Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants

Wu, Linwei; Ning, Daliang; Zhang, Bing; Yong, Li; Zhang, Ping; Shan, Xiaoyu; Zhang, Qiuting; Brown, Mathew; Li, Zhenxin; Nostrand, Joy D. Van; Ling, Fangqiong; Xiao, Naijia; Zhang, Ya; Vierheilig, Julia; Wells, George F.; Yang, Yunfeng; Deng, Ye; Tu, Qichao; Wang, Aijie; Zhang, Tong; He, Zi; Keller, Jürg; Nielsen, Per Halkjær; Alvarez, Pedro J. J.; Criddle, Craig S.; Wagner, Michael; Tiedje, James M.; He, Qiang; Curtis, Thomas P.; Stahl, David A.; Alvarez‐Cohen, Lisa; Rittmann, Bruce E.; Wen, Xianghua; Zhou, Jizhong

doi:10.1038/s41564-019-0617-0

Cited by 19 publications

(16 citation statements)

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“…b OTUs’ rrn copy number of the abundant, intermediate, and rare biospheres. The OTUs were classified based on their relative abundance and occurrence frequency: (i) abundant biosphere, OTUs with relative abundance ≥0.1% 53 in >50% 26 samples, and occurred in more than 80% 26 , 54 samples; (ii) rare biosphere, OTUs with relative abundance <0.1% in all samples; (iii) intermediate biosphere, OTUs other than those belonging to the rare biosphere or abundant biosphere. The bars indicate mean values and the error bars indicate standard errors.…”

Section: Resultsmentioning

confidence: 99%

“…The ribosomal RNA gene operon ( rrn ) copy number in bacterial genomes is a phylogenetically conserved trait at the genus and species levels 22 , which can predict the growth rate and nutrient utilization efficiency for individual organisms well 10 , 11 , 23 . Accordingly, we examined whether the average rrn copy number of community members was positively correlated with environmental nutrient contents, which was verified in natural 24 and engineered systems 25 , 26 . We also mathematically modeled a microbial community as a network to explore potential ecological interactions with nutrient availability.…”

Section: Introductionmentioning

confidence: 97%

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Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

et al. 2022

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Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

et al. 2022

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“…Although several previous studies had investigated ARG pollution in natural sediments, mainly focusing on rivers, 63 fish farms, 64 estuaries, 19 coastal, 65 and deep sea, 20 to the best of our knowledge, there has been no related study to profile the probable ARG pollution in hadal sediments and diverse patterns with different depths; however, a recent study identified the MT as a major depository for plastic pollution 66 indicating its potential to receive pollutants. Thus, our novel insights of a sudden high ARG abundance and diversity motivated us to suspect whether With this concern and hypothesis, the Bayesian-modeling classification SourceTracker, 50 which had been frequently used for tracing the source of bacterial communities 67 and genes, 68 was employed to predict potential sources of ARGs in the MT sediments, and we observed a significant ARG origin from human feces in the surface layer of the MT sediments at 2−3 cm (63.6%) and 0−2 cm (46.1%), but zero below 4 cm. Although the prediction results were highly data-and modeldependent, we collected 584 metagenomic data sets for source modeling covering as many ecotypes and continents as possible, and we could get some clues on their probable contributors from the prediction results.…”

Section: Resultsmentioning

confidence: 99%

“…With this concern and hypothesis, the Bayesian-modeling classification SourceTracker, which had been frequently used for tracing the source of bacterial communities and genes, was employed to predict potential sources of ARGs in the MT sediments, and we observed a significant ARG origin from human feces in the surface layer of the MT sediments at 2–3 cm (63.6%) and 0–2 cm (46.1%), but zero below 4 cm. Although the prediction results were highly data- and model-dependent, we collected 584 metagenomic data sets for source modeling covering as many ecotypes and continents as possible, and we could get some clues on their probable contributors from the prediction results.…”

Section: Results and Discussionmentioning

confidence: 99%

Evidence for Long-Term Anthropogenic Pollution: The Hadal Trench as a Depository and Indicator for Dissemination of Antibiotic Resistance Genes

Yang

Liu

et al. 2021

Environ. Sci. Technol.

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Knowledge of the distribution and dissemination of antibiotic resistance genes (ARGs) is essential for understanding anthropogenic impacts on natural ecosystems. The transportation of ARGs via aquatic environments is significant and has received great attention, but whether there has been anthropogenic ARG pollution to the hadal ocean ecosystem has not been well explored. For investigating ecological health concerns, we profiled the ARG occurrence in sediments of the Mariana Trench (MT) (10 890 m), the deepest region of the ocean. Metagenomic-based ARG profiles showed a sudden increase of abundance and diversity in the surface layer of MT sediments reaching 2.73 × 10–2 copy/cell and 81 subtypes, and a high percentage of ∼63.6% anthropogenic pollution sources was predicted by the Bayesian-modeling classification method. These together suggested that ARG accumulation and anthropogenic impacts have already permeated into the bottom of the deepest corner on the earth. Moreover, six ARG-carrying draft genomes were retrieved using a metagenomic binning strategy, one of which assigned as Streptococcus was identified as a potential bacterial host to contribute to the ARG accumulation in MT, carrying ermF, tetM, tetQ, cfxA2, PBP-2X, and PBP-1A. We propose that the MT ecosystem needs further long-term monitoring for the assessment of human impacts, and our identified three biomarkers (cfxA2, ermF, and mefA) could be used for the rapid monitoring of anthropogenic pollution. Together our findings imply that anthropogenic pollution has penetrated into the deepest region of the ocean and urge for better pollution control to reduce the risk of ARG dissemination to prevent the consistent accumulation and potential threat to the natural environment.

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“…This result allows us to screen different species as indigenous internal standards for different sample groups if there are no common species in all samples because of sample diversity. For example, no single species was shared between 1,186 samples from global wastewater treatment plants, but Macellibacteroides fermentans was detected in all 11 wastewater treatment plants sampled from South America (29). Thus, this species could be a candidate for use as the indigenous internal standard for the corresponding sample group.…”

Section: Discussionmentioning

confidence: 99%

Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards

2020

Appl Environ Microbiol

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Identifying the functional microbes in spontaneous food fermentation is important for improving food quality. To identify the key flavor producers in Chinese liquor fermentation, we propose a novel quantitative microbiome profiling method that uses indigenous internal standards to normalize high-throughput amplicon sequencing results. We screened Lactobacillus acetotolerans and Lactobacillus jinshani as indigenous internal standards based on their high distribution frequencies and relative abundances. After determining the absolute abundance of indigenous internal standards using quantitative PCR with species-specific primers, the liquor-fermented bacterial community and its dynamics were better characterized by internal standards normalization. Based on quantitative microbiome profiling, we identified that Lactobacillus was a key flavor producer correlated with eight flavor compounds. Metatranscriptomic analysis indicated that Lactobacillus was active in transcribing genes involving the biosynthesis of flavor compounds and their precursors. This work has developed a novel and extensible absolute quantification method for microbiota that will alleviate concerns in the statistical analyses based on relative microbiome profiling, and shed insights into the function of Lactobacillus in food fermentation. It can potentially be applied to other microbial ecology studies. IMPORTANCE In this study, we developed a novel strategy using indigenous internal standards to normalize the high-throughput amplicon sequencing results. We chose two Lactobacillus species as indigenous internal standards and characterized the absolute abundance of the bacterial community. Further, we identified Lactobacillus as the key flavor producer using quantitative microbiome profiling combined with multivariate statistics and metatranscriptomic analysis. This work developed a novel strategy for absolute quantitative abundance analysis of microbiota and expanded our understanding of the role of Lactobacillus in food fermentation.

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Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants

Cited by 19 publications

References 0 publications

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Evidence for Long-Term Anthropogenic Pollution: The Hadal Trench as a Depository and Indicator for Dissemination of Antibiotic Resistance Genes

Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards

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