Frontiers in Microbiology最新文献

{"title":"Improvement of silage characteristics of <i>Lactobacillus salivarius</i> HMC4 and improvement of silage quality of king grass.","authors":"Jinsong Yang, Songsong Zhao, Wenbo Zhi, Tianyu Lu, Huahua Qiao, Wei Liu, Ying Dou, Haisheng Tan, Hanlin Zhou","doi":"10.3389/fmicb.2024.1468577","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1468577","url":null,"abstract":"<p><p>The effect of HMC4 produced by protoplast fusion on silage was studied. The silage formula was composed of heterozygote HMC4 (Group C), parent Lactobacillus (Group A) and a combination of two parents (Group B). The fermentation quality and microbial composition of each batch of silage were evaluated. The results showed that the propionic acid concentration in group C was the lowest, but the organic acid content in feed was significantly increased. Groups B and C had slightly lower crude fiber levels than group A, while groups A and C had higher levels of soluble sugars. The dynamic observation of C group showed that the nutrient composition of feed changed gradually with the extension of silage period. High-throughput sequencing revealed fluctuations in microbial composition before and after silage. Over time, Lactobacillus became the dominant strain and its numbers steadily increased.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1468577"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>SlDLK2</i> receptor, involved in the control of arbuscular mycorrhizal symbiosis, regulates hormonal balance in roots.","authors":"Martín Ramos-Alvelo, Nuria Molinero-Rosales, María Isabel Tamayo-Navarrete, Sanja Ćavar Zeljković, Petr Tarkowski, José Manuel García-Garrido, Tania Ho-Plágaro","doi":"10.3389/fmicb.2024.1472449","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1472449","url":null,"abstract":"<p><p>Arbuscular mycorrhiza (AM) represents a symbiotic mutualistic association between most land plants and <i>Glomeromycota</i> fungi. AM fungi develops specialized intraradical and highly branched structures, called arbuscules, where bidirectional exchange of nutrients between plant and fungi partners occurs, improving plant growth and fitness. Transcriptional reprogramming and hormonal regulation are necessary for the formation of the arbuscules. <i>SlDLK2</i>, a member of the third clade from the DWARF14 family of <i>α</i>, <i>β</i>-hydrolases closely related to the strigolactone receptor D14, is a negative regulator of arbuscule branching in tomato, but the underlying mechanisms are unknown. We explored the possible role of <i>SlDLK2</i> on the regulation of hormonal balance. RNA-seq analysis was performed on roots from composite tomato plants overexpressing <i>SlDLK2</i> and in control plants transformed with the empty vector. Analysis of transcriptomic data predicted that significantly repressed genes were enriched for genes related to hormone biosynthesis pathways, with a special relevance of carotenoid/apocarotenoid biosynthesis genes. Stable transgenic <i>SlDLK2</i> overexpressing (OE) tomato lines were obtained, and hormone contents were analyzed in their roots and leaves. Interesting significant hormonal changes were found in roots of <i>SlDLK2</i> OE lines with respect to the control lines, with a strong decrease on jasmonic acid and ABA. In addition, <i>SlDLK2</i> OE roots showed a slight reduction in auxin contents and in one of the major strigolactones in tomato, solanacol. Overall, our results suggest that the negative regulation of AM symbiosis by <i>SlDLK2</i> is associated with the repression of genes involved in the biosynthesis of AM-promoting hormones.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1472449"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effects of different doses of compound enzyme preparations on the production performance, meat quality and rumen microorganisms of yak were studied by metagenomics and transcriptomics.","authors":"Chenyang Zhang, YongFu La, Xiaoming Ma, Pingcuo Zhandui, Xiaoyun Wu, Xian Guo, Ping Yan, Luosan Dunzhu, Chunnian Liang","doi":"10.3389/fmicb.2024.1491551","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1491551","url":null,"abstract":"<p><p>Yak (<i>Bos grunniens</i>) is a large ruminant endemic to the Tibetan plateau. The addition of enzyme complexes to feed can significantly improve their growth performance. Therefore, studying the