1
|
Ding Y, Wang L, Wang H, Li H. Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation. Foods 2024; 13:1580. [PMID: 38790880 DOI: 10.3390/foods13101580] [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: 03/17/2024] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.
Collapse
Affiliation(s)
- Yinting Ding
- College of Enology, Northwest A&F University, Xianyang 712100, China
| | - Lin Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
| | - Hua Li
- College of Enology, Northwest A&F University, Xianyang 712100, China
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
| |
Collapse
|
2
|
Cheng Y, Meng Y, Xu L, Yu H, Guo Y, Xie Y, Yao W, Qian H. Study on the Correlations between Quality Indicators of Dry-Aged Beef and Microbial Succession during Fermentation. Foods 2024; 13:1552. [PMID: 38790852 DOI: 10.3390/foods13101552] [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: 04/18/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Dry-aged beef has been long favored by people due to its unique flavor and taste. However, the inner relationship between its overall quality formation and microbial changes during dry aging has not yet received much attention and research. To deeply reveal the forming mechanism of the unique flavor and taste of dry-aged beef, correlations between its three main quality indicators, i.e., texture, free amino acids (FAAs), volatile flavor compounds (VFCs), and microbial succession were analyzed in this study. The results showed that Staphylococcus spp. and Macrococcus spp. were key strains that influenced the total quality of dry-aged beef and strongly correlated with chewiness, hardness, and sweet FAAs (Ala), providing beef with unique palatability and taste. Additionally, among VFCs, Staphylococcus spp. and Macrococcus spp. showed a strong correlation with octanal and heptanal, and meanwhile, those highly correlated with nonanal, pentanol, and oct-1-en-3-ol were Debaryomyces spp., Psychrobacter spp., and Brochothrix spp., respectively, providing beef with a unique flavor. Staphylococcus spp. was proposed to be the dominant genus for dry-aged beef. This study provides valuable reference for the understanding of the role of microorganisms involved in dry aging.
Collapse
Affiliation(s)
- Yuliang Cheng
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yiyun Meng
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Lin Xu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hang Yu
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Yahui Guo
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Yunfei Xie
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - Weirong Yao
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| | - He Qian
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
3
|
Ban S, Cheng W, Wang X, Niu J, Wu Q, Xu Y. Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making. mSystems 2024; 9:e0058623. [PMID: 38206013 PMCID: PMC10878095 DOI: 10.1128/msystems.00586-23] [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: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024] Open
Abstract
Microbial inoculation is an effective way to improve the quality of fermented foods via affecting the microbiota structure. However, it is unclear how the inoculation regulates the microbiota structure, and it is still difficult to directionally control the microbiota function via the inoculation. In this work, using the spontaneous fermentation of the starter (Daqu) for Chinese liquor fermentation as a case, we inoculated different microbiota groups at different time points in Daqu fermentation, and analyzed the effect of the inoculation on the final metabolic profile of Daqu. The inoculated microbiota and inoculated time points both significantly affected the final metabolites via regulating the microbial succession (P < 0.001), and multiple inoculations can promote deterministic assembly. Twenty-seven genera were identified to be related to microbial succession, and drove the variation of 121 metabolites. We then constructed an elastic network model to predict the profile of these 121 metabolites based on the abundances of 27 succession-related genera in Daqu fermentation. Procrustes analysis showed that the model could accurately predict the metabolic abundances (average Spearman correlation coefficients >0.3). This work revealed the effect of inoculation on the microbiota succession and the metabolic profile. The established predicted model of metabolic profile would be beneficial for directionally improving the food quality.IMPORTANCEThis work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality.
Collapse
Affiliation(s)
- Shibo Ban
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Cheng
- Sichuan Langjiu Group Co., Ltd, Luzhou, China
| | - Xi Wang
- Sichuan Langjiu Group Co., Ltd, Luzhou, China
| | - Jiao Niu
- Sichuan Langjiu Group Co., Ltd, Luzhou, China
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, State Key Laboratory of Food Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
4
|
Yu J, Lee JYY, Tang SN, Lee PKH. Niche differentiation in microbial communities with stable genomic traits over time in engineered systems. ISME J 2024; 18:wrae042. [PMID: 38470313 PMCID: PMC10987969 DOI: 10.1093/ismejo/wrae042] [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: 12/02/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions was correlated with the kinetics of treatment processes in the activated sludge systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.
Collapse
Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Kowloon, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| |
Collapse
|
5
|
Chen C, Yao W, Yu H, Yuan H, Guo W, Huang K, Tian H. Dynamics of microbial communities associated with flavor formation during sour juice fermentation and the milk fan drying process. J Dairy Sci 2023; 106:7432-7446. [PMID: 37641282 DOI: 10.3168/jds.2023-23244] [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: 01/09/2023] [Accepted: 05/04/2023] [Indexed: 08/31/2023]
Abstract
Milk fan is an acid-curd cheese with strong national characteristics (a traditional dairy product of the Bai nationality with a shape like a piece of paper) and a long history in Yunnan province, China. In our previous study, we characterized the microbial community diversity of milk fan, but the succession of microorganisms associated with flavor formation in milk fan is still unknown. Therefore, we examined the predominant microorganisms and their correlations with the formation of flavor in the fermentation of sour juice and drying of milk fan by gas chromatography mass spectrometry, high-throughput 16S rDNA sequencing, intergenic spacer sequencing and metatranscriptome analysis. We found that the relative abundances of Lactobacillus and Issatchenkia initially decreased and then increased with time during the fermentation of sour juice. However, the relative abundances of Acetobacter, Leuconostoc, Lactococcus, Geotrichum, and Dipodascus initially increased and then decreased. During the drying step, the relative abundances of Lactobacillus and Issatchenkia continuously increased and became the dominant microorganisms in the milk fan. The metatranscriptomes generated from the milk fan showed that "carbohydrate metabolism," "translation," and "signal transduction" were the main metabolic functions of the microbial communities. Rhodotorula and Yarrowia contained more differentially expressed genes than other genera, which indicated they may be associated with the production of the characteristic flavor. Furthermore, a Pearson correlation analysis showed that Lactococcus, Rhodotorula, Candida, Cutaneotrichosporon, and Yarrowia were significantly positively correlated with more aroma-active compounds, mainly ethyl acetate, 2-heptanone, isovaleraldehyde, butyric acid, nonanal, and hexanal. In conclusion, these findings contribute to a better understanding of the flavor production mechanism during the production of milk fan.
Collapse
Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Wenqian Yao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Wei Guo
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Ke Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, China.
| |
Collapse
|
6
|
Huang L, Tang Y, Zheng J, Kan J, Wu Y, Wu Y, Awad S, Ibrahim A, Du M. Relationship between the Dynamics of Flavor Compounds and Microbial Succession in the Natural Fermentation of Zhalajiao, a Popular Traditional Chinese Fermented Chili Paste. Foods 2023; 12:3849. [PMID: 37893743 PMCID: PMC10606277 DOI: 10.3390/foods12203849] [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: 08/20/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/29/2023] Open
Abstract
Zhalajiao, a traditional Chinese fermented food, is popular due to its unique flavor. Traditional Zhalajiao fermentation is closely related to flavor compounds production. However, the mechanisms underlying the formation of these crucial flavor components in Zhalajiao remain unclear. Here, we explored the dynamic changes in physical and chemical properties, microbial diversity, and flavor components of Zhalajiao at various fermentation times. In total, 6 organic acids, 17 amino acids, and 21 key volatile compounds were determined as flavor components. In Zhalajiao, Lactobacillus and Cyanobacterium were the main bacteria that were involved in the formation of crucial flavor compounds. Candida showed a significant correlation with 14 key flavor compounds during fermentation (p < 0.05) and was the main fungal genus associated with flavor formation in Zhalajiao. This research offers a theoretical foundation for the flavor regulation and quality assurance of Zhalajiao.
Collapse
Affiliation(s)
- Luhan Huang
- College of Food Science, Southwest University, Chongqing 400715, China
- Chinese-Hungarian Cooperative Research Center for Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China
| | - Yanyan Tang
- Chongqing Houjie Pharmaceutical Group Co., Ltd., Chongqing 404100, China
| | - Jiong Zheng
- College of Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China
| | - Jianquan Kan
- College of Food Science, Southwest University, Chongqing 400715, China
- Chinese-Hungarian Cooperative Research Center for Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China
| | - Yun Wu
- College of Food Science and Pharmaceutical Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yating Wu
- College of Food Science and Pharmaceutical Science, Xinjiang Agricultural University, Urumqi 830052, China
- Institute of Quality Standards & Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Sameh Awad
- Faculty of Agriculture, Alexandria University, Alexandria 21500, Egypt
| | - Amel Ibrahim
- Faculty of Agriculture, Alexandria University, Alexandria 21500, Egypt
| | - Muying Du
- College of Food Science, Southwest University, Chongqing 400715, China
- Chinese-Hungarian Cooperative Research Center for Food Science, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China
| |
Collapse
|
7
|
Singleton SL, Davis EW, Arnold HK, Daniels AMY, Brander SM, Parsons RJ, Sharpton TJ, Giovannoni SJ. Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment. Front Microbiol 2023; 14:1259014. [PMID: 37869676 PMCID: PMC10585116 DOI: 10.3389/fmicb.2023.1259014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Plastic waste accumulation in marine environments has complex, unintended impacts on ecology that cross levels of community organization. To measure succession in polyolefin-colonizing marine bacterial communities, an in situ time-series experiment was conducted in the oligotrophic coastal waters of the Bermuda Platform. Our goals were to identify polyolefin colonizing taxa and isolate bacterial cultures for future studies of the biochemistry of microbe-plastic interactions. HDPE, LDPE, PP, and glass coupons were incubated in surface seawater for 11 weeks and sampled at two-week intervals. 16S rDNA sequencing and ATR-FTIR/HIM were used to assess biofilm community structure and chemical changes in polymer surfaces. The dominant colonizing taxa were previously reported cosmopolitan colonizers of surfaces in marine environments, which were highly similar among the different plastic types. However, significant differences in rare community composition were observed between plastic types, potentially indicating specific interactions based on surface chemistry. Unexpectedly, a major transition in community composition occurred in all material treatments between days 42 and 56 (p < 0.01). Before the transition, Alteromonadaceae, Marinomonadaceae, Saccharospirillaceae, Vibrionaceae, Thalassospiraceae, and Flavobacteriaceae were the dominant colonizers. Following the transition, the relative abundance of these taxa declined, while Hyphomonadaceae, Rhodobacteraceae and Saprospiraceae increased. Over the course of the incubation, 8,641 colonizing taxa were observed, of which 25 were significantly enriched on specific polyolefins. Seven enriched taxa from families known to include hydrocarbon degraders (Hyphomonadaceae, Parvularculaceae and Rhodobacteraceae) and one n-alkane degrader (Ketobacter sp.). The ASVs that exhibited associations with specific polyolefins are targets of ongoing investigations aimed at retrieving plastic-degrading microbes in culture.
