1
|
Cicala F, Cisterna-Céliz JA, Paolinelli M, Moore JD, Sevigny J, Rocha-Olivares A. The Role of Diversity in Mediating Microbiota Structural and Functional Differences in Two Sympatric Species of Abalone Under Stressed Withering Syndrome Conditions. Microb Ecol 2023; 85:277-287. [PMID: 35064808 DOI: 10.1007/s00248-022-01970-5] [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: 06/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Withering syndrome (WS) is a gastro-intestinal (GI) infectious disease likely affecting all abalone species worldwide. Structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. It is unclear if interspecific microbiota differences, such as the presence of certain microbes, their abundance, and functional capabilities, may be involved in the occurrence of this disease. Bacterial microbiotas of healthy Haliotis fulgens and Haliotis corrugata are mainly composed by Tenericutes, Proteobacteria, Fusobacteria, and Spirochaetes. We previously reported species-specific structural and functional profiles of those communities and suggested that they are of consequence to the different susceptibility of each species to WS. Here, we address this question by comparing the structure and function of healthy and dysbiotic microbiota through 454 pyrosequencing and PICRUSt 2, respectively. Our findings suggest that the extent to which WS-stressed conditions may explain structural and functional differences in GI microbiota is contingent on the microbiota diversity itself. Indeed, microbiota differences between stressed and healthy abalone were marginal in the more complex bacterial communities of H. corrugata, in which no significant structural or functional changes were detected. Conversely, significant structural changes were observed in the less complex bacterial microbiota of H. fulgens. Moreover, structural alterations led to a significant downregulation of some metabolic activities conducted by GI bacteria. Accordingly, results suggest that gastro-intestinal bacterial diversity appears to be related with both the health of abalone and the etiology of WS.
Collapse
Affiliation(s)
- Francesco Cicala
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
- Department of Biomedical Innovation, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico
| | | | - Marcos Paolinelli
- National Council of Scientific and Technical Research (CONICET), Av. Rivadavia 1917, C1033AAJ, Buenos Aires, Argentina
- National Institute of Agricultural Technology INTA EEA Mendoza, San Martin 3853, Luján de Cuyo, 5507, Mendoza, Argentina
| | - James D Moore
- Bodega Marine Laboratory, University of California at Davis, P.O. Box 247, Bodega Bay, CA, USA
| | - Joseph Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH, 03824, USA
| | - Axayácatl Rocha-Olivares
- Department of Biological Oceanography, CICESE, Carretera Tijuana-Ensenada km 3918, 22860, Ensenada, Baja CA, Mexico.
| |
Collapse
|
2
|
Li J, Ren A, van der Mark E, Liu G. Direct evidence of microbiological water quality changes on bacterial quantity and community caused by plumbing system. J Environ Sci (China) 2022; 116:175-183. [PMID: 35219416 DOI: 10.1016/j.jes.2021.04.028] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 06/14/2023]
Abstract
Drinking water quality deteriorates from treatment plant to customer taps, especially in the plumbing system. There is no direct evidence about what the differences are contributed by plumbing system. This study compared the water quality in the water main and at customer tap by preparing a sampling tap on the water main. The biomass was quantified by adenosine triphosphate (ATP) and the microbial community was profiled by 454 pyrosequencing. The results showed that in distribution pipes, biofilm contributed >94% of the total biomass, while loose deposits showed little contribution (< 2%) because of the low amount of loose deposits. The distribution of biological stable water had minor effects on the microbiocidal water quality regarding both quantity (ATP 1 ng/L vs. 1.7 ng/L) and community of the bacteria. Whereas the plumbing system has significant contribution to the increase of active biomass (1.7 ng/L vs. 2.9 ng/L) and the changes of bacterial community. The relative abundance of Sphingomonas spp. at tap (22%) was higher than that at water main (2%), while the relative abundance of Pseudomonas spp. in tap water (15%) was lower than that in the water from street water main (29%). Though only one location was prepared and studied, the present study showed that the protocol of making sampling tap on water main offered directly evidences about the impacts of plumbing system on tap water quality, which makes it possible to distinguish and study the processes in distribution system and plumbing system separately.
Collapse
Affiliation(s)
- Jun Li
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anran Ren
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ed van der Mark
- Dunea Water Company, Plaza of the United Nations 11-15, Zoetermeer 2700 AT, the Netherlands
| | - Gang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sanitary engineering, Department of Water management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Delft 2600 GA, the Netherlands.
| |
Collapse
|
3
|
Bahadur A, Zhang W, Sajjad W, Nasir F, Zhang G, Liu G, Chen T. Bacterial diversity patterns of desert dunes in the northeastern Qinghai-Tibet Plateau, China. Arch Microbiol 2021; 203:2809-2823. [PMID: 33730221 DOI: 10.1007/s00203-021-02272-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/02/2023]
Abstract
Limited knowledge about the variation patterns of bacterial community composition in the sand and vegetative ecosystems confines our understanding regarding the contribution of the sand dune to desert areas. In this study, 454 pyrosequencing platforms were adopted to determine the community structure of bacteria and diversity of sand dunes in northeastern Qinghai-Tibet Plateau, China: 50 cm deep, rhizosphere, physical crusts, and biological crusts representing sand and vegetative ecosystems, respectively. The findings revealed significant variation in bacterial diversities and the structure of communities in the sand and vegetative ecosystems. The dominant bacterial phyla of sand and vegetative ecosystems were Firmicutes (47%), Actinobacteria (21%), Proteobacteria (16%), and Bacteroidetes (13%), while Lactococcus (50%) was found to be the dominant genus. Furthermore, samples with high alpha-diversity indices (Chao 1 and Shannon) for the vegetative ecosystem have the lowest modularity index and the largest number of biomarkers, with some exceptions. Redundancy analysis exhibited that environmental factors could explain 72% (phyla) and 67% (genera) of the bacterial communities, with EC, TC, and TOC being the major driving factors. This study expands our understanding of bacterial community composition in the desert ecosystem. The findings suggest that variations in the sand and vegetative ecosystems, such as those predicted by environmental factors, may reduce the abundance and diversity of bacteria, a response that likely affects the provision of key ecosystem processes by desert regions.
Collapse
Affiliation(s)
- Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences (CAS), ChangchunJilin Province, 130102, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| |
Collapse
|
4
|
Alaux PL, Mison C, Senés-Guerrero C, Moreau V, Manssens G, Foucart G, Cranenbrouck S, Declerck S. Diversity and species composition of arbuscular mycorrhizal fungi across maize fields in the southern part of Belgium. Mycorrhiza 2021; 31:265-272. [PMID: 33211191 DOI: 10.1007/s00572-020-01007-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/14/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are key actors among soil microbial inhabitants, forming beneficial associations with most horticultural plants and crops (e.g., maize). For maize, the world most cultivated cereal, data on AMF species diversity in fields is sparse and even totally nonexistent in the southern part of Belgium where maize represents 8% of the cultivated area. In the present study, 14 maize fields in South Belgium under conventional, conversion, or organic management were analyzed for AMF diversity and species composition using 454 pyrosequencing. A large part (54%) of the 49 AMF species observed were unknown or have not been described in the literature. AMF diversity highly varied among fields, with the number of species ranging between 1 and 37 according to the field. A statistically significant effect of management was measured on AMF diversity, with the highest Hill index values (diversity and richness) under the organic management system compared with conventional management or conversion. Our results suggest a positive effects of organic management on AMF diversity in maize. They also highlight the rather high diversity or richness of AMF and the large portion of sequences not yet ascribed to species, thereby emphasizing a need to intensify AMF identification in cropping systems.
Collapse
Affiliation(s)
- Pierre-Louis Alaux
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Coralie Mison
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Carolina Senés-Guerrero
- Escuela de Ingeniería Y Ciencias, Tecnológico de Monterrey, General Ramón Corona 2514, 45138, Zapopan, Jalisco, Mexico
| | - Virginie Moreau
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Gilles Manssens
- Centre Indépendant de Promotion Fourragère (CIPF), Croix du Sud, 2 L7.05.11, Louvain-la-Neuve, Belgium
| | - Guy Foucart
- Centre Indépendant de Promotion Fourragère (CIPF), Croix du Sud, 2 L7.05.11, Louvain-la-Neuve, Belgium
| | - Sylvie Cranenbrouck
- Earth and Life Institute, Applied Microbiology, Mycology, Mycothèque de L'Université Catholique de Louvain (BCCM/MUCL), Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Earth and Life Institute, Applied Microbiology, Mycology, Université Catholique de Louvain, Croix du Sud 2, box L7.05.06, 1348, Louvain-la-Neuve, Belgium.
| |
Collapse
|
5
|
Bibi F, Azhar EI. Analysis of bacterial communities in sponges and coral inhabiting Red Sea, using barcoded 454 pyrosequencing. Saudi J Biol Sci 2020; 28:847-854. [PMID: 33424375 PMCID: PMC7783839 DOI: 10.1016/j.sjbs.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are linked with marine sponge are diverse in their structure and function. Our understanding of the sponge-associated microbial diversity is limited especially from Red Sea in Saudi Arabia where few species of sponges have been studied. Here we used pyrosequencing to study two marine sponges and coral species sampled from Obhur region from Red sea in Jeddah. A total of 168 operational taxonomic units (OTUs) were identified from Haliclona caerulea, Stylissa carteri and Rhytisma fulvum. Taxonomic identification of tag sequences of 16S ribosomal RNA revealed 6 different bacterial phyla and 9 different classes. A proportion of unclassified reads were was also observed in sponges and coral sample. We found diverse bacterial communities associated with two sponges and a coral sample. Diversity and richness estimates based on OUTs revealed that sponge H. caerulea had significantly high bacterial diversity. The identified OTUs showed unique clustering in three sponge samples as revealed by Principal coordinate analysis (PCoA). Proteobacteria (88-95%) was dominant phyla alonwith Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes and Nitrospirae. Seventeen different genera were identified where genus Pseudoalteromonas was dominant in all three samples. This is first study to assess bacterial communities of sponge and coral sample that have never been studied before to unravel their microbial communities using 454-pyrosequencing method.
