1
|
Xie G, Sun C, Luo W, Gong Y, Tang X. Distinct ecological niches and community dynamics: understanding free-living and particle-attached bacterial communities in an oligotrophic deep lake. Appl Environ Microbiol 2024; 90:e0071424. [PMID: 38940583 PMCID: PMC11267872 DOI: 10.1128/aem.00714-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
Oligotrophic deep-water lakes are unique and sensitive ecosystems with limited nutrient availability. Understanding bacterial communities within these lakes is crucial for assessing ecosystem health, biogeochemical cycling, and responses to environmental changes. In this study, we investigated the seasonal and vertical dynamics of both free-living (FL) and particle-attached (PA) bacteria in Lake Fuxian, a typical oligotrophic deep freshwater lake in southeast China. Our findings revealed distinct seasonal and vertical dynamics of FL and PA bacterial communities, driven by similar physiochemical environmental factors. PA bacteria exhibited higher α- and β-diversity and were enriched with Proteobacteria, Cyanobacteria, Firmicutes, Patescibacteria, Planctomycetota, and Verrucomicrobiota, while FL bacteria were enriched with Actinobacteria and Bacteroidota. FL bacteria showed enrichment in putative functions related to chemoheterotrophy and aerobic anoxygenic photosynthesis, whereas the PA fraction was enriched with intracellular parasites (mainly contributed by Rickettsiales, Chlamydiales, and Legionellales) and nitrogen metabolism functions. Deterministic processes predominantly shaped the assembly of both FL and PA bacterial communities, with stochastic processes playing a greater role in the FL fraction. Network analysis revealed extensive species interactions, with a higher proportion of positively correlated edges in the PA network, indicating mutualistic or cooperative interactions. Cyanobium, Comamonadaceae, and Roseomonas were identified as keystone taxa in the PA network, underscoring potential cooperation between autotrophic and heterotrophic bacteria in organic particle microhabitats. Overall, the disparities in bacterial diversity, community composition, putative function, and network characteristics between FL and PA fractions highlight their adaptation to distinct ecological niches within these unique lake ecosystems.IMPORTANCEUnderstanding the diversity of microbial communities, their assembly mechanisms, and their responses to environmental changes is fundamental to the study of aquatic microbial ecology. Oligotrophic deep-water lakes are fragile ecosystems with limited nutrient resources, rendering them highly susceptible to environmental fluctuations. Examining different bacterial types within these lakes offers valuable insights into the intricate mechanisms governing community dynamics and adaptation strategies across various scales. In our investigation of oligotrophic deep freshwater Lake Fuxian in China, we explored the seasonal and vertical dynamics of two bacterial types: free-living (FL) and particle-attached (PA). Our findings unveiled distinct patterns in the diversity, composition, and putative functions of these bacteria, all shaped by environmental factors. Understanding these subtleties provides insight into bacterial interactions, thereby influencing the overall ecosystem functioning. Ultimately, our research illuminates the adaptation and roles of FL and PA bacteria within these unique lake environments, contributing significantly to our broader comprehension of ecosystem stability and health.
Collapse
Affiliation(s)
- Guijuan Xie
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Chuanbo Sun
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Wenlei Luo
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- The Fuxianhu Station of Plateau Deep Lake Field Scientific Observation and Research, Yunnan, Yuxi, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
2
|
Gao M, Zhang Q, Wu S, Wu L, Cao P, Zhang Y, Rong L, Fang B, Yuan C, Yao Y, Wang Y, Sun H. Contamination Status of Novel Organophosphate Esters Derived from Organophosphite Antioxidants in Soil and the Effects on Soil Bacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10740-10751. [PMID: 38771797 DOI: 10.1021/acs.est.3c10611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The contamination status of novel organophosphate esters (NOPEs) and their precursors organophosphite antioxidants (OPAs) and hydroxylated/diester transformation products (OH-OPEs/di-OPEs) in soils across a large-scale area in China were investigated. The total concentrations of the three test NOPEs in soil were 82.4-716 ng g-1, which were considerably higher than those of traditional OPEs (4.50-430 ng g-1), OPAs (n.d.-30.8 ng g-1), OH-OPEs (n.d.-0.49 ng g-1), and di-OPEs (0.57-21.1 ng g-1). One NOPE compound, i.e., tris(2,4-di-tert-butylphenyl) phosphate (AO168 = O) contributed over 65% of the concentrations of the studied OPE-associated contaminants. A 30-day soil incubation experiment was performed to confirm the influence of AO168 = O on soil bacterial communities. Specific genera belonging to Proteobacteria, such as Lysobacter and Ensifer, were enriched in AO168 = O-contaminated soils. Moreover, the ecological function of methylotrophy was observed to be significantly enhanced (t-test, p < 0.01) in soil treated with AO168 = O, while nitrogen fixation was significantly inhibited (t-test, p < 0.01). These findings comprehensively revealed the contamination status of OPE-associated contaminants in the soil environment and provided the first evidence of the effects of NOPEs on soil microbial communities.