Collapse
Affiliation(s)
| | - Edward W. Davis
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K. Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - Susanne M. Brander
- Department of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR, United States
| | | | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | |
Collapse
|
8
|
Miao Z, Bai Y, Wang X, Han C, Wang B, Li Z, Sun J, Zheng F, Zhang Y, Sun B. Unravelling Metabolic Heterogeneity of Chinese Baijiu Fermentation in Age-Gradient Vessels. Foods 2023; 12:3425. [PMID: 37761135 PMCID: PMC10530105 DOI: 10.3390/foods12183425] [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: 08/14/2023] [Revised: 09/04/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Fermentation vessels affect the characteristics of food fermentation; however, we lack an approach to identify the biomarkers indicating fermentation. In this study, we applied metabolomics and high-throughput sequencing analysis to reveal the dynamic of metabolites and microbial communities in age-gradient fermentation vessels for baijiu production. Furthermore, we identified 64 metabolites during fermentation, and 19 metabolites significantly varied among the three vessels (p < 0.05). Moreover, the formation of these 19 metabolites were positively correlated with the core microbiota (including Aspergillus, Saccharomyces, Lactobacillus, and Bacillus). In addition, ethyl lactate or ethyl acetate were identified as the biomarkers for indicating the metabolism among age-gradient fermentation vessels by BP-ANN (R2 > 0.40). Therefore, this study combined the biological analysis and predictive model to identify the biomarkers indicating metabolism in different fermentation vessels, and it also provides a potential approach to assess the profiling of food fermentations.
Collapse
Affiliation(s)
- Zijian Miao
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Yu Bai
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xinlei Wang
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Chao Han
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Bowen Wang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Zexia Li
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Jinyuan Sun
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Fuping Zheng
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Yuhang Zhang
- Hebei Solid State Fermentation Making Industry Technology Research Institute, Hebei Baijiu Making Technology Innovation Center, Hebei Hengshui Laobaigan Liquor Co., Ltd., Hengshui 053000, China; (X.W.); (C.H.); (Z.L.); (Y.Z.)
| | - Baoguo Sun
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing Technology and Business University, Beijing 100048, China; (Z.M.); (Y.B.); (J.S.); (F.Z.); (B.S.)
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Laboratory for Food Quality and Safety, School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| |
Collapse
|
9
|
Dlugosch L, Bunse C, Bunk B, Böttcher L, Den TQ, Dittmar T, Hartmann M, Heinrichs M, Hintz NH, Milke F, Mori C, Niggemann J, Spröer C, Striebel M, Simon M. Naturally-induced biphasic phytoplankton spring bloom reveals rapid and distinct substrate and bacterial community dynamics. FEMS Microbiol Ecol 2023:fiad078. [PMID: 37442617 DOI: 10.1093/femsec/fiad078] [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] [Indexed: 07/15/2023] Open
Abstract
Phytoplankton spring blooms are typical features in coastal seas and provide heterotrophic bacteria with a rich blend of dissolved substrates. However, they are difficult to study in coastal seas in-situ. Here, we induced a phytoplankton spring bloom and followed its fate for 37 days in four 600 L-mesocosms. To specifically investigate the significance of phytoplankton-born dissolved organic carbon (DOC) we used artificial seawater with low DOC background and inoculated it with a 100 µm-prefiltered plankton community from the North Sea. A biphasic bloom developed, dominated by diatoms and Phaeocystis globosa respectively. In between, bacterial numbers peaked, followed by a peak in virus-like particles, implying that virus infection caused the collapse. Concentrations of dissolved free amino acids exhibited rapid changes, in particular during the diatom bloom and until the peak in bacterial abundance. Dissolved combined amino acids and neutral monosaccharides accumulated continuously, accounting for 22% of DOC as a mean and reaching levels as high as 44%. Bacterial communities were largely dominated by Bacteroidetes, especially the NS3a marine group (family Flavobacteriaceae), but Rhodobacteraceae and Gammaproteobacteria were also prominent members. Our study shows rapid organic matter and community composition dynamics that are hard to trace in natural coastal ecosystems.
Collapse
Affiliation(s)
- Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Carina Bunse
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, D-26129 Oldenburg, Germany
- Department of Marine Sciences, University of Gothenburg, Carl Skottsbergs gata 22 B, 41319 Göteborg, Sweden
| | - Boyke Bunk
- DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Lea Böttcher
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Tran Quoc Den
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, D-26129 Oldenburg, Germany
| | - Maike Hartmann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Mara Heinrichs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Nils H Hintz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstr. 1, D-26382 Wilhelmshaven, Germany
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Corinna Mori
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
| | - Cathrin Spröer
- DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Maren Striebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Schleusenstr. 1, D-26382 Wilhelmshaven, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, D-26129 Oldenburg, Germany
| |
Collapse
|
10
|
Tamarelle J, Creze MM, Savathdy V, Phonekeo S, Wallenborn J, Siengsounthone L, Fink G, Odermatt P, Kounnavong S, Sayasone S, Vonaesch P. Dynamics and consequences of nutrition-related microbial dysbiosis in early life: study protocol of the VITERBI GUT project. Front Nutr 2023; 10:1111478. [PMID: 37275646 PMCID: PMC10232750 DOI: 10.3389/fnut.2023.1111478] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Early life under- and overnutrition (jointly termed malnutrition) is increasingly recognized as an important risk factor for adult obesity and metabolic syndrome, a diet-related cluster of conditions including high blood sugar, fat and cholesterol. Nevertheless, the exact factors linking early life malnutrition with metabolic syndrome remain poorly characterized. We hypothesize that the microbiota plays a crucial role in this trajectory and that the pathophysiological mechanisms underlying under- and overnutrition are, to some extent, shared. We further hypothesize that a "dysbiotic seed microbiota" is transmitted to children during the birth process, altering the children's microbiota composition and metabolic health. The overall objective of this project is to understand the precise causes and biological mechanisms linking prenatal or early life under- or overnutrition with the predisposition to develop overnutrition and/or metabolic disease in later life, as well as to investigate the possibility of a dysbiotic seed microbiota inheritance in the context of maternal malnutrition. Methods/design VITERBI GUT is a prospective birth cohort allowing to study the link between early life malnutrition, the microbiota and metabolic health. VITERBI GUT will include 100 undernourished, 100 normally nourished and 100 overnourished pregnant women living in Vientiane, Lao People's Democratic Republic (PDR). Women will be recruited during their third trimester of pregnancy and followed with their child until its second birthday. Anthropometric, clinical, metabolic and nutritional data are collected from both the mother and the child. The microbiota composition of maternal and child's fecal and oral samples as well as maternal vaginal and breast milk samples will be determined using amplicon and shotgun metagenomic sequencing. Epigenetic modifications and lipid profiles will be assessed in the child's blood at 2 years of age. We will investigate for possible associations between metabolic health, epigenetics, and microbial changes. Discussion We expect the VITERBI GUT project to contribute to the emerging literature linking the early life microbiota, epigenetic changes and growth/metabolic health. We also expect this project to give new (molecular) insights into the mechanisms linking malnutrition-induced early life dysbiosis and metabolic health in later life, opening new avenues for microbiota-engineering using microbiota-targeted interventions.