Collapse
Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
- Corresponding author at: Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| |
Collapse
|
6
|
Ibaba JD, Gubba A. High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later. Plants (Basel) 2020; 9:E1376. [PMID: 33081084 PMCID: PMC7602839 DOI: 10.3390/plants9101376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.
Collapse
Affiliation(s)
- Jacques Davy Ibaba
- Discipline of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, Agriculture Campus, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa;
| | | |
Collapse
|
7
|
Wu Y, He G, Chen S, Wang Z. Three-dimensional carbon-based anodes promoted the accumulation of exoelectrogens in bioelectrochemical systems. Water Environ Res 2020; 92:997-1005. [PMID: 31891435 DOI: 10.1002/wer.1293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/08/2019] [Revised: 12/17/2019] [Accepted: 12/24/2019] [Indexed: 06/10/2023]
Abstract
To achieve deep understandings on the effects of structure and surface properties of anode material on the performance of bioelectrochemical systems, the present research investigated the bacterial community structures of biofilms attached to different three-dimensional anodes including carbon felt and materials derived from pomelo peel, kenaf stem, and cardboard with 454 pyrosequencing analysis based on the bacterial 16S rRNA gene. The results showed that bacterial community structures, especially the relative abundance of exoelectrogens, were significantly related to the types of adopted three-dimensional anode materials. Proteobacteria was the shared predominant phylum, accounting for 55.4%, 52.1%, 66.7%, and 56.1% for carbon felt, cardboard, pomelo peel, and kenaf stem carbon, respectively. The most abundant OTU was phylogenetically related to the well-known exoelectrogen of Geobacter, with a relative abundance of 16.3%, 19.0%, 36.3%, and 28.6% in carbon felt, cardboard, pomelo peel, and kenaf stem, respectively. Moreover, another exoelectrogen of Pseudomonas sp. accounted for 4.9% in kenaf stem and 3.9% in carbonboard, respectively. The results implied the macrostructure and properties of different anode materials might result in different niches such as hydrodynamics and substrate transport dynamics, leading to different bacterial structure, especially different relative abundance of exoelectrogens, which consequently affected the performance of bioelectrochemical systems. PRACTITIONER POINTS: Bioelectrochemical systems (BESs) represent a novel biotechnology platform to simultaneously treat wastewaters and produce electrical power. Three-dimensional materials derived from nature plant as anode to promote electricity output from BESs and reduce the construct cost of BESs. Macrostructure of the three-dimensional anode material affected phylotype richness and phylogenetic diversity of microorganisms in anodic biofilm of BESs. Geobacter as well-known exoelectrogen was the most abundant in biofilm attached to three-dimensional anode.
Collapse
Affiliation(s)
- Yicheng Wu
- Fujian Engineering and Research Center of Rural Sewage Treatment and Water Safety, Xiamen University of Technology, Xiamen, China
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Guanghua He
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Department of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, China
| | - Shuiliang Chen
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Department of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, China
| | - Zejie Wang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| |
Collapse
|
8
|
Mohideen AM, Johansen SD, Babiak I. High-Throughput Identification of Adapters in Single-Read Sequencing Data. Biomolecules 2020; 10:biom10060878. [PMID: 32521604 PMCID: PMC7356586 DOI: 10.3390/biom10060878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/20/2022] Open
Abstract
Sequencing datasets available in public repositories are already high in number, and their growth is exponential. Raw sequencing data files constitute a substantial portion of these data, and they need to be pre-processed for any downstream analyses. The removal of adapter sequences is the first essential step. Tools available for the automated detection of adapters in single-read sequencing protocol datasets have certain limitations. To explore these datasets, one needs to retrieve the information on adapter sequences from the methods sections of appropriate research articles. This can be time-consuming in metadata analyses. Moreover, not all research articles provide the information on adapter sequences. We have developed adapt_find, a tool that automates the process of adapter sequences identification in raw single-read sequencing datasets. We have verified adapt_find through testing a number of publicly available datasets. adapt_find secures a robust, reliable and high-throughput process across different sequencing technologies and various adapter designs. It does not need prior knowledge of the adapter sequences. We also produced associated tools: random_mer, for the detection of random N bases either on one or both termini of the reads, and fastqc_parser, for consolidating the results from FASTQC outputs. Together, this is a valuable tool set for metadata analyses on multiple sequencing datasets.
Collapse
|
9
|
Andongma AA, Wan L, Dong YC, Wang YL, He J, Niu CY. Assessment of the Bacteria community structure across life stages of the Chinese Citrus Fly, Bactrocera minax (Diptera: Tephritidae). BMC Microbiol 2019; 19:285. [PMID: 31870291 PMCID: PMC6929268 DOI: 10.1186/s12866-019-1646-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Indexed: 01/23/2023] Open
Abstract
Background Symbiotic bacteria play a critical role in insect’s biology. They also offer great opportunities to improve on current pest management techniques. In order to exploit and integrate the roles played by the gut microbiota on pest management programs, a better understanding of the structural organization of the microbial community in the Chinese citrus fly Bactrocera minax is essential. Results The results revealed a total of 162 OTUs at 97% similarity interval. The dominant bacteria phyla were Proteobacteria, Bacteroidetes, Antinobacteria and Firmicutes, with the Proteobacteria having the highest relative abundance (more than 80% in all life stages). There was also a shift in the dominant OTUs from the early developmental stages to the late developmental stages and adult stages in B. minax. These OTUs related to Klebsiella pneumoniae, Providencia rettgeri and Enterobacter aerogenes, respectively. Six bacteria OTU were shared by all the life stages. These belonged to the Enterobacteriaceae and the Enterococcaceae families. Conclusion The common bacteria groups shared by all the life stages and other fruit flies could be important targets for further research. This should aim towards realizing how these bacteria affect the biology of the fly and how their relationship could be exploited in the development of sustainable management strategies against fruit flies.
Collapse
Affiliation(s)
| | - Lun Wan
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong-Cheng Dong
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu-Lei Wang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin He
- State key laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang-Ying Niu
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
10
|
Bibi F, Alvi SA, Al-Sofyani A, Naseer MI, Yasir M, Azhar EI. Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia. Saudi J Biol Sci 2019; 27:67-73. [PMID: 31889819 PMCID: PMC6933160 DOI: 10.1016/j.sjbs.2019.05.002] [Citation(s) in RCA: 5] [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: 03/11/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022] Open
Abstract
Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.
Collapse
Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Sana Akhtar Alvi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Abdulmohsin Al-Sofyani
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King AbdulAziz University, 21589, Jeddah, Saudi Arabia
| |
Collapse
|
11
|
Gadhave KR, Devlin PF, Ebertz A, Ross A, Gange AC. Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner. Microb Ecol 2018; 76:741-750. [PMID: 29511840 PMCID: PMC6132550 DOI: 10.1007/s00248-018-1160-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 09/22/2017] [Accepted: 02/13/2018] [Indexed: 05/22/2023]
Abstract
The use of microbial inoculants containing plant growth-promoting rhizobacteria as a promoter of plant fitness and health is becoming increasingly popular in agriculture. However, whether and how these bacteria affect indigenous bacterial communities in field conditions is sparsely explored. We studied the effects of seed inoculation and field soil application of ubiquitous soil bacteria, B. cereus, B. subtilis, and B. amyloliquefaciens, on the diversity, evenness, and richness of endophytic bacterial communities in sprouting broccoli roots using high-throughput metagenome sequencing. The multiple operational taxonomic units (OTUs) assigned to different bacterial taxa clearly showed changes in ecological measures and relative abundances of certain taxa between control and treatment groups. The Bacillus inocula, themselves, failed to flourish as endophytes; however, the effects they extended on the endophytic bacterial community were both generic as well as species specific. In each case, Pseudomonadales, Rhizobiales, Xanthomonadales, and Burkholderiales were the most abundant orders in the endosphere. B. amyloliquefaciens drastically reduced the most abundant genus, Pseudomonas, while increasing the relative abundance of a range of minor taxa. The Shannon-Weiner diversity and Buzas and Gibson's evenness indices showed that the diversity and evenness were increased in both B. amyloliquefaciens and mixed treated plants. The UniFrac measurement of beta diversity showed that all treatments affected the specific composition of the endophytic bacterial community, with an apparent interspecies competition in the mixed treatment. Taken together, Bacillus species influenced the diversity, evenness, and composition of the endophytic bacterial community. However, these effects varied between different Bacillus spp. in a context-specific manner.