effects of ruminant compound enzyme preparations dosage on yak rumen microorganisms and production performance is crucial to promoting the development of the yak industry. This study aimed to determine the effects of feeding yaks with different doses of ruminant enzyme compounds on the performance, meat quality, and rumen microorganisms of yaks. Three kinds of experimental diets with doses of 0.5 g/kg (LE group), 1 g/kg (ME group), and 2 g/kg (HE group) were selected to determine the growth index, meat quality, serum biochemical indexes, rumen fluid pH and other indexes of the three experimental groups. Metagenomics studies were used to investigate the differences in rumen microbial composition and function among yak groups, and transcriptome sequencing of the longest dorsal muscle was performed to reveal the expression of differential genes among different groups. It was determined that the levels of dietary enzyme complexes significantly affected growth performance, rumen fluid pH, and serum biochemical indices. At the phylum level, the dominant phylum in all three treatment groups was Bacteroidota, Bacillota, Kiritimatiellota, and Pseudomonadota. At the genus level, Prevotella, Methanobrevibacter, Oscillibacter. Fibrobacter showed statistically significant differences in abundance (<i>p</i> < 0.05). CAZymes family analysis revealed significant differences in GHs, CTs, and CEs among the three groups. Genome-wide differential gene expression in the longest muscle of the yak back was analyzed by RNA-seq between the three experimental groups. Some DEGs were found to be enriched in the ECM, PI3K-Akt, PPAR, and protein digestion and absorption receptor pathways. Combined metagenomics and transcriptomics analyses revealed that some microorganisms were significantly associated with the genes COL11A1, POSTN, and PTHLH, which are involved in growth metabolism. In summary, this study investigated the effects and interrelationships of ruminant complex enzymes on yak performance, meat quality, and rumen environment. The results of this study provide a scientific basis for adding ruminant enzymes to yaks.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1491551"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11670318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Possible biocontrol of bacterial blight in pomegranate using native endophytic <i>Bacillus</i> spp. under field conditions.","authors":"N Manjunatha, Somnath S Pokhare, Ruchi Agarrwal, Nripendra V Singh, Jyotsana Sharma, Mallikarjun M Harsur, Rajiv A Marathe","doi":"10.3389/fmicb.2024.1491124","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1491124","url":null,"abstract":"<p><p>Bacterial blight in pomegranate, caused by <i>Xanthomonas citri</i> pv. <i>punicae</i> (Xcp), is one of the most devastating diseases, leading to substantial economic losses in pomegranate production. Methods for blight management in pomegranate production are scarce and not well established. To date, the major control strategy is targeting the pathogen with antibiotics and copper-based compounds. However, excessive use of antibiotics has resulted in the development of antibiotic resistance in the field population of Xcp. Hence, as a means of eco-friendly and sustainable management of bacterial blight, the use of native endophytes was investigated under field conditions in the current study. Endophytic bacteria were isolated from micro-propagated nodal explants of pomegranate and were identified as <i>Bacillus haynesii</i>, <i>B. tequilensis</i>, and <i>B. subtilis</i>. They were found to produce volatiles that inhibited Xcp growth during <i>in vitro</i> antibiosis assay. GC-MS-based volatile profiling revealed the presence of several bioactive compounds with reported antimicrobial activities. These endophytes (CFU of 10⁸/mL) were then spray-inoculated on leaves of 6-month-old pomegranate plants in the polyhouse. They were found to induce ROS-scavenging enzymes such as catalase and peroxidase. This alteration was a manifestation of host tissue colonization by the endophytes as ROS scavenging is one of the mechanisms by which endophytes colonize the host plants. Furthermore, two-season field trials with endophytes for blight control resulted in a reduction of disease index by 47-68%, which was considerably higher than the reduction due to the chemical immune modulator (2-bromo-2-nitro-1, 3-propanediol) currently being recommended for blight control. In addition, these endophytes also exhibited reduced sensitivity to this immune modulator; thus, the current study advocates the use of <i>B. haynesii</i>, <i>B. subtilis</i>, and <i>B. tequilensis</i> as biocontrol agents for bacterial blight of pomegranate either alone or as a part of integrated disease management.