Collapse
Affiliation(s)
- Jeanne Tamarelle
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Margaux M. Creze
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vanthanom Savathdy
- Lao Tropical and Public Health Institute, Ministry of Health, Vientiane, Lao People’s Democratic Republic (PDR)
| | - Sengrloun Phonekeo
- Lao Tropical and Public Health Institute, Ministry of Health, Vientiane, Lao People’s Democratic Republic (PDR)
| | - Jordyn Wallenborn
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Latsamy Siengsounthone
- Lao Tropical and Public Health Institute, Ministry of Health, Vientiane, Lao People’s Democratic Republic (PDR)
| | - Günther Fink
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Peter Odermatt
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sengchanh Kounnavong
- Lao Tropical and Public Health Institute, Ministry of Health, Vientiane, Lao People’s Democratic Republic (PDR)
| | - Somphou Sayasone
- Lao Tropical and Public Health Institute, Ministry of Health, Vientiane, Lao People’s Democratic Republic (PDR)
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
11
|
Li X, Gao Y, Han Y, Zhang R, Wang C, Wu X. Microbial communities and metabolite profiles during the fermentation of Chinese Dongbei suancai with Chinese baijiu as supplementary material. J Sci Food Agric 2023; 103:3521-3530. [PMID: 36799142 DOI: 10.1002/jsfa.12510] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/11/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In industrial production of suancai, baijiu is commonly used to inhibit the spoilage bacteria and enhance the flavor. However, the effects of baijiu on the microbial diversity and metabolic pathways of suancai are rarely reported in the literature. This study aimed to explore the microbial community, its predicted functional roles, and the metabolites formed during fermentation of Chinese Dongbei suancai fermented using a mixed starter with Chinese baijiu as supplementary material. RESULTS Results showed that Lactobacillus, Enterobacter, and Leuconostoc were the major bacterial genera in the Dongbei suancai fermented by adding baijiu. Linear discriminant analysis effect size indicated that Leuconostoc was the major biomarker in the early stage of fermentation, whereas Lactococcus, Weissella, and Lactobacillus plantarum were biomarkers in the middle and later stages of fermentation. A total of 638 metabolites were detected in suancai fermented by adding baijiu. However, the principal component analysis showed that baijiu significantly affected the metabolites of suancai in the early and later stages of fermentation. Furthermore, 58, 22, and 26 significantly differential metabolites (P < 0.01) were found on day 0, day 2, and day 30 of fermentation respectively. Moreover, Lactobacillus, Lactococcus, and Enterobacter had positive correlations with amino acids, nucleotides, organic acids, alcohols, and esters. Functional analysis implied that carbohydrate, amino acid, energy, and nucleotide metabolism were the major determinants of the characteristics of suancai fermented with baijiu as supplementary material. CONCLUSION Baijiu changed the metabolites of inoculated fermented Dongbei suancai. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Xiao Li
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Ya Gao
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanqiu Han
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Rui Zhang
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Chen Wang
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xingzhuang Wu
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| |
Collapse
|
12
|
Luo Y, Li D, Liao H, Xia X. Patterns of biogenic amine during broad bean paste fermentation: microbial diversity and functionality via Bacillus bioaugmentation. J Sci Food Agric 2023; 103:1315-1325. [PMID: 36114594 DOI: 10.1002/jsfa.12225] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Broad bean paste is a high nitrogen and high salt traditional Chinese condiment, which triggers biosynthesis of nitrogen hazards like biogenic amines (BAs). Mechanisms of association and applied research of functional safety and community assembly within multiple-microbial fermentation are currently lacking. Here, bioaugmentation was performed based on the profiles of BAs accumulation and microbial succession to evaluate the functional variation within broad bean paste fermentation. RESULTS Putrescine, spermine, and spermidine were the main BAs during traditional broad bean paste fermentation. Staphylococcus, Streptococcus, Lactococcus, Lactobacillus, Leuconostoc, and Bacillus were the predominant bacteria, whereas Aspergillus and Zygosaccharomyces dominated in fungal species, and community structure shifted upon salt exposure. PICRUSt software uncovered that Bacillus contributed significantly (>1%) to the amine oxidase gene family. Bacillus amyloliquefaciens 1-G6 and Bacillus licheniformis 2-B3 were screened to perform the bioaugmentation of broad bean paste, which achieved a 29% and 16% BA decrease respectively. Interaction network analysis showed that Cronobacter and Lactobacillus were significantly negatively correlated with Bacillus (ρ = -0.829 and ρ = -0.714, respectively, P < 0.05) in the B. amyloliquefaciens 1-G6 group, and Staphylococcus and Buttiauxella were inhibited by Bacillus (ρ = -0.657 and ρ = -0.543, respectively, P < 0.05) in the B. licheniformis 2-B3 group. CONCLUSION The synergism of amine oxidase activity and microbial interactions led to the decline of BAs. Thus, this study improves our understanding of the underlying mechanisms of microbial succession and functional variation to further facilitate the optimization of the fermented food industry.
Collapse
Affiliation(s)
- Yi Luo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Dongrui Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Hui Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| |
Collapse
|
13
|
Diehl JMC, Keller A, Biedermann PHW. Comparing the succession of microbial communities throughout development in field and laboratory nests of the ambrosia beetle Xyleborinus saxesenii. Front Microbiol 2023; 14:1151208. [PMID: 37152720 PMCID: PMC10159272 DOI: 10.3389/fmicb.2023.1151208] [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: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Some fungus-farming ambrosia beetles rely on multiple nutritional cultivars (Ascomycota: Ophiostomatales and/or yeasts) that seem to change in relative abundance over time. The succession of these fungi could benefit beetle hosts by optimal consumption of the substrate and extended longevity of the nest. However, abundances of fungal cultivars and other symbionts are poorly known and their culture-independent quantification over development has been studied in only a single species. Here, for the first time, we compared the diversity and succession of both fungal and bacterial communities of fungus gardens in the fruit-tree pinhole borer, Xyleborinus saxesenii, from field and laboratory nests over time. By amplicon sequencing of probed fungus gardens of both nest types at three development phases we showed an extreme reduction of diversity in both bacterial and fungal symbionts in laboratory nests. Furthermore, we observed a general transition from nutritional to non-beneficial fungal symbionts during beetle development. While one known nutritional mutualist, Raffaelea canadensis, was occurring more or less stable over time, the second mutualist R. sulphurea was dominating young nests and decreased in abundance at the expense of other secondary fungi. The quicker the succession proceeded, the slower offspring beetles developed, suggesting a negative role of these secondary symbionts. Finally, we found signs of transgenerational costs of late dispersal for daughters, possibly as early dispersers transmitted and started their own nests with less of the non-beneficial taxa. Future studies should focus on the functional roles of the few bacterial taxa that were present in both field and laboratory nests.
Collapse
Affiliation(s)
- Janina M. C. Diehl
- Chair of Forest Entomology and Protection, Institute of Forestry, University of Freiburg, Freiburg im Breisgau, Germany
- Insect-Fungus Interactions Research Group, Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
- *Correspondence: Janina M. C. Diehl,
| | - Alexander Keller
- Faculty of Biology, Cellular and Organismic Networks, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Peter H. W. Biedermann
- Chair of Forest Entomology and Protection, Institute of Forestry, University of Freiburg, Freiburg im Breisgau, Germany
- Peter H. W. Biedermann,
| |
Collapse
|
14
|
Abstract
Gut microbiome maturation in infants born prematurely is uniquely influenced by the physiological, clinical, and environmental factors surrounding preterm birth and early life, leading to altered patterns of microbial succession relative to term infants during the first months of life. These differences in microbiome composition are implicated in acute clinical conditions that disproportionately affect preterm infants, including necrotizing enterocolitis (NEC) and late-onset sepsis (LOS). Probiotic supplementation initiated early in life is an effective prophylactic measure for preventing NEC, LOS, and other clinical concerns relevant to preterm infants. In parallel, reported benefits of probiotics on the preterm gut microbiome, metabolome, and immune function are beginning to emerge. This review summarizes the current literature on the influence of probiotics on the gut microbiome of preterm infants, outlines potential mechanisms by which these effects are exerted, and highlights important clinical considerations for determining the best practices for probiotic use in premature infants.
Collapse
Affiliation(s)
- Emily M Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
15
|
Martínez-Cuesta R, Conlon R, Wang M, Blanco-Romero E, Durán D, Redondo-Nieto M, Dowling D, Garrido-Sanz D, Martin M, Germaine K, Rivilla R. Field scale biodegradation of total petroleum hydrocarbons and soil restoration by Ecopiles: microbiological analysis of the process. Front Microbiol 2023; 14:1158130. [PMID: 37152743 PMCID: PMC10160625 DOI: 10.3389/fmicb.2023.1158130] [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: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Ecopiling is a method for biodegradation of hydrocarbons in soils. It derives from Biopiles, but phytoremediation is added to biostimulation with nitrogen fertilization and bioaugmentation with local bacteria. We have constructed seven Ecopiles with soil heavily polluted with hydrocarbons in Carlow (Ireland). The aim of the study was to analyze changes in the microbial community during ecopiling. In the course of 18 months of remediation, total petroleum hydrocarbons values decreased in 99 and 88% on average for aliphatics and aromatics, respectively, indicating a successful biodegradation. Community analysis showed that bacterial alfa diversity (Shannon Index), increased with the degradation of hydrocarbons, starting at an average value of 7.59 and ending at an average value of 9.38. Beta-diversity analysis, was performed using Bray-Curtis distances and PCoA ordination, where the two first principal components (PCs) explain the 17 and 14% of the observed variance, respectively. The results show that samples tend to cluster by sampling time instead of by Ecopile. This pattern is supported by the hierarchical clustering analysis, where most samples from the same timepoint clustered together. We used DSeq2 to determine the differential abundance of bacterial populations in Ecopiles at the beginning and the end of the treatment. While TPHs degraders are more abundant at the start of the experiment, these populations are substituted by bacterial populations typical of clean soils by the end of the biodegradation process. Similar results are found for the fungal community, indicating that the microbial community follows a succession along the process. This succession starts with a TPH degraders or tolerant enriched community, and finish with a microbial community typical of clean soils.
