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Klick SA, Pitula JS, Collick AS, May EB, Pisani O. Bacterial diversity in agricultural drainage ditches shifts with increasing urea-N concentrations. FEMS Microbiol Ecol 2024:fiae057. [PMID: 38609337 DOI: 10.1093/femsec/fiae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Urea-based fertilizers applied to crop fields can enter surface waters of adjacent agricultural drainage ditches and contribute to nitrogen (N) loading to nearby watersheds. Management practices applied in drainage ditches promote N removal by the microbial communities, but little is known about the impacts of excess urea fertilizer from crop fields on the microbial diversity in these ditches. In 2017, sediments from drainage ditches next to corn and soybean fields were sampled to determine if fertilizer application and high urea-N concentrations alters bacterial diversity and urease gene abundances. A mesocosm experiment was paired with a field study to determine which bacterial groups respond to high urea-N concentrations. The bacterial diversity in the ditch next to corn fields was significantly different from the other site. The bacterial orders of Rhizobiales, Bacteroidales, Acidobacteriales, Burkholderiales, and Anaerolineales were most abundant in the ditch next to corn and increased after the addition of urea-N (0.5 mg N L-1) during the mesocosm experiment. The results of our study suggests that urea-N concentrations >0.07 mg N L-1, which are higher than concentrations associated with downstream harmful algal blooms, can lead to shifts in the bacterial communities of agricultural drainage ditches.
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Affiliation(s)
- Sabrina A Klick
- USDA - ARS, Southeast Watershed Research Laboratory, Tifton, GA 31793, USA
| | - Joseph S Pitula
- University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | | | - Eric B May
- University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Oliva Pisani
- USDA - ARS, Southeast Watershed Research Laboratory, Tifton, GA 31793, USA
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Zhang L, Yuan L, Xiang J, Liao Q, Zhang D, Liu J. Response of the microbial community structure to the environmental factors during the extreme flood season in Poyang Lake, the largest freshwater lake in China. Front Microbiol 2024; 15:1362968. [PMID: 38633691 PMCID: PMC11021660 DOI: 10.3389/fmicb.2024.1362968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024] Open
Abstract
Background Poyang Lake is the largest freshwater lake in China, and there are several studies on the composition and diversity of bacteria in Poyang Lake, while few quantitative studies were carried out on the response of the bacterial community to environmental factors during the extreme flood season in Poyang Lake. Methods The connected-lake heterogeneity of bacterial community composition (BCC) was investigated in Poyang Lake during the flood season in 2020. Illumina high-throughput sequencing technology was used in this study. Results The bacterial community structure in the water was different from that in the sediment of Poyang Lake during extreme flood seasons. The bacterial diversity in water was much lower than that in sediment. In the water column, the dominant phyla were Actinobacteriota, while the composition of bacteria in sediment was more complex than that in water, and the dominant phyla in sediment were Proteobacteria, Chloroflexi, Acidobacteriota, and Actinobacteriota. The bacterial diversity in the water of Poyang Lake showed seasonal dynamics, while no seasonal variation of bacterial communities in sediment was observed. The bacterial community structure in the sediment from the two bays and channel areas of Poyang Lake can be distinguished from each other. The microbial diversity in sediment gradually increased from the Sancha Bay to the Zhouxi Bay and then to the channel, but the total nitrogen (TN) concentration in sediment (STN) and the total phosphorus (TP) concentration in sediment (STP) showed opposite trends. This might be due to the anthropogenic disturbances from the extreme flood. The bacterial community structure in, water column was significantly correlated with WT, NH4-N, STP, SOM, Chl a, DO, TP, and Eh, while the bacterial community structure in sediment was significantly correlated with SOM and STP. Conclusion The bacterial community structure in water was greatly different from that in sediment in Poyang Lake during extreme flood seasons. The bacterial community structure in the water column was not only sensitive to the geochemical characteristics of the water but also affected by some nutrient concentrations in the sediment. During the wet seasons, bacterial diversity was only affected by SOM and STP.
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Affiliation(s)
- Li Zhang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Lijuan Yuan
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Jianjun Xiang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Qiegen Liao
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Dawen Zhang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Jutao Liu
- Jiangxi Provincial Institute of Water Sciences, Nanchang, Jiangxi, China
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Pagac MP, Stalder M, Campiche R. Menopause and facial skin microbiomes: a pilot study revealing novel insights into their relationship. Front Aging 2024; 5:1353082. [PMID: 38577131 PMCID: PMC10991793 DOI: 10.3389/fragi.2024.1353082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024]
Abstract
Introduction: The human skin microbial composition is affected by age. Previous studies reported skin microbiome diversity shifts between elderly and significantly younger subjects. Some studies implied that menopausal status, which is inherently linked to age, could be associated with changes in skin microbial compositions. Nevertheless, the influence of menopausal status on skin microbiome profiles while minimizing the impact of aging-associated changes in skin parameters still needs further clarification. Methods: We performed an observational study on healthy Caucasian female volunteers, which were grouped according to their pre- or postmenopausal status. Bacterial community structures on facial skin were analyzed using 16S rRNA gene sequencing. Cutometer® measurements were performed to evaluate aging-associated changes in facial skin biophysical properties. Results: The relative abundance of the lipophilic Cutibacterium genus was decreased, and bacterial diversity was increased in skin samples of postmenopausal volunteers. The mean age difference between examined groups in this study was 12.4 years only. Accordingly, Cutometer® measurements revealed no differences in aging-associated skin biophysical parameters between pre- and postmenopausal groups. Consequently, no correlation was detected between Shannon diversity and measured age-dependent biomechanical properties of facial skin. Discussion: These findings are in line with previous studies, which investigated the wide-ranging impact of chronological aging on skin microbial communities. However, this work reports for the first time a direct association between menopausal status and facial microbiomes on skin of similarly aged study participants, and hence uncouples aging-associated skin biophysical parameters, such as viscoelastic properties, from the equation. These findings open avenues for the development of microbiome-targeting strategies for treatment of menopause-associated skin disorders.
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Xian WD, Chen J, Zheng Z, Ding J, Xi Y, Zhang Y, Qu W, Tang C, Li C, Liu X, Li W, Wang J. Water masses influence the variation of microbial communities in the Yangtze River Estuary and its adjacent waters. Front Microbiol 2024; 15:1367062. [PMID: 38572235 PMCID: PMC10987813 DOI: 10.3389/fmicb.2024.1367062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
The Yangtze River estuary (YRE) are strongly influenced by the Kuroshio and terrigenous input from rivers, leading to the formation of distinct water masses, however, there remains a limited understanding of the full extent of this influence. Here the variation of water masses and bacterial communities of 58 seawater samples from the YRE and its adjacent waters were investigated. Our findings suggested that there were 5 water masses in the studied area: Black stream (BS), coastal water in the East China Sea (CW), nearshore mixed water (NM), mixed water in the middle and deep layers of the East China Sea (MM), and deep water blocks in the middle of the East China Sea (DM). The CW mass harbors the highest alpha diversity across all layers, whereas the NM mass exhibits higher diversity in the surface layer but lower in the middle layers. Proteobacteria was the most abundant taxa in all water masses, apart from that, in the surface layer masses, Cyanobacterium, Bacteroidota, and Actinobacteriota were the highest proportion in CW, while Bacteroidota and Actinobacteriota were the highest proportion in NM and BS; in the middle layer, Bacteroidota and Actinobacteriota were dominant phylum in CW and BS masses, but Cyanobacterium was main phylum in NM mass; in the bottom layer, Bacteroidota and Actinobacteriota were the dominant phylum in CW, while Marininimicrobia was the dominated phylum in DM and MM masses. Network analysis suggests water masses have obvious influence on community topological characteristics, moreover, community assembly across masses also differ greatly. Taken together, these results emphasized the significant impact of water masses on the bacterial composition, topological characteristics and assembly process, which may provide a theoretical foundation for predicting alterations in microbial communities within estuarine ecosystems under the influence of water masses.
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Affiliation(s)
- Wen-Dong Xian
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Jinhui Chen
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Zheng Zheng
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Junjie Ding
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yinli Xi
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Yiying Zhang
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wu Qu
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Chunyu Tang
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Changlin Li
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Xuezhu Liu
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Wei Li
- College of Science, Shantou University, Shantou, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
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Sun M, Shao W, Liu Z, Ma X, Chen H, Zheng N, Zhao Y. Microbial diversity in camel milk from Xinjiang, China as revealed by metataxonomic analysis. Front Microbiol 2024; 15:1367116. [PMID: 38533337 PMCID: PMC10964795 DOI: 10.3389/fmicb.2024.1367116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The quality of raw camel milk is affected by its bacterial composition and diversity. However, few studies have investigated the bacterial composition and diversity of raw camel milk. In this study, we obtained 20 samples of camel milk during spring and summer in Urumqi and Hami, Xinjiang, China. Single-molecule real-time sequencing technology was used to analyze the bacterial community composition. The results revealed that there were significant seasonal differences in the bacterial composition and diversity of camel milk. Overall, Epilithonimonas was the most abundant bacterial genus in our samples. Through the annotated genes inferred by PICRUSt2 were mapped against KEGG database. Non-parametric analysis of the bacterial community prediction function revealed a strong bacterial interdependence with metabolic pathways (81.83%). There were clear regional and seasonal differences in level 3 metabolic pathways such as fat, vitamins, and amino acids in camel milk. In addition, we identified lactic acid bacteria in camel milk with antibacterial and anti-tumor activities. Our findings revealed that camel milk from Xinjiang had serious risk of contamination by psychrophilic and pathogenic bacteria. Our research established a crucial theoretical foundation for ensuring the quality and safety of camel milk, thereby contributing significantly to the robust growth of China's camel milk industry.
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Affiliation(s)
- Miao Sun
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Wei Shao
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Zhengyu Liu
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Xianlan Ma
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
| | - He Chen
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yankun Zhao
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Tenea GN, Reyes P. Bacterial community changes in strawberry fruits ( Fragaria × ananassa variety "Monterey") from farm field to retail market stands, an indicator of postharvest contamination. Front Microbiol 2024; 15:1348316. [PMID: 38435684 PMCID: PMC10904649 DOI: 10.3389/fmicb.2024.1348316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Background Strawberry (Fragaria × ananassa) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and diversity at different ripe stages is a key determinant of the fruit health, productivity, and quality. Methodology An amplicon metagenomic approach on the 16S rRNA region was used to identify the bacterial diversity in exocarp of fruits collected from a farm field at two ripe stages: breaking (white, phase two) and ripe (red, phase four) and purchased from different retail market stands at ripe (red, phase four, ready-to-eat) stage. Besides, the fruit quality was assessed. Results Strawberries carries a high microorganisms diversity, with Pseudomonaceae, Yearsiniaceae, and Hafniaceae being the most abundant families across the samples. Among the groups, Pseudomonaceae and Clostridiaceae were the most abundant families at breaking (phase two) and ripe (phase four), whereas Yearsiniaceae, Hafniaceae, Aeromonadaceae, and Streptococcaceae were the most abundant families in the market group. Although samples from group four-field and market were at the same ripe stage, the bacterial species composition was divergent. Serratia spp. were prevalent (above 60%) in samples collected from the market group, and Pseudomonas (above 70%) species were mostly found in the samples collected from the field settings regardless of the phase. Besides, Escherichia coli and Salmonella enterica were detected in the ready-to-eat samples from both the field and the market, while Enterococcus gallinarum was detected in the samples that originated from the market. Interestingly, Shewanella putrefaciens and Shewanella profunda, two human opportunistic pathogens, were detected in the fruits from the market only. According to alpha and beta diversity analyses, strawberry fruits displayed significant differences (P < 0.05) in bacterial communities within the ripe group, with the samples from the market showing the most bacterial diversity. Although we do not directly correlate the quality attributes with bacterial diversity, the results indicated a clear separation between groups according with their ripe stage and origin. Conclusion This study provides a comprehensive framework of the bacterial diversity throughout the transition from unripe to ripe strawberries which may aid in the development of preventative measures to manage the postharvest contamination.