Collapse
Affiliation(s)
- Meng Gao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qiuyue Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shanxing Wu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lina Wu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Peiyu Cao
- Department of Global Development, College of Agriculture and Life Science, and Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York 14850, United States
| | - Yaozhi Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lili Rong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Bo Fang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Chaolei Yuan
- School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| |
Collapse
|
3
|
Guo P, Du H, Zhao W, Xiong B, Wang M, He M, Flemetakis E, Hänsch R, Ma M, Rennenberg H, Wang D. Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133236. [PMID: 38141298 DOI: 10.1016/j.jhazmat.2023.133236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 12/10/2023] [Indexed: 12/25/2023]
Abstract
Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.
Collapse
Affiliation(s)
- Pan Guo
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Hongxia Du
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Wancang Zhao
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing 400715, PR China
| | - Bingcai Xiong
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Mingxing Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
| | - Mingyan He
- Chongqing Ecological Environment Monitoring Center, Chongqing 401147, PR China
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Robert Hänsch
- Institute for Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, D-38106, Braunschweig, Germany
| | - Ming Ma
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China.
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Dingyong Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
| |
Collapse
|
4
|
Tie J, Qiao Y, Jin N, Gao X, Liu Y, Lyu J, Zhang G, Hu L, Yu J. Yield and Rhizosphere Soil Environment of Greenhouse Zucchini in Response to Different Planting and Breeding Waste Composts. Microorganisms 2023; 11:microorganisms11041026. [PMID: 37110447 PMCID: PMC10143665 DOI: 10.3390/microorganisms11041026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Composting, planting, and breeding waste for return to the field is the most crucial soil improvement method under the resource utilization of agricultural waste. However, how the vegetable yield and rhizosphere soil environment respond to different composts is still unknown. Therefore, eight formulations were designed for compost fermentation using agricultural waste [sheep manure (SM), tail vegetable (TV), cow manure (CM), mushroom residue (MR), and corn straw (CS)] without fertilizer (CK1) and local commercial organic fertilizer (CK2) as controls to study the yield and rhizosphere soil environment of greenhouse zucchini in response to different planting and breeding waste compost. Applying planting and breeding waste compost significantly increased the soil's organic matter and nutrient content. It inhibited soil acidification, which T4 (SM:TV:CS = 6:3:1) and T7 (SM:TV:MR:CS = 6:2:1:1) treatments affected significantly. Compared to CK2 treatment, T4 and T7 treatments showed a greater increase, with a significant increase of 14.69% and 11.01%, respectively. Therefore, T4, T7, and two control treatments were selected for high-throughput sequencing based on yield performance. Compared with the CK1 treatment, although multiple applications of chemical fertilizers led to a decrease in bacterial and fungal richness, planting and breeding waste compost maintained bacterial diversity and enhanced fungal diversity. Compared to CK2, the relative abundance increased in T7-treated Proteobacteria (Sphingomonas, Pseudomonas, and Lysobacter) and T4-treated Bacteroidetes (Flavobacterium) among bacteria. An increase in T4-treated Ascomycota (Zopfiella and Fusarium) and Basidiomycota among fungi and a decrease in T7-treated Mortierellomycota have been observed. Functional predictions of the bacterial Tax4Fun and fungal FUNGuild revealed that applying planting and breeding waste compost from the T4 treatment significantly increased the abundance of soil bacterial Metabolism of Cities, Genetic Information Processing, and Cellular Processes decreased the abundance of Pathotroph and Saprotroph-Symbiotroph fungi and increased the abundance of Saprotroph fungi. Overall, planting and breeding waste compost increased zucchini yield by improving soil fertility and microbial community structure. Among them, T4 treatment has the most significant effect, so T4 treatment can be selected as the optimized formulation of local commercial organic fertilizer. These findings have valuable implications for sustainable agricultural development.
Collapse
Affiliation(s)
- Jianzhong Tie
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yali Qiao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Ning Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Xueqin Gao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yayu Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Guobin Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Linli Hu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Provincial Key Laboratory of Arid Land Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| |
Collapse
|
5
|
Zhu H, Zhang H, Hou B, Xu B, Ji L, Wu Y. Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:9110560. [PMID: 36467550 PMCID: PMC9715342 DOI: 10.1155/2022/9110560] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 10/29/2023]
Abstract
OBJECTIVES The experiment aimed to explore the effects of curcumin on motor impairment, dopamine neurons, and gut microbiota in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mice model. METHODS Mice were randomly assigned to six groups: normal control group, solvent control group, MPTP group, curcumin-low-dose group (40 mg/kg), curcumin-medium-dose group (80 mg/kg), and curcumin-high-dose group (160 mg/kg). After 14 days, each group of mice was subjected to the pole text, the hanging test, and the open-field test. Tyrosine hydroxylase (TH) immunohistochemistry was used to observe the survival of nigrostriatal dopamine neurons. Moreover, ultrastructural changes were observed with a transmission electron microscope in mice striatal tissue cells. Then, 16S rRNA was used to assess changes in the gut microbiota. RESULTS (1) Each dose of curcumin reduced pole climbing time and increased suspension score and total distance moved dose-dependently. (2) All curcumin groups improved cell wrinkling and vacuolar degeneration, increased the number of TH positives, improved cell survival, and the higher the dose of curcumin, the better the effect. (3) There were differences in microbiota composition and a relative abundance among the groups. The relative abundance of Patescibacteria, Proteobacteria, and Verrucomicrobia was higher in the MPTP group. The relative abundance of Patescibacteria, Enterobacteriaceae, Enterococcaceae all decreased in all curcumin groups. In addition, the Kyoto Encyclopedia of Genes and Genomes pathways showed a reduction in the superpathway of N-acetylneuraminate degradation after medium- and high-dose curcumin administration. CONCLUSIONS Curcumin regulates gut microbiota and exerts a neuroprotective effect in the MPTP mice model. This preliminary study demonstrates the therapeutic potential of curcumin for Parkinson's disease, providing clues for microbially targeted therapies for Parkinson's disease.