Collapse
Affiliation(s)
| | - Robert Conlon
- EnviroCore, Dargan Research Centre, South East Technological University, Carlow, Ireland
| | - Mutian Wang
- EnviroCore, Dargan Research Centre, South East Technological University, Carlow, Ireland
| | | | - David Durán
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - David Dowling
- EnviroCore, Dargan Research Centre, South East Technological University, Carlow, Ireland
| | | | - Marta Martin
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Kieran Germaine
- EnviroCore, Dargan Research Centre, South East Technological University, Carlow, Ireland
| | - Rafael Rivilla
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
- *Correspondence: Rafael Rivilla,
| |
Collapse
|
16
|
Vimercati L, Bueno de Mesquita CP, Johnson BW, Mineart D, DeForce E, Vimercati Molano Y, Ducklow H, Schmidt SK. Dynamic trophic shifts in bacterial and eukaryotic communities during the first 30 years of microbial succession following retreat of an Antarctic glacier. FEMS Microbiol Ecol 2022; 98:6762214. [PMID: 36251461 DOI: 10.1093/femsec/fiac122] [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: 06/02/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 01/21/2023] Open
Abstract
We examined microbial succession along a glacier forefront in the Antarctic Peninsula representing ∼30 years of deglaciation to contrast bacterial and eukaryotic successional dynamics and abiotic drivers of community assembly using sequencing and soil properties. Microbial communities changed most rapidly early along the chronosequence, and co-occurrence network analysis showed the most complex topology at the earliest stage. Initial microbial communities were dominated by microorganisms derived from the glacial environment, whereas later stages hosted a mixed community of taxa associated with soils. Eukaryotes became increasingly dominated by Cercozoa, particularly Vampyrellidae, indicating a previously unappreciated role for cercozoan predators during early stages of primary succession. Chlorophytes and Charophytes (rather than cyanobacteria) were the dominant primary producers and there was a spatio-temporal sequence in which major groups became abundant succeeding from simple ice Chlorophytes to Ochrophytes and Bryophytes. Time since deglaciation and pH were the main abiotic drivers structuring both bacterial and eukaryotic communities. Determinism was the dominant assembly mechanism for Bacteria, while the balance between stochastic/deterministic processes in eukaryotes varied along the distance from the glacier front. This study provides new insights into the unexpected dynamic changes and interactions across multiple trophic groups during primary succession in a rapidly changing polar ecosystem.
Collapse
Affiliation(s)
- Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Clifton P Bueno de Mesquita
- DOE Joint Genome Institute Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Ben W Johnson
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Dana Mineart
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Emelia DeForce
- Integrative Oceanography Division Scripps Institution of Oceanography 9500 Gilman Drive La Jolla, CA 92093 5, United States
| | - Ylenia Vimercati Molano
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Hugh Ducklow
- Lamont-Doherty Earth Observatory P.O. Box 1000 61 Route 9W Palisades, NY 10964-1000, United States
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| |
Collapse
|
17
|
Rey-Mariño A, Francino MP. Nutrition, Gut Microbiota, and Allergy Development in Infants. Nutrients 2022; 14:nu14204316. [PMID: 36297000 PMCID: PMC9609088 DOI: 10.3390/nu14204316] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
The process of gut microbiota development in infants is currently being challenged by numerous factors associated with the contemporary lifestyle, including diet. A thorough understanding of all aspects of microbiota development will be necessary for engineering strategies that can modulate it in a beneficial direction. The long-term consequences for human development and health of alterations in the succession pattern that forms the gut microbiota are just beginning to be explored and require much further investigation. Nevertheless, it is clear that gut microbiota development in infancy bears strong associations with the risk for allergic disease. A useful understanding of microbial succession in the gut of infants needs to reveal not only changes in taxonomic composition but also the development of functional capacities through time and how these are related to diet and various environmental factors. Metagenomic and metatranscriptomic studies have started to produce insights into the trends of functional repertoire and gene expression change within the first year after birth. This understanding is critical as during this period the most substantial development of the gut microbiota takes place and the relations between gut microbes and host immunity are established. However, further research needs to focus on the impact of diet on these changes and on how diet can be used to counteract the challenges posed by modern lifestyles to microbiota development and reduce the risk of allergic disease.
Collapse
Affiliation(s)
- Alejandra Rey-Mariño
- Genomics and Health Department, Foundation for the Promotion of Health and Biomedical Research of the Valencia Region (FISABIO), 46020 València, Spain
| | - M. Pilar Francino
- Genomics and Health Department, Foundation for the Promotion of Health and Biomedical Research of the Valencia Region (FISABIO), 46020 València, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), 28001 Madrid, Spain
- Correspondence:
| |
Collapse
|
18
|
Ferrer A, Heath KD, Mosquera SL, Suaréz Y, Dalling JW. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS Microbiol Ecol 2022; 98:6566339. [PMID: 35404430 DOI: 10.1093/femsec/fiac040] [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: 07/17/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.
Collapse
Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sergio L Mosquera
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Yaraví Suaréz
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| |
Collapse
|
19
|
Chalkos D, Karamanoli K, Vokou D. Monoterpene Enrichments Have Positive Impacts on Soil Bacterial Communities and the Potential of Application in Bioremediation. Plants (Basel) 2021; 10:plants10112536. [PMID: 34834898 PMCID: PMC8623845 DOI: 10.3390/plants10112536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
We study here how soil bacterial communities of different ecosystems respond to disturbances caused by enrichments with monoterpenes that are common essential oil constituents. We used fenchone, 1,8-cineol and α-pinene, and soils from phrygana, a typical Mediterranean-type ecosystem where aromatic plants abound, and from another five ecosystem types, focusing on culturable bacteria. Patterns of response were common to all ecosystems, but responses themselves were not always as pronounced in phrygana as in the other ecosystems, suggesting that these enrichments are less of a disturbance there. More specifically, soil respiration and abundance of the bacterial communities increased, becoming from below two up to 16 times as high as in control soils (for both attributes) and remained at high levels as long as these compounds were present. Bacteria that can utilize these three compounds as substrates of growth became dominant members of the bacterial communities in the enriched soils. All changes were readily reversible once monoterpene addition stopped. Bacteria with the ability to utilize these monoterpenes as carbon sources were found in soils from all ecosystems, 15 strains in total, suggesting a rather universal presence; of these, six could also utilize the organic pollutants toluene or p-xylene. These results suggest also potential novel applications of monoterpenes in combating soil pollution.
Collapse
Affiliation(s)
- Dimitris Chalkos
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Faculty of Agriculture Forestry and Natural Environment, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| |
Collapse
|
20
|
Dai D, Zhang HJ, Qiu K, Qi GH, Wang J, Wu SG. Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model. Front Nutr 2021; 8:692305. [PMID: 34692742 PMCID: PMC8526724 DOI: 10.3389/fnut.2021.692305] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
Early colonization of intestinal microbiota plays an important role in intestinal development. However, the microbial succession at an embryonic stage and its assembly patterns induced by prenatal nutrition are unknown. In the present study, we used a chick embryo model to investigate the effects of in ovo feeding (IOF) of L-arginine (Arg) on the intestinal development and microbial succession of embryos. A total of 216 fertile eggs were randomly distributed into 2 groups including the non-injected control group and IOF of Arg group with 7 mg/egg. The results showed that IOF Arg increased the intestinal index, absolute weight of jejunum, and improved jejunal morphology in terms of villus width and surface area (p < 0.05). The relative mRNA expressions of mTOR and 4E-BP1 were up-regulated and accompanied by higher contents of Mucin-2 in the Arg group (p < 0.05). There was a significant elevation in contents of serum glucose and high-density lipoprotein cholesterol, whereas there was a decreased low-density lipoprotein cholesterol in the Arg group (p < 0.05). Additionally, Proteobacteria and Firmicutes were major intestinal bacteria species at the embryonic stage. However, Arg supplementation targeted to shape assembly patterns of microbial succession and then changed microbial composition (p = 0.05). Meanwhile, several short-chain fatty acids (SCFAs)-producing bacteria, such as Roseburia, Blautia, and Ruminococcus were identified as biomarkers in the Arg group (LDA > 3, p < 0.05). Accordingly, significant elevated concentrations of SCFAs, including lactic acid and formic acid, were observed in the Arg group (p < 0.05), accompanied by the higher concentration of butyric acid (0.05 < p < 0.10). In conclusion, prenatal Arg supplementation improved embryonic intestine development by regulating glucose and lipid homeostasis to supply more energy for chick embryos. The possible mechanism could be the roles of Arg in shaping the microbial assembly pattern and succession of the embryonic intestine, particularly the enrichment of potential probiotics. These findings may contribute to exploring nutritional strategies to establish health-promoting microbiota by manipulating prenatal host-microbe interactions for the healthy development of neonates.
Collapse
Affiliation(s)
- Dong Dai
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-Jun Zhang
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Qiu
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guang-Hai Qi
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shu-Geng Wu
- Laboratory of Quality and Safety Risk Assessment for Animal Products on Feed Hazards (Beijing) of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
21
|
Varliero G, Anesio AM, Barker GLA. A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems. Front Microbiol 2021; 12:627437. [PMID: 34621246 PMCID: PMC8491546 DOI: 10.3389/fmicb.2021.627437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.
Collapse
Affiliation(s)
- Gilda Varliero
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Gary L. A. Barker
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
22
|
Fanin N, Lin D, Freschet GT, Keiser AD, Augusto L, Wardle DA, Veen GFC. Home-field advantage of litter decomposition: from the phyllosphere to the soil. New Phytol 2021; 231:1353-1358. [PMID: 34008201 DOI: 10.1111/nph.17475] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Plants often associate with specialized decomposer communities that increase plant litter breakdown, a phenomenon that is known as the 'home-field advantage' (HFA). Although the concept of HFA has long considered only the role of the soil microbial community, explicit consideration of the role of the microbial community on the foliage before litter fall (i.e. the phyllosphere community) may help us to better understand HFA. We investigated the occurrence of HFA in the presence vs absence of phyllosphere communities and found that HFA effects were smaller when phyllosphere communities were removed. We propose that priority effects and interactions between phyllosphere and soil organisms can help explain the positive effects of the phyllosphere at home, and suggest a path forward for further investigation.