Collapse
Affiliation(s)
- Kiran R Gadhave
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Paul F Devlin
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
- Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
| | - Andreas Ebertz
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Arabella Ross
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Alan C Gange
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| |
Collapse
|
12
|
García-Maldonado JQ, Escobar-Zepeda A, Raggi L, Bebout BM, Sanchez-Flores A, López-Cortés A. Bacterial and archaeal profiling of hypersaline microbial mats and endoevaporites, under natural conditions and methanogenic microcosm experiments. Extremophiles 2018; 22:903-916. [PMID: 30120599 DOI: 10.1007/s00792-018-1047-2] [Citation(s) in RCA: 12] [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: 06/14/2018] [Accepted: 08/08/2018] [Indexed: 11/29/2022]
Abstract
Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA sequencing. The response of the microbial community to artificial changes in salinity-sulfate concentrations and to addition of trimethylamine was also evaluated in microcosm experiments. Ordination analyses of the microbial community structure showed that microbial composition was distinctive for each hypersaline site. Members of bacteria were dominated by Bacteroidetes and Proteobacteria phyla, while Halobacteria of the Euryarchaeota phylum was the most represented class of archaea for all the environmental samples. At a higher phylogenetic resolution, methanogenic communities were dominated by members of the Methanosarcinales, Methanobacteriales and Methanococcales orders. Incubation experiments showed that putative hydrogenotrophic methanogens of the Methanomicrobiales increased in abundance only under lowest salinity and sulfate concentrations. Trimethylamine addition effectively increased the abundance of methylotrophic members from the Methanosarcinales, but also increased the relative abundance of the Thermoplasmata class, suggesting the potential capability of these microorganisms to use trimethylamine in hypersaline environments. These results contribute to the knowledge of microbial diversity in hypersaline environments from Baja California Sur, Mexico, and expand upon the available information for uncultured methanogenic archaea in these ecosystems.
Collapse
Affiliation(s)
- José Q García-Maldonado
- CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Antigua Carretera a Progreso Km. 6, Yucatán, 97310, Mexico.
| | - Alejandra Escobar-Zepeda
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Luciana Raggi
- CONACYT - Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Brad M Bebout
- Exobiology Branch, Ames Research Center, National Aeronautics and Space Administration, Moffett Field, CA, USA
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Alejandro López-Cortés
- Laboratorio de Geomicrobiología y Biotecnología, Instituto Politécnico Nacional 195, Centro de Investigaciones Biológicas del Noroeste, Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, 23096, Mexico.
| |
Collapse
|
13
|
Kisková J, Stramová Z, Javorský P, Sedláková-Kaduková J, Pristaš P. Analysis of the bacterial community from high alkaline (pH > 13) drainage water at a brown mud disposal site near Žiar nad Hronom (Banská Bystrica region, Slovakia) using 454 pyrosequencing. Folia Microbiol (Praha) 2018; 64:83-90. [PMID: 30084086 DOI: 10.1007/s12223-018-0634-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 11/07/2017] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
Abstract
Brown mud, as a waste product of the industrial process of aluminum production, represents a great environmental burden due to its toxicity to living organisms. However, some microorganisms are able to survive in this habitat, and they can be used in bioremediation processes. Traditional cultivation methods have a limited capacity to characterize bacterial composition in environmental samples. Recently, next-generation sequencing methods have provided new perspectives on microbial community studies. The aim of this study was to analyze the bacterial community in the drainage water of brown mud disposal site near Žiar nad Hronom (Banská Bystrica region, Slovakia) using 454 pyrosequencing. We obtained 9964 sequences assigned to 163 operational taxonomic units belonging to 10 bacterial phyla. The phylum Proteobacteria showed the highest abundance (80.39%) within the bacterial community, followed by Firmicutes (13.05%) and Bacteroidetes (5.64%). Other bacterial phyla showed an abundance lower than 1%. The classification yielded 85 genera. Sulfurospirillum spp. (45.19%) dominated the bacterial population, followed by Pseudomonas spp. (13.76%) and Exiguobacterium spp. (13.02%). These results indicate that high heavy metals content, high pH, and lack of essential nutrients are the drivers of a dramatic reduction of diversity in the bacterial population in this environment.
Collapse
Affiliation(s)
- Jana Kisková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Šrobarova 2, 04154, Košice, Slovakia.
| | - Zuzana Stramová
- Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, 04001, Košice, Slovakia
| | - Peter Javorský
- Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, 04001, Košice, Slovakia
| | - Jana Sedláková-Kaduková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Šrobarova 2, 04154, Košice, Slovakia
| | - Peter Pristaš
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Šrobarova 2, 04154, Košice, Slovakia.,Institute of Animal Physiology, Centre of Biosciences of the Slovak Academy of Sciences, Šoltésovej 4-6, 04001, Košice, Slovakia
| |
Collapse
|
14
|
Molins A, Moya P, García-Breijo FJ, Reig-Armiñana J, Barreno E. Molecular and morphological diversity of Trebouxia microalgae in sphaerothallioid Circinaria spp. lichens 1. J Phycol 2018; 54:494-504. [PMID: 29791719 DOI: 10.1111/jpy.12751] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 11/29/2017] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Three vagrant (Circinaria hispida, Circinaria gyrosa, and Circinaria sp. 'paramerae') and one crustose (semi-vagrant, Circinaria sp. 'oromediterranea') lichens growing in very continental areas in the Iberian Peninsula were selected to study the phycobiont diversity. Mycobiont identification was checked using nrITS DNA barcoding: Circinaria sp. 'oromediterranea' and Circinaria sp. 'paramerae' formed a new clade. Phycobiont diversity was analyzed in 50 thalli of Circinaria spp. using nrITS DNA and LSU rDNA, with microalgae coexistence being found in all the species analyzed by Sanger sequencing. The survey of phycobiont diversity showed up to four different Trebouxia spp. as the primary phycobiont in 20 thalli of C. hispida, in comparison with the remaining Circinaria spp., where only one Trebouxia was the primary microalga. In lichen species showing coexistence, some complementary approaches are needed (454 pyrosequencing and/or ultrastructural analyses). Five specimens were selected for high-throughput screening (HTS) analyses: 22 Trebouxia OTUs were detected, 10 of them not previously known. TEM analyses showed three different cell morphotypes (Trebouxia sp. OTU A12, OTU S51, and T. cretacea) whose ultrastructure is described here in detail for the first time. HTS revealed a different microalgae pool in each species studied, and we cannot assume a specific pattern between these pools and the ecological and/or morphological characteristics. The mechanisms involved in the selection of the primary phycobiont and the other microalgae by the mycobiont are unknown, and require complex experimental designs. The systematics of the genus Circinaria is not yet well resolved, and more analyses are needed to establish a precise delimitation of the species.
Collapse
Affiliation(s)
- Arántzazu Molins
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Patricia Moya
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Francisco J García-Breijo
- Dpto. Ecosistemas Agroforestales, Universitat Politècnica de València, Camino de Vera s/n. 46022, Valencia, Spain
| | - José Reig-Armiñana
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| | - Eva Barreno
- Botánica, ICBIBE and Jardí Botànic. Fac. CC. Biológicas, Universitat de València, C/Dr. Moliner, 50. 46100-Burjassot, Valencia, Spain
| |
Collapse
|
15
|
Ziegler M, Stone E, Colman D, Takacs-Vesbach C, Shepherd U. Patterns of Symbiodinium (Dinophyceae) diversity and assemblages among diverse hosts and the coral reef environment of Lizard Island, Australia. J Phycol 2018; 54:447-460. [PMID: 29696650 PMCID: PMC6105428 DOI: 10.1111/jpy.12749] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Large-scale environmental disturbances may impact both partners in coral host-Symbiodinium systems. Elucidation of the assembly patterns in such complex and interdependent communities may enable better prediction of environmental impacts across coral reef ecosystems. In this study, we investigated how the community composition and diversity of dinoflagellate symbionts in the genus Symbiodinium were distributed among 12 host species from six taxonomic orders (Actinaria, Alcyonacea, Miliolida, Porifera, Rhizostoma, Scleractinia) and in the reef water and sediments at Lizard Island, Great Barrier Reef before the 3rd Global Coral Bleaching Event. 454 pyrosequencing of the ITS2 region of Symbiodinium yielded 83 operational taxonomic units (OTUs) at a 97% similarity cut-off. Approximately half of the Symbiodinium OTUs from reef water or sediments were also present in symbio. OTUs belonged to six clades (A-D, F-G), but community structure was uneven. The two most abundant OTUs (100% matches to types C1 and A3) comprised 91% of reads and OTU C1 was shared by all species. However, sequence-based analysis of these dominant OTUs revealed host species specificity, suggesting that genetic similarity cut-offs of Symbiodinium ITS2 data sets need careful evaluation. Of the less abundant OTUs, roughly half occurred at only one site or in one species and the background Symbiodinium communities were distinct between individual samples. We conclude that sampling multiple host taxa with differing life history traits will be critical to fully understand the symbiont diversity of a given system and to predict coral ecosystem responses to environmental change and disturbance considering the differential stress response of the taxa within.