Collapse
Affiliation(s)
- Hong Zhu
- Department of Neurology, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province), Hangzhou 310000, China
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Houwen Zhang
- Department of Neurology, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province), Hangzhou 310000, China
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Bonan Hou
- Department of Neurology, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province), Hangzhou 310000, China
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Bin Xu
- Department of Neurology, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province), Hangzhou 310000, China
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Liting Ji
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - You Wu
- Department of Neurology, The Second Affiliated Hospital of Zhejiang Chinese Medical University (Xinhua Hospital of Zhejiang Province), Hangzhou 310000, China
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou 310000, China
| |
Collapse
|
6
|
Zhang N, He Y, Yi X, Yan Y, Xu W. Rapid start-up of autotrophic shortcut nitrification system in SBR and microbial community analysis. ENVIRONMENTAL TECHNOLOGY 2022; 43:4363-4375. [PMID: 34187308 DOI: 10.1080/09593330.2021.1950213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Shortcut nitrification is crucial for application of autotrophic nitrogen removal which is beneficial for treating carbon-limited wastewater. In this experiment, rapid start-up of autotrophic shortcut nitrification system was studied in a small sequencing batch reactor (SBR) built in laboratory with intermittent aeration operation mode. The influent was artificially simulated inorganic domestic wastewater (the ammonium nitrogen concentration was 35.19-57.54 mg/L), the pH value was 7.6-7.8, the hydraulic loading was 1L, the operating temperature was 24.3-28.3 °C, and the dissolved oxygen (DO) was 2-4 mg/L and 0.5-0.9 mg/L at the stage of complete nitrification sludge domestication and shortcut nitrification sludge domestication. High-throughput sequencing technology was used to analyse the composition and changes of microbial populations in sludge. The experimental results showed that on the 24th day of the experiment, shortcut nitrification was started successfully, the accumulation rate of nitrite was 81.63% and the removal efficiency of ammonium nitrogen was 99.25%; the richness of the main denitrifying bacteria phylum Proteobacteria increased from 30.21% to 42.85%; the richness of Nitrosomonas (ammonia oxidizing bacteria, AOB) increased from 0.37% to 22.43%, and at the species level, AOB was the salt-tolerant bacteria Nitrosomonas. europaea; the richness of Nitrospira (nitrite oxidizing bacteria, NOB) decreased from 2.59% to 0.47%.
Collapse
Affiliation(s)
- Nan Zhang
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, People's Republic of China
| | - Yuecheng He
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, People's Republic of China
| | - Xiang Yi
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, People's Republic of China
| | - Yunan Yan
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, People's Republic of China
| | - Wenlai Xu
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, People's Republic of China
| |
Collapse
|
7
|
Oliveira MET, Paulino GVB, Dos Santos Júnior ED, da Silva Oliveira FA, Melo VMM, Ursulino JS, de Aquino TM, Shetty AK, Landell MF, Gitaí DLG. Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy. Mol Neurobiol 2022; 59:6429-6446. [PMID: 35962889 DOI: 10.1007/s12035-022-02984-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 07/29/2022] [Indexed: 11/25/2022]
Abstract
Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.
Collapse
Affiliation(s)
- Maria Eduarda T Oliveira
- Laboratory of Cellular and Molecular Biology (LBCM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Gustavo V B Paulino
- Laboratory of Molecular Diversity (LDM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Erivaldo D Dos Santos Júnior
- Laboratory of Cellular and Molecular Biology (LBCM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Francisca A da Silva Oliveira
- Laboratory of Microbial Ecology and Biotechnology (Lembiotech), Department of Biology, Universidade Federal Do Ceará, Campus do Pici, Bloco 909, Fortaleza, CE, 60455-760, Brazil
| | - Vânia M M Melo
- Laboratory of Microbial Ecology and Biotechnology (Lembiotech), Department of Biology, Universidade Federal Do Ceará, Campus do Pici, Bloco 909, Fortaleza, CE, 60455-760, Brazil
| | - Jeferson S Ursulino
- Nucleus of Analysis and Research in Nuclear Magnetic Resonance - NAPRMN, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Thiago M de Aquino
- Nucleus of Analysis and Research in Nuclear Magnetic Resonance - NAPRMN, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center College of Medicine, College Station, TX, USA
| | - Melissa Fontes Landell
- Laboratory of Molecular Diversity (LDM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil.