Collapse
Affiliation(s)
- Nicolas Fanin
- INRAE, UMR 1391 ISPA, Bordeaux Sciences Agro, 71 Avenue Edouard Bourlaux, CS 20032, Villenave-d'Ornon Cedex, F33882, France
| | - Dunmei Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, 174th Shapingba Zhengjie Street, Shapingba District, Chongqing, 400045, China
| | - Grégoire T Freschet
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, Moulis, 09200, France
| | - Ashley D Keiser
- Stockbridge School of Agriculture, 311 Paige Laboratory, University of Massachusetts, 161 Holdsworth Way, Amherst, MA, 01003, USA
| | - Laurent Augusto
- INRAE, UMR 1391 ISPA, Bordeaux Sciences Agro, 71 Avenue Edouard Bourlaux, CS 20032, Villenave-d'Ornon Cedex, F33882, France
| | - David A Wardle
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - G F Ciska Veen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Droevendaalstesteeg 10, Wageningen, 6708 PB, the Netherlands
| |
Collapse
|
23
|
Gyeong H, Hyun CU, Kim SC, Tripathi BM, Yun J, Kim J, Kang H, Kim JH, Kim S, Kim M. Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic. Mol Ecol 2021; 30:4231-4244. [PMID: 34214230 DOI: 10.1111/mec.16054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/04/2023]
Abstract
Although microorganisms are the very first colonizers of recently deglaciated soils even prior to plant colonization, the drivers and patterns of microbial community succession at early-successional stages remain poorly understood. The successional dynamics and assembly processes of bacterial and fungal communities were compared on a glacier foreland in the maritime Antarctic across the ~10-year soil-age gradient from bare soil to sparsely vegetated area. Bacterial communities shifted more rapidly than fungal communities in response to glacial retreat; species turnover (primarily the transition from glacier- to soil-favouring taxa) contributed greatly to bacterial beta diversity, but this pattern was less clear in fungi. Bacterial communities underwent more predictable (more deterministic) changes along the soil-age gradient, with compositional changes paralleling the direction of changes in soil physicochemical properties following deglaciation. In contrast, the compositional shift in fungal communities was less associated with changes in deglaciation-induced changes in soil geochemistry and most fungal taxa displayed mosaic abundance distribution across the landscape, suggesting that the successional dynamics of fungal communities are largely governed by stochastic processes. A co-occurrence network analysis revealed that biotic interactions between bacteria and fungi are very weak in early succession. Taken together, these results collectively suggest that bacterial and fungal communities in recently deglaciated soils are largely decoupled from each other during succession and exert very divergent trajectories of succession and assembly under different selective forces.
Collapse
Affiliation(s)
| | - Chang-Uk Hyun
- Department of Energy and Mineral Resources Engineering, Dong-A University, Busan, Korea
| | | | | | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Ji Hee Kim
- Korea Polar Research Institute (KOPRI), Incheon, Korea
| | - Sanghee Kim
- Korea Polar Research Institute (KOPRI), Incheon, Korea
| | - Mincheol Kim
- Korea Polar Research Institute (KOPRI), Incheon, Korea
| |
Collapse
|
24
|
Phillips AA, Speth DR, Miller LG, Wang XT, Wu F, Medeiros PM, Monteverde DR, Osburn MR, Berelson WM, Betts HL, Wijker RS, Mullin SW, Johnson HA, Orphan VJ, Fischer WW, Sessions AL. Microbial succession and dynamics in meromictic Mono Lake, California. Geobiology 2021; 19:376-393. [PMID: 33629529 PMCID: PMC8359280 DOI: 10.1111/gbi.12437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/29/2020] [Revised: 11/18/2020] [Accepted: 02/08/2021] [Indexed: 05/30/2023]
Abstract
Mono Lake is a closed-basin, hypersaline, alkaline lake located in Eastern Sierra Nevada, California, that is dominated by microbial life. This unique ecosystem offers a natural laboratory for probing microbial community responses to environmental change. In 2017, a heavy snowpack and subsequent runoff led Mono Lake to transition from annually mixed (monomictic) to indefinitely stratified (meromictic). We followed microbial succession during this limnological shift, establishing a two-year (2017-2018) water-column time series of geochemical and microbiological data. Following meromictic conditions, anoxia persisted below the chemocline and reduced compounds such as sulfide and ammonium increased in concentration from near 0 to ~400 and ~150 µM, respectively, throughout 2018. We observed significant microbial succession, with trends varying by water depth. In the epilimnion (above the chemocline), aerobic heterotrophs were displaced by phototrophic genera when a large bloom of cyanobacteria appeared in fall 2018. Bacteria in the hypolimnion (below the chemocline) had a delayed, but systematic, response reflecting colonization by sediment "seed bank" communities. Phototrophic sulfide-oxidizing bacteria appeared first in summer 2017, followed by microbes associated with anaerobic fermentation in spring 2018, and eventually sulfate-reducing taxa by fall 2018. This slow shift indicated that multi-year meromixis was required to establish a sulfate-reducing community in Mono Lake, although sulfide oxidizers thrive throughout mixing regimes. The abundant green alga Picocystis remained the dominant primary producer during the meromixis event, abundant throughout the water column including in the hypolimnion despite the absence of light and prevalence of sulfide. Our study adds to the growing literature describing microbial resistance and resilience during lake mixing events related to climatic events and environmental change.
Collapse
Affiliation(s)
- Alexandra A. Phillips
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Daan R. Speth
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Laurence G. Miller
- United States Geological Survey, Earth Systems Process DivisionMenlo ParkCAUSA
| | - Xingchen T. Wang
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Earth and Environmental SciencesBoston CollegeChestnut HillMAUSA
| | - Fenfang Wu
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | | | - Danielle R. Monteverde
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Magdalena R. Osburn
- Department of Earth and Planetary SciencesNorthwestern UniversityEvanstonILUSA
| | - William M. Berelson
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | - Reto S. Wijker
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Sean W. Mullin
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Hope A. Johnson
- Department of Biological ScienceCalifornia State University FullertonFullertonCAUSA
| | - Victoria J. Orphan
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Woodward W. Fischer
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Geobiology Course 2017
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Geobiology Course 2018
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Alex L. Sessions
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| |
Collapse
|
25
|
Figueiredo Dos Santos L, Fernandes Souta J, de Paula Soares C, Oliveira da Rocha L, Luiza Carvalho Santos M, Grativol C, Fernando Wurdig Roesch L, Lopes Olivares F. Insights into the structure and role of seed-borne bacteriome during maize germination. FEMS Microbiol Ecol 2021; 97:6133469. [PMID: 33571355 DOI: 10.1093/femsec/fiab024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 06/02/2020] [Accepted: 02/09/2021] [Indexed: 12/30/2022] Open
Abstract
Seed germination events modulate microbial community composition, which ultimately influences seed-to-seedling growth performance. Here, we evaluate the germinated maize (variety SHS 5050) root bacterial community of disinfected seed (DS) and non-disinfected seed (NDS). Using a gnotobiotic system, sodium hypochlorite (1.25%; 30 min)-treated seeds showed a reduction of bacterial population size and an apparent increase of bacterial community diversity associated with a significant selective reduction of Burkholderia-related sequences. The shift in the bacterial community composition in DS negatively affects germination speed, seedling growth and reserve mobilization rates compared with NDS. A synthetic bacterial community (syncom) formed by 12 isolates (9 Burkholderia spp., 2 Bacillus spp., and 1 Staphylococcus sp.) obtained from natural microbiota maize seeds herein was capable of recovering germination and seedling growth when reintroduced in DS. Overall, results showed that changes in bacterial community composition and selective reduction of Burkholderia-related members' dominance interfere with germination events and the initial growth of the maize. By cultivation-dependent and -independent approaches, we deciphered seed-maize microbiome structure, bacterial niches location and bacterial taxa with relevant roles in seedling growth performance. A causal relationship between seed microbial community succession and germination performance opens opportunities in seed technologies to build-up microbial communities to boost plant growth and health.
Collapse
Affiliation(s)
- Lidiane Figueiredo Dos Santos
- Laboratório de Biologia Celular e Tecidual (LBCT) & Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA) da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Julie Fernandes Souta
- Laboratório de Biologia Celular e Tecidual (LBCT) & Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA) da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Cleiton de Paula Soares
- Laboratório de Biologia Celular e Tecidual (LBCT) & Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA) da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Letícia Oliveira da Rocha
- Laboratório de Biologia Celular e Tecidual (LBCT) & Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA) da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Maria Luiza Carvalho Santos
- Laboratório de Química e Função de Proteínas e Peptídeos da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Clicia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Luiz Fernando Wurdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia (CIP-Biotec) da Universidade Federal do Pampa (UNIPAMPA), 97300-000 São Gabriel, Rio Grande do Sul, Brazil
| | - Fabio Lopes Olivares
- Laboratório de Biologia Celular e Tecidual (LBCT) & Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA) da Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil
| |
Collapse
|
26
|
Mullin SW, Wanger G, Kruger BR, Sackett JD, Hamilton-Brehm SD, Bhartia R, Amend JP, Moser DP, Orphan VJ. Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer. Front Microbiol 2020; 11:536535. [PMID: 33329414 PMCID: PMC7711152 DOI: 10.3389/fmicb.2020.536535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 09/24/2020] [Indexed: 11/13/2022] Open
Abstract
The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.