Collapse
Affiliation(s)
- Maren Ziegler
- Author for correspondence: Maren Ziegler, 4700 King Abdullah University of Science and Technology (KAUST), Building 2, Office 2227, 3955-6900 Thuwal, Saudi Arabia, Tel.: +966 12 808 2446,
| | - Elizabeth Stone
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Daniel Colman
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Cristina Takacs-Vesbach
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Ursula Shepherd
- Department of Biology, University of New Mexico, Castetter Hall, MSC03-2020 1 University of New Mexico, Albuquerque, New Mexico 87131, USA; Honors College, University of New Mexico, Student Health Center Building, MSCO6-3890 1 University of New Mexico, Albuquerque, New Mexico 87131, USA
| |
Collapse
|
16
|
Cheng Z, Chen Y, Zhang F. Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China. Sci Total Environ 2018; 630:799-808. [PMID: 29494981 DOI: 10.1016/j.scitotenv.2018.02.259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 11/23/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Understanding the impact of reclamation of abandoned salinized farmland on soil bacterial community is of great importance for maintaining soil health and sustainability in arid regions. In this study, we used field sampling and 454 pyrosequencing methods to investigate the effects of 5-year reclamation treatments on soil properties, bacterial community composition and diversity. The four reclamation treatments are: abandoned salinized farmland (CK), cropland (CL), grassland (GL) and woodland (WL). We have found soil properties are significantly altered by abandoned salinized farmland reclamation. In particular, the lowest soil pH and electrical conductivity (EC) values are observed in CL (P<0.05). The dominant phyla are Firmicutes, Proteobacteria, Chloroflexi, Actinobacteria and Acidobacteria in all treatments. At the genus levels, the relative abundance of Bacillus, Lactococcus, Streptococcus and Enterococcus in CK, GL and WL is significantly higher than in CL. Bacterial diversity indices (i.e. ACE, Chao and Shannon) dramatically increase after the reclamation, with the highest in CL. Similar patterns of bacterial communities have been observed in CK, GL and WL soils, but significantly different from CL. Regression analyses indicate that the relative abundance of these phyla are significantly correlated with soil Fe, pH and EC. Results from non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) indicate that soil Fe content, EC and pH are the most important factors in shaping soil bacterial communities. Overall, results indicate that abandoned salinized farmland reclaimed for CL significantly decrease soil pH and EC, and increase soil bacterial community diversity. Soil Fe concentration, EC and pH are the dominant environmental factors affecting soil bacterial community composition. The important role of Fe concentration in shaping bacterial community composition is a new discovery among the similar studies.
Collapse
Affiliation(s)
- Zhibo Cheng
- Agricultural College, Shihezi University, Shihezi City, 832003, China; CSIRO Land and Water, Canberra, ACT, 2601, Australia
| | - Yun Chen
- CSIRO Land and Water, Canberra, ACT, 2601, Australia
| | - Fenghua Zhang
- Agricultural College, Shihezi University, Shihezi City, 832003, China.
| |
Collapse
|
17
|
Najafi A, Moradinasab M, Nabipour I. First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing. Front Microbiol 2018; 9:1500. [PMID: 30034382 PMCID: PMC6043863 DOI: 10.3389/fmicb.2018.01500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 02/05/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
The Persian Gulf is a special habitat of marine sponges whose bacterial communities are under-investigated. Recently, next-generation sequencing technology has comprehensively improved the knowledge of marine sponge-associated bacteria. For the first time, this study aimed to evaluate the diversity of the Persian Gulf sponge-associated bacteria using tag pyrosequencing in Iran. In this study, 10 sponge samples from 6 different taxonomic orders were collected from the Persian Gulf using SCUBA diving. The diversity of the bacteria associated with the marine sponges was investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. A total of 68,628 high-quality sequences were obtained and clustered at a 97% similarity into 724 unique operational taxonomic units (OTUs), representing 17 bacterial phyla. Cyanobacteria was the most abundant phylum in the sponges, followed by Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria. Other phyla were detected as minor groups of bacteria. Bacterial community richness, Shannon, and Simpson indices revealed the highest diversity in sponge S11 (Dictyoceratida sp.) compared to other sponges. This study showed a diverse structure of bacterial communities associated with the Persian Gulf sponges. The dominance of Cyanobacteria may suggest an ecological importance of this phylum in the Persian Gulf sponges.
Collapse
Affiliation(s)
- Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Moradinasab
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| |
Collapse
|
18
|
Xu Y, Jia YH, Chen L, Huang WM, Yang DQ. Metagenomic analysis of oral microbiome in young children aged 6-8 years living in a rural isolated Chinese province. Oral Dis 2018; 24:1115-1125. [PMID: 29667264 DOI: 10.1111/odi.12871] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 01/08/2018] [Revised: 03/07/2018] [Accepted: 04/08/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND The mixed dentition is an important transition period from primary teeth to permanent teeth. However, the caries prevalence of first permanent molar in mixed dentitions was about 30%, which almost represent the caries rate of permanent teeth in this period of time. Therefore, we assessed the oral bacterial profiles in young children (age 6-8) with mixed dentition with or without first molar caries for providing the research basis of caries etiology. METHODS We collected samples of supragingival plaque and saliva from the children living in Guizhou, a rural isolated province in China. Then, we performed DNA extraction and purification followed by 454 pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA and compared our results with those of previous research. RESULTS (i) We analyzed 48,320 unique sequences that represented 18 phyla, 29 classes, 44 orders, 74 families, 129 genera, 15,003 species-level OUT in plaque and saliva samples; (ii) longitudinally, there was the "healthy core microbiome" between healthy deciduous dentition and early mixed dentition, for example, Neisseria, Porphyromonas, Selenomonas etc.; (iii) horizontally, there also existed the "healthy core microbiome" in early mixed dentition, for example, Neisseria, Streptococcus, Prevotella etc.; (iv) the dominant bacteria detected by Lefse in caries group including Actinomycetaceae, Streptobacillus (p < 0.05) and those in caries-free group including Gammaproteobacteria, Pasteurellaceae, Aggregatibacter, Chloroflexi, (p < 0.05). CONCLUSIONS The oral cavity is a highly heterogeneous ecosystem with the "healthy core microbiome" in children, although microbial composition shifts along with aging. In addition, the abundance and diversity of microbiota vary between caries and caries-free groups verify the ecological plaque hypothesis.
Collapse
Affiliation(s)
- Y Xu
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Y H Jia
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - L Chen
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - W M Huang
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - D Q Yang
- College of Stomatology, Chongqing Medical University, Chongqing, China.,Chongqing key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| |
Collapse
|
19
|
Onming S, Thongda W, Li C, Sawatdichaikul O, McMillan N, Klinbunga S, Peatman E, Poompuang S. Bioinformatics characterization of a cathepsin B transcript from the giant river prawn, Macrobrachium rosenbergii: Homology modeling and expression analysis after Aeromonas hydrophila infection. Comp Biochem Physiol B Biochem Mol Biol 2018; 221-222:18-28. [PMID: 29649577 DOI: 10.1016/j.cbpb.2018.04.002] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36.04 kDa and 4.73. The major characteristics of MrCTSB protein consisted of a propeptide of C1 peptidase family at the N-terminus and a cysteine protease (Pept_C1) domain at the C-terminus. The 3-dimentional structure of MrCTSB was constructed by computer-assisted homology modeling. The folding of MrCTSB was highly conserved to human CTSB structure and the modeled MrCTSB displayed characteristics of cysteine proteinases superfamily. The docking study was performed to investigate binding interactions between known inhibitors against MrCTSB. Known inhibitors were oriented in the groove of catalytic site cleft. They bound to subsites from S2, S1, S1', and S2', respectively, with key residues in each subsite. Challenge of juvenile prawns with Aeromonas hydrophila revealed that the MrCTSB transcript in hepatopancreas significantly increased at 60-96 h post injection (hpi). This suggested that MrCTSB may play roles in innate immunity of M. rosenbergii. Our results provide useful information for a more comprehensive study in immune-related functions of MrCTSB.
Collapse
Affiliation(s)
- Saowalak Onming
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Chao Li
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, Bangkok 10900, Thailand
| | - Nichanun McMillan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand
| | - Sirawut Klinbunga
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; Center of Excellence for Marine Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Supawadee Poompuang
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan Road, Bangkok 10900, Thailand.
| |
Collapse
|
20
|
Siegel-Hertz K, Edel-Hermann V, Chapelle E, Terrat S, Raaijmakers JM, Steinberg C. Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region. Front Microbiol 2018; 9:568. [PMID: 29670584 PMCID: PMC5893819 DOI: 10.3389/fmicb.2018.00568] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [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: 10/11/2017] [Accepted: 03/13/2018] [Indexed: 12/30/2022] Open
Abstract
Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.
Collapse
Affiliation(s)
- Katarzyna Siegel-Hertz
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Véronique Edel-Hermann
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Emilie Chapelle
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| |
Collapse
|
21
|
Zenk FL, Firmer C, Wöhrmann T, da Silva LV, Weising K, Huettel B, Paggi GM. Development of 15 nuclear microsatellite markers in Deuterocohnia (Pitcairnioideae; Bromeliaceae) using 454 pyrosequencing. Appl Plant Sci 2018; 6:e1147. [PMID: 30131889 PMCID: PMC5947610 DOI: 10.1002/aps3.1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed in Deuterocohnia longipetala (Bromeliaceae) to investigate species and subspecies boundaries within the genus and the genetic diversity of natural populations. METHODS AND RESULTS We used 454 pyrosequencing to isolate 835 microsatellite loci in D. longipetala. Of 64 loci selected for primer design, 15 were polymorphic among 23 individuals of D. longipetala and 76 individuals of the heterologous subspecies D. meziana subsp. meziana and D. meziana subsp. carmineo-viridiflora. Twelve and 13 of these loci were also polymorphic in one population each of D. brevispicata and D. seramisiana, respectively. Numbers of alleles per locus varied from two to 14 in D. longipetala, two to 12 in D. meziana, one to nine in D. brevispicata, and one to 10 in D. seramisiana. STRUCTURE analyses clearly separated the taxa from each other. CONCLUSIONS The 15 new microsatellite markers are promising tools for studying population genetics in Deuterocohnia species.