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Affiliation(s)
- Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
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Zhu Y, An M, Anwar T, Wang H. Differences in soil bacterial community structure during the remediation of Cd-polluted cotton fields by biochar and biofertilizer in Xinjiang, China. Front Microbiol 2024; 15:1288526. [PMID: 38404600 PMCID: PMC10884324 DOI: 10.3389/fmicb.2024.1288526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Heavy metal pollution is a major worldwide environmental problem. Many remediation techniques have been developed, these techniques have different performance in different environments. Methods In this study, soil sampling was conducted in multiple cotton fields in Xinjiang, China, and found that cadmium (Cd) was the most abundant soil heavy metal. Then, to find the most suitable technique for the remediation of Cd pollution in cotton fields, a two-year study was conducted to explore the effects of cotton straw-derived biochar (BC, 3%) and Bacillus-based biofertilizer (BF, 1.5%) on cotton Cd uptake and transport and soil microbial community structure under Cd exposure conditions (soil Cd contents: 1, 2, and 4 mg·kg-1). Results The results showed that the bioaccumulation coefficients (Cd content of cotton organs / soil available Cd content) of cotton roots, stems, leaves, and buds/bolls reduced by 15.93%, 14.41%, 23.53%, and 20.68%, respectively after the application of BC, and reduced by 16.83%, 17.15%, 22.21%, and 26.25%, respectively after the application of BF, compared with the control (no BC and BF). Besides, the application of BC and BF reduced the transport of Cd from soil to root system, and enhanced the diversity of soil bacterial communities (dominant species: Alphaproteobacteria and Actinobacteria) and the metabolic functions related to amino acid synthesis. It was worth noting that the differential species for BF group vs BC group including Alphaproteobacteria, Gemmatimonadetes, Bacilli, and Vicinamibacteria were associated with the enrichment and transport of Cd, especially the transport of Cd from cotton roots to stems. Discussion Therefore, the application of BC and BF changed the soil bacterial diversity in Cd-polluted cotton field, and then promoted the transport of Cd in cotton, ultimately improving soil quality. This study will provide a reference for the selection of soil heavy metal pollution remediation techniques in Xinjiang, China.
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Affiliation(s)
- Yongqi Zhu
- Key Laboratory of Biological Resources and Genetic Engineering of Xinjiang Uygur Autonomous Region, College of Life Science and Technology, Xinjiang University, Ürümqi, Xinjiang, China
| | - Mengjie An
- Key Laboratory of Biological Resources and Genetic Engineering of Xinjiang Uygur Autonomous Region, College of Life Science and Technology, Xinjiang University, Ürümqi, Xinjiang, China
| | - Tumur Anwar
- Key Laboratory of Biological Resources and Genetic Engineering of Xinjiang Uygur Autonomous Region, College of Life Science and Technology, Xinjiang University, Ürümqi, Xinjiang, China
| | - Haijiang Wang
- Agricultural College, Shihezi University, Shihezi, Xinjiang, China
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Yan J, Green K, Noel K, Kim CH, Stone CM. Effects of seasonality and developed land cover on Culex mosquito abundance and microbiome diversity. Front Microbiol 2024; 15:1332970. [PMID: 38404602 PMCID: PMC10885804 DOI: 10.3389/fmicb.2024.1332970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
The vectorial capacity of mosquitoes, which influences the dynamics of vector-borne disease transmission, is intricately linked to mosquito abundance and the composition and diversity of their associated microbiomes. However, the influence of environmental factors on mosquito populations and microbiome diversity remains underexplored. Here we examined the effects of seasonality and developed land cover on Culex mosquito abundance and bacterial diversity. Biweekly field sampling of female Culex mosquitoes was conducted using gravid and CDC light traps, spanning summer to autumn across varying developed land cover levels in two urban areas in Central Illinois. Mosquito abundance was assessed by the number of mosquitoes captured per trap night and compared across seasons and developed levels. The mean mosquito abundance for gravid and light traps was 12.96 ± 2.15 and 7.67 ± 1.44, respectively. Notably, higher levels of developed land cover exhibited higher Culex abundance than the low level for light traps, but no significant difference was found between summer and early autumn. In gravid traps, no significant differences were detected across seasons or developed levels. Microbial analysis of the mosquito microbiome revealed that Proteobacteria and Wolbachia, with a mean relative abundance of 80.77 and 52.66% respectively, were identified as the most dominant bacterial phylum and genus. Their relative abundance remained consistent across seasons and developed land cover levels, with negligible variations. Alpha diversity, as measured by observed species, Chao1, Shannon, and Simpson, showed slightly higher values in early-autumn compared to late-summer. A notable pattern of bacterial diversity, as indicated by all four diversity indexes, is evident across varying levels of land development. Significantly, high or intermediate developed levels consistently showed reduced alpha diversity when compared to the lower level. This underscores the pronounced impact of anthropogenic ecological disturbances in shaping mosquito microbiomes. Beta diversity analysis revealed no significant dissimilarities in bacterial community composition across seasons and developed levels, although some separation was noted among different levels of developed land cover. These findings highlight the significant role of environmental factors in shaping mosquito abundance and their associated microbiomes, with potential implications for the vectorial capacity in the transmission of vector-borne diseases.
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Affiliation(s)
- Jiayue Yan
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | | | | | | | - Chris M. Stone
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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Zhang W, Ren F, Zang C, Yang F, Li X, Huang X, Chen K, Li X. Effects of dietary addition of ellagic acid on rumen metabolism, nutrient apparent digestibility, and growth performance in Kazakh sheep. Front Vet Sci 2024; 11:1334026. [PMID: 38379922 PMCID: PMC10877003 DOI: 10.3389/fvets.2024.1334026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Plant extracts have shown promise as natural feed additives to improve animal health and growth. Ellagic acid (EA), widely present in various plant tissues, offers diverse biological benefits. However, limited research has explored its effects on ruminants. This study aimed to investigate the effects of dietary addition EA on rumen metabolism, apparent digestibility of nutrients, and growth performance in Kazakh sheep. Ten 5-month-old Kazakh sheep with similar body weight (BW), fitted with rumen fistulas, were randomly assigned to two groups: the CON group (basal diet) and the EA group (basal diet + 30 mg/kg BW EA). The experiment lasted 30 days, and individual growth performance was assessed under identical feeding and management conditions. During the experimental period, rumen fluid, fecal, and blood samples were collected for analysis. The results indicated a trend toward increased average daily gain in the EA group compared to the CON group (p = 0.094). Compared with the CON group, the rumen contents of acetic acid and propionic acid were significantly increased in the EA group and reached the highest value at 2 h to 4 h after feeding (p < 0.05). Moreover, the relative abundances of specific rumen microbiota (Ruminococcaceae, uncultured_rumen_bacterium, unclassified_Prevotella, Bacteroidales, Bacteroidota, Bacteroidia, unclassified_Rikenellaceae, and Prevotella_spBP1_145) at the family and genus levels were significantly higher in the EA group (p < 0.05) compared to the CON group. The EA group exhibited significantly higher dry matter intake (p < 0.05) and increased the digestibility of neutral detergent fiber and ether extract when compared with the CON group (p < 0.05). Additionally, the plasma activities of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) were significantly higher, while malondialdehyde (MDA) concentration was significantly lower in the EA group compared to the CON group (p < 0.05). In conclusion, dietary supplementation with 30 mg/kg BW EA in 5-month-old Kazakh sheep increased the dry matter intakQ16e, apparent digestibility of neutral detergent fiber, and ether extract, as well as the contents of acetic acid and propionic acid in rumen fluid. Moreover, EA supplementation regulated the ruminal microbiota, enhanced antioxidant capacity, and improved daily weight gain.
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Affiliation(s)
| | | | | | | | | | | | - Kaixu Chen
- College of Animal Science and Technology, Xinjiang Key Laboratory of Meat & Milk Production Herbivore Nutrition, Xinjiang Agricultural University, Urumqi, China
| | - Xiaobin Li
- College of Animal Science and Technology, Xinjiang Key Laboratory of Meat & Milk Production Herbivore Nutrition, Xinjiang Agricultural University, Urumqi, China
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Corral-García LS, Molina MC, Bautista LF, Simarro R, Espinosa CI, Gorines-Cordero G, González-Benítez N. Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins. Toxics 2024; 12:119. [PMID: 38393214 PMCID: PMC10892221 DOI: 10.3390/toxics12020119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
The Ecuadorian Amazon rainforest stands out as one of the world's most biodiverse regions, yet faces significant threats due to oil extraction activities dating back to the 1970s in the northeastern provinces. This research investigates the environmental and societal consequences of prolonged petroleum exploitation and oil spills in Ecuador's Amazon. Conducted in June 2015, the study involved a comprehensive analysis of freshwater sediment samples from 24 locations in the Rio Aguarico and Napo basins. Parameters such as water and air temperature, conductivity, soil pH, and hydrocarbon concentrations were examined. Total petroleum hydrocarbon (TPH) concentrations ranged from 9.4 to 847.4 mg kg-1, with polycyclic aromatic hydrocarbon (PAH) levels varying from 10.15 to 711.1 mg kg-1. The pristane/phytane ratio indicated historic hydrocarbon pollution in 8 of the 15 chemically analyzed sediments. Using non-culturable techniques (Illumina), bacterial analyses identified over 350 ASV, with prominent families including Comamonadaceae, Chitinophagaceae, Anaeromyxobacteraceae, Sphingomonadaceae, and Xanthobacteraceae. Bacterial diversity, assessed in eight samples, exhibited a positive correlation with PAH concentrations. The study provides insights into how microbial communities respond to varying levels of hydrocarbon pollution, shedding light on the enduring impact of oil exploitation in the Amazonian region. Its objective is to deepen our understanding of the environmental and human well-being in the affected area, underscoring the pressing need for remedial actions in the face of ongoing ecological challenges.
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Affiliation(s)
- Lara S. Corral-García
- Centro de Investigación en Biodiversidad y Cambio Global, Department of Ecology, Universidad Autónoma de Madrid, C/Darwin, 2, 28049 Madrid, Spain
| | - María Carmen Molina
- Biodiversity and Conservation Unit, Department of Biology and Geology, Physics and Inorganic Chemistry, Instituto de Investigación en Cambio Global, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain; (M.C.M.); (N.G.-B.)
| | - Luis Fernando Bautista
- Department of Chemical and Environmental Technology, ESCET, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain;
| | - Raquel Simarro
- Plant Pathology Laboratory (DTEVL), INIA-CSIC, Ctra, de La Coruña, Km 7.5, 28040 Madrid, Spain;
| | - Carlos Iván Espinosa
- Department of Biological and Agricultural Sciences, Universidad Técnica Particular de Loja, San Cayetano alto s/n, Loja 1101608, Ecuador;
| | - Guillermo Gorines-Cordero
- Biodiversity and Conservation Unit, Department of Biology and Geology, Physics and Inorganic Chemistry, Instituto de Investigación en Cambio Global, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain; (M.C.M.); (N.G.-B.)
| | - Natalia González-Benítez
- Biodiversity and Conservation Unit, Department of Biology and Geology, Physics and Inorganic Chemistry, Instituto de Investigación en Cambio Global, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain; (M.C.M.); (N.G.-B.)
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Zheng H, Chen T, Li W, Hong J, Xu J, Yu Z. Endosymbiotic bacteria within the nematode-trapping fungus Arthrobotrys musiformis and their potential roles in nitrogen cycling. Front Microbiol 2024; 15:1349447. [PMID: 38348183 PMCID: PMC10860758 DOI: 10.3389/fmicb.2024.1349447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Endosymbiotic bacteria (ESB) have important effects on their hosts, contributing to its growth, reproduction and biological functions. Although the effects of exogenous bacteria on the trap formation of nematode-trapping fungi (NTF) have been revealed, the effects of ESB on NTF remain unknown. In this study, we investigated the species diversity of ESB in the NTF Arthrobotrys musiformis using high-throughput sequencing and culture-dependent approaches, and compared bacterial profiles to assess the effects of strain source and culture media on A. musiformis. PICRUSt2 and FAPROTAX were used to predict bacterial function. Our study revealed that bacterial communities in A. musiformis displayed high diversity and heterogeneity, with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the dominant phyla. The ESB between A. musiformis groups isolated from different habitats and cultured in the same medium were more similar to each other than the other groups isolated from the same habitat but cultured in different media. Function analysis predicted a broad and diverse functional repertoire of ESB in A. musiformis, and unveiled that ESB have the potential to function in five modules of the nitrogen metabolism. We isolated nitrogen-fixing and denitrifying bacteria from the ESB and demonstrated their effects on trap formation of A. musiformis. Among seven bacteria that we tested, three bacterial species Bacillus licheniformis, Achromobacter xylosoxidans and Stenotrophomonas maltophilia were found to be efficient in inducing trap formation. In conclusion, this study revealed extensive ESB diversity within NTF and demonstrated that these bacteria likely play important roles in nitrogen cycling, including nematode trap formation.