Collapse
Affiliation(s)
- Sean W Mullin
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Greg Wanger
- Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Brittany R Kruger
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States
| | - Joshua D Sackett
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, United States
| | - Rohit Bhartia
- Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| |
Collapse
|
27
|
Guan T, Lin Y, Chen K, Ou M, Zhang J. Physicochemical Factors Affecting Microbiota Dynamics During Traditional Solid-State Fermentation of Chinese Strong-Flavor Baijiu. Front Microbiol 2020; 11:2090. [PMID: 33013762 PMCID: PMC7509048 DOI: 10.3389/fmicb.2020.02090] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/08/2020] [Indexed: 12/16/2022] Open
Abstract
Spontaneous solid-state fermentation (SSF) of Chinese Baijiu involves diverse microbes from Daqu and pit mud (PM). Given that the transfer of interphase microflora during the fermentation is a continuous and dynamic process, longitudinal studies are essential to provide ecological insights into community stability and response to consecutive disturbances in the process. In this context, this study aimed to generate a comprehensive longitudinal characterization of the microbiota during the fermentation processes of Chinese strong-flavor Baijiu (CSFB) differing in cellar ages with consideration for potential relation to physicochemical variables. The microecology variations observed during the 6-years cellar SSF (SCSSF) and 30-years cellar SSF (TCSSF) processes reveal that fungal composition contributes to a larger extent than bacterial composition to such variations. Orders of Lactobacillales, Anaerolineales, Enterobacteriales, Bacillales, Eurotiales, and Saccharomycetales dominated (average relative abundances >10%) the microbiota in both SCSSF and TCSSF processes but with a different percentage in the operational taxonomic unit (out) abundances. Compared with the SCSSF process, TCSSF possessed slower microbial succession rates, which were in accordance with the profile of physicochemical properties. From a network perspective, the microbial community structure observed in the TCSSF processes was more stable than that in the SCSSF. This may benefit from the milder physicochemical conditions of the TCSSF processes, especially the temperature, which is also more beneficial to the growth of some groups that have negative effects on fermentation, such as Staphylococcus, Pseudomonas, and Acinetobacter.
Collapse
Affiliation(s)
- Tongwei Guan
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Yijin Lin
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Kebao Chen
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Mengying Ou
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Jiaxu Zhang
- Chengdu Shuzhiyuan of Liquor Co., Ltd., Chengdu, China
| |
Collapse
|
28
|
Luo Y, Huang Y, Xu RX, Qian B, Zhou JW, Xia XL. Primary and Secondary Succession Mediate the Accumulation of Biogenic Amines during Industrial Semidry Chinese Rice Wine Fermentation. Appl Environ Microbiol 2020; 86:e01177-20. [PMID: 32591381 PMCID: PMC7440807 DOI: 10.1128/aem.01177-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/18/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023] Open
Abstract
The use of exogenous functional microorganisms to regulate biogenic amine (BA) content is a common approach in fermentation systems. Here, to better understand the microbial traits of succession trajectories in resource-based and biotic interference systems, the BA-related primary and secondary succession were tracked during industrial semidry Chinese rice wine (CRW) fermentation. Dominant abundance and BA-associated microbial functionality based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that Citrobacter, Acinetobacter, Lactobacillus, Exiguobacterium, Bacillus, Pseudomonas, and Enterobacter spp. prominently contributed to the decarboxylase gene family in CRW. The expression levels of tyrosine decarboxylase (tyrDC), ornithine decarboxylase (odc), and agmatine deiminase (aguA) genes were assessed by quantitative PCR (qPCR). The transcription levels of these genes did not correlate with the BA formation rate during postfermentation, indicating that acidification and carbon source depletion upregulated the expression and microbes launch the dormancy strategy to respond to unfavorable conditions. Furthermore, microbial interference with CRW fermentation by Lactobacillus plantarum (ACBC271) and Staphylococcus xylosus (CGMCC1.8382) coinoculated at a ratio of 1:2 exhibited the best synergetic control of BA content. Spearman correlations revealed that Lactobacillus and Staphylococcus exhibited influence on BA-associated microbiota (|ρ| > 0), Exiguobacterium and Pseudomonas were strongly suppressed by Lactobacillus (ρ = -0.867 and ρ = -0.782, respectively; P < 0.05), and Staphylococcus showed the strongest inhibitory effect toward Lactobacillus (ρ = -0.115) and Citrobacter (ρ = -0.188) in the coinoculated 1:2 group. The high inhibitory effect of exogenous added strains on specific bacteria presented evidence for the obtained BA-associated contributors. Overall, this work provides important insight into the microbial traits that rely on resource usage and functional microbiota within food microbial ecology.IMPORTANCE Understanding the shifting patterns of substance usage and microbial interactions is a fundamental objective within microbiology and ecology. Analyses of primary and secondary microbial succession allow for determinations of taxonomic diversity, community traits, and functional transformations over time or after a disturbance. The kinetics of BA generation and the patterns of resource consumption, functional metagenome prediction, and microbial interactions were profiled to elucidate the equilibrium mechanism of microbial systems. Secondary succession after a disturbance triggers a change in resource usage, which in turn affects primary succession and metabolism. In this study, the functional potential of exogenous microorganisms under disturbance synergized with secondary succession strategies, including rebalancing and dormancy, which ultimately reduced BA accumulation. Thus, this succession system could facilitate the settling of essential issues with respect to microbial traits that rely on resource usage and microbial interactions that occur in natural ecosystems.
Collapse
Affiliation(s)
- Yi Luo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Yang Huang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Rui-Xian Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Bin Qian
- Zhejiang Guyue Longshan Shaoxing Wine Co. Ltd., Shaoxing, People's Republic of China
| | - Jing-Wen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Xiao-le Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| |
Collapse
|
29
|
Abstract
Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70 m × 1 m) microbial mat formed at 10 m water depth in the Ross Sea, Antarctica which we identify here to be a high latitude hydrogen sulfide and methane seep. Through 16S rRNA gene analysis on samples collected 1 year and 5 years after the methane seep formed, we identify the taxa involved in the Antarctic methane cycle and quantify the response rate of the microbial community to a novel input of methane. One year after the seep formed, ANaerobic MEthane oxidizing archaea (ANME), the dominant sink of methane globally, were absent. Five years later, ANME were found to make up to 4% of the microbial community, however the dominant member of this group observed (ANME-1) were unexpected considering the cold temperature (-1.8°C) and high sulfate concentrations (greater than 24 mM) present at this site. Additionally, the microbial community had not yet formed a sufficient filter to mitigate the release of methane from the sediment; methane flux from the sediment was still significant at 3.1 mmol CH4 m-2 d-1. We hypothesize that this 5 year time point represents an early successional stage of the microbiota in response to methane input. This study provides the first report of the evolution of a seep system from a non-seep environment, and reveals that the rate of microbial succession may have an unrealized impact on greenhouse gas emission from marine methane reservoirs.
Collapse
Affiliation(s)
- Andrew R Thurber
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
| | - Sarah Seabrook
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Rory M Welsh
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
30
|
I Otoni, R Paula, J Alves, J Roseira, F Pimentel, K Ribeiro, O Pereira. PSVIII-35 Isolation and identification of lactic acid bacteria in guinea grass silages. J Anim Sci 2018; 96. [ DOI: 10.1093/jas/sky404.476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024] Open
Abstract
The objectives of this study were to isolate and identify lactic acid bacteria (LAB) in guinea grass (Panicum maximum Jacq. cultivar Mombasa) silage harvested in the summer (February) and winter (August) of 2017, at 60 and 122 days of regrowth, respectively. The grass was chopped into 1.5 cm particle size and ensiled in bags measuring 25.4 × 35.56 cm. The bags were stored at room temperature and triplicate bags were opened after 1, 3, 7, 14, 28, 56, and 90 days of fermentation. The 16s rRNA gene sequences were obtained by pre-selecting cells grown in 5 mL MRS broth at 37 ºC for 18 h. The 16S rRNA sequences that showed similarity equal to or greater than 97% were considered of the same Operational Taxonomic Unit. A total of 366 strains (170 in the summer and 196 in the winter) belonging to 21 different LAB species were isolated. The following species were identified: Enterococcus canintestini (1.27%), E. faecium (0.55%), E. gallinarum (2.19%), E. saccharolyticus (0.27%), Lactobacillus brevis (7.92%), L. buchneri (0.27%), L. coryniformis (0.27%), L. curieae (0.27%), L. hordei (0.55%), L. mali (3.28%), L. pantheris (4.10%), L. paracasei (10.38%), L. plantarum (24.04%), Lactococcus garvieae (0.55%), L. lactis (5.19%), Leuconostoc mesenteroides (6.01%), Leuconostoc pseudomesenteroides (1.37%), Pediococcus pentosaceus (26.23%), Weissella confusa (1.09%), W. oryzae (0.27%), and W. paramesenteroides (3.83%). Of these, only Lactobacillus brevis , L. plantarum ,and Lactococcus lactis were common to both grass growing seasons. At 56 days of fermentation, Pediococcus pentosaceus (60%) and Lactobacillus pantheris (32%) were the predominant LAB species in summer and winter, respectively. On the last day of fermentation, P. pentosaceus (100%) and L. paracasei (28%) were the dominant species in the respective seasons. Greater heterogeneity of species was observed in the winter period.