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1491124"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and distinction of <i>Enterococcus faecium</i> and <i>Enterococcus lactis</i> in traditional Montenegrin brine cheeses and salamis.","authors":"Beatriz Daza Prieto, Nadja Raicevic, Aleksandra Martinovic, Johann Ladstätter, Ivana Zuber Bogdanovic, Anika Schorpp, Anna Stoeger, Robert L Mach, Werner Ruppitsch, Adriana Cabal","doi":"10.3389/fmicb.2024.1473938","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1473938","url":null,"abstract":"<p><strong>Introduction: </strong><i>Enterococcus faecium</i> is a widespread acid-lactic bacterium found in the environment, humans, and animal microbiota, and it also plays a role in the production of traditional food. However, the worldwide emergence of multidrug-resistant <i>E. faecium</i> strains represents a major public health threat and is the primary reason that the genus <i>Enterococcus</i> is not recommended for the Qualified Presumption of Safety (QPS) list of the European Food Safety Authority (EFSA), raising concerns about its presence in food products.</p><p><strong>Methods: </strong>In this study, 39 <i>E. faecium</i> and 5 <i>E. lactis</i> isolates were obtained from artisanal brine cheeses and dry sausages, sourced from 21 different Montenegrin producers. The isolates were collected following the ISO 15214:1998 international method and processed for whole-genome sequencing (WGS).</p><p><strong>Results: </strong>Genome analysis based on core genome multilocus sequence type (cgMLST) revealed a high diversity among isolates. Furthermore, the isolates carried antimicrobial resistance genes; the virulence genes <i>acm</i>, <i>sgrA</i>, and <i>ecbA</i>; the bacteriocin genes <i>Enterolysin A</i>, <i>Enterocin A, Enterocin P, Duracin Q, Enterocin B, Bacteriocin 31, Enterocin EJ97, Sactipeptides</i>, and <i>Enterocin SEK4</i>; the secondary metabolite genes <i>T3PKS</i>, cyclic lactone autoinducer, RiPP-like, and <i>NRPS</i> and a maximum of eight plasmids.</p><p><strong>Conclusion: </strong>This study highlights the need for careful monitoring of <i>E. faecium</i> and <i>E. lactis</i> strains in food to ensure they do not pose any potential risks to consumer safety.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1473938"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668737/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Porcine peritoneal macrophages are susceptible to porcine reproductive and respiratory syndrome virus infection.","authors":"Kassandra Durazo-Martinez, Jayeshbhai Chaudhari, Sushmita Kumari, Hiep L X Vu","doi":"10.3389/fmicb.2024.1505900","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1505900","url":null,"abstract":"<p><p>Previous studies have suggested that porcine peritoneal macrophages (PPMs) are resistant to PRRSV infection, whereas porcine alveolar macrophages (PAMs) are highly susceptible. This contrast is intriguing, as both cell types belong to the same monocyte/macrophage family. The current study aimed to investigate the host factors contributing to the differing susceptibility of PPMs and PAMs to PRRSV infection. We found that PPMs exhibit a higher frequency of CD14⁺ cells compared to PAMs, suggesting a more immature macrophage phenotype in PPMs. Importantly, PPMs expressed both CD163 and CD169, the key receptors for PRRSV entry, although the frequency and intensity of CD163 and CD169 expression were lower in PPMs than in PAMs. Despite these differences, PPMs were susceptible to both PRRSV-1 and PRRSV-2 isolates. Notably, PPMs susceptibility increased 10-fold when the cells were cultured for 1 day before infection. PRRSV infection in PPMs was dependent on CD163, as pretreatment with an anti-CD163 antibody significantly reduced infection. Overall, our results demonstrate that PPMs are susceptible to PRRSV infection, thereby expanding the understanding of PRRSV tropism.