Collapse
Affiliation(s)
- Fides Lea Zenk
- Max Planck Institute of Immunobiology and EpigeneticsStübeweg 5179108Freiburg im BreisgauGermany
| | - Cynthia Firmer
- Systematics and Morphology of PlantsInstitute of BiologyUniversity of KasselHeinrich‐Plett‐Str. 4034132KasselGermany
| | - Tina Wöhrmann
- Systematics and Morphology of PlantsInstitute of BiologyUniversity of KasselHeinrich‐Plett‐Str. 4034132KasselGermany
| | - Luciana Vicente da Silva
- Ecology and Conservation Postgraduate ProgramFederal University of Mato Grosso do Sul State79070‐900Campo GrandeBrazil
| | - Kurt Weising
- Systematics and Morphology of PlantsInstitute of BiologyUniversity of KasselHeinrich‐Plett‐Str. 4034132KasselGermany
| | - Bruno Huettel
- Max Planck‐Genome‐centre CologneMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829CologneGermany
| | - Gecele Matos Paggi
- Biological SciencesPantanal Campus/Federal University of Mato Grosso do Sul StateC.P. 25279304‐902CorumbáBrazil
| |
Collapse
|
22
|
Chirkov S, Ivanov P, Sheveleva A, Kudryavtseva A, Mitrofanova I. Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain. Virus Genes 2018; 54:328-332. [PMID: 29460128 DOI: 10.1007/s11262-018-1541-8] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/11/2018] [Indexed: 11/29/2022]
Abstract
Field isolates of Plum pox virus (PPV), belonging to the strain Rec, have been found for the first time in Russia. Full-size genomes of the isolates K28 and Kisl-1pl from myrobalan and plum, respectively, were sequenced on the 454 platform. Analysis of all known PPV-Rec complete genomes using the Recombination Detection Program (RDP4) revealed yet another recombination event in the 5'-terminal region. This event was detected by seven algorithms, implemented in the RDP4, with statistically significant P values and supported by a phylogenetic analysis with the bootstrap value of 87%. A putative PPV-M-derived segment, encompassing the C-terminus of the P1 gene and approximately two-thirds of the HcPro gene, is bordered by breakpoints at positions 760-940 and 1838-1964, depending on the recombinant isolate. The predicted 5'-distal breakpoint for the isolate Valjevka is located at position 2804. The Dideron (strain D) and SK68 (strain M) isolates were inferred as major and minor parents, respectively. Finding of another recombination event suggests more complex evolutionary history of PPV-Rec than previously assumed. Perhaps the first recombination event led to the formation of a PPV-D variant harboring the PPV-M-derived fragment within the 5'-proximal part of the genome. Subsequent recombination of its descendant with PPV-M in the 3'-proximal genomic region resulted in the emergence of the evolutionary successful strain Rec.
Collapse
Affiliation(s)
- Sergei Chirkov
- Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Peter Ivanov
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna Sheveleva
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Irina Mitrofanova
- Nikita Botanical Gardens - National Scientific Center, Yalta, 298648, Russia
| |
Collapse
|
23
|
Cuartas JH, Alzate JF, Moreno-Herrera CX, Marquez EJ. Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758). PeerJ 2018; 6:e4307. [PMID: 29472996 PMCID: PMC5816965 DOI: 10.7717/peerj.4307] [Citation(s) in RCA: 3] [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: 01/20/2017] [Accepted: 01/10/2018] [Indexed: 11/25/2022] Open
Abstract
The endangered marine gastropod, Lobatus gigas, is an important fishery resource in the Caribbean region. Microbiological and parasitological research of this species have been poorly addressed despite its role in ecological fitness, conservation status and prevention of potential pathogenic infections. This study identified taxonomic groups associated with orange colored protrusions in the muscle of queen conchs using histological analysis, 454 pyrosequencing, and a combination of PCR amplification and automated Sanger sequencing. The molecular approaches indicate that the etiological agent of the muscle protrusions is a parasite belonging to the subclass Digenea. Additionally, the scope of the molecular technique allowed the detection of bacterial and fungi clades in the assignment analysis. This is the first evidence of a digenean infection in the muscle of this valuable Caribbean resource.
Collapse
Affiliation(s)
- Jaison H. Cuartas
- Facultad de Ciencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Juan F. Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Claudia X. Moreno-Herrera
- Facultad de Ciencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Edna J. Marquez
- Facultad de Ciencias, Laboratorio de Biología Molecular y Celular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| |
Collapse
|
24
|
Ren G, Ma Y, Guo D, Gentry TJ, Hu P, Pierson EA, Gu M. Soil Bacterial Community Was Changed after Brassicaceous Seed Meal Application for Suppression of Fusarium Wilt on Pepper. Front Microbiol 2018; 9:185. [PMID: 29487582 PMCID: PMC5816756 DOI: 10.3389/fmicb.2018.00185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 10/14/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Application of Brassicaceous seed meal (BSM) is a promising biologically based disease-control practice but BSM could directly and indirectly also affect the non-target bacterial communities, including the beneficial populations. Understanding the bacterial response to BSM at the community level is of great significance for directing plant disease management through the manipulation of resident bacterial communities. Fusarium wilt is a devastating disease on pepper. However, little is known about the response of bacterial communities, especially the rhizosphere bacterial community, to BSM application to soil heavily infested with Fusarium wilt pathogen and cropped with peppers. In this study, a 25-day microcosm incubation of a natural Fusarium wilt pathogen-infested soil supplemented with three BSMs, i.e., Camelina sativa 'Crantz' (CAME), Brassica juncea 'Pacific Gold' (PG), and a mixture of PG and Sinapis alba cv. 'IdaGold' (IG) (PG+IG, 1:1 ratio), was performed. Then, a further 35-day pot experiment was established with pepper plants growing in the BSM treated soils. The changes in the bacterial community in the soil after 25 days of incubation and changes in the rhizosphere after an additional 35 days of pepper growth were investigated by 454 pyrosequencing technique. The results show that the application of PG and PG+IG reduced the disease index by 100% and 72.8%, respectively, after 35 days of pepper growth, while the application of CAME did not have an evident suppressive effect. All BSM treatments altered the bacterial community structure and decreased the bacterial richness and diversity after 25 days of incubation, although this effect was weakened after an additional 35 days of pepper growth. At the phylum/class and the genus levels, the changes in specific bacterial populations resulting from the PG and PG+IG treatments, especially the significant increase in Actinobacteria-affiliated Streptomyces and an unclassified genus and the significant decrease in Chloroflexi, were suspected to be one of the microbial mechanisms involved in PG-containing BSM-induced disease suppression. This study is helpful for our understanding of the mechanisms that lead to contrasting plant disease severity after the addition of different BSMs.
Collapse
Affiliation(s)
- Gaidi Ren
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Yan Ma
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Dejie Guo
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Terry J. Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Ping Hu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Elizabeth A. Pierson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Mengmeng Gu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
25
|
Liu J, Yu Z, Yao Q, Sui Y, Shi Y, Chu H, Tang C, Franks AE, Jin J, Liu X, Wang G. Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China. Front Microbiol 2018; 9:171. [PMID: 29497404 PMCID: PMC5819564 DOI: 10.3389/fmicb.2018.00171] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 11/23/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Black soils (Mollisols) of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001) but not with soil pH (p > 0.05). In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009) but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR) was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048), whereas PNR significantly correlated positively with the richness (p = 0.003), diversity (p = 0.001) and abundance (p < 0.001) of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA community in the black soils when ammonium is readily available.
Collapse
Affiliation(s)
- Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qin Yao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora VIC, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora VIC, Australia
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| |
Collapse
|
26
|
Vaidya JD, van den Bogert B, Edwards JE, Boekhorst J, van Gastelen S, Saccenti E, Plugge CM, Smidt H. The Effect of DNA Extraction Methods on Observed Microbial Communities from Fibrous and Liquid Rumen Fractions of Dairy Cows. Front Microbiol 2018; 9:92. [PMID: 29445366 PMCID: PMC5797766 DOI: 10.3389/fmicb.2018.00092] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 07/26/2017] [Accepted: 01/16/2018] [Indexed: 12/01/2022] Open
Abstract
DNA based methods have been widely used to study the complexity of the rumen microbiota, and it is well known that the method of DNA extraction is a critical step in enabling accurate assessment of this complexity. Rumen fluid (RF) and fibrous content (FC) fractions differ substantially in terms of their physical nature and associated microorganisms. The aim of this study was therefore to assess the effect of four DNA extraction methods (RBB, PBB, FDSS, PQIAmini) differing in cell lysis and/or DNA recovery methods on the observed microbial diversity in RF and FC fractions using samples from four rumen cannulated dairy cows fed 100% grass silage (GS100), 67% GS and 33% maize silage (GS67MS33), 33% GS and 67% MS (GS33MS67), or 100% MS (MS100). An ANOVA statistical test was applied on DNA quality and yield measurements, and it was found that the DNA yield was significantly affected by extraction method (p < 0.001) and fraction (p < 0.001). The 260/280 ratio was not affected by extraction (p = 0.08) but was affected by fraction (p = 0.03). On the other hand, the 260/230 ratio was affected by extraction method (p < 0.001) but not affected by fraction (p = 0.8). However, all four extraction procedures yielded DNA suitable for further analysis of bacterial, archaeal and anaerobic fungal communities using quantitative PCR and pyrosequencing of relevant taxonomic markers. Redundancy analysis (RDA) of bacterial 16S rRNA gene sequence data at the family level showed that there was a significant effect of rumen fraction (p = 0.012), and that PBB (p = 0.012) and FDSS (p = 0.024) also significantly contributed to explaining the observed variation in bacterial community composition. Whilst the DNA extraction method affected the apparent bacterial community composition, no single extraction method could be concluded to be ineffective. No obvious effect of DNA extraction method on the anaerobic fungi or archaea was observed, although fraction effects were evident for both. In summary, the comprehensive assessment of observed communities of bacteria, archaea and anaerobic fungi described here provides insight into a rational basis for selecting an optimal methodology to obtain a representative picture of the rumen microbiota.