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Affiliation(s)
- Hua Zheng
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Tong Chen
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Wenjie Li
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianan Hong
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, China
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12
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Duan X, Li J, He W, Huang J, Xiong W, Chi S, Luo S, Liu J, Zhang X, Li J. Microbial diversity and their extracellular enzyme activities among different soil particle sizes in mossy biocrust under N limitation in the southeastern Tengger Desert, China. Front Microbiol 2024; 15:1328641. [PMID: 38357343 PMCID: PMC10866007 DOI: 10.3389/fmicb.2024.1328641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Mossy biocrust represents a stable stage in the succession of biological soil crust in arid and semi-arid areas, providing a microhabitat that maintains microbial diversity. However, the impact of mossy biocrust rhizoid soil and different particle sizes within the mossy biocrust layer and sublayer on microbial diversity and soil enzyme activities remains unclear. Methods This study utilized Illumina MiSeq sequencing and high-throughput fluorometric technique to assess the differences in microbial diversity and soil extracellular enzymes between mossy biocrust rhizoid soil and different particle sizes within the mossy biocrust sifting and sublayer soil. Results The results revealed that the total organic carbon (TOC), total nitrogen (TN), ammonium (NH4+) and nitrate (NO3-) in mossy biocrust rhizoid soil were the highest, with significantly higher TOC, TN, and total phosphorus (TP) in mossy biocrust sifting soil than those in mossy biocrust sublayer soil. Extracellular enzyme activities (EAAs) exhibited different responses to various soil particle sizes in mossy biocrust. Biocrust rhizoid soil (BRS) showed higher C-degrading enzyme activity and lower P-degrading enzyme activity, leading to a significant increase in enzyme C: P and N: P ratios. Mossy biocrust soils were all limited by microbial relative nitrogen while pronounced relative nitrogen limitation and microbial maximum relative carbon limitation in BRS. The diversity and richness of the bacterial community in the 0.2 mm mossy biocrust soil (BSS0.2) were notably lower than those in mossy biocrust sublayer, whereas the diversity and richness of the fungal community in the rhizoid soil were significantly higher than those in mossy biocrust sublayer. The predominant bacterial phyla in mossy biocrust were Actinobacteriota, Protebacteria, Chloroflexi, and Acidobacteriota, whereas in BSS0.2, the predominant bacterial phyla were Actinobacteriota, Protebacteria, and Cyanobacteria. Ascomycota and Basidiomycota were dominant phyla in mossy biocrust. The bacterial and fungal community species composition exhibited significant differences. The mean proportions of Actinobacteriota, Protebacteria, Chloroflexi, Acidobacteriota, Acidobacteria, Cyanobacteria, and Bacteroidota varied significantly between mossy biocrust rhizoid and different particle sizes of mossy biocrust sifting and sublayer soil (p < 0.05). Similarly, significant differences (p < 0.05) were observed in the mean proportions of Ascomycota, Basidiomycota, and Glomeromycota between mossy biocrust rhizoid and different particle sizes within the mossy biocrust sifting and sublayer soil. The complexity and connectivity of bacterial and fungal networks were higher in mossy biocrust rhizoid soil compared with different particle sizes within the mossy biocrust sifting and sublayer soil. Discussion These results offer valuable insights to enhance our understanding of the involvement of mossy biocrust in the biogeochemical cycle of desert ecosystems.
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Affiliation(s)
- Xiaomin Duan
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
| | - Jiajia Li
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
| | - Wangping He
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Jingjing Huang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Wanxiang Xiong
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Shijia Chi
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Siyuan Luo
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Jianli Liu
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
| | - Xiu Zhang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
| | - Jingyu Li
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Yinchuan, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, China
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13
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Amara J, Itani T, Hajal J, Bakhos JJ, Saliba Y, Aboushanab SA, Kovaleva EG, Fares N, Mondragon AC, Miranda JM. Circadian Rhythm Perturbation Aggravates Gut Microbiota Dysbiosis in Dextran Sulfate Sodium-Induced Colitis in Mice. Nutrients 2024; 16:247. [PMID: 38257139 PMCID: PMC10819604 DOI: 10.3390/nu16020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Circadian rhythm disruption is increasingly considered an environmental risk factor for the development and exacerbation of inflammatory bowel disease. We have reported in a previous study that nychthemeral dysregulation is associated with an increase in intestinal barrier permeability and inflammation in mice with dextran sulfate sodium (DSS)-induced colitis. To investigate the effect of circadian rhythm disruption on the composition and diversity of the gut microbiota (GM), sixty male C57BL/6J mice were initially divided to two groups, with the shifted group (n = 30) exposed to circadian shifts for three months and the non-shifted group (n = 30) kept under a normal light-dark cycle. The mice of the shifted group were cyclically housed for five days under the normal 12:12 h light-dark cycle, followed by another five days under a reversed light-dark cycle. At the end of the three months, a colitis was induced by 2% DSS given in the drinking water of 30 mice. Animals were then divided into four groups (n = 15 per group): sham group non-shifted (Sham-NS), sham group shifted (Sham-S), DSS non-shifted (DSS-NS) and DSS shifted (DSS-S). Fecal samples were collected from rectal content to investigate changes in GM composition via DNA extraction, followed by high-throughput sequencing of the bacterial 16S rRNA gene. The mouse GM was dominated by three phyla: Firmicutes, Bacteroidetes and Actinobacteria. The Firmicutes/Bacteroidetes ratio decreased in mice with induced colitis. The richness and diversity of the GM were reduced in the colitis group, especially in the group with inverted circadian rhythm. Moreover, the GM composition was modified in the inverted circadian rhythm group, with an increase in Alloprevotella, Turicibacter, Bacteroides and Streptococcus genera. Circadian rhythm inversion exacerbates GM dysbiosis to a less rich and diversified extent in a DSS-induced colitis model. These findings show possible interplay between circadian rhythm disruption, GM dynamics and colitis pathogenesis.
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Affiliation(s)
- Joseph Amara
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Tarek Itani
- Laboratoire de Microbiologie, Faculté de Pharmacie, Université Saint Joseph, Beirut 1104 2020, Lebanon;
| | - Joelle Hajal
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Jules-Joel Bakhos
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Youakim Saliba
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Saied A. Aboushanab
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Mira 19, Yekaterinburg 620002, Russia; (S.A.A.); (E.G.K.)
| | - Elena G. Kovaleva
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Mira 19, Yekaterinburg 620002, Russia; (S.A.A.); (E.G.K.)
| | - Nassim Fares
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Alicia C. Mondragon
- Laboratorio de Higiene, Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade da Santiago de Compostela, 27002 Lugo, Spain;
| | - Jose Manuel Miranda
- Laboratorio de Higiene, Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade da Santiago de Compostela, 27002 Lugo, Spain;
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14
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Wang Z, Liu K. Effect of Intertidal Vegetation ( Suaeda salsa) Restoration on Microbial Diversity in the Offshore Areas of the Yellow River Delta. Plants (Basel) 2024; 13:213. [PMID: 38256766 PMCID: PMC10820354 DOI: 10.3390/plants13020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024]
Abstract
The coastal wetlands in the Yellow River Delta play a vital role in the ecological function of the area. However, the impact of primary restoration on microbial communities is not yet fully understood. Hence, this study aimed to analyze the bacterial and archaeal communities in the soil. The results indicated that Marinobacter and Halomonas were predominant in the bacterial community during spring and winter. On the other hand, Muribaculaceae and Helicobacter were prevalent during the core remediation of soil, while Inhella and Halanaerobium were predominant in non-vegetation-covered high-salinity soil. The bacterial Shannon index showed significant differences in vegetation-covered areas. For archaea, Salinigranum, Halorubrum, and Halogranum were dominant in vegetation areas, while Halolamina, Halogranum, and Halorubrum were prevalent in non-vegetation areas. The colonization of Suaeda salsa led to differences in the composition of bacteria (22.6%) and archaea (29.5%), and salt was one of the significant reasons for this difference. The microflora was more diverse, and the elements circulated after vegetation grounding, while the microbial composition in non-vegetation areas was similar, but there was potential competition. Therefore, vegetation restoration can effectively restore soil ecological function, while the microorganisms in the soil before restoration provide germplasm resources for pollutant degradation and antimicrobial development.
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Affiliation(s)
- Zhaohua Wang
- First Institute of Oceanography, MNR, Qingdao 266061, China;
| | - Kai Liu
- Dongying Research Institute for Oceanography Development, Dongying 257000, China
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15
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Xing T, Liu K, Ji M, Chen Y, Liu Y. Bacterial diversity in a continuum from supraglacial habitats to a proglacial lake on the Tibetan Plateau. FEMS Microbiol Lett 2024; 371:fnae021. [PMID: 38521984 DOI: 10.1093/femsle/fnae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/14/2024] [Accepted: 03/22/2024] [Indexed: 03/25/2024] Open
Abstract
Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
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16
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Smutin D, Taldaev A, Lebedev E, Adonin L. Shotgun Metagenomics Reveals Minor Micro" bee"omes Diversity Defining Differences between Larvae and Pupae Brood Combs. Int J Mol Sci 2024; 25:741. [PMID: 38255816 PMCID: PMC10815634 DOI: 10.3390/ijms25020741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Bees represent not only a valuable asset in agriculture, but also serve as a model organism within contemporary microbiology. The metagenomic composition of the bee superorganism has been substantially characterized. Nevertheless, traditional cultural methods served as the approach to studying brood combs in the past. Indeed, the comb microbiome may contribute to determining larval caste differentiation and hive immunity. To further this understanding, we conducted a shotgun sequencing analysis of the brood comb microbiome. While we found certain similarities regarding species diversity, it exhibits significant differentiation from all previously described hive metagenomes. Many microbiome members maintain a relatively constant ratio, yet taxa with the highest abundance level tend to be ephemeral. More than 90% of classified metagenomes were Gammaproteobacteria, Bacilli and Actinobacteria genetic signatures. Jaccard dissimilarity between samples based on bacteria genus classifications hesitate from 0.63 to 0.77, which for shotgun sequencing indicates a high consistency in bacterial composition. Concurrently, we identified antagonistic relationships between certain bacterial clusters. The presence of genes related to antibiotic synthesis and antibiotic resistance suggests potential mechanisms underlying the stability of comb microbiomes. Differences between pupal and larval combs emerge in the total metagenome, while taxa with the highest abundance remained consistent. All this suggests that a key role in the functioning of the comb microbiome is played by minor biodiversity, the function of which remains to be established experimentally.
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Affiliation(s)
- Daniil Smutin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen 625003, Russia
- Faculty of Information Technology and Programming, ITMO University, St. Petersburg 197101, Russia
| | - Amir Taldaev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen 625003, Russia
- Institute of Biomedical Chemistry, Moscow 119121, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen 625003, Russia
| | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen 625003, Russia
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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Ren K, Mo Y, Xiao P, Rønn R, Xu Z, Xue Y, Chen H, Rivera WL, Rensing C, Yang J. Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions. ISME Commun 2024; 4:ycae026. [PMID: 38559570 PMCID: PMC10980835 DOI: 10.1093/ismeco/ycae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.
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Affiliation(s)
- Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Peng Xiao
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- National and Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Regin Rønn
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Department of Biology, University of Copenhagen, Copenhagen DK2100, Denmark
| | - Zijie Xu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Christopher Rensing
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Institute of Environmental Microbiology, College of Resources and the Environment, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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18
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Cortazar-Chinarro M, Richter-Boix A, Rödin-Mörch P, Halvarsson P, Logue JB, Laurila A, Höglund J. Association between the skin microbiome and MHC class II diversity in an amphibian. Mol Ecol 2024; 33:e17198. [PMID: 37933583 DOI: 10.1111/mec.17198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
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Affiliation(s)
- M Cortazar-Chinarro
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- MEMEG/Department of Biology, Lund University, Lund, Sweden
- Department of Earth Ocean and Atmospheric Sciences, Faculty of Science 2020-2207, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Richter-Boix
- Department of Political and Social Science, Pompeu Fabra University, Barcelona, Spain
| | - P Rödin-Mörch
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - P Halvarsson
- Parasitology/Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J B Logue
- Aquatic Ecology/Department of Biology, Lund University, Lund, Sweden
- SLU University Library, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Laurila
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Höglund
- Animal Ecology/Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Peng Z, Yang Y, Liu Y, Bu L, Qi J, Gao H, Chen S, Pan H, Chen B, Liang C, Li X, An Y, Wang S, Wei G, Jiao S. The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems. Glob Chang Biol 2024; 30:e16996. [PMID: 37916454 DOI: 10.1111/gcb.16996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.