Collapse
|
31
|
Wu X, Wu L, Liu Y, Zhang P, Li Q, Zhou J, Hess NJ, Hazen TC, Yang W, Chakraborty R. Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession. Front Microbiol 2018; 9:1234. [PMID: 29937762 PMCID: PMC6002664 DOI: 10.3389/fmicb.2018.01234] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater.
Collapse
Affiliation(s)
- Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Yina Liu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, United States
| | - Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States
| | - Qinghao Li
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,National Key Laboratory of Crystal Materials, School of Physics, Shandong University, Jinan, China
| | - Jizhong Zhou
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, United States.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Nancy J Hess
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Institute for a Secure and Sustainable Environment, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wanli Yang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
32
|
Xu S, Zhang J, Luo S, Zhou X, Shi S, Tian C. Similar soil microbial community structure across different environments after long-term succession: evidence from volcanoes of different ages. J Basic Microbiol 2018; 58:704-711. [PMID: 29882593 DOI: 10.1002/jobm.201800016] [Citation(s) in RCA: 6] [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: 01/10/2018] [Revised: 04/03/2018] [Accepted: 04/07/2018] [Indexed: 11/09/2022]
Abstract
Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession.
Collapse
Affiliation(s)
- Shangqi Xu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jianfeng Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,School of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Shasha Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xue Zhou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| |
Collapse
|
33
|
Cao B, Zhang Y, Wang Z, Li M, Yang F, Jiang D, Jiang Z. Insight Into the Variation of Bacterial Structure in Atrazine-Contaminated Soil Regulating by Potential Phytoremediator: Pennisetum americanum (L.) K. Schum. Front Microbiol 2018; 9:864. [PMID: 29780374 PMCID: PMC5945882 DOI: 10.3389/fmicb.2018.00864] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/13/2018] [Indexed: 11/13/2022] Open
Abstract
Although plants of the genus Pennisetum can accelerate the removal of atrazine from its rhizosphere, the roles played by this plant in adjusting the soil environment and soil microorganism properties that might contribute to pollutant removal are incompletely understood. We selected Pennisetum americanum (L.) K. Schum (P. americanum) as the test plant and investigated the interaction between P. americanum and atrazine-contaminated soil, focusing on the adjustment of the soil biochemical properties as well as bacterial functional and community diversity in the rhizosphere using Biolog EcoPlates and high-throughput sequencing of the 16S rRNA gene. The results demonstrate that the rhizosphere soil of P. americanum exhibited higher catalase activity, urease activity and water soluble organic carbon (WSOC) content, as well as a suitable pH for microorganisms after a 28-day incubation. The bacterial functional diversity indices (Shannon and McIntosh) for rhizosphere soil were 3.17 ± 0.04 and 6.43 ± 0.86 respectively, while these indices for non-rhizosphere soil were 2.95 ± 0.06 and 3.98 ± 0.27. Thus, bacteria in the P. americanum rhizosphere exhibited better carbon substrate utilization than non-rhizosphere bacteria. Though atrazine decreased the richness of the soil bacterial community, rhizosphere soil had higher bacterial community traits. For example, the Shannon diversity indices for rhizosphere and non-rhizosphere soil were 5.821 and 5.670 respectively. Meanwhile, some bacteria, such as those of the genera Paenibacillus, Rhizobium, Sphingobium, and Mycoplana, which facilitate soil nutrient cycling or organic pollutants degradation, were only found in rhizosphere soil after a 28-day remediation. Moreover, redundancy analysis suggests that the soil biochemical properties that were adjusted by the test plant exhibited correlations with the bacterial community composition and functional diversity. These results suggest that the soil environment and bacterial properties could be adjusted by P. americanum during phytoremediation of atrazine-contaminated soil.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Zhao Jiang
- School of Resources and Environment, Northeast Agricultural University, Harbin, China
| |
Collapse
|
34
|
Wilmoth JL, Doak PW, Timm A, Halsted M, Anderson JD, Ginovart M, Prats C, Portell X, Retterer ST, Fuentes-Cabrera M. A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions. Front Microbiol 2018; 9:33. [PMID: 29467721 PMCID: PMC5808251 DOI: 10.3389/fmicb.2018.00033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/09/2018] [Indexed: 12/17/2022] Open
Abstract
The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.
Collapse
Affiliation(s)
- Jared L Wilmoth
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Peter W Doak
- Computational Sciences and Engineering Division, Oak Ridge, TN, United States
| | - Andrea Timm
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Michelle Halsted
- The Bredesen Center, University of Tennessee, Knoxville, TN, United States
| | - John D Anderson
- The Bredesen Center, University of Tennessee, Knoxville, TN, United States
| | - Marta Ginovart
- Department of Mathematics, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Clara Prats
- Department of Physics, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Xavier Portell
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Scott T Retterer
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States.,Computational Sciences and Engineering Division, Oak Ridge, TN, United States
| | - Miguel Fuentes-Cabrera
- Computational Sciences and Engineering Division, Oak Ridge, TN, United States.,Computational Sciences and Engineering Division, Oak Ridge, TN, United States
| |
Collapse
|
35
|
Wang X, Du H, Zhang Y, Xu Y. Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation. Appl Environ Microbiol 2018; 84:e02369-17. [PMID: 29196296 DOI: 10.1128/AEM.02369-17] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/28/2017] [Indexed: 01/14/2023] Open
Abstract
Many microorganisms in the environment participate in the fermentation process of Chinese liquor. However, it is unknown to what extent the environmental microbiota influences fermentation. In this study, high-throughput sequencing combined with multiphasic metabolite target analysis was applied to study the microbial succession and metabolism changes during Chinese liquor fermentation from two environments (old and new workshops). SourceTracker was applied to evaluate the contribution of environmental microbiota to fermentation. Results showed that Daqu contributed 9.10 to 27.39% of bacterial communities and 61.06 to 80.00% of fungal communities to fermentation, whereas environments (outdoor ground, indoor ground, tools, and other unknown environments) contributed 62.61 to 90.90% of bacterial communities and 20.00 to 38.94% of fungal communities to fermentation. In the old workshop, six bacterial genera (Lactobacillus [11.73% average relative abundance], Bacillus [20.78%], Pseudomonas [6.13%], Kroppenstedtia [10.99%], Weissella [16.64%], and Pantoea [3.40%]) and five fungal genera (Pichia [55.10%], Candida [1.47%], Aspergillus [10.66%], Saccharomycopsis [22.11%], and Wickerhamomyces [3.35%]) were abundant at the beginning of fermentation. However, in the new workshop, the change of environmental microbiota decreased the abundances of Bacillus (5.74%), Weissella (6.64%), Pichia (33.91%), Aspergillus (7.08%), and Wickerhamomyces (0.12%), and increased the abundances of Pseudomonas (17.04%), Kroppenstedtia (13.31%), Pantoea (11.41%), Acinetobacter (3.02%), Candida (16.47%), and Kazachstania (1.31%). Meanwhile, in the new workshop, the changes of microbial community resulted in the increase of acetic acid, lactic acid, malic acid, and ethyl acetate, and the decrease of ethyl lactate during fermentation. This study showed that the environmental microbiota was an important source of fermentation microbiota and could drive both microbial succession and metabolic profiles during liquor fermentation.IMPORTANCE Traditional solid-state fermentation of foods and beverages is mainly carried out by complex microbial communities from raw materials, starters, and the processing environments. However, it is still unclear how the environmental microbiota influences the quality of fermented foods and beverages, especially for Chinese liquors. In this study, we utilized high-throughput sequencing, microbial source tracking, and multiphasic metabolite target analysis to analyze the origins of microbiota and the metabolic profiles during liquor fermentation. This study contributes to a deeper understanding of the role of environmental microbiota during fermentation.
Collapse
|
36
|
Shukla SP, Vogel H, Heckel DG, Vilcinskas A, Kaltenpoth M. Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring. Mol Ecol 2017; 27:1980-1991. [PMID: 28748615 DOI: 10.1111/mec.14269] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 03/23/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 11/28/2022]
Abstract
Necrophagous beetles utilize carrion, a highly nutritious resource that is susceptible to intense microbial competition, by treating it with antimicrobial anal and oral secretions. However, how this regulates the carcass microbiota remains unclear. Here, we show that carcasses prepared by the burying beetle Nicrophorus vespilloides undergo significant changes in their microbial communities subsequent to their burial and "preparation." Prepared carcasses hosted a microbial community that was more similar to that of beetles' anal and oral secretions than to the native carcass community or the surrounding soil, indicating that the beetles regulated the carcass microbiota. A core microbial community (Xanthomonadaceae, Enterococcaceae, Enterobacteriaceae and Yarrowia yeasts) was transmitted by the beetles to the larvae via the anal and oral secretions and the carcass surface. These core taxa proliferated on the carcass, indicating a growth conducive environment for these microbes when associated with beetles. However, total bacterial loads were higher on decomposing carcasses without beetles than on beetle-prepared carcasses, indicating that the beetles and/or their associated symbionts suppress the growth of competing microbes. Thus, apart from being a nutritional resource, the carcass provides a medium for vertical transmission of a tightly regulated symbiotic microbiota, whose activity on the carcass and in the larval gut may involve carcass preservation as well as digestion.