Collapse
Affiliation(s)
- Jueeli D. Vaidya
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Bartholomeus van den Bogert
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Joan E. Edwards
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Sanne van Gastelen
- Top Institute Food and Nutrition, Wageningen, Netherlands
- Animal Nutrition Group, Wageningen University and Research, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| |
Collapse
|
27
|
Lee CG, Iida T, Uwagaki Y, Otani Y, Nakaho K, Ohkuma M. Comparison of Prokaryotic and Eukaryotic Communities in Soil Samples with and without Tomato Bacterial Wilt Collected from Different Fields. Microbes Environ 2017; 32:376-385. [PMID: 29187707 PMCID: PMC5745023 DOI: 10.1264/jsme2.me17131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/17/2017] [Accepted: 10/15/2017] [Indexed: 11/24/2022] Open
Abstract
Biocontrol agents (BCA) effectively suppress soil-borne disease symptoms using natural antagonistic prokaryotes or eukaryotes. The main issue associated with the application of BCA is that disease reduction effects are unstable under different field conditions. In order to identify potentially effective BCA among several fields, we compared prokaryotic and eukaryotic communities in soil with and without tomato bacterial wilt from three different fields, each of which had the same field management and similar soil characteristics. Soil samples were collected from three fields and two depths because bacterial wilt pathogens were present in soil at a depth greater than 40 cm. We classified soil samples based on the presence or absence of the bacterial phcA gene, a key gene for bacterial wilt pathogenicity and tomato disease symptoms. Pyrosequencing of the prokaryotic 16S rRNA gene and eukaryotic internal transcribed spacer region sequences showed that the diversity and richness of the communities mostly did not correlate with disease symptoms. Prokaryotic and eukaryotic community structures were affected more by regional differences than the appearance of disease. Several prokaryotes and eukaryotes were more abundant in soil that lacked disease symptoms, and eight prokaryotes and one eukaryote of this group were commonly detected among the three fields. Some of these taxa were not previously found in disease-suppressive soil. Our results suggest that several prokaryotes and eukaryotes control plant disease symptoms.
Collapse
Affiliation(s)
- Chol Gyu Lee
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| | - Toshiya Iida
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| | - Yohei Uwagaki
- Ishikawa Agriculture and Forestry Research CenterKanazawa, Ishikawa, 920–3198Japan
| | - Yoko Otani
- Wakayama Agricultural Experiment StationKoinokawa, Wakayama, 640–0423Japan
| | - Kazuhiro Nakaho
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research OrganizationTsu, Mie 514–2392Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| |
Collapse
|
28
|
Détrée C, López-Landavery E, Gallardo-Escárate C, Lafarga-De la Cruz F. Transcriptome mining of immune-related genes in the muricid snail Concholepas concholepas. Fish Shellfish Immunol 2017; 71:69-75. [PMID: 28962882 DOI: 10.1016/j.fsi.2017.09.061] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 08/30/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
The population of the Chilean endemic marine gastropod Concholepas concholepas locally called "loco" has dramatically decreased in the past 50 years as a result of intense activity of local fisheries and high environmental variability observed along the Chilean coast, including episodes of hypoxia, changes in sea surface temperature, ocean acidification and diseases. In this study, we set out to explore the molecular basis of C. concholepas to cope with biotic stressors such as exposure to the pathogenic bacterium Vibrio anguillarum. Here, 454pyrosequencing was conducted and 61 transcripts related to the immune response in this muricid species were identified. Among these, the expression of six genes (CcNFκβ, CcIκβ, CcLITAF, CcTLR, CcCas8 and CcCath) involved in the regulation of inflammatory, apoptotic and immune processes upon stimuli, were evaluated during the first 33 h post challenge (hpc). The results showed that CcTLR, CcCas8 and CcCath have an initial response at 4 hpc, evidencing an up-regulation from 4 to 24 hpc. Notably, the response of CcNFKB occurred 2 h later with a statistically significant up-regulation at 6 hpc and 10 hpc. Furthermore, the challenge with V. anguillarum induced a statistically significant down-regulation of CcIKB between 2 and 10 hpc as well as a down-regulation of CcLITAF between 2 and 4 hpc followed in both cases by an up-regulation between 24 and 33 hpc. This work describes the first transcriptomic effort to characterize the immune response of C. concholepas and constitutes a valuable transcriptomic resource for future efforts to develop sustainable aquaculture and conservations tools for this endemic marine snail species.
Collapse
Affiliation(s)
- Camille Détrée
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Edgar López-Landavery
- Department of Marine Biotechnology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, BC, Mexico
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Fabiola Lafarga-De la Cruz
- Laboratory of Aquatic Genomics, Aquaculture Department, Center for Scientific Research and Higher Education at Ensenada (CICESE), Ensenada, BC, Mexico.
| |
Collapse
|
29
|
Cho K, Shin SG, Kim W, Lee J, Lee C, Hwang S. Microbial community shifts in a farm-scale anaerobic digester treating swine waste: Correlations between bacteria communities associated with hydrogenotrophic methanogens and environmental conditions. Sci Total Environ 2017; 601-602:167-176. [PMID: 28551535 DOI: 10.1016/j.scitotenv.2017.05.188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 03/31/2017] [Revised: 05/19/2017] [Accepted: 05/20/2017] [Indexed: 06/07/2023]
Abstract
Microbial community structure in a farm-scale anaerobic digester treating swine manure was investigated during three process events: 1) prolonged starvation, and changes of 2) operating temperature (between meso- and thermophilic) and 3) hydraulic retention time (HRT). Except during the initial period, the digester was dominated by hydrogenotrophic methanogens (HMs). The bacterial community structure significantly shifted with operating temperature and HRT but not with long-term starvation. Clostridiales (26.5-54.4%) and Bacteroidales (2.5-13.7%) became dominant orders in the digester during the period of HM dominance. Abundance of diverse meso- and thermophilic bacteria increased during the same period; many of these species may be H2 producers, and/or syntrophic acetate oxidizers. Some of these species showed positive correlations with [NH4+-N] (p<0.1); this relationship suggests that ammonia was a significant parameter for bacterial selection. The bacterial niche information reported in this study can be useful to understand the ecophysiology of anaerobic digesters treating swine manure that contains high ammonia content.
Collapse
Affiliation(s)
- Kyungjin Cho
- Center for Water Resource Cycle Research, Korea Institute of Science and Technology, 39-1 Hawolgok-Dong, Seongbuk-Gu, Seoul 136-791, Republic of Korea
| | - Seung Gu Shin
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea.
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Joonyeob Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Seokhwan Hwang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea.
| |
Collapse
|
30
|
Lozano YM, Armas C, Hortal S, Casanoves F, Pugnaire FI. Disentangling above- and below-ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat. New Phytol 2017; 216:1236-1246. [PMID: 28262957 DOI: 10.1111/nph.14499] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 09/16/2016] [Accepted: 01/11/2017] [Indexed: 05/22/2023]
Abstract
Nurse plants promote establishment of other plant species by buffering climate extremes and improving soil properties. Soil biota plays an important role, but an analysis to disentangle the effects of soil microorganisms, soil properties and microclimate on facilitation is lacking. In three microhabitats (gaps, small and large Retama shrubs), we placed six microcosms with sterilized soil, two per soil origin (i.e. from each microhabitat). One in every pair received an alive, and the other a sterile, inoculum from its own soil. Seeds of annual plants were sown into the microcosms. Germination, survival and biomass were monitored. Soil bacterial communities were characterized by pyrosequencing. Germination in living Retama inoculum was nearly double that of germination in sterile inoculum. Germination was greater under Retama canopies than in gaps. Biomass was up to three times higher in nurse than in gap soils. Soil microorganisms, soil properties and microclimate showed a range of positive to negative effects on understory plants depending on species identity and life stage. Nurse soil microorganisms promoted germination, but the effect was smaller than the positive effects of soil properties and microclimate under nurses. Nurse below-ground environment (soil properties and microorganisms) promoted plant growth and survival more than nurse microhabitat.
Collapse
Affiliation(s)
- Yudi M Lozano
- Estación Experimental de Zonas Áridas, Spanish National Research Council (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| | - Cristina Armas
- Estación Experimental de Zonas Áridas, Spanish National Research Council (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| | - Sara Hortal
- Western Sydney University, Hawkesbury Institute for the Environment, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Fernando Casanoves
- Unidad de Bioestadística del Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Turrialba, 7170, Costa Rica
| | - Francisco I Pugnaire
- Estación Experimental de Zonas Áridas, Spanish National Research Council (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| |
Collapse
|
31
|
Meng L, Li X, Wang X, Ma K, Liu G, Zhang J. Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system. J Environ Sci (China) 2017; 61:110-117. [PMID: 29191308 DOI: 10.1016/j.jes.2017.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/16/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to reveal how amoxicillin (AMX) affected the microbial community and the spread mechanism of antibiotic resistance genes (ARGs) in the AMX manufacture wastewater treatment system. For this purpose, a 1.47 L expanded granular sludge bed (EGSB) reactor was designed and run for 241days treating artificial AMX manufacture wastewater. 454 pyrosequencing was applied to analyze functional microorganisms in the system. The antibiotic genes OXA-1, OXA-2, OXA-10, TEM-1, CTX-M-1, class I integrons (intI1) and 16S rRNA genes were also examined in sludge samples. The results showed that the genera Ignavibacterium, Phocoenobacter, Spirochaeta, Aminobacterium and Cloacibacillus contributed to the degradation of different organic compounds (such as various sugars and amines). And the relative quantification of each β-lactam resistance gene in the study was changed with the increasing of AMX concentration. Furthermore the vertical gene transfer was the main driver for the spread of ARGs rather than horizontal transfer pathways in the system.