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Affiliation(s)
- Ziheng Peng
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yu Liu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lianyan Bu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiejun Qi
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hang Gao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shi Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Haibo Pan
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Beibei Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunling Liang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Li
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yining An
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shaopeng Wang
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Obayori OS, Adesina OD, Salam LB, Ashade AO, Nwaokorie FO. Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil. Environ Technol 2023:1-16. [PMID: 38118139 DOI: 10.1080/09593330.2023.2291421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/26/2023] [Indexed: 12/22/2023]
Abstract
Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.
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Affiliation(s)
| | | | - Lateef Babatunde Salam
- Microbiology Unit, Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
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21
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Tamai S, Suzuki Y. Diversity of Fecal Indicator Enterococci among Different Hosts: Importance to Water Contamination Source Tracking. Microorganisms 2023; 11:2981. [PMID: 38138125 PMCID: PMC10745335 DOI: 10.3390/microorganisms11122981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Enterococcus spp. are common bacteria present in the intestinal tracts of animals and are used as fecal indicators in aquatic environments. On the other hand, enterococci are also known as opportunistic pathogens. Elucidating their composition in the intestinal tracts of domestic animals can assist in estimating the sources of fecal contamination in aquatic environments. However, information on the species and composition of enterococci in animal hosts (except humans) is still lacking. In this study, enterococci were isolated from the feces of cattle, pigs, birds, and humans using selective media. Enterococcal species were identified using mass spectrometry technology, and each host was characterized by diversity and cluster analysis. The most dominant species were E. hirae in cattle, E. faecium in birds, and E. faecalis in pigs and humans. Cattle had the highest alpha diversity, with high interindividual and livestock farm diversity. The dominant enterococcal species in pigs and humans were identical, and cluster analysis showed that the majority of the two hosts' species clustered together.
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Affiliation(s)
| | - Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan;
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Lin TT, Zheng J, Zhu GF, Luan L, Yang YYP, Liu J, Xu QS, Sun B, Jiang YJ. [Effects of Organic Fertilization on Bacterial Community and Maize Productivity in Dryland Red Soil]. Huan Jing Ke Xue 2023; 44:6965-6972. [PMID: 38098419 DOI: 10.13227/j.hjkx.202301133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Since 2002, a long-term field experiment has been conducted to determine the effects of different organic fertilization treatments on the bacterial community characteristics and maize productivity in dryland red soil using high-throughput sequencing technology. The experiment consisted of four treatments:no manure, M0; low manure, M1; high manure, M2; and high manure with lime addition, M3. Our results showed that the different organic fertilization treatments(M1, M2, and M3) significantly promoted maize productivity with the highest values of pH, soil organic matter(SOM), total nitrogen(TN), and total phosphorus(TP) compared to that under the M0 treatment, and the high manure with lime addition(M3) treatment had the highest level of maize production. The different organic fertilization treatments significantly increased the Shannon index, Evenness index, Chao1 index, and ACE index and significantly shaped the composition of the bacterial community. TP and pH were the main variables determining soil bacterial diversity index based on random forest modeling analysis, whereas pH, SOM, TP, and TN were the main variables determining the structure of the soil bacterial community. Correlation analysis and structural equation modeling determined that TP and SOM indirectly affected maize productivity by varying the bacterial diversity and community structure. The results of this study provide the scientific basis for ensuring food security and sustainable agricultural development by improving the fertility and bacterial diversity in dryland red soil.
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Affiliation(s)
- Ting-Ting Lin
- College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China
| | - Guo-Fan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China
| | - Ye-Yu-Ping Yang
- College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Jia Liu
- Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qin-Song Xu
- College of Life Science, Nanjing Normal University, Nanjing 210023, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China
| | - Yu-Ji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan 335211, China
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Guan L, Wang H, Chen J, Yang F, Yang J, Li J, Jin L. Isolation and Identification of Culturable Bacteria from South China Seawater and Preliminary Screening of Marine Biocontrol Bacteria. Microorganisms 2023; 11:2933. [PMID: 38138077 PMCID: PMC10746102 DOI: 10.3390/microorganisms11122933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Marine microorganisms have evolved special metabolic pathways to produce numerous bioactive substances with novel structures and unique functions. This study analyzed the diversity of culturable bacteria in marine water samples from the South China Sea and screened the isolated bacteria with pathogenic fungi. A total of 200 culturable strains of 72 different bacteria were obtained from 56 water samples from the South China Sea. They belonged to three phyla and four classes, namely Gammaproteobacteria, Alphaproteobacteria, Bacilli and Actinomycetia. Bacilli was the dominant class, comprising up to 59.72%, followed by Gammaproteobacteria (20.83%). Bacillus, Pseudomonas, Paenibacillus and Rhizobium were the most dominant genera. Among these strains, HY-88 and HY-91 encoding BamC, FenB and PKSI genes were selected and identified as Bacillus subtilis. The respective inhibition rates of the HY-88 caused by plate confrontation against Magnaporthe grisea, Fusarium oxysporum, Botrytis cinerea, anthrax and Botrytis cinerea were 90.91%, 54.29%, 52.17% and 51.72%, in comparison with HY-91 86.36%, 48.57%, 47.83% and 34.48%. In addition, the supernatant of HY-88 showed a lesion inhibition rate of 74.5%, which was significantly higher than HY-91 (60.55%). In addition, HY-88 and HY-91 showed strong antifungal activity to Colletotrichum viniferum on detached Shine Muscat grapes. Tolerance tests showed that the HY-88 and HY-91 grew at 10-40 °C, 7-10% NaCl and pH 3-11. HY-88 and HY-91 could inhibit various fungal plant diseases, which lays a foundation for the development of new biopesticides.
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Affiliation(s)
- Limei Guan
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Hongxiu Wang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330029, China;
| | - Junhui Chen
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Feiying Yang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Jian Yang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Jianghuai Li
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Liang Jin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
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Zhu J, Chen X, Chen SC, Qiu W, Yu J, Guo T, Wang X. Diversity and community composition of strictly anaerobic and culturable bacteria from the feces of Styrofoam-fed Tenebrio molitor larvae: a culturomics-based study. Front Microbiol 2023; 14:1309806. [PMID: 38116533 PMCID: PMC10728288 DOI: 10.3389/fmicb.2023.1309806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/09/2023] [Indexed: 12/21/2023] Open
Abstract
Introduction In recent years, researchers have been exploring the plastic-degrading abilities of bacteria residing in the guts of Styrofoam-eating Tenebrio molitor larvae. However, none of the reported strains have displayed highly efficient plastic degradation capabilities, and it's noteworthy that none of the existing studies have focused on strictly anaerobic microbes. Methods In this study, we exclusively fed Styrofoam to T. molitor larvae and examined how this dietary change influence the gut's bacterial community composition, as observed through fecal bacteria using bacterial 16S rRNA gene amplicon sequencing and the small-scale culturomics method with 20 types of anaerobic media under four different conditions. Results The results revealed a significant shift in the dominant phylogroup from Lactococcus (37.8%) to Escherichia-Shigella (54.7%) when comparing the feces of larvae fed with bran and Styrofoam, as analyzing through the bacterial 16S rRNA gene amplicon sequencing. For small-scale culturomics method, a total of 226 strains of anaerobic bacteria were isolated and purified using the rolling-tube/strictly anaerobic technique. Among them, 226 strains were classified into 3 phyla, 7 classes, 9 orders, 17 families, 29 genera, 42 known species and 34 potential novel species. Discussion Interestingly, 24 genera in total, identified through the culturomics method, were not found in the results obtained from amplicon sequencing. Here, we present a collection of culturable anaerobic bacteria from the feces of T. molitor larvae, which might be a promising avenue for investigating the biodegradability of plastics by combining specific strains, either randomly or intentionally, while considering the abundance ratio of the microbial community composition.
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Affiliation(s)
- Junyu Zhu
- Innovation Center for Soil Remediation and Restoration Technologies, College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, China
| | - Xiaochen Chen
- Innovation Center for Soil Remediation and Restoration Technologies, College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Sheng-Chung Chen
- Innovation Center for Soil Remediation and Restoration Technologies, College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, China
| | - Jianying Yu
- Innovation Center for Soil Remediation and Restoration Technologies, College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- The Second Geological Exploration Institute, China Metallurgical Geology Bureau, Fuzhou, Fujian, China
| | - Tengfei Guo
- Innovation Center for Soil Remediation and Restoration Technologies, College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- The Second Geological Exploration Institute, China Metallurgical Geology Bureau, Fuzhou, Fujian, China
| | - Xianxing Wang
- Innovation Center for Soil Remediation and Restoration Technologies, College of Environment and Safety Engineering, Fuzhou University, Fuzhou, Fujian, China
- The Second Geological Exploration Institute, China Metallurgical Geology Bureau, Fuzhou, Fujian, China
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Chen S, He F, Cheng X. Analysis of subgingival bacterial and fungal diversity in patients with peri-implantitis based on 16sRNA and internal transcribed spacer sequencing. Future Microbiol 2023. [PMID: 38047905 DOI: 10.2217/fmb-2023-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Aim: To analyze subgingival fungal diversity in peri-implant inflammation patients and their relationship with bacteria. Methods: We collected saliva samples from four groups. 16sRNA and internal transcribed spacer sequencing was performed preceded by quantitative PCR and enzyme-linked immunosorbent assay tests. Analyses were done using R and Cytoscape software. Results: Significant differences were observed in the Abundance-based Coverage Estimator (ACE) index between control and peri-implantitis samples. Basidiomycota was the dominant fungal species, while Firmicutes dominated the bacteria. The most abundant fungal and bacterial species were 's_unclassified g Apiotrichum' and 's_unclassified g Streptococcus', respectively. Dothiorella was strongly associated with immunoglobulin G levels, with positive correlations between specific microorganisms and peri-implantitis in Q-PCR. Conclusion: Our findings have significant clinical implications, suggesting specific fungal and bacterial taxa roles in peri-implant inflammation.
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Affiliation(s)
- Song Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Fuming He
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Xi Cheng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
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26
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Basharat S, Meng T, Zhai L, Hussain A, Aqeel SM, Khan S, Shah OU, Liao X. Bacterial diversity of stingless bee honey in Yunnan, China: isolation and genome sequencing of a novel acid-resistant Lactobacillus pentosus (SYBC-MI) with probiotic and L. tryptophan producing potential via millet fermentation. Front Bioeng Biotechnol 2023; 11:1272308. [PMID: 38107618 PMCID: PMC10722240 DOI: 10.3389/fbioe.2023.1272308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023] Open
Abstract
Stingless bee (Hymenoptera, Apidae, and Trigona) honey is a remarkable "miracle liquid" with a wide range of medical benefits for conditions including gastroenteritis, cataracts, and wound healing. Our study aimed to isolate, identify, and characterize acid-resistant Lactobacillus spp. from sour honey distributed in Yunnan, China. To assess the safety of an entirely novel Lactobacillus pentosus strain, S4 (OM618128), based on probiotic property evaluation and whole-genome sequencing analysis. A 16S rRNA gene high-throughput sequencing analysis showed that Lactobacillus was abundant at the genus level in sour honey. Seven Lactobacillus strains (viz. S1-7) were isolated from sour honey using a multiple-anaerobic culture enrichment method. One potential acid-resistant isolate, Lactobacillus sp. S4, was obtained after screening the seven Lactobacillus isolates, and it had the highest lactic acid production (17.62 g/L), followed by Lactobacillus sp. S3 (17.07 g/L). Phylogenetic and comparative analyses of conserved sequence regions have shown that all seven strains are phylogenetically located in the Lactobacillus pentosus sub-cluster. In L. pentosus SYBC-MI, there is a circular chromosome (3288615 bps) and 11,466 bps plasmids. GC content is 44.03%. The number of predicted genes is 3,129, with 16 rRNAs and 74 tRNAs present. During the fermentation of foxtail millet by seven Lactobacillus pentosus (S1-7) strains isolated from sour honey, a potential tryptophan accumulating isolate, Lactobacillus pentosus S4, was obtained, which could reach a maximum tryptophan content of 238.43 mgL-1 that is 1.80 times the initial tryptophan content in the fermentation broth. This strain has strong acid tolerance, salt tolerance, and fermentation acid production abilities. This strain degrades nitrite at a rate of over 99%, and it has high probiotic potential as well. This project has established a solid foundation for further exploring the excellent lactic acid bacteria in sour honey. It is also investigating the key taxa and their role in the environment. According to the results of our studies, these LAB isolates provide a lot of potential for use in the future, as a source of probiotics for human, animals, and starter cultures for food applications.