| | - Daniel Leite Góes Gitaí
- Laboratory of Cellular and Molecular Biology (LBCM), Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, 57072-900, Brazil.
| |
Collapse
|
8
|
Ray AE, Zaugg J, Benaud N, Chelliah DS, Bay S, Wong HL, Leung PM, Ji M, Terauds A, Montgomery K, Greening C, Cowan DA, Kong W, Williams TJ, Hugenholtz P, Ferrari BC. Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. THE ISME JOURNAL 2022; 16:2547-2560. [PMID: 35933499 PMCID: PMC9561532 DOI: 10.1038/s41396-022-01298-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
Collapse
|
9
|
Administration of Hookworm Excretory/Secretory Proteins Improves Glucose Tolerance in a Mouse Model of Type 2 Diabetes. Biomolecules 2022; 12:biom12050637. [PMID: 35625566 PMCID: PMC9138508 DOI: 10.3390/biom12050637] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 01/27/2023] Open
Abstract
Diabetes is recognised as the world’s fastest growing chronic condition globally. Helminth infections have been shown to be associated with a lower prevalence of type 2 diabetes (T2D), in part due to their ability to induce a type 2 immune response. Therefore, to understand the molecular mechanisms that underlie the development of T2D-induced insulin resistance, we treated mice fed on normal or diabetes-promoting diets with excretory/secretory products (ES) from the gastrointestinal helminth Nippostrongylus brasiliensis. We demonstrated that treatment with crude ES products from adult worms (AES) or infective third-stage larvae (L3ES) from N. brasiliensis improved glucose tolerance and attenuated body weight gain in mice fed on a high glycaemic index diet. N. brasiliensis ES administration to mice was associated with a type 2 immune response measured by increased eosinophils and IL-5 in peripheral tissues but not IL-4, and with a decrease in the level of IL-6 in adipose tissue and corresponding increase in IL-6 levels in the liver. Moreover, treatment with AES or L3ES was associated with significant changes in the community composition of the gut microbiota at the phylum and order levels. These data highlight a role for N. brasiliensis ES in modulating the immune response associated with T2D, and suggest that N. brasiliensis ES contain molecules with therapeutic potential for treating metabolic syndrome and T2D.
Collapse
|
10
|
Xia WJ, Xu ML, Yu XJ, Du MM, Li XH, Yang T, Li L, Li Y, Kang KB, Su Q, Xu JX, Shi XL, Wang XM, Li HB, Kang YM. Antihypertensive effects of exercise involve reshaping of gut microbiota and improvement of gut-brain axis in spontaneously hypertensive rat. Gut Microbes 2022; 13:1-24. [PMID: 33382364 PMCID: PMC7781639 DOI: 10.1080/19490976.2020.1854642] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Exercise (Ex) has long been recognized to produce beneficial effects on hypertension (HTN). This coupled with evidence of gut dysbiosis and an impaired gut-brain axis led us to hypothesize that reshaping of gut microbiota and improvement in impaired gut-brain axis would, in part, be associated with beneficial influence of exercise. Male spontaneously hypertensive rats (SHR) and Wistar Kyoto (WKY) rats were randomized into sedentary, trained, and detrained groups. Trained rats underwent moderate-intensity exercise for 12 weeks, whereas, detrained groups underwent 8 weeks of moderate-intensity exercise followed by 4 weeks of detraining. Fecal microbiota, gut pathology, intestinal inflammation, and permeability, brain microglia and neuroinflammation were analyzed. We observed that exercise training resulted in a persistent decrease in systolic blood pressure in the SHR. This was associated with increase in microbial α diversity, altered β diversity, and enrichment of beneficial bacterial genera. Furthermore, decrease in the number of activated microglia, neuroinflammation in the hypothalamic paraventricular nucleus, improved gut pathology, inflammation, and permeability were also observed in the SHR following exercise. Interestingly, short-term detraining did not abolish these exercise-mediated improvements. Finally, fecal microbiota transplantation from exercised SHR into sedentary SHR resulted in attenuated SBP and an improved gut-brain axis. These observations support our concept that an impaired gut-brain axis is linked to HTN and exercise ameliorates this impairment to induce antihypertensive effects.