Collapse
Affiliation(s)
- Lingwei Meng
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiangkun Li
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Xinran Wang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kaili Ma
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Gaige Liu
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Zhang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| |
Collapse
|
32
|
Tan S, Liu H. Unravel the hidden protistan diversity: application of blocking primers to suppress PCR amplification of metazoan DNA. Appl Microbiol Biotechnol 2017; 102:389-401. [PMID: 29080999 DOI: 10.1007/s00253-017-8565-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/08/2017] [Accepted: 09/28/2017] [Indexed: 11/28/2022]
Abstract
Planktonic protists, including both autotroph and heterotroph, have been recognized as a major contributor to primary production and consumers of bacteria, archaea and picophytoplankton. However, the understanding of protistan diversity is typically impeded by the large amount of metazoans when employing universal primers to environmental samples. In this study, we developed 3 blocking primers to inhibit the amplification of metazoan DNA in PCR. First, we optimized the design and concentration of blocking primers by using 2 metazoans and 3 protists in quantitative PCR. No significant difference (q > 0.05) was found in protistan community structure at phylum, family or OTU levels and genetic diversity between samples amplified with and without adding blocking primers, indicating that the blocking primer does not alter the composition of protistan community. An application to samples with a high abundance of metazoans showed that the blocking primer can reduce 42.1-72.4% of metazoan sequences, resulting the retrieval of a higher protistan richness and diversity. The use of the blocking primer helped to identify protistan community composition from a large size fraction, which is usually dominated by metazoans. Protistan community from the small (0.2-10 μm) and large (> 10 μm) size fractions exhibited a low similarity of 36.6% and shared 14.7% OTUs. About 63.8% of the OTUs were unique to the large fraction. Species from groups, such as Lepidodinium, Warnowia, Kareniaceae, Torodiniales, Phaeocystis, Chrysochromulina and Chrysophyceae, were enriched in the large fraction, indicating that they could be largely underestimated in studies that exclude the large-sized cells. Blocking primers are a promising tool to increase the efficiency for the characterization of protistan diversity in aquatic planktonic ecosystems.
Collapse
Affiliation(s)
- Shangjin Tan
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, CYT5004, Clear Water Bay, Kowloon, Hong Kong, SAR, China.
| |
Collapse
|
33
|
Cho SK, Jung KW, Kim DH, Kwon JC, Ijaz UZ, Shin SG. Bacterial community analysis in upflow multilayer anaerobic reactor treating high-solids organic wastes. Biotechnol Prog 2017; 33:1226-1234. [PMID: 28840641 PMCID: PMC6585729 DOI: 10.1002/btpr.2540] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/26/2017] [Indexed: 11/05/2022]
Abstract
A novel anaerobic digestion configuration, the upflow multi-layer anaerobic reactor (UMAR), was developed to treat high-solids organic wastes. The UMAR was hypothesized to form multi-layer along depth due to the upflow plug flow; use of a recirculation system and a rotating distributor and baffles aimed to assist treating high-solids influent. The chemical oxygen demand (COD) removal efficiency and methane (CH4 ) production rate were 89% and 2.10 L CH4 /L/d, respectively, at the peak influent COD concentration (110.4 g/L) and organic loading rate (7.5 g COD/L/d). The 454 pyrosequencing results clearly indicated heterogeneous distribution of bacterial communities at different vertical locations (upper, middle, and bottom) of the UMAR. Firmicutes was the dominant (>70%) phylum at the middle and bottom parts, while Deltaproteobacteria and Chloroflexi were only found in the upper part. Potential functions of the bacteria were discussed to speculate on their roles in the anaerobic performance of the UMAR system. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1226-1234, 2017.
Collapse
Affiliation(s)
- Si-Kyung Cho
- Dept. of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Kyung-Won Jung
- Department of Earth and Environmental Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Dong-Hoon Kim
- Dept. of Civil Engineering, Inha University, 100 Inharo, Nam-gu, Incheon, Republic of Korea
| | - Joong-Chun Kwon
- Ecodigm, 10-6, 339 Expo-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Umer Zeeshan Ijaz
- Infrastructure and Environment Division, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Seung Gu Shin
- Department of Energy Engineering, Gyeongnam National University of Science and Technology (GNTECH), Jinju, Republic of Korea
| |
Collapse
|
34
|
Zheng Y, Yu M, Liu J, Qiao Y, Wang L, Li Z, Zhang XH, Yu M. Bacterial Community Associated with Healthy and Diseased Pacific White Shrimp ( Litopenaeus vannamei) Larvae and Rearing Water across Different Growth Stages. Front Microbiol 2017; 8:1362. [PMID: 28769916 PMCID: PMC5513922 DOI: 10.3389/fmicb.2017.01362] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [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: 12/09/2016] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities are called another "organ" for aquatic animals and their important influence on the health of host has drawn increasing attention. Thus, it is important to study the relationships between aquatic animals and bacterial communities. Here, bacterial communities associated with Litopenaeus vannamei larvae at different healthy statuses (diseased and healthy) and growth stages (i.e., zoea, mysis, and early postlarvae periods) were examined using 454-pyrosequencing of the 16S rRNA gene. Bacterial communities with significant difference were observed between healthy and diseased rearing water, and several bacterial groups, such as genera Nautella and Kordiimonas could also distinguish healthy and diseased shrimp. Rhodobacteraceae was widely distributed in rearing water at all growth stages but there were several stage-specific groups, indicating that bacterial members in rearing water assembled into distinct communities throughout the larval development. However, Gammaproteobacteria, mainly family Enterobacteriaceae, was the most abundant group (accounting for more than 85%) in shrimp larvae at all growth stages. This study compared bacterial communities associated with healthy and diseased L. vannamei larvae and rearing water, and identified several health- and growth stage-specific bacterial groups, which might be provided as indicators for monitoring the healthy status of shrimp larvae in hatchery.
Collapse
Affiliation(s)
- Yanfen Zheng
- Marine Microbiology Lab, College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Min Yu
- Marine Microbiology Lab, College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Jiwen Liu
- Marine Microbiology Lab, College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Yanlu Qiao
- Marine Microbiology Lab, College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | - Long Wang
- Marine Microbiology Lab, College of Marine Life Sciences, Ocean University of ChinaQingdao, China
| | | | - Xiao-Hua Zhang
- Marine Microbiology Lab, College of Marine Life Sciences, Ocean University of ChinaQingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | | |
Collapse
|
35
|
Zhang Y, Shen H, He X, Thomas BW, Lupwayi NZ, Hao X, Thomas MC, Shi X. Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH. Front Microbiol 2017; 8:1325. [PMID: 28769896 PMCID: PMC5513969 DOI: 10.3389/fmicb.2017.01325] [Citation(s) in RCA: 82] [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: 03/17/2017] [Accepted: 06/30/2017] [Indexed: 11/13/2022] Open
Abstract
Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.
Collapse
Affiliation(s)
- Yuting Zhang
- College of Resources and Environment, Southwest UniversityChongqing, China.,Agriculture and Agri-Food Canada, Lethbridge Research and Development CentreLethbridge, AB, Canada
| | - Hong Shen
- College of Resources and Environment, Southwest UniversityChongqing, China.,Centre of Excellence for Soil Biology, College of Resources and Environment, Southwest UniversityChongqing, China
| | - Xinhua He
- Centre of Excellence for Soil Biology, College of Resources and Environment, Southwest UniversityChongqing, China.,School of Biological Sciences, University of Western AustraliaCrawley, WA, Australia
| | - Ben W Thomas
- Agriculture and Agri-Food Canada, Lethbridge Research and Development CentreLethbridge, AB, Canada
| | - Newton Z Lupwayi
- Agriculture and Agri-Food Canada, Lethbridge Research and Development CentreLethbridge, AB, Canada
| | - Xiying Hao
- Agriculture and Agri-Food Canada, Lethbridge Research and Development CentreLethbridge, AB, Canada
| | - Matthew C Thomas
- Calgary Laboratory, Canadian Food Inspection AgencyCalgary, AB, Canada
| | - Xiaojun Shi
- College of Resources and Environment, Southwest UniversityChongqing, China.,Centre of Excellence for Soil Biology, College of Resources and Environment, Southwest UniversityChongqing, China.,Academy of Agricultural Sciences, Southwest UniversityChongqing, China
| |
Collapse
|
36
|
Abstract
Bacteria, actinomycetes and fungi are the three major groups of soil microbes. Soil microbes play a critical role in ecological and biodegradation processes in petroleum-contaminated soils. Based on the actual situation, this study took the oil polluted soil around the abandoned oil well in Shehong County, Suining City, Sichuan Province as the test soil. First, we determined the physiochemical properties of the tested soil; then we analyzed the changes of physiochemical properties and the three major microbes in petroleum contaminated soils. The number of the three major microbes in contaminated soils was relatively fewer than uncontaminated samples, and the water content of the soil was in positive correlation with the number of microbes. Also we assessed the soil bacteria community diversity and changes therein in petroleum-contaminated soils using 454 pyrosequencing of 16S rRNA genes. No less than 23 982 valid reads and 6 123 operational taxonomic units (OTUs) were obtained from all 4 studied samples. OTU richness was relatively higher in contaminated soils than uncontaminated samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. However, the prokaryotes community abundance of phyla was significantly different in the four samples. The most abundant OTUs associated with petroleum-contaminated soil sample were the sequences related to Acidobacteria, Actinobacteria and Proteobacteria, whereas the most abundance sequences with uncontaminated sample were those related to Actinobacteria, Bacteroidetes and Proteobacteria.