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Affiliation(s)
- Samra Basharat
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Tiantian Meng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Lixin Zhai
- Henan Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety, Institute of Molecular Detection Technology and Equipment, Xuchang University, Xuchang, Henan, China
| | - Asif Hussain
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Sahibzada Muhammad Aqeel
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Salman Khan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Obaid Ullah Shah
- Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou, China
| | - Xiangru Liao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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27
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Mathrani A, Lu LW, Sequeira-Bisson IR, Silvestre MP, Hoggard M, Barnett D, Fogelholm M, Raben A, Poppitt SD, Taylor MW. Gut microbiota profiles in two New Zealand cohorts with overweight and prediabetes: a Tū Ora/PREVIEW comparative study. Front Microbiol 2023; 14:1244179. [PMID: 38033566 PMCID: PMC10687470 DOI: 10.3389/fmicb.2023.1244179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
Obesity-related metabolic diseases such as type 2 diabetes (T2D) are major global health issues, affecting hundreds of millions of people worldwide. The underlying factors are both diverse and complex, incorporating biological as well as cultural considerations. A role for ethnicity - a measure of self-perceived cultural affiliation which encompasses diet, lifestyle and genetic components - in susceptibility to metabolic diseases such as T2D is well established. For example, Asian populations may be disproportionally affected by the adverse 'TOFI' (Thin on the Outside, Fat on the Inside) profile, whereby outwardly lean individuals have increased susceptibility due to excess visceral and ectopic organ fat deposition. A potential link between the gut microbiota and metabolic disease has more recently come under consideration, yet our understanding of the interplay between ethnicity, the microbiota and T2D remains incomplete. We present here a 16S rRNA gene-based comparison of the fecal microbiota of European-ancestry and Chinese-ancestry cohorts with overweight and prediabetes, residing in New Zealand. The cohorts were matched for mean fasting plasma glucose (FPG: mean ± SD, European-ancestry: 6.1 ± 0.4; Chinese-ancestry: 6.0 ± 0.4 mmol/L), a consequence of which was a significantly higher mean body mass index in the European group (BMI: European-ancestry: 37.4 ± 6.8; Chinese-ancestry: 27.7 ± 4.0 kg/m2; p < 0.001). Our findings reveal significant microbiota differences between the two ethnicities, though we cannot determine the underpinning factors. In both cohorts Firmicutes was by far the dominant bacterial phylum (European-ancestry: 93.4 ± 5.5%; Chinese-ancestry: 79.6 ± 10.4% of 16S rRNA gene sequences), with Bacteroidetes and Actinobacteria the next most abundant. Among the more abundant (≥1% overall relative sequence abundance) genus-level taxa, four zero-radius operational taxonomic units (zOTUs) were significantly higher in the European-ancestry cohort, namely members of the Subdoligranulum, Blautia, Ruminoclostridium, and Dorea genera. Differential abundance analysis further identified a number of additional zOTUs to be disproportionately overrepresented across the two ethnicities, with the majority of taxa exhibiting a higher abundance in the Chinese-ancestry cohort. Our findings underscore a potential influence of ethnicity on gut microbiota composition in the context of individuals with overweight and prediabetes.
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Affiliation(s)
- Akarsh Mathrani
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Louise W. Lu
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Human Nutrition Unit, University of Auckland, Auckland, New Zealand
| | - Ivana R. Sequeira-Bisson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Human Nutrition Unit, University of Auckland, Auckland, New Zealand
| | - Marta P. Silvestre
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Human Nutrition Unit, University of Auckland, Auckland, New Zealand
- Centro de Investigação em Tecnologias e Serviços de Saúde (CINTESIS), NOVA University of Lisbon, Lisbon, Portugal
| | - Michael Hoggard
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Daniel Barnett
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Mikael Fogelholm
- Department of Food and Nutrition, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Anne Raben
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Clinical Research, Copenhagen University Hospital – Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Sally D. Poppitt
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Human Nutrition Unit, University of Auckland, Auckland, New Zealand
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
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Shu X, Liu W, Huang H, Ye Q, Zhu S, Peng Z, Li Y, Deng L, Yang Z, Chen H, Liu D, Shi J. Meta-Analysis of Organic Fertilization Effects on Soil Bacterial Diversity and Community Composition in Agroecosystems. Plants (Basel) 2023; 12:3801. [PMID: 38005698 PMCID: PMC10675672 DOI: 10.3390/plants12223801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023]
Abstract
Application of organic fertilizers or their combination with chemical fertilizers is a feasible practice for improving soil fertility and reducing soil degradation in agroecosystems, and these regulations are mainly mediated though soil microbial communities. Despite bacteria ranking among the most abundant and diverse groups of soil microorganisms, the effects of long-term organic fertilization (OF) and chemical-organic fertilization (COF) on soil bacterial diversity and community composition remain unclear. In this study, we conducted a meta-analysis and demonstrated that OF had no significant effect on bacterial alpha diversity. Application of chemical fertilizer and crop residue significantly decreased bacterial Richness index. Both OF and COF significantly altered bacterial community structure, with these changes being predominately attributed to shifts in soil pH. For bacterial phyla, both OF and COF significantly increased the relative abundance of Proteobacteria and Bacteroidetes, suggesting that OF and COF may cause the enrichment of copiotrophic taxa. In addition, COF significantly increased the relative abundance of Gammaproteobacteria but decreased the relative abundance of Acidobacteria. Overall, our results suggest that organic and chemical-organic fertilization can effectively maintain bacterial diversity and enhance soil fertility in agroecosystems, and the alteration of soil bacterial community structure is closely intertwined with soil pH.
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Affiliation(s)
- Xiangyang Shu
- Key Lab of Land Resources Evaluation and Monitoring in Southwest, Ministry of Education, Sichuan Normal University, Chengdu 610068, China
| | - Weijia Liu
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Han Huang
- College of Economics and Management, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Qinxin Ye
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Shunxi Zhu
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Zhaohui Peng
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China; (W.L.); (Q.Y.); (S.Z.)
| | - Yiding Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (L.D.)
| | - Liangji Deng
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (Y.L.); (L.D.)
| | - Zepeng Yang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Z.Y.); (H.C.); (D.L.)
| | - Honglin Chen
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Z.Y.); (H.C.); (D.L.)
| | - Dinghui Liu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Z.Y.); (H.C.); (D.L.)
| | - Jialing Shi
- Chengdu Agricultural and Rural Bureau, Chengdu 610066, China;
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Tambong JT, Bilodeau GJ, Fall ML. Editorial: Insights on plant-associated microorganisms: diversity, systematics and genomics. Front Microbiol 2023; 14:1323823. [PMID: 38029201 PMCID: PMC10644803 DOI: 10.3389/fmicb.2023.1323823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
- James T. Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Ottawa, ON, Canada
| | | | - Mamadou L. Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Saint-Jean-sur-Richelieu, QC, Canada
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30
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György É, Unguran KA, Laslo É. Biocide Tolerance and Impact of Sanitizer Concentrations on the Antibiotic Resistance of Bacteria Originating from Cheese. Foods 2023; 12:3937. [PMID: 37959056 PMCID: PMC10648639 DOI: 10.3390/foods12213937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
In this study, we determined and identified the bacterial diversity of different types of artisanal and industrially produced cheese. The antibiotic (erythromycin, chloramphenicol, kanamycin, ampicillin, clindamycin, streptomycin, tetracycline, and gentamicin) and biocide (peracetic acid, sodium hypochlorite, and benzalkonium chloride) resistance of clinically relevant bacteria was determined as follows: Staphylococcus aureus, Macrococcus caseolyticus, Bacillus sp., Kocuria varians, Escherichia coli, Enterococcus faecalis, Citrobacter freundii, Citrobacter pasteurii, Klebsiella oxytoca, Klebsiella michiganensis, Enterobacter sp., Enterobacter cloacae, Enterobacter sichuanensis, Raoultella ornithinolytica, Shigella flexneri, and Salmonella enterica. Also, the effect of the sub-inhibitory concentration of three biocides on antibiotic resistance was determined. The microbiota of evaluated dairy products comprise diverse and heterogeneous groups of bacteria with respect to antibiotic and disinfectant tolerance. The results indicated that resistance was common in the case of ampicillin, chloramphenicol, erythromycin, and streptomycin. Bacillus sp. SCSSZT2/3, Enterococcus faecalis SRGT/1, E. coli SAT/1, Raoultella ornithinolytica MTT/5, and S. aureus SIJ/2 showed resistance to most antibiotics. The tested bacteria showed sensitivity to peracetic acid and a different level of tolerance to benzalkonium chloride and sodium hypochlorite. The inhibition zone diameter of antibiotics against Enterococcus faecalis SZT/2, S. aureus JS11, E. coli CSKO2, and Kocuria varians GRT/10 was affected only by the sub-inhibitory concentration of peracetic acid.
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Affiliation(s)
- Éva György
- Department of Food Science, Faculty of Economics, Socio-Human Sciences and Engineering, Sapientia Hungarian University of Transylvania, 530104 Miercurea Ciuc, Romania; (K.A.U.); (É.L.)
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31
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Zhai K, Hua Y, Liang J, Li J, Wang Z, Liu L, Gao M, Sa R, Zhao M. Soil microbial diversity under different types of interference in birch secondary forest in the Greater Khingan Mountains in China. Front Microbiol 2023; 14:1267746. [PMID: 37954244 PMCID: PMC10635414 DOI: 10.3389/fmicb.2023.1267746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/05/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Soil microorganisms are an important component of soil ecosystems with an indispensable role in forest ecosystems. We analyzed the soil microbial diversity in birch secondary forest formed by natural restoration or artificial reconstruction after interference by burning, clear cutting, and gradient cutting, and the Betula platyphylla Suk undisturbed forest in the Greater Khingan Mountains in China. Methods Illumina high-throughput sequencing technology was used to analyze the characteristics of the soil microbial community during the restoration process of birch secondary forest caused by the different types of interference. The relationships between bacteria and fungi were analyzed. The gene functions of the soil bacterial community and the ecological functions of soil fungi were predicted using PICRUSt and FunGuild, respectively. Results At the phylum level, the species and quantity of bacteria were more abundant than that of fungi. At the genus level, no obvious differences in the abundance of bacteria were observed; there were obvious differences in the abundance of fungi. Among the eight sample plots, the artificial larch forest belt had the highest bacterial and fungal alpha diversity, which was slightly higher than undisturbed forest, while the other sample plots were significantly lower. Gradual cutting pure birch forest bacteria and fungi had the highest beta diversity, and artificial larch forest belt bacteria and heavy burn sample plot fungi had the lowest beta diversity. Samples from the cutting and burning sample plots were significantly different from the undisturbed forest at the phylum level of Acidobacteriae, Acidimicrobiia, Mortierellomycetes and Sordariomycetes. We found statistical differences in biomarkers between bacterial and fungal communities in undisturbed forest and artificial larch forest belt and burn sample plots. PICRUSt prediction and FunGuild prediction showed that soil bacterial and fungal communities were rich in gene and ecological functions, respectively. In the microbial network, the stability or anti-interference performance of the fungal community was higher than that of bacteria. Conclusion Our data reveal the characteristics of the soil microbial community during the restoration process of Betula platyphylla Suk secondary forest under different types of disturbance, which is of great significance for understanding the role of soil microorganisms in the forest ecological cycle.