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1505900"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Fundamental and practical advances in bioremediation of emerging pollutants as add-on treatments for polluted waters.","authors":"Francis Hassard, Victor Castro-Gutierrez","doi":"10.3389/fmicb.2024.1514698","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1514698","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1514698"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of <i>Salmonella</i> isolated from surface water and animal sources in Chile reveals new T6SS effector protein candidates.","authors":"Fernando A Amaya, Carlos J Blondel, Felipe Reyes-Méndez, Dácil Rivera, Andrea Moreno-Switt, Magaly Toro, Consuelo Badilla, Carlos A Santiviago, David Pezoa","doi":"10.3389/fmicb.2024.1496223","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1496223","url":null,"abstract":"<p><p>Type VI Secretion Systems (T6SS), widely distributed in Gram-negative bacteria, contribute to interbacterial competition and pathogenesis through the translocation of effector proteins to target cells. <i>Salmonella</i> harbor 5 pathogenicity islands encoding T6SS (SPI-6, SPI-19, SPI-20, SPI-21 and SPI-22), in which a limited number of effector proteins have been identified. Previous analyses by our group focused on the identification of candidate T6SS effectors and cognate immunity proteins in <i>Salmonella</i> genomes deposited in public databases. In this study, the analysis was centered on <i>Salmonella</i> isolates obtained from environmental sources in Chile. To this end, bioinformatics and comparative genomics analyses were performed using 695 genomes of <i>Salmonella</i> isolates representing 44 serotypes obtained from surface water and animal sources in Chile to identify new T6SS effector proteins. First, T6SS gene clusters were identified using the SecreT6 server. This analysis revealed that most isolates carry the SPI-6 T6SS gene cluster, whereas the SPI-19 and SPI-21 T6SS gene clusters were detected in isolates from a limited number of serotypes. In contrast, the SPI-20 and SPI-22 T6SS gene clusters were not detected. Subsequently, each ORF in the T6SS gene clusters identified was analyzed using bioinformatics tools for effector prediction, identification of immunity proteins and functional biochemical prediction. This analysis detected 20 of the 37 T6SS effector proteins previously reported in <i>Salmonella</i>. In addition, 4 new effector proteins with potential antibacterial activity were identified in SPI-6: 2 Rhs effectors with potential DNase activity (PAAR-RhsA-NucA_B and PAAR-RhsA-GH-E) and 2 effectors with potential RNase activity (PAAR-RhsA-CdiA and RhsA-CdiA). Interestingly, the repertoire of SPI-6 T6SS effectors varies among isolates of the same serotype. In SPI-19, no new effector protein was detected. Of note, some Rhs effectors of SPI-19 and SPI-6 present C-terminal ends with unknown function. The presence of cognate immunity proteins carrying domains present in <i>bona fide</i> immunity proteins suggests that these effectors have antibacterial activity. Finally, two new effectors were identified in SPI-21: one with potential peptidoglycan hydrolase activity and another with potential membrane pore-forming activity. Altogether, our work broadens the repertoire of <i>Salmonella</i> T6SS effector proteins and provides evidence that SPI-6, SPI-19 and SPI-21 T6SS gene clusters harbor a vast array of antibacterial effectors.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1496223"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kaempferol restores the susceptibility of ESBLs <i>Escherichia coli</i> to Ceftiofur.","authors":"Peng-Cheng Li, Yin-Chao Tong, Xing-Lan Xiao, Yun-Peng Fan, Wu-Ren Ma, Ying-Qiu Liu, Shen Zhuang, Su-Zhu Qing, Wei-Min Zhang","doi":"10.3389/fmicb.2024.1474919","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1474919","url":null,"abstract":"<p><strong>Introduction: </strong>The development of extended-spectrum-beta-lactamase (ESBLs) <i>Escherichia coli</i> (<i>E. coli</i>) has become a global threat to public health. An alternative strategy to alleviate this is identifying potential natural compounds to restore antibiotic activity against ESBLs <i>E. coli</i>. This study aimed to find a possible compound to restore ESBLs <i>E. coli</i> sensitivity to ceftiofur.