Collapse
Affiliation(s)
- Wen-Jie Xia
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina,CONTACT Hong-Bao Li, Xi’an 710061, China
| | - Meng-Lu Xu
- Department of Nephrology, The First Affiliated Hospital of Xi’an Medical University, Xi’anChina,CONTACT Hong-Bao Li, Xi’an 710061, China
| | - Xiao-Jing Yu
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina,CONTACT Hong-Bao Li, Xi’an 710061, China
| | - Meng-Meng Du
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina
| | - Xu-Hui Li
- Center for Neuron and Disease, Frontier Institutes of Science and Technology, Xi’an Jiaotong University, Xi’anChina
| | - Tao Yang
- Microbiome Consortium and Center for Hypertension and Precision Medicine, Department of Physiology and Pharmacology, College of Medicine and Life Sciences, University of Toledo, Toledo, OHUSA
| | - Lu Li
- Department of Nephrology, The First Affiliated Hospital of Xi’an Medical University, Xi’anChina
| | - Ying Li
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina
| | - Kai B. Kang
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Qing Su
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina
| | - Jia-Xi Xu
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina
| | - Xiao-Lian Shi
- Department of Pharmacology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’anChina
| | - Xiao-Min Wang
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina
| | - Hong-Bao Li
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina,CONTACT Hong-Bao Li, Xi’an 710061, China
| | - Yu-Ming Kang
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Shaanxi Engineering and Research Center of Vaccine, Key Laboratory of Environment and Genes Related to Diseases of Education Ministry of China, Xi’anChina,CONTACT Hong-Bao Li, Xi’an 710061, China
| |
Collapse
|
11
|
Li H, Li Z, Song B, Gu Z. Microbial community response of the full-scale MBR system for mixed leachates treatment. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 94:e1677. [PMID: 34897880 DOI: 10.1002/wer.1677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/29/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
In practice, mature landfill leachate and incineration (young) leachate are mixed to improve the biodegradability and enhance biological treatment performance. However, the ratio of mature-to-young leachates greatly influences MBR treatment efficiency and microbial community structure. This study investigated the treatment efficiency and microbial community structure of full-scale MBR systems operated under two mix ratios, mature leachate: young leachate = 7:3 (v/v, denoted as LL) and 3:7 (v/v, denoted as IL). LL group showed lower Cl- and COD concentrations but a higher aromatic organic content comparing to IL group, and the COD and UV254 removals for LL were significantly lower than those for IL by MBR treatment. Microbial community structures were similar in both groups at phylum level, with dominant phyla being Proteobacteria (23.8%-32.3%), Bacteroidetes (15.25%-20.7%), Chloroflexi (10.5%-23.1%), and Patescibacteria (9.9%-13.2%). However, the richness and diversity of LL group were lower, and differences were observed at lower taxonomy levels. Results indicated that salinity mainly changed the structure of microbial community, resulting in greater abundance of salt-tolerant microbials, while refractory organics affected microbial community structure, and also led to decreased diversity and metabolic activity. Therefore, in mixed leachates biological treatment, a higher young leachate ratio is recommended for better organics removal performance. PRACTITIONER POINTS: The trade-off between refractory organics and salinity in mixed leachate treatment should be paid attention. Refractory organics reduced alpha and functional diversities of microorganisms. Mixed leachate with a higher young leachate ratio reached a better organic removal.
Collapse
Affiliation(s)
- Huan Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Zhiheng Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Bowen Song
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Zhepei Gu
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| |
Collapse
|
12
|
Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res 2021; 49:11050-11066. [PMID: 34614190 PMCID: PMC8565304 DOI: 10.1093/nar/gkab773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.
Collapse
Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Mark Lee
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Ivan Erill
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| |
Collapse
|
13
|
Liu X, Ma Y, Wang J. Genetic variation and function: revealing potential factors associated with microbial phenotypes. BIOPHYSICS REPORTS 2021; 7:111-126. [PMID: 37288143 PMCID: PMC10235906 DOI: 10.52601/bpr.2021.200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/09/2021] [Indexed: 06/09/2023] Open
Abstract
Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.
Collapse
Affiliation(s)
- Xiaolin Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
14
|
Ni L, Shi Q, Wu M, Ma J, Wang Y. Fouling behavior and mechanism of hydrophilic modified membrane in anammox membrane bioreactor: Role of gel layer. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2020.118988] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
Kursa O, Tomczyk G, Sawicka-Durkalec A, Giza A, Słomiany-Szwarc M. Bacterial communities of the upper respiratory tract of turkeys. Sci Rep 2021; 11:2544. [PMID: 33510238 PMCID: PMC7843632 DOI: 10.1038/s41598-021-81984-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/13/2021] [Indexed: 02/02/2023] Open
Abstract
The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.
Collapse
Affiliation(s)
- Olimpia Kursa
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland.
| | - Grzegorz Tomczyk
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| | - Anna Sawicka-Durkalec
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| | - Aleksandra Giza
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| | - Magdalena Słomiany-Szwarc
- Department of Omics Analyses, National Veterinary Research Institute, Al. Partyzantów 57, 24-100, Pulawy, Poland
| |
Collapse
|
16
|
Kılıç S, Sánchez-Osuna M, Collado-Padilla A, Barbé J, Erill I. Flexible comparative genomics of prokaryotic transcriptional regulatory networks. BMC Genomics 2020; 21:466. [PMID: 33327941 PMCID: PMC7739468 DOI: 10.1186/s12864-020-06838-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evolution of bacterial regulons, few comparative genomics suites have been developed for the automated analysis of these regulatory systems. Available solutions typically rely on precomputed databases for operon and ortholog predictions, limiting the scope of analyses to processed complete genomes, and several key issues such as the transfer of experimental information or the integration of regulatory information in a probabilistic setting remain largely unaddressed. Results Here we introduce CGB, a flexible platform for comparative genomics of prokaryotic regulons. CGB has few external dependencies and enables fully customized analyses of newly available genome data. The platform automates the merging of experimental information and uses a gene-centered, Bayesian framework to generate and integrate easily interpretable results. We demonstrate its flexibility and power by analyzing the evolution of type III secretion system regulation in pathogenic Proteobacteria and by characterizing the SOS regulon of a new bacterial phylum, the Balneolaeota. Conclusions Our results demonstrate the applicability of the CGB pipeline in multiple settings. CGB’s ability to automatically integrate experimental information from multiple sources and use complete and draft genomic data, coupled with its non-reliance on precomputed databases and its easily interpretable display of gene-centered posterior probabilities of regulation provide users with an unprecedented level of flexibility in launching comparative genomics analyses of prokaryotic transcriptional regulatory networks. The analyses of type III secretion and SOS response regulatory networks illustrate instances of convergent and divergent evolution of these regulatory systems, showcasing the power of formal ancestral state reconstruction at inferring the evolutionary history of regulatory networks.
Collapse
Affiliation(s)
- Sefa Kılıç
- University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | | | | | - Jordi Barbé
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ivan Erill
- University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
| |
Collapse
|
17
|
Wang M, Ma Y, Feng C, Cai L, Li W. Diversity of Pelagic and Benthic Bacterial Assemblages in the Western Pacific Ocean. Front Microbiol 2020; 11:1730. [PMID: 33071990 PMCID: PMC7533643 DOI: 10.3389/fmicb.2020.01730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity data in the water column and sediments of the Western Pacific Ocean were explored. The OTU richness declined along the water column after peaking between 100 to 200 m deep. Relative abundance of Cyanobacteria and SAR11 decreased significantly with depth, while Actinobacteria and Gammaproteobacteria increased. This clearly mirrors the vertical distribution pattern of the predicted functional composition with the shift between phototrophic to chemoheterotrophic groups from the surface to the deeper layers. In terms of community composition and functional structure, the epipelagic zone differed from other deeper ones (i.e., meso-, bathy-, and abyssopelagic zones) where no obvious differences were detected. For the epipelagic zone, temperature, dissolved oxygen, and salinity were recognized as the crucial factors shaping both community composition and the functional structure of bacteria. Compared with water samples, benthic sediment samples harbored unexpectedly higher read abundance of Proteobacteria, presenting distinguishable taxonomic and functional compositions. This study provides novel knowledge on the vertical distribution of bacterial taxonomic and functional compositions in the western Pacific.
Collapse
Affiliation(s)
- Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiyuan Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chunhui Feng
- Beihai Ocean Engineering Survey Research Institute, State Oceanic Administration, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| |
Collapse
|
18
|
Naufal M, Wu JH. Stability of microbial functionality in anammox sludge adaptation to various salt concentrations and different salt-adding steps. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114713. [PMID: 32388308 DOI: 10.1016/j.envpol.2020.114713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/08/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
The stability of community functioning in anaerobic ammonia oxidation (anammox) sludge adaptation to various salinity changes are concerned but not fully explored. In this study, two anammox reactors were designed in response to different salt levels and salt-adding methods. The reactor PI, run with small stepwise salt increments (0.5%-1.0%), removed >90% of nitrite and ammonium in the influent over the range of 0%-4% salt. By contrast, the reactor SI, run with a sharp salt increment (>2.5%), exhibited a reduced performance (by up to 44%) over the same salt range with a new steady state. The observed resilience times after salt perturbations indicated that the PI reactor recovered substantially and rapidly at all imposed salt levels. Principal coordinates analysis of 16S rRNA gene amplicon sequences revealed that bacterial community structures of the anammox sludge altered conspicuously in response to the salinity changes. However, quantitative PCR analysis showed that the shift in copy number of studied nitrogen-converting genes encoding hydrazine synthase (hzsA), bacterial and archaeal ammonia monooxygenases (amoA), nitrite oxidoreductase (nxrB), nitrite reductase (nirK), and nitrous oxide reductase (nosZ) was not significant (p > 0.05) in anammox sludge across the salt levels of 0.5%-4%, which suggests the stability of microbial community functioning in the osmoadaptation processes. The freshwater anammox Ca. Kuenenia showed high osmoadaptation by potentially adopting both high-salt-in and low-salt-in strategies to dominate in both reactors. The quantitative transcript analysis showed that the active anammox bacteria represented by hzsA transcripts in the SI reactor were approximately two orders of magnitude lower than those in the PI reactor during the long-term exposure to 4% salinity, manifesting the influence by the salt-increasing methods. These results provided new insight into osmo-adaptation of the anammox microbiome and will be useful for managing salinity effects on nitrogen removal processes.