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Affiliation(s)
- Kaitao Zhai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongchun Hua
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jingwen Liang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Li
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Zirui Wang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Lei Liu
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Minglong Gao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Rula Sa
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
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Salam MTB, Kataoka R. Changes in the Endophytic Bacterial Community of Brassica rapa after Application of Systemic Insecticides. Int J Mol Sci 2023; 24:15306. [PMID: 37894986 PMCID: PMC10607537 DOI: 10.3390/ijms242015306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted to compare the trends in endophytic bacterial response after insecticide application. Endophytic bacteria were isolated at 2 and 4 weeks after germination. Most insecticide treatments showed a declining trend in bacterial diversity and abundance, whereas an increasing trend was observed in the control. Therefore, insecticide use negatively affected non-target endophytic bacterial communities. Bacillus spp. was mostly dominant in the early stage in both insecticide treatment and control groups. Nevertheless, in the matured stage, mostly bacteria including Pseudomonas spp., Priestia spp. were dominant in groups treated with high insecticide concentrations. Therefore, plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions.
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Affiliation(s)
- Md. Tareq Bin Salam
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
- Soil, Water and Environment Discipline, Khulna University, Khulna 9208, Bangladesh
| | - Ryota Kataoka
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
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Kadoya R, Soga H, Matsuda M, Sato M, Taguchi S. Bacterial Population Changes during the Degradation Process of a Lactate (LA)-Enriched Biodegradable Polymer in River Water: LA-Cluster Preferable Bacterial Consortium. Polymers (Basel) 2023; 15:4111. [PMID: 37896354 PMCID: PMC10610160 DOI: 10.3390/polym15204111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/06/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
The lactate-based polyester poly[lactate (LA)-co-3-hydroxybutyrate (3HB)], termed LAHB, is a highly transparent and flexible bio-based polymeric material. There are many unknowns regarding its degradation process in riverine environments, especially the changes in bacterial flora that might result from its degradation and the identities of any LAHB-degrading bacteria. LAHB were immersed in the river water samples (A and B), and LAHB degradation was observed in terms of the weight change of the polymer and the microscopic changes on the polymer surfaces. A metagenomic analysis of microorganisms was conducted to determine the effect of LAHB degradation on the aquatic environment. The bacterial flora obtained from beta diversity analysis differed between the two river samples. The river A water sample showed the simultaneous degradation of LA and 3HB even though the copolymer was LA-enriched, suggesting preferable hydrolysis of the LA-enriched segments. In contrast, only 3HB degraded for the LAHB in the river B water sample. The linear discriminant analysis effect size (LEfSe) analysis revealed 14 bacteria that were significantly increased in the river A water sample during LAHB degradation, suggesting that these bacteria preferentially degraded and assimilated LA-clustering polymers. Our metagenomic analysis provides useful insights into the dynamic changes in microbial communities and LA-clustering polymer-degrading bacteria.
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Affiliation(s)
- Ryosuke Kadoya
- Department of Food and Nutrition, School of Life Studies, Sugiyama Jogakuen University, 17-3 Hoshigaoka Motomachi, Chikusa-ku, Nagoya 464-8662, Aichi, Japan; (H.S.); (M.M.)
| | - Hitomi Soga
- Department of Food and Nutrition, School of Life Studies, Sugiyama Jogakuen University, 17-3 Hoshigaoka Motomachi, Chikusa-ku, Nagoya 464-8662, Aichi, Japan; (H.S.); (M.M.)
| | - Miki Matsuda
- Department of Food and Nutrition, School of Life Studies, Sugiyama Jogakuen University, 17-3 Hoshigaoka Motomachi, Chikusa-ku, Nagoya 464-8662, Aichi, Japan; (H.S.); (M.M.)
| | - Michio Sato
- Microbial Genetics Laboratory, Department of Agricultural Chemistry, Graduate School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawsaki 214-8571, Kanagawa, Japan;
| | - Seiichi Taguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada, Kobe 657-8501, Hyogo, Japan;
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34
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DeVilbiss SE, Taylor JM, Hicks M. Salinization and sedimentation drive contrasting assembly mechanisms of planktonic and sediment-bound bacterial communities in agricultural streams. Glob Chang Biol 2023; 29:5615-5633. [PMID: 37548955 DOI: 10.1111/gcb.16905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Agriculture is the most dominant land use globally and is projected to increase in the future to support a growing human population but also threatens ecosystem structure and services. Bacteria mediate numerous biogeochemical pathways within ecosystems. Therefore, identifying linkages between stressors associated with agricultural land use and responses of bacterial diversity is an important step in understanding and improving resource management. Here, we use the Mississippi Alluvial Plain (MAP) ecoregion, a highly modified agroecosystem, as a case study to better understand agriculturally associated drivers of stream bacterial diversity and assembly mechanisms. In the MAP, we found that planktonic bacterial communities were strongly influenced by salinity. Tolerant taxa increased with increasing ion concentrations, likely driving homogenous selection which accounted for ~90% of assembly processes. Sediment bacterial phylogenetic diversity increased with increasing agricultural land use and was influenced by sediment particle size, with assembly mechanisms shifting from homogenous to variable selection as differences in median particle size increased. Within individual streams, sediment heterogeneity was correlated with bacterial diversity and a subsidy-stress relationship along the particle size gradient was observed. Planktonic and sediment communities within the same stream also diverged as sediment particle size decreased. Nutrients including carbon, nitrogen, and phosphorus, which tend to be elevated in agroecosystems, were also associated with detectable shifts in bacterial community structure. Collectively, our results establish that two understudied variables, salinity and sediment texture, are the primary drivers of bacterial diversity within the studied agroecosystem, whereas nutrients are secondary drivers. Although numerous macrobiological communities respond negatively, we observed increasing bacterial diversity in response to agricultural stressors including salinization and sedimentation. Elevated taxonomic and phylogenetic bacterial diversity likely increases the probability of detecting community responses to stressors. Thus, bacteria community responses may be more reliable for establishing water quality goals within highly modified agroecosystems that have experienced shifting baselines.
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Affiliation(s)
- Stephen E DeVilbiss
- U.S. Geological Survey, Lower Mississippi-Gulf Water Science Center, Oxford, Mississippi, USA
| | - Jason M Taylor
- United States Department of Agriculture-Agricultural Research Service, National Sedimentation Laboratory, Oxford, Mississippi, USA
| | - Matthew Hicks
- United States Geological Survey, Lower Mississippi-Gulf Water Science Center, Jackson, Mississippi, USA
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Siebielec S, Marzec-Grządziel A, Siebielec G, Ukalska-Jaruga A, Kozieł M, Gałązka A, Przybyś M, Sugier P, Urbaniak M. Microbial Community Response to Various Types of Exogenous Organic Matter Applied to Soil. Int J Mol Sci 2023; 24:14559. [PMID: 37834007 PMCID: PMC10572811 DOI: 10.3390/ijms241914559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/23/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023] Open
Abstract
Recycling of solid biowaste and manure would reduce the dependence of agriculture on synthetic products. Most of the available studies on the effects of exogenous organic matter (EOM) application to soil were focused on nutrients and crop yield, with much less attention to microbiological processes in soil, especially using modern molecular methods. The aim of this study was to evaluate the effects of various types of manure, sewage sludge and bottom sediment on the biochemical activity and biodiversity of soil and plant yield in a pot experiment. The soil was treated with a range of EOM types: six types of manure (cattle, pig, goat, poultry, rabbit and horse manure; two bottom sediments (from urban and rural systems); and two types of municipal sewage sludge. All EOMs stimulated dehydrogenases activity at a rate of 20 t ha-1. Alkaline phosphatase was mostly stimulated by poultry manure and one of the sludges. In general, the two-fold greater rate of EOMs did not further accelerate the soil enzymes. The functional diversity of the soil microbiome was stimulated the most by cattle and goat manure. EOMs produce a shift in distribution of the most abundant bacterial phyla and additionally introduce exogenous bacterial genera to soil. Poultry and horse manure introduced the greatest number of new genera that were able to survive the strong competition in soil. EOMs differentiated plant growth in our study, which was correlated to the rate of nitrate release to soil. The detailed impacts of particular amendments were EOM-specific, but in general, no harm for microbial parameters was observed for manure and sludge application, regardless of their type. There was also no proof that the PAH and pesticide contents measured in manure or sludge had any effect on microbial activity and diversity.
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Affiliation(s)
- Sylwia Siebielec
- Department of Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland; (A.M.-G.); (M.K.); (A.G.)
| | - Anna Marzec-Grządziel
- Department of Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland; (A.M.-G.); (M.K.); (A.G.)
| | - Grzegorz Siebielec
- Department of Soil Science Erosion and Land Protection, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland; (G.S.); (A.U.-J.)
| | - Aleksandra Ukalska-Jaruga
- Department of Soil Science Erosion and Land Protection, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland; (G.S.); (A.U.-J.)
| | - Monika Kozieł
- Department of Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland; (A.M.-G.); (M.K.); (A.G.)
| | - Anna Gałązka
- Department of Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland; (A.M.-G.); (M.K.); (A.G.)
| | - Marcin Przybyś
- Department of Plant Breeding and Biotechnology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Pulawy, Poland;
| | - Piotr Sugier
- Department of Botany, Mycology and Ecology, Institute of Biological Sciences, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Magdalena Urbaniak
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
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36
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Pérez-Losada M, Crandall KA. Spatial diversity of the skin bacteriome. Front Microbiol 2023; 14:1257276. [PMID: 37795302 PMCID: PMC10546022 DOI: 10.3389/fmicb.2023.1257276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
The bacterial communities of the human skin impact its physiology and homeostasis, hence elucidating the composition and structure of the healthy skin bacteriome is paramount to understand how bacterial imbalance (i.e., dysbiosis) may lead to disease. To obtain an integrated view of the spatial diversity of the skin bacteriome, we surveyed from 2019 to 2023 five skin regions (belly button, behind ears, between toes, calves and forearms) with different physiological characteristics (dry, moist and sebaceous) in 129 healthy adults (579 samples - after data cleaning). Estimating bacterial diversity through 16S rRNA metataxonomics, we identified significant (p < 0.0001) differences in the bacterial relative abundance of the four most abundant phyla and 11 genera, alpha- and beta-diversity indices and predicted functional profiles (36 to 400 metabolic pathways) across skin regions and microenvironments. No significant differences, however, were observed across genders, ages, and ethnicities. As previously suggested, dry skin regions (forearms and calves) were more even, richer, and functionally distinct than sebaceous (behind ears) and moist (belly button and between toes) regions. Within skin regions, bacterial alpha- and beta-diversity also varied significantly for some of the years compared, suggesting that skin bacterial stability may be region and subject dependent. Our results, hence, confirm that the skin bacteriome varies systematically across skin regions and microenvironments and provides new insights into the internal and external factors driving bacterial diversity.
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Affiliation(s)
- Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
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Fang J, Wei S, Gao Y, Zhang X, Cheng Y, Wang J, Ma J, Shi G, Bai L, Xie R, Zhao X, Ren Y, Lu Z. Character variation of root space microbial community composition in the response of drought-tolerant spring wheat to drought stress. Front Microbiol 2023; 14:1235708. [PMID: 37779714 PMCID: PMC10541208 DOI: 10.3389/fmicb.2023.1235708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Drought is the most prevalent environmental stress in crop production, posing a significant danger to food security. Microorganisms in the crop root zone affect crop growth and development, enhance effective nutrient use, and resist adversity hazards. To analyze the changes and functional differences of root space microbial (endosphere-rhizosphere-bulk soil) communities in spring wheat under drought stress. In this study, the root, rhizosphere, and bulk soil of the drought-tolerant group (DTG, three varieties) and drought-sensitive group (DSG, three varieties) were collected. The control (CK, 25-28%), moderate drought (MD, 15-18%), and severe drought (SD, 9-12%) were analyzed by high-throughput sequencing and bioinformatics. The results showed significant differences in the diversity of Bacteria and Fungi in the root space of spring wheat under drought stress (P < 0.05), with the drought-tolerant group exhibiting higher microbial diversity. The microbial community change in spring wheat root space was mainly determined by the niche differentiation of endosphere, rhizosphere, and bulk soil and declined from endosphere to bulk soil due to drought. The antagonism between microbial and root-space species increased, and the community's complexity and stability deteriorated. Enriching drought-resistant preference groups like Actinobaciota, Variovorax, Streptomyces, and Conocybe altered the structure and function of the microbial community in the root space of spring wheat. Spring wheat's root space Bacteria and Fungi have different strategies to respond to drought.