Collapse
Affiliation(s)
- Xiaolou Li
- Sichuan Vocational and Technological College, Suining 629000, Sichuan, China
| |
Collapse
|
37
|
Lee CG, Iida T, Inoue Y, Muramoto Y, Watanabe H, Nakaho K, Ohkuma M. Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse. Microbes Environ 2017; 32:118-124. [PMID: 28502968 PMCID: PMC5478534 DOI: 10.1264/jsme2.me16136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 09/05/2016] [Accepted: 02/13/2017] [Indexed: 11/30/2022] Open
Abstract
The characterization of microbial communities that promote or suppress soil-borne pathogens is important for controlling plant diseases. We compared prokaryotic communities in soil with or without the signs of tomato bacterial wilt caused by Ralstonia solanacearum. Soil samples were collected from a greenhouse at two different depths because this pathogen is present in deep soil. We used samples from sites in which we detected phcA, a key gene regulating R. solanacearum pathogenicity. The pyrosequencing of prokaryotic 16S rRNA sequences in four soil samples without disease symptoms but with phcA and in two soil samples with disease symptoms indicated that community richness was not significantly different between these two soils; however, microbial diversity in the lower soil layer was higher in soil samples without disease symptoms but with phcA. A difference in prokaryotic community structures between soil samples with and without bacterial wilt was only observed in the upper soil layer despite apparent similarities in the communities at the phylum level. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and several Archaea were more abundant in soil samples without disease symptoms, whereas taxa in another eight phyla were more abundant in soil samples with disease symptoms. Furthermore, some prokaryotic taxa were abundant specifically in the lower layer of soil, regardless of whether disease was present. These prokaryotic taxa may suppress or accelerate the pathogenesis of bacterial wilt and are good targets for future studies on disease control.
Collapse
Affiliation(s)
- Chol Gyu Lee
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| | - Toshiya Iida
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| | - Yasuhiro Inoue
- Central Region Agricultural Research Center, National Agriculture and Food Research OrganizationTsukuba, Ibaraki, 305–8666Japan
| | - Yasunori Muramoto
- Gifu Prefectural Agricultural Technology Center729 Matamaru, Gifu 501–1152Japan
| | - Hideki Watanabe
- Gifu Prefectural Agricultural Technology Center729 Matamaru, Gifu 501–1152Japan
| | - Kazuhiro Nakaho
- Central Region Agricultural Research Center, National Agriculture and Food Research OrganizationTsukuba, Ibaraki, 305–8666Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource CenterTsukuba, Ibaraki, 305–0074Japan
| |
Collapse
|
38
|
Liu F, Yuan Z, Zhang X, Zhang G, Xie B. Characteristics and diversity of endophytic bacteria in moso bamboo (Phyllostachys edulis) based on 16S rDNA sequencing. Arch Microbiol 2017; 199:1259-1266. [PMID: 28601968 DOI: 10.1007/s00203-017-1397-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 09/07/2016] [Revised: 02/17/2017] [Accepted: 06/05/2017] [Indexed: 11/28/2022]
Abstract
To understand the diversity and distribution of endophytic bacteria in moso bamboo (Phyllostachys edulis), we used 16S rDNA sequencing to investigate the characteristics and diversity of endophytic bacteria in different moso bamboo tissues. After 454 pyrosequencing, we obtained 141,269 sequences from seven moso bamboo tissue samples. The taxonomic origins of unique sequences were identified using RDP classifier. The results showed that these sequences belonged to 26 bacterial orders, including the Actinomycetales, Rickettsiales, Burkholderiales, Enterobacteriales, and Rhizobiales. Among these, Enterobacteriales was widely found in all bamboo tissues. Endophytic bacterial communities differed between the moso bamboo shoot and pole. With continuous growth and development, the number of endophytic species in the moso bamboo pole increased gradually.
Collapse
Affiliation(s)
- Fang Liu
- The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zongsheng Yuan
- The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xintao Zhang
- The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Nanjing Wanchen Biological Technology co., LTD, Nanjing, 211299, Jiangsu, China
| | - Guofang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Baogui Xie
- The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| |
Collapse
|
39
|
Khomich M, Kauserud H, Logares R, Rasconi S, Andersen T. Planktonic protistan communities in lakes along a large-scale environmental gradient. FEMS Microbiol Ecol 2017; 93:fiw231. [PMID: 27827804 DOI: 10.1093/femsec/fiw231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 08/15/2016] [Accepted: 11/04/2016] [Indexed: 11/14/2022] Open
Abstract
Despite their obvious importance, our knowledge about the eukaryotic microbial diversity of inland waters is still limited and poorly documented. We applied 18S rDNA amplicon sequencing to provide a comprehensive analysis of eukaryotic diversity in 74 low-productivity lakes along a 750 km longitudinal transect (5.40-18.52°E) across southern Scandinavia. We detected a wide diversity of pelagic microbial eukaryotes, classified into 1882 operational taxonomic units (OTUs). The highest OTU richness was found in traditional phytoplankton groups like Dinoflagellata, Chrysophyceae, Chlorophyta and Cryptophyta. A total of 53.6% OTUs were primarily autotrophic, while 19.4% of the heterotrophic OTUs belonged to putative parasitic taxa. Except for a longitudinal trend in the relative influence of mixotrophs, there were no significant associations between major functional groups (autotrophs, heterotrophs and parasites) and spatial and environmental variables. Community dissimilarity increased significantly with increasing geographical distance between lakes. In accordance with earlier, microscopy-based surveys in this region, we demonstrate distinct gradients in protistan diversity and community composition, which are better explained by spatial structure than local environment. The strong association between longitude and protistan diversity is probably better explained by differences in regional species pools due to differences in landscape productivity than by dispersal limitation or climatic constraints.
Collapse
Affiliation(s)
- Maryia Khomich
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway.,Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, 08003 Barcelona, Spain
| | - Serena Rasconi
- WasserCluster-Biological Station Lunz, Inter-university Centre for Aquatic Ecosystem Research, A-3293 Lunz am See, Austria
| | - Tom Andersen
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| |
Collapse
|
40
|
Bouffaud ML, Bragalini C, Berruti A, Peyret-Guzzon M, Voyron S, Stockinger H, van Tuinen D, Lumini E, Wipf D, Plassart P, Lemanceau P, Bianciotto V, Redecker D, Girlanda M. Arbuscular mycorrhizal fungal community differences among European long-term observatories. Mycorrhiza 2017; 27:331-343. [PMID: 27942957 DOI: 10.1007/s00572-016-0753-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 06/27/2016] [Accepted: 11/25/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungal (AMF) communities have been demonstrated to respond to a variety of biotic and abiotic factors, including various aspects of land management. Numerous studies have specifically addressed the impact of land use on AMF communities, but usually have been confined to one or a few sites. In this study, soil AMF assemblages were described in four different long-term observatories (LTOs) across Europe, each of which included a site-specific high-intensity and a low-intensity land use. AMF communities were characterized on the basis of 454 sequencing of the internal transcribed spacer 2 (ITS2) rDNA region. The primary goals of this study were (i) to determine the main factors that shape AMF communities in differentially managed sites in Europe and (ii) to identify individual AMF taxa or combinations of taxa suitable for use as biomarkers of land use intensification. AMF communities were distinct among LTOs, and we detected significant effects of management type and soil properties within the sites, but not across all sites. Similarly, indicator species were identified for specific LTOs and land use types but not universally for high- or low-intensity land uses. Different subsets of soil properties, including several chemical and physical variables, were found to be able to explain an important fraction of AMF community variation alone or together with other examined factors in most sites. The important factors were different from those for other microorganisms studied in the same sites, highlighting particularities of AMF biology.
Collapse
Affiliation(s)
- M-L Bouffaud
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
- Helmholtz Center for Environmental Research - UFZ, Halle, Germany, German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - C Bragalini
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy
- Université Claude Bernard Lyon1, Lyon, France
| | - A Berruti
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - M Peyret-Guzzon
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - S Voyron
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy
| | - H Stockinger
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - D van Tuinen
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - E Lumini
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - D Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - P Plassart
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - P Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - V Bianciotto
- CNR-Istituto per la Protezione Sostenibile delle Piante, UOS Turin (CNR-IPSP), Torino, Italy
| | - D Redecker
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France.
| | - M Girlanda
- Department of Life Sciences and System Biology (DBios), University of Torino, 25 Viale Mattioli, 10125, Torino, Italy.
- Université Claude Bernard Lyon1, Lyon, France.
| |
Collapse
|
41
|
Kegler HF, Lukman M, Teichberg M, Plass-Johnson J, Hassenrück C, Wild C, Gärdes A. Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia. Front Microbiol 2017; 8:662. [PMID: 28473810 PMCID: PMC5397486 DOI: 10.3389/fmicb.2017.00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 01/15/2016] [Accepted: 03/31/2017] [Indexed: 12/04/2022] Open
Abstract
Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.
Collapse
Affiliation(s)
- Hauke F Kegler
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Muhammad Lukman
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin UniversitySouth Sulawesi, Indonesia
| | - Mirta Teichberg
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany
| | - Jeremiah Plass-Johnson
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Centre for Ocean Life, National Institute of Aquatic Resources (DTU-Aqua), Technical University of DenmarkCharlottenlund, Denmark
| | - Christiane Hassenrück
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany
| |
Collapse
|
42
|
Egan CP, Callaway RM, Hart MM, Pither J, Klironomos J. Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient. Mycorrhiza 2017; 27:273-282. [PMID: 27909817 DOI: 10.1007/s00572-016-0752-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 09/17/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.
Collapse
Affiliation(s)
- Cameron P Egan
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada.
| | - Ragan M Callