus‐utilization, sulfur oxidation, and metal‐detoxification and had lower metabolic potentials of carbon and nitrogen fixation, and the degradation of starch, hemicellulose, cellulose, chitin, and lignin than those in the WAL. By performing null model and network analyses, we observed stronger deterministic effects of the functional gene assemblages and greater clustering among the co‐occurring functional genes in the AML than those in the WAL. Altogether, we demonstrated contrasting patterns of freshwater microbial metabolic potentials and functional gene interactions between an AML and a WAL, which may advance the understanding of microbial functional response to acidification in freshwater lakes.

Bacterial communities comprise large numbers of species and normally include a few abundant taxa and many rare taxa. These two subcommunities may have fundamentally different ecological roles, and it is not clear whether their diversity patterns along elevation gradients vary. In this study, we investigated the diversity of bacterioplankton and their subcommunities, i.e., abundant and rare bacterioplankton, in lakes across gradual elevations from 525 m to 4652 m at Siguniang Mountain in western China via the high‐throughput sequencing of bacterial 16S rRNA genes. Elevation showed strong influence on bacterioplankton community composition (BCC) and that the dissimilarity of BCC increased with increasing differences in elevation. However, the elevational distance‐decay rate of abundant bacterioplankton was higher than that of rare bacterioplankton. Abundant bacterioplankton were more sensitive to changes of environmental factors than rare bacterioplankton. We observed a marginal increase in alpha diversity, estimated as operational taxonomic unit richness and phylogenetic diversity, of overall bacterioplankton with increasing elevation. The alpha diversity of abundant bacterioplankton decreased monotonically with elevation; in contrast, the alpha diversity of rare bacterioplankton increased monotonically with elevation. Null model tests indicated that environmental filtering played a dominant role in overall bacterioplankton community assembly along the elevation gradient, while there was decreased contribution of environmental selection to rare bacterioplankton in smaller lakes at higher elevation. Our results revealed that abundant bacterioplankton followed the general elevation diversity theory commonly found for plants and animals in freshwater lakes, whereas rare bacterioplankton did not follow this tenet.

A new method combined continuum topology with discrete truss is proposed for truss optimization. The optimized material distribution is obtained by means of continuum topology optimization and then transformed into initial truss. Based on the element principal stress and 8-neighborhood elements of continuum, force flow path extraction method is presented to obtain the initial truss layout. For section size optimization, criterion is deduced from a mathematical model by Lagrange multiplier method. Leveraging the free-form nature of continuum, this method can avoid the restriction of traditional ground structure. And it can achieve a better solution with less mass, smaller deformation and more uniform stress.

The current climate warming and eutrophication are known to interactively threaten freshwater biodiversity; however, the interactive effects on lacustrine bacterioplankton diversity remain to be determined. Here, we analyzed the spring bacterioplankton community composition (BCC) in 24 outdoor, flow-through mesocosms (mimicking shallow lake environments) under 3 temperature scenarios and 2 nutrient regimes. Our results revealed that neither long-term warming (8.5 years) nor nutrient enrichment had significant effects on bacterioplankton alpha diversity, whereas long-term enhanced warming (elevated 50% above the IPCC A2 climate scenario) and nutrient enrichment in combination increased bacterioplankton beta diversity. We also found that BCC shifted significantly under enhanced warming and nutrient-enriched conditions towards decreased relative abundances of Actinobacteria, Bacteroidetesand Betaproteobacteria, whereas the percentages of Cyanobacteria, total rare phyla and unclassified phyla significantly increased. Null-model tests indicated that deterministic processes played a more important role than stochastic processes in determining BCC. However, the relative importance of stochasticity, primarily ecological drift, was enhanced and contributed to the increased beta diversity of BCC under enhanced warming and nutrient-enriched conditions. Overall, our study suggests that the synergetic effects of warming and nutrient enrichment may result in high variability in the composition of bacterioplankton communities in lacustrine water bodies.

The current climate warming and eutrophication are known to interactively threaten freshwater biodiversity; however, the interactive effects on lacustrine bacterioplankton diversity remain to be determined. Here, we analyzed the spring bacterioplankton community composition (BCC) in 24 outdoor, flow-through mesocosms (mimicking shallow lake environments) under 3 temperature scenarios and 2 nutrient regimes. Our results revealed that neither long-term warming (8.5 years) nor nutrient enrichment had significant effects on bacterioplankton alpha diversity, whereas long-term enhanced warming (elevated 50% above the IPCC A2 climate scenario) and nutrient enrichment in combination increased bacterioplankton beta diversity. We also found that BCC shifted significantly under enhanced warming and nutrient-enriched conditions towards decreased relative abundances of Actinobacteria, Bacteroidetes and Betaproteobacteria, whereas the percentages of Cyanobacteria, total rare phyla and unclassified phyla significantly increased. Null-model tests indicated that deterministic processes played a more important role than stochastic processes in determining BCC. However, the relative importance of stochasticity, primarily ecological drift, was enhanced and contributed to the increased beta diversity of BCC under enhanced warming and nutrient-enriched conditions. Overall, our study suggests that the synergetic effects of warming and nutrient enrichment may result in high variability in the composition of bacterioplankton communities in lacustrine water bodies.