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Affiliation(s)
- Jing Fang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yanrong Gao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Xiangqian Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Jianguo Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Gongfu Shi
- School of Life Science, Inner Mongolia University, Hohhot, China
| | - Lanfang Bai
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Yongfeng Ren
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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Yao L, Ding J, Zhang T, Jia Y, Dai J, Zheng X, Yu J, Yang C, Chen X. Heterogeneity changes of active bacterial community on cigar filler leaves after fermentation based on metagenome. Biosci Biotechnol Biochem 2023; 87:1056-1067. [PMID: 37279907 DOI: 10.1093/bbb/zbad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Microorganisms play an important role in cigar fermentation. To further explore the dynamic changes of bacterial community composition, the changes of surface bacterial diversity of cigar filler leaves were investigated in the present study by high-throughput sequencing technology. It was found that the surface bacterial richness was declined after fermentation, and the dominant microorganisms on the surface of cigar filler leaves evolved from Pseudomonas spp. and Sphingomonas spp. before fermentation to Staphylococcus spp. after fermentation. The chemical composition and sensory quality evaluation of cigar filler leaves were closely related to the changes of surface bacterial community. The changes of the dominant surface bacterial community led to the differences of metabolic functions, among which the metabolic pathways such as the synthesis of secondary metabolites, carbon metabolism, and amino acid biosynthesis were significantly different. The results provide a basis for clarifying the roles of bacteria in fermentation of cigar filler leaves.
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Affiliation(s)
- Lan Yao
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
| | - Jingyi Ding
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
| | - Tongtong Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
| | - Youpiao Jia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
| | - Jun Dai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
| | - Xueyun Zheng
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
| | - Jun Yu
- Tobacco Research Institute of Hubei Province, Wuhan, China
| | - Chunlei Yang
- Tobacco Research Institute of Hubei Province, Wuhan, China
| | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), College of Bioengineering, Hubei University of Technology, 28th of Nanli Road, Wuhan, China
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Weng X, Wang M, Sui X, Frey B, Liu Y, Zhang R, Ni H, Li M. High Ammonium Addition Changes the Diversity and Structure of Bacterial Communities in Temperate Wetland Soils of Northeastern China. Microorganisms 2023; 11:2033. [PMID: 37630593 PMCID: PMC10459003 DOI: 10.3390/microorganisms11082033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
The soil microbiome is an important component of wetland ecosystems and plays a pivotal role in nutrient cycling and climate regulation. Nitrogen (N) addition influences the soil's microbial diversity, composition, and function by affecting the soil's nutrient status. The change in soil bacterial diversity and composition in temperate wetland ecosystems in response to high ammonium nitrogen additions remains unclear. In this study, we used high-throughput sequencing technology to study the changes of soil bacterial diversity and community structure with increasing ammonium concentrations [CK (control, 0 kg ha-1 a-1), LN (low nitrogen addition, 40 kg ha-1 a-1), and HN (high nitrogen addition, 80 kg ha-1 a-1)] at a field experimental site in the Sanjiang Plain wetland, China. Our results showed that except for soil organic carbon (SOC), other soil physicochemical parameters, i.e., soil moisture content (SMC), dissolved organic nitrogen (DON), total nitrogen (TN), pH, ammonium nitrogen (NH4+), and dissolved organic carbon (DOC), changed significantly among three ammonium nitrogen addition concentrations (p < 0.05). Compared to CK, LN did not change soil bacterial α-diversity (p > 0.05), and HN only decreased the Shannon (p < 0.05) and did not change the Chao (p > 0.05) indices of soil bacterial community. Ammonium nitrogen addition did not significantly affect the soil's bacterial community structure based on non-metric multidimensional scaling (NMDS) and PERMANOVA (ADONIS) analyses. Acidobacteriota (24.96-31.11%), Proteobacteria (16.82-26.78%), Chloroflexi (10.34-18.09%), Verrucomicrobiota (5.23-11.56%), and Actinobacteriota (5.63-8.75%) were the most abundant bacterial phyla in the soils. Nitrogen addition changed the complexity and stability of the bacterial network. SMC, NO3-, and pH were the main drivers of the bacterial community structure. These findings indicate that enhanced atmospheric nitrogen addition may have an impact on bacterial communities in soil, and this study will allow us to better understand the response of the soil microbiome in wetland ecosystems in the framework of increasing nitrogen deposition.
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Affiliation(s)
- Xiaohong Weng
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (X.W.); (M.W.)
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (X.W.); (M.W.)
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (X.W.); (M.W.)
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland;
| | - Yingnan Liu
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150001, China; (Y.L.); (R.Z.)
| | - Rongtao Zhang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150001, China; (Y.L.); (R.Z.)
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, Harbin 150022, China;
| | - Maihe Li
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland;
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
- School of Life Science, Hebei University, Baoding 071002, China
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40
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Luzardo-Ocampo I, Ocampo-Ruiz AL, Dena-Beltrán JL, Martínez de la Escalera G, Clapp C, Macotela Y. The Diversity of Gut Microbiota at Weaning Is Altered in Prolactin Receptor-Null Mice. Nutrients 2023; 15:3447. [PMID: 37571383 PMCID: PMC10420910 DOI: 10.3390/nu15153447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Maternal milk supports offspring development by providing microbiota, macronutrients, micronutrients, immune factors, and hormones. The hormone prolactin (PRL) is an important milk component with protective effects against metabolic diseases. Because maternal milk regulates microbiota composition and adequate microbiota protect against the development of metabolic diseases, we aimed to investigate whether PRL/PRL receptor signaling regulates gut microbiota composition in newborn mice at weaning. 16SrRNA sequencing of feces and bioinformatics analysis was performed to evaluate gut microbiota in PRL receptor-null mice (Prlr-KO) at weaning (postnatal day 21). The normalized colon and cecal weights were higher and lower, respectively, in the Prlr-KO mice relative to the wild-type mice (Prlr-WT). Relative abundances (Simpson Evenness Index), phylogenetic diversity, and bacterial concentrations were lower in the Prlr-KO mice. Eleven bacteria species out of 470 differed between the Prlr-KO and Prlr-WT mice, with two genera (Anaerotruncus and Lachnospiraceae) related to metabolic disease development being the most common in the Prlr-KO mice. A higher metabolism of terpenoids and polyketides was predicted in the Prlr-KO mice compared to the Prlr-WT mice, and these metabolites had antimicrobial properties and were present in microbe-associated pathogenicity. We concluded that the absence of the PRL receptor altered gut microbiota, resulting in lower abundance and richness, which could contribute to metabolic disease development.
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Affiliation(s)
| | | | | | | | | | - Yazmín Macotela
- Instituto de Neurobiología, Universidad Nacional Autónoma de México (UNAM), Querétaro 76230, Mexico; (I.L.-O.); (A.L.O.-R.); (J.L.D.-B.); (G.M.d.l.E.); (C.C.)
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Frias J, Garriga A, Peñalver Á, Teixeira M, Beltrí R, Toubarro D, Simões N. Exploring Gut Microbiome Variations between Popillia japonica Populations of Azores. Microorganisms 2023; 11:1972. [PMID: 37630532 PMCID: PMC10459852 DOI: 10.3390/microorganisms11081972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
Popillia japonica (Coleoptera: Scarabaeidae), is an emerging invasive pest in Europe and America. In the Azores, this pest was first found on Terceira Island during the sixties and soon spread to other islands. The rate of infestation differs between islands, and we hypothesized that microbiome composition could play a role. Therefore, we sampled 3rd instar larvae and soil from sites with high and low infestation rates to analyze the microbiome using next-generation sequencing. We analyzed twenty-four 16S DNA libraries, which resulted in 3278 operational taxonomic units. The alpha and beta diversity of the soil microbiome was similar between sites. In contrast, the larvae from high-density sites presented a higher bacterial gut diversity than larvae from low-density sites, with biomarkers linked to plant digestion, nutrient acquisition, and detoxification. Consequently, larvae from high-density sites displayed several enriched molecular functions associated with the families Ruminococcaceae, Clostridiaceae and Rikenellaceae. These bacteria revealed a supportive function by producing several CAZyme families and other proteins. These findings suggest that the microbiome must be one drive for the increase in P. japonica populations, thus providing a checkpoint in the establishment and spread of this pest.
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Affiliation(s)
- Jorge Frias
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Anna Garriga
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
- Departament de Biologia Animal, Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ángel Peñalver
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Mário Teixeira
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Rubén Beltrí
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Duarte Toubarro
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
| | - Nelson Simões
- Centro de Biotecnologia dos Açores, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9500-321 Ponta Delgada, Portugal
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Cheng A, Gajic G, Doni F. Editorial: Soil biota and climate smart crops. Front Plant Sci 2023; 14:1250831. [PMID: 37538065 PMCID: PMC10395117 DOI: 10.3389/fpls.2023.1250831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023]
Affiliation(s)
- Acga Cheng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Gordana Gajic
- Department of Ecology, Institute for Biological Research `Sinisa Stankovic`, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Febri Doni
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, West Java, Indonesia
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Ohan JA, Siani R, Kurth JK, Sommer V, Glaser K, Karsten U, Schloter M, Schulz S. Microbiome convergence and deterministic community assembly along successional biocrust gradients on potash salt heaps. FEMS Microbiol Ecol 2023:fiad081. [PMID: 37463797 DOI: 10.1093/femsec/fiad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Potash mining, typically performed for agricultural fertilizer production, can create piles of residual salt waste that are ecologically detrimental and difficult to revegetate. Biological soil crusts (biocrusts) have been found growing on and around these heaps, suggesting resilience to the hypersaline environment. We set out to understand the community dynamics of biocrust formation by examining two succesionary salinity gradients at historical mining sites using a high throughput amplicon sequencing. Bare heaps were distinct, with little overlap between sites, and were characterized by high salinity, low nutrient availability, and specialized, low diversity microbial communities, dominated by Halobacteria, Chloroflexia, and Deinococci. 'Initial' stages of biocrust development were dominated by site-specific Cyanobacteria, with significant overlap between sites. Established biocrusts were the most diverse, with large proportions of Alphaproteobacteria, Anaerolineae, and Planctomycetacia. Along the salinity gradient at both sites, salinity decreased, pH decreased, and nutrients and Chlorophyll a increased. Microbiomes between sites converged during succession and community assembly process analysis revealed biocrusts at both sites were dominated by deterministic, niche-based processes; indicating a high degree of phylogenetic turnover. We posit early cyanobacterial colonization is essential for biocrust initiation, and facilitates later establishment of plant and other higher-level biota.
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Affiliation(s)
- Juliette A Ohan
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Julia K Kurth
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Veronika Sommer
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Strasse 3, 18051, Rostock, Germany
- upi Umweltprojektingenieurgesellschaft, Stendal, Germany
| | - Karin Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Strasse 3, 18051, Rostock, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Strasse 3, 18051, Rostock, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
- Department of Ecology and Ecosystem Management, School of Life Sciences, Technical University Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Center Munich, Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Munich, Germany
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Khan A, Wei Y, Adnan M, Ali I, Zhang M. Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane. Front Microbiol 2023; 14:1197246. [PMID: 37492263 PMCID: PMC10364612 DOI: 10.3389/fmicb.2023.1197246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023] Open
Abstract
Ratooning in sugarcane often leads to soil problems such as degradation, acidification, and soil-borne diseases that negatively impact agriculture output and sustainability. Understanding the alteration in bacterial communities, activities, and their diversity connected to the plant and soil under consecutive ratooning still needs to be clarified. To address this gap, multidisciplinary approaches such as Illumina sequencing and measurement of soil nutrients and enzymes were used in this study to analyze soil samples in a field with three consecutive ratooning sugarcane crops. The results revealed a decline in crop yield and significant changes (P < 0.05) in soil nutrients and bacterial diversity. Ratooning resulted in an acidic environment that potentially affected soil nutrients and enzyme activity responsible for the cycling of carbon, nitrogen, and phosphorous. Non-metric dimensional scaling (NMDS) confirmed the effect of ratooning on soil attributes. Moreover, a positive correlation between soil physiochemical properties and soil enzymes was observed. Alpha diversity indices indicated greater bacterial diversity in ratooning sugarcane. Bacterial diversity varied throughout the ratooning crop, and significant (P < 0.05) changes in the relative abundance of specific phyla were observed. For example, the relative abundance of Proteobacteria was decreased, and Acidobacteria was increased. Furthermore, the relative abundance of bacterial phyla was strongly correlated with soil attributes (enzymes and nutrients). Additionally, ratooning results in the depletion or enrichment of important agriculture microbial genera such as Sphingomonas, Burkholderia, and Acidothermus (P < 0.05), respectively. In conclusion, ratooning led to soil acidification, decreased fertility, and altered microbial structure and activity. Thus, restraining soil acidity by means of liming or biofertilizers to maintain soil nutrients, enzymatic activities, and microbial structure could benefit plants and soil to help create a long-term eco-friendly sugarcane cropping system.