Collapse
Affiliation(s)
- Shantanu P Shukla
- Research Group Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.,Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Martin Kaltenpoth
- Research Group Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany.,Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
37
|
Li J, Cui J, Yang Q, Cui G, Wei B, Wu Z, Wang Y, Zhou H. Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney. Front Microbiol 2017; 8:1378. [PMID: 28785251 PMCID: PMC5519607 DOI: 10.3389/fmicb.2017.01378] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/06/2017] [Indexed: 12/25/2022] Open
Abstract
When its hydrothermal supply ceases, hydrothermal sulfide chimneys become inactive and commonly experience oxidative weathering on the seafloor. However, little is known about the oxidative weathering of inactive sulfide chimneys, nor about associated microbial community structures and their succession during this weathering process. In this work, an inactive sulfide chimney and a young chimney in the early sulfate stage of formation were collected from the Main Endeavor Field of the Juan de Fuca Ridge. To assess oxidative weathering, the ultrastructures of secondary alteration products accumulating on the chimney surface were examined and the presence of possible Fe-oxidizing bacteria (FeOB) was investigated. The results of ultrastructure observation revealed that FeOB-associated ultrastructures with indicative morphologies were abundantly present. Iron oxidizers primarily consisted of members closely related to Gallionella spp. and Mariprofundus spp., indicating Fe-oxidizing species likely promote the oxidative weathering of inactive sulfide chimneys. Abiotic accumulation of Fe-rich substances further indicates that oxidative weathering is a complex, dynamic process, alternately controlled by FeOB and by abiotic oxidization. Although hydrothermal fluid flow had ceased, inactive chimneys still accommodate an abundant and diverse microbiome whose microbial composition and metabolic potential dramatically differ from their counterparts at active vents. Bacterial lineages within current inactive chimney are dominated by members of α-, δ-, and γ-Proteobacteria and they are deduced to be closely involved in a diverse set of geochemical processes including iron oxidation, nitrogen fixation, ammonia oxidation and denitrification. At last, by examining microbial communities within hydrothermal chimneys at different formation stages, a general microbial community succession can be deduced from early formation stages of a sulfate chimney to actively mature sulfide structures, and then to the final inactive altered sulfide chimney. Our findings provide valuable insights into the microbe-involved oxidative weathering process and into microbial succession occurring at inactive hydrothermal sulfide chimney after high-temperature hydrothermal fluids have ceased venting.
Collapse
Affiliation(s)
- Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Jiamei Cui
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Qunhui Yang
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Guojie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanya, China
| | - Bingbing Wei
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Zijun Wu
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of SciencesSanya, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| |
Collapse
|
38
|
Song Z, Du H, Zhang Y, Xu Y. Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing. Front Microbiol 2017; 8:1294. [PMID: 28769888 PMCID: PMC5509801 DOI: 10.3389/fmicb.2017.01294] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022] Open
Abstract
Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces) and lactic acid bacteria (genus Lactobacillus) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into the effects of the core functional microbiota in soy sauce aroma type liquor production and the characteristics of the fermentation microbiota under different environmental conditions.
Collapse
Affiliation(s)
- Zhewei Song
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan UniversityWuxi, China
| | - Hai Du
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan UniversityWuxi, China
| | - Yan Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology - Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai, China
| | - Yan Xu
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology of Ministry of Education, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan UniversityWuxi, China
| |
Collapse
|
39
|
Jiao S, Zhang Z, Yang F, Lin Y, Chen W, Wei G. Temporal dynamics of microbial communities in microcosms in response to pollutants. Mol Ecol 2017; 26:923-936. [PMID: 28012222 DOI: 10.1111/mec.13978] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 08/08/2016] [Accepted: 12/08/2016] [Indexed: 01/18/2023]
Abstract
Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.
Collapse
Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhengqing Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
40
|
Gorzelak MA, Pickles BJ, Hart MM. Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts. Mol Ecol 2017; 26:1586-1597. [PMID: 28099772 DOI: 10.1111/mec.14023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 10/15/2016] [Revised: 12/26/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long-lived woody perennial species in undisturbed ecosystems. Here we examined AMF communities associated with roots and soils of young, mature and old western redcedar (Thuja plicata) at two sites in the old-growth temperate rainforests of British Columbia. Due to the unique biology of AMF, community richness and structure were assessed using a conservative, clade-based approach. We found 91 AMF OTUs across all samples, with significantly greater AMF richness in the southern site, but no differences in richness along the host chronosequence at either site. All host age classes harboured AMF communities that were overdispersed (more different to each other than expected by chance), with young tree communities most resembling old tree communities. A comparison with similar clade richness data obtained from the literature indicates that western redcedar AMF communities are as rich as those of grasses, tropical trees and palms. Our examination of undisturbed temperate old-growth rainforests suggests that priority effects, rather than succession, are an important aspect of AMF community assembly in this ecosystem.
Collapse
Affiliation(s)
- Monika A Gorzelak
- Department of Forest and Conservation Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Brian J Pickles
- School of Biological Sciences, University of Reading, Harborne Building, Whiteknights, Reading, RG6 8AS, UK
| | - Miranda M Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, V1V 1V7, Canada
| |
Collapse
|
41
|
Dini-Andreote F, Brossi MJDL, van Elsas JD, Salles JF. Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem. Front Microbiol 2016; 7:902. [PMID: 27379042 PMCID: PMC4908922 DOI: 10.3389/fmicb.2016.00902] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/26/2016] [Indexed: 11/25/2022] Open
Abstract
Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., NO3−, NH4+), salinity and pH (explaining 73.8% of the total variation, R2 = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, NO3−, NH4+ and SO42−, across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine and impacted salt marsh areas. Such models should account for the ecology as well as the historical contingency of N cycling communities.
Collapse
Affiliation(s)
- Francisco Dini-Andreote
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Maria Julia de L Brossi
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Jan Dirk van Elsas
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Joana F Salles
- Microbial Ecology Group, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| |
Collapse
|
42
|
Abstract
Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.
Collapse
Affiliation(s)
- James A Bradley
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
| | - Joy S Singarayer
- Department of Meteorology, University of Reading, Reading RG6 6BB, UK
| | - Alexandre M Anesio
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
| |
Collapse
|
43
|
Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2013; 2:e01104. [PMID: 24137541 PMCID: PMC3796315 DOI: 10.7554/elife.01104] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/20/2013] [Indexed: 12/13/2022] Open
Abstract
Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI:http://dx.doi.org/10.7554/eLife.01104.001 Our bodies—especially our skin, our saliva, the lining of our mouth and our gastrointestinal tract—are home to a diverse collection of bacteria and other microorganisms called the microbiome. While the roles played by many of these microorganisms have yet to be identified, it is known that they contribute to the health and wellbeing of their host by metabolizing indigestible compounds, producing essential vitamins, and preventing the growth of harmful bacteria. They are important for nutrient and carbon cycling in the environment. The advent of advanced sequencing techniques has made it feasible to study the composition of this microbial community, and to monitor how it changes over time or how it responds to events such as antibiotic treatment. Sequencing studies have been used to highlight the significant differences between microbial communities found in different parts of the body, and to follow the evolution of the gut microbiome from birth. Most of these studies have focused on live animals, so little is known about what happens to the microbiome after its host dies. In particular, it is not known if the changes that occur after death are similar for all individuals. Moreover, the decomposing animal supplies nutrients and carbon to the surrounding ecosystem, but its influence on the microbial community of its immediate environment is not well understood. Now Metcalf et al. have used high-throughput sequencing to study the bacteria and other microorganisms (such as nematodes and fungi) in dead and decomposing mice, and also in the soil beneath them, over the course of 48 days. The changes were significant and also consistent across the corpses, with the microbial communities in the corpses influencing those in the soil, and vice versa. Metcalf et al. also showed that these measurements could be used to estimate the postmortem interval (the time since death) to within approximately 3 days, which suggests that the work could have applications in forensic science. DOI:http://dx.doi.org/10.7554/eLife.01104.002
Collapse
Affiliation(s)
- Jessica L Metcalf
- Biofrontiers Institute , University of Colorado at Boulder , Boulder , United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Devi S, Sharma CR, Singh K. Microbiological biodiversity in poultry and paddy straw wastes in composting systems. Braz J Microbiol 2012; 43:288-96. [PMID: 24031831 PMCID: PMC3768964 DOI: 10.1590/s1517-838220120001000034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 08/30/2011] [Indexed: 12/03/2022]
Abstract
Immense quantity of waste is generated in association with poultry meat egg and crop production. The potential risks due to disposal of these wastes are magnified as a result of dense refinement of poultry production and the decreasing amount of land available for waste disposal. The study aims at studying the microbiological biodiversity of poultry waste and paddy straw based co-composting system. The predominant microflora of the poultry manure were bacteria, fungi, enteric bacteria and spore forming bacteria whose population was high at the initiation of composting but decreased significantly as the compost approached maturity. The initial load of inherent enteric groups of bacteria in poultry waste, that also includes some pathogenic ones, is considerably reduced and some new vital groups contributed to compost quality as the microbiological biodiversity sets in the system and becomes stable. Major fraction of nitrogen of poultry waste was subjected to ammonia volatilization and a fraction of it conserved by co-composting it in conjunction with wastes having low nitrogen contents. In the treatment T1 and T5, where poultry manure and paddy straws alone were composted, 60 and 30 percent of organic carbon, respectively, was lost over a period of six months. Whereas in treatments T2,T3 and T4, poultry manure and paddy straw were co-composted in the ratio of 3:1, 2:2 and 1:3, respectively, 51.4,45.0 and 37.0 percent of carbon, respectively, was lost during decomposition. The C: N ratio in all the treatments decreased significantly to 18.3 for T1, 24.7 for T2, 27.0 for T3, 34.9 for T4 and 38.5 for T5 at the end of composting period.
Collapse
Affiliation(s)
- Sunita Devi
- Department of Microbiology, College of Basic Sciences, CSK HPKV , Palampur-176062 India
| | | | | |
Collapse
|