Collapse
Affiliation(s)
- Muhammad Naufal
- Department of Environmental Engineering, National Cheng Kung University, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Taiwan.
| |
Collapse
|
19
|
Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Bacterial communities associated with cell phones and shoes. PeerJ 2020; 8:e9235. [PMID: 32551196 PMCID: PMC7292020 DOI: 10.7717/peerj.9235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.
Collapse
Affiliation(s)
- David A Coil
- Genome Center, University of California, Davis, CA, United States of America
| | - Russell Y Neches
- Genome Center, University of California, Davis, CA, United States of America
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, United States of America
| | - Wendy E Brown
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America.,Science Cheerleaders, Inc., Philadelphia, PA, United States of America
| | - Darlene Cavalier
- Science Cheerleaders, Inc., Philadelphia, PA, United States of America.,SciStarter.org, Philadelphia, PA, United States of America
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, University of Chicago, Lemont, IL, United States of America
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, UC San Diego School of Medicine, San Diego, CA, United States of America
| | - Jonathan A Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America
| |
Collapse
|
20
|
Zhou J, You X, Niu B, Yang X, Gong L, Zhou Y, Wang J, Zhang H. Enhancement of methanogenic activity in anaerobic digestion of high solids sludge by nano zero-valent iron. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:135532. [PMID: 31759718 DOI: 10.1016/j.scitotenv.2019.135532] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
This study evaluated the effects of nano zero-valent iron (NZVI, 50 nm) on anaerobic digestion of high solids sludge (10 ± 0.5%). Compared to the blank group without NZVI, the group with NZVI at all levels (10, 20 and 30 mM) played a driving role in methane production. The maximal methane production was increased by 37.5% in the group of 30 mM NZVI. The dynamic changes of hydrogen content and VFAs showed that rapid hydrogen evolutional corrosion of NZVI made lower hydrogen partial pressure in the later stage, which was more conducive to conversion of propionic acid. The microscopic analysis indicated that NZVI could flocculate and adsorb on the extracellular polymeric substances (EPS) around the anaerobic microorganisms, protecting most active microbial cell membrane from contact damage. On the other hand, some decaying microbial cells membrane could be destroyed by NZVI and intracellular substances would be released due to the reduction of EPS.
Collapse
Affiliation(s)
- Jun Zhou
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| | - Xiaogang You
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| | - Baowei Niu
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| | - Xiaoqi Yang
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| | - Lei Gong
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China.
| | - Ying Zhou
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| | - Jin Wang
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| | - Haonan Zhang
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, 53, Zhengzhou Road, Qingdao, Shandong Province 266042, PR China
| |
Collapse
|
21
|
Ren CC, Sylvia KE, Munley KM, Deyoe JE, Henderson SG, Vu MP, Demas GE. Photoperiod modulates the gut microbiome and aggressive behavior in Siberian hamsters. ACTA ACUST UNITED AC 2020; 223:jeb.212548. [PMID: 31862850 DOI: 10.1242/jeb.212548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022]
Abstract
Seasonally breeding animals undergo shifts in physiology and behavior in response to changes in photoperiod (day length). Interestingly, some species, such as Siberian hamsters (Phodopus sungorus), are more aggressive during the short-day photoperiods of the non-breeding season, despite gonadal regression. While our previous data suggest that Siberian hamsters employ a 'seasonal switch' from gonadal to adrenal regulation of aggression during short-day photoperiods, there is emerging evidence that the gut microbiome, an environment of symbiotic bacteria within the gastrointestinal tract, may also change seasonally and modulate social behaviors. The goal of this study was to compare seasonal shifts in the gut microbiome, circulating levels of adrenal dehydroepiandrosterone (DHEA) and aggression in male and female Siberian hamsters. Hamsters were housed in either long-day (LD) or short-day (SD) photoperiods for 9 weeks. Fecal samples were collected and behaviors were recorded following 3, 6 and 9 weeks of housing, and circulating DHEA was measured at week 9. SD females that were responsive to changes in photoperiod (SD-R), but not SD-R males, displayed increased aggression following 9 weeks of treatment. SD-R males and females also exhibited distinct changes in the relative abundance of gut bacterial phyla and families, yet showed no change in circulating DHEA. The relative abundance of some bacterial families (e.g. Anaeroplasmataceae in females) was associated with aggression in SD-R but not LD or SD non-responder (SD-NR) hamsters after 9 weeks of treatment. Collectively, this study provides insight into the complex role of the microbiome in regulating social behavior in seasonally breeding species.
Collapse
Affiliation(s)
- Clarissa C Ren
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Kristyn E Sylvia
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kathleen M Munley
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Jessica E Deyoe
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Sarah G Henderson
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Michael P Vu
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| | - Gregory E Demas
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
22
|
Filippini G, Bugnot AB, Johnston EL, Ruszczyk J, Potts J, Scanes P, Ferguson A, Ostrowski M, Varkey D, Dafforn KA. Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133462. [PMID: 31374508 DOI: 10.1016/j.scitotenv.2019.07.268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) related to increasing TOC that could be investigated further as potential indicators of excess enrichment.
Collapse
Affiliation(s)
- Giulia Filippini
- Department of Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Ana B Bugnot
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia; School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Emma L Johnston
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jason Ruszczyk
- Coast and Catchments, Northern Beaches Council, Manly, NSW 1655, Australia
| | - Jaimie Potts
- NSW Department of Planning, Industry and Environment, Lidcombe, NSW 2141, Australia
| | - Peter Scanes
- NSW Department of Planning, Industry and Environment, Lidcombe, NSW 2141, Australia
| | - Angus Ferguson
- NSW Department of Planning, Industry and Environment, Lidcombe, NSW 2141, Australia
| | - Martin Ostrowski
- Climate Change Cluster, University of Technology, Sydney, NSW 2007, Australia
| | - Deepa Varkey
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Katherine A Dafforn
- Department of Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia; Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| |
Collapse
|
23
|
Meyer JL, Castellanos-Gell J, Aeby GS, Häse CC, Ushijima B, Paul VJ. Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract. Front Microbiol 2019; 10:2244. [PMID: 31608047 PMCID: PMC6769089 DOI: 10.3389/fmicb.2019.02244] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/12/2019] [Indexed: 12/31/2022] Open
Abstract
As many as 22 of the 45 coral species on the Florida Reef Tract are currently affected by stony coral tissue loss disease (SCTLD). The ongoing disease outbreak was first observed in 2014 in Southeast Florida near Miami and as of early 2019 has been documented from the northernmost reaches of the reef tract in Martin County down to Key West. We examined the microbiota associated with disease lesions and apparently healthy tissue on diseased colonies of Montastraea cavernosa, Orbicella faveolata, Diploria labyrinthiformis, and Dichocoenia stokesii. Analysis of differentially abundant taxa between disease lesions and apparently healthy tissue identified five unique amplicon sequence variants enriched in the diseased tissue in three of the coral species (all except O. faveolata), namely an unclassified genus of Flavobacteriales and sequences identified as Fusibacter (Clostridiales), Planktotalea (Rhodobacterales), Algicola (Alteromonadales), and Vibrio (Vibrionales). In addition, several groups of likely opportunistic or saprophytic colonizers such as Epsilonbacteraeota, Patescibacteria, Clostridiales, Bacteroidetes, and Rhodobacterales were also enriched in SCTLD disease lesions. This work represents the first microbiological characterization of SCTLD, as an initial step toward identifying the potential pathogen(s) responsible for SCTLD.
Collapse
Affiliation(s)
- Julie L. Meyer
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, United States
| | - Jessy Castellanos-Gell
- Soil and Water Sciences Department, University of Florida, Gainesville, FL, United States
| | - Greta S. Aeby
- Smithsonian Marine Station, Fort Pierce, FL, United States
| | - Claudia C. Häse
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Blake Ushijima
- Smithsonian Marine Station, Fort Pierce, FL, United States
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | | |
Collapse
|
24
|
Lemos LN, Medeiros JD, Dini-Andreote F, Fernandes GR, Varani AM, Oliveira G, Pylro VS. Genomic signatures and co-occurrence patterns of the ultra-small Saccharimonadia (phylum CPR/Patescibacteria) suggest a symbiotic lifestyle. Mol Ecol 2019; 28:4259-4271. [PMID: 31446647 DOI: 10.1111/mec.15208] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/29/2019] [Indexed: 01/31/2023]
Abstract
The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co-metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co-occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives.
Collapse
Affiliation(s)
- Leandro N Lemos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, Brazil
| | - Julliane D Medeiros
- Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Brazil
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Gabriel R Fernandes
- Biosystems Informatics and Genomics Group, René Rachou Institute, FIOCRUZ-Minas, Belo Horizonte, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, Brazil
| | | | - Victor S Pylro
- Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Brazil
| |
Collapse
|
25
|
Metagenomic survey of the bacterial communities in the rhizosphere of three Andean tuber crops. Symbiosis 2019. [DOI: 10.1007/s13199-019-00631-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
26
|
Fiedler CJ, Schönher C, Proksch P, Kerschbaumer DJ, Mayr E, Zunabovic-Pichler M, Domig KJ, Perfler R. Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry. Front Microbiol 2018; 9:2887. [PMID: 30555435 PMCID: PMC6281747 DOI: 10.3389/fmicb.2018.02887] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.
Collapse
Affiliation(s)
- Christina J Fiedler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Schönher
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Philipp Proksch
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - David Johannes Kerschbaumer
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ernest Mayr
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marija Zunabovic-Pichler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Konrad J Domig
- Laboratory of Food Microbiology and Hygiene, Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reinhard Perfler
- Laboratory of Microbiology, Institute of Sanitary Engineering and Water Pollution Control (SIG), Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|