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Affiliation(s)
- Abdullah Khan
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Department of Plant Protection, College of Agriculture, Guangxi University, Nanning, China
- Department of Plant Sciences, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Yibin Wei
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Muhammad Adnan
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Izhar Ali
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Department of Plant Protection, College of Agriculture, Guangxi University, Nanning, China
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Mourgela RN, Kioukis A, Pourjam M, Lagkouvardos I. Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments. Microorganisms 2023; 11:1767. [PMID: 37512939 PMCID: PMC10384058 DOI: 10.3390/microorganisms11071767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.
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Affiliation(s)
- Rafaila Nikola Mourgela
- School of Chemical and Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Antonios Kioukis
- Department of Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, 71500 Heraklion, Greece
| | - Mohsen Pourjam
- ZIEL Institute of Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Ilias Lagkouvardos
- Department of Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, 71500 Heraklion, Greece
- ZIEL Institute of Food and Health, Technical University of Munich, 85354 Freising, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece
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Kumar R, Choudhary JS, Naik SK, Mondal S, Mishra JS, Poonia SP, Kumar S, Hans H, Kumar S, Das A, Kumar V, Bhatt BP, Chaudhari SK, Malik RK, Craufurd P, McDonald A, Sherpa SR. Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India. Front Microbiol 2023; 14:1181317. [PMID: 37485518 PMCID: PMC10356824 DOI: 10.3389/fmicb.2023.1181317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied. Methods Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods. Results and Discussion Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50-23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2-13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.
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Affiliation(s)
- Rakesh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Jaipal Singh Choudhary
- ICAR Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, Jharkhand, India
| | - Sushanta Kumar Naik
- ICAR Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, Jharkhand, India
| | - Surajit Mondal
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | | | - Shish Pal Poonia
- Cereal Systems Initiative for South Asia (CSISA)-CIMMYT, Patna, India
| | - Saurabh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Hansraj Hans
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Sanjeev Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Anup Das
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Virender Kumar
- International Rice Research Institute, Los Banos, Philippines
| | | | | | - Ram Kanwar Malik
- Cereal Systems Initiative for South Asia (CSISA)-CIMMYT, Patna, India
| | | | - Andrew McDonald
- Soil and Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
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Xiong H, Liu YL, Li Y, Zhang YR, Huang XC, Yang YH, Zhu HQ, Jiang TM. Effects of long-term fertilization patterns on bacterial community structure and soil nutrients in dryland of yellow soil. Ying Yong Sheng Tai Xue Bao 2023; 34:1949-1956. [PMID: 37694479 DOI: 10.13287/j.1001-9332.202307.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Understanding the responses of soil bacterial community to long-term fertilization in dryland of yellow soil could provide theoretical basis for establishing scientific fertilization system and cultivating healthy soil. Based on a 25-year long-term fertilization experiment on yellow soil, we collected soil samples from 0-20 cm layer under different fertilization treatments: no fertilization (CK), balanced application of N, P and K fertilizers (NPK), single application of organic fertilizer (M), combined application of constant organic and inorganic fertilizer (MNPK), and 1/2 organic fertilizer instead of 1/2 chemical fertilizer (MNP). Illumina MiSeq high-throughput sequencing technology was used to examine the effects of different fertilization patterns on soil bacterial community structure and soil nutrient content. The main driving factors of soil bacterial community were explored. The results showed that soil pH and organic matter content under treatments with organic fertilizer increased by 11.4%-13.5% and 28.8%-52.0%, respectively, compared to that under NPK treatment. Long-term fertilization did not affect soil bacterial α diversity, but significantly affected soil bacterial β diversity. Compared with CK and NPK treatment, treatments of M, MNP, and MNPK significantly changed soil bacterial community structure, and increased the relative abundance of Fusobacteria and Anaerobes. Four fertilization treatments increased the relative abundance of Bacteroidetes, and decreased the relative abundance of Actinomyces and Campylobacter, compared to CK. Soil pH was the most important factor affecting soil bacterial community structure. Fertilization-stimulated rare microbial taxa (Pumilomyces and Anaerobes) were more sensitive to changes in different environmental factors and were the main drivers of the formation of community versatility. In conclusion, organic fertilizer improved soil properties and fertility and changed soil bacterial community structure, which are conducive to cultivating healthy soil.
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Affiliation(s)
- Han Xiong
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Yan-Ling Liu
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Yu Li
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Ya-Rong Zhang
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Xing-Cheng Huang
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Ye-Hua Yang
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Hua-Qing Zhu
- Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
| | - Tai-Ming Jiang
- Scientific Observing and Experimental Station of Arable Land Conservation and Agriculture Environment (Guizhou), Ministry of Agriculture and Rural Affairs, Guiyang 550006, China
- Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
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Gupta S, Gupta SL, Singh A, Oswal N, Bal V, Rath S, George A, Basu S. IgA Determines Bacterial Composition in the Gut. Crohns Colitis 360 2023; 5:otad030. [PMID: 37288325 PMCID: PMC10244000 DOI: 10.1093/crocol/otad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 06/09/2023] Open
Abstract
Background Classically, IgA in the gut prevents the invasion of microorganisms to systemic organs through the process of neutralization and immune exclusion. Interestingly, recent reports suggest that IgA might help in biofilm formation and promote bacterial growth inside the intestine. Methods In this study, we used flow cytometry, ELISA, and chemical models of colitis to test whether the quality and quantity of IgA can select for bacterial persistence in the gut. Results We found that members of Proteobacteria, such as γ-Proteobacteria and SFB, are preferentially coated by IgA in WT mice. In the partial absence of either T-dependent or -independent IgA responses, there are no significant differences in the frequency of bacteria coated with IgA in mice. However, Rag-/- mice that lack all antibodies had a severe reduction in Proteobacteria and were resistant to DSS-induced colitis, suggesting that secretory IgA might be essential for differential retention of these taxa in the mouse gut. Rag-/- littermates in the F2 generation generated from (B6 × Rag-/-) F1 mice acquired the underrepresented bacteria taxa such as γ-Proteobacteria through vertical transmission of flora. They died soon after weaning, possibly due to the acquired flora. Additionally, continued exposure of Rag-/- mice to B6 flora by cohousing mice led to the acquisition of γ-Proteobacteria and mortality. Conclusions Together, our results indicate that host survival in the complete absence of an IgA response necessitates the exclusion of specific bacterial taxa from the gut microbiome.
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Affiliation(s)
| | | | - Aashima Singh
- Mucosa Immunology Laboratory, National Institute of Immunology, New Delhi, India
| | - Neelam Oswal
- Mucosa Immunology Laboratory, National Institute of Immunology, New Delhi, India
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, New Jersey, USA
| | - Vineeta Bal
- Mucosa Immunology Laboratory, National Institute of Immunology, New Delhi, India
- Indian Institute of Science Education and Research, Pune, India
| | - Satyajit Rath
- Mucosa Immunology Laboratory, National Institute of Immunology, New Delhi, India
- Translational Health Science and Technology Institute, Faridabad, India
| | - Anna George
- Mucosa Immunology Laboratory, National Institute of Immunology, New Delhi, India
| | - Srijani Basu
- Address correspondence to: Srijani Basu, PhD, Department of Medicine, Weill Cornell Medicine, New York, NY, USA ()
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Wang S, Zhou T, Zhao H, Zhang K, Cui J. Temporal and spatial changes in rhizosphere bacterial diversity of mountain Rhododendron mucronulatum. Front Microbiol 2023; 14:1201274. [PMID: 37415822 PMCID: PMC10321304 DOI: 10.3389/fmicb.2023.1201274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
To better conserve the ecology of the wild Rhododendron mucronulatum range, we studied the rhizosphere microenvironment of R. mucronulatum in Beijing's Yunmeng Mountain National Forest Park. R. mucronulatum rhizosphere soil physicochemical properties and enzyme activities changed significantly with temporal and elevational gradients. The correlations between soil water content (SWC), electrical conductivity (EC), organic matter content (OM), total nitrogen content (TN), catalase activity (CAT), sucrose-converting enzyme activity (INV), and urease activity (URE) were significant and positive in the flowering and deciduous periods. The alpha diversity of the rhizosphere bacterial community was significantly higher in the flowering period than in the deciduous period, and the effect of elevation was insignificant. The diversity of the R. mucronulatum rhizosphere bacterial community changed significantly with the change in the growing period. A network analysis of the correlations revealed stronger linkages between the rhizosphere bacterial communities in the deciduous period than in the flowering period. Rhizomicrobium was the dominant genus in both periods, but its relative abundance decreased in the deciduous period. Changes in the relative abundance of Rhizomicrobium may be the main factor influencing the changes in the R. mucronulatum rhizosphere bacterial community. Moreover, the R. mucronulatum rhizosphere bacterial community and soil characteristics were significantly correlated. Additionally, the influence of soil physicochemical properties on the rhizosphere bacterial community was larger than that of enzyme activity on the bacterial community. We mainly analyzed the change patterns in the rhizosphere soil properties and rhizosphere bacterial diversity of R. mucronulatum during temporal and spatial variation, laying the foundation for further understanding of the ecology of wild R. mucronulatum.
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Affiliation(s)
- Sirui Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Tiantian Zhou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Hewen Zhao
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Jinteng Cui
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Ancient Tree Health and Culture Engineering Technology Research Center, Beijing University of Agriculture, Beijing, China
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Parchemin C, Raviglione D, Mejait A, Sasal P, Faliex E, Clerissi C, Tapissier-Bontemps N. Antibacterial Activities and Life Cycle Stages of Asparagopsis armata: Implications of the Metabolome and Microbiome. Mar Drugs 2023; 21:363. [PMID: 37367688 DOI: 10.3390/md21060363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
The red alga Asparagopsis armata is a species with a haplodiplophasic life cycle alternating between morphologically distinct stages. The species is known for its various biological activities linked to the production of halogenated compounds, which are described as having several roles for the algae such as the control of epiphytic bacterial communities. Several studies have reported differences in targeted halogenated compounds (using gas chromatography-mass spectrometry analysis (GC-MS)) and antibacterial activities between the tetrasporophyte and the gametophyte stages. To enlarge this picture, we analysed the metabolome (using liquid chromatography-mass spectrometry (LC-MS)), the antibacterial activity and the bacterial communities associated with several stages of the life cycle of A. armata: gametophytes, tetrasporophytes and female gametophytes with developed cystocarps. Our results revealed that the relative abundance of several halogenated molecules including dibromoacetic acid and some more halogenated molecules fluctuated depending on the different stages of the algae. The antibacterial activity of the tetrasporophyte extract was significantly higher than that of the extracts of the other two stages. Several highly halogenated compounds, which discriminate algal stages, were identified as candidate molecules responsible for the observed variation in antibacterial activity. The tetrasporophyte also harboured a significantly higher specific bacterial diversity, which is associated with a different bacterial community composition than the other two stages. This study provides elements that could help in understanding the processes that take place throughout the life cycle of A. armata with different potential energy investments between the development of reproductive elements, the production of halogenated molecules and the dynamics of bacterial communities.
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Affiliation(s)
- Christelle Parchemin
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Delphine Raviglione
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Anouar Mejait
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Pierre Sasal
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Elisabeth Faliex
- Centre de Formation et de Recherche sur les Environnements Méditerranéens (CEFREM), UMR 5110 UPVD-CNRS, Université de Perpignan-Via Domitia, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Camille Clerissi
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Nathalie Tapissier-Bontemps
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
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