</p><p><strong>Methods: </strong>The synergistic effect of kaempferol and ceftiofur against ESBLs <i>E. coli</i> was investigated by checkerboard assays, time-kill, growth curves, and scanning electronic microscope. The impact of kaempferol with ceftiofur on the biofilm of ESBLs <i>E. coli</i> was evaluated by crystal violet staining and laser scanning confocal microscopy and this study also assessed the effect of kaempferol on the initial adhesion and aggregation of <i>E. coli</i> (SY20) by examining motility, adhesion, and surface characteristics. The RT-qPCR was used to determine the effect of kaempferol on the expression of genes related to the <i>LuxS</i>/AI-2 quorum sensing system in ESBLs <i>E. coli</i>, and the effect of kaempferol on AI-2 signaling molecules was determined by molecular docking and bioassay. The impact of kaempferol on the activity of <i>bla_CTX-M-27</i> protein was determined by RT-qPCR, molecular docking, and nitrofen experiments, the results were further verified by transcriptome analysis. The mouse infection model was established, and the inhibitory mechanism of kaempferol with ceftiofur on bacteria in vivo was further verified by HE staining and immunohistochemistry.</p><p><strong>Results and discussion: </strong>Kaempferol with ceftiofur exerts synergistic antibacterial and bactericidal effects on ESBLs <i>E. coli</i> by influencing β-lactamase activity, biofilm formation, and <i>LuxS</i>/AI-2 QS system. In vivo, kaempferol protected the small intestinal villi from the damage of ESBLs <i>E. coli</i>. Furthermore, kaempferol fully restores the activity of ceftiofur in animal infection models by relieving the TLR₄/NF-κb pathway. In conclusion, the sensitivity of ESBLs <i>E. coli</i> to ceftiofur in vitro and in vivo could be enhanced by kaempferol, which showed that kaempferol may be a kind of antibiotic adjuvant.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1474919"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatiotemporal distributions, co-occurrence networks, and assembly mechanisms of the bacterial community in sediments of the Yangtze River: comprehensive insights into abundant and rare taxa.","authors":"Guohua Zhang, Shufeng Liu, Wenran Du, Yinghao Li, Zongzhi Wu, Tang Liu, Yichu Wang","doi":"10.3389/fmicb.2024.1444206","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1444206","url":null,"abstract":"<p><p>Sediments are key reservoirs for rare bacterial biospheres that provide broad ecological services and resilience in riverine ecosystems. Compared with planktons, there is a lack of knowledge regarding the ecological differences between abundant and rare taxa in benthic bacteria along a large river. Here, we offer comprehensive insights into the spatiotemporal distributions, co-occurrence networks, and assembly processes of three divided categories namely always rare taxa (ART), conditionally rare taxa (CRT), and conditionally rare and abundant taxa (CRAT) in sediments covering a distance of 4,300 km in the Yangtze River. Our study demonstrated that ART/CRT contributed greatly to the higher Chao-1 index, Shannon-Wiener index, and phylogenetic alpha diversity of benthic bacteria in autumn than in spring. ART showed high overall beta diversity, and CRT/CRAT exhibited more significant distance-decay patterns than ART in both seasons, mainly corresponding to macroscopic landform types. CRT predominated the nonrandom co-occurrence network, with 97% of the keystone species mostly affiliated with Acidobacteriota flourishing in the lower-reach plain. Two selection processes had the greatest influences on the assembly of CRT (74.7-77.6%), whereas CRAT were driven primarily by dispersal limitation (74.9-86.8%) and ART were driven by heterogeneous selection (33.9-48.5%) and undominated stochasticity (32.7-36.5%). Natural factors such as river flow and channel slope exhibited more significant correlations with community variation than nutrients in all three groups, and total organic carbon mediated the balance among the distinct assembly processes of the ART and CRT in both seasons. Taken together, these results provide an improved ecological understanding of the discrepancy in biogeographic patterns between abundant and rare bacterial taxa in the sediments of Asia's largest river.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1444206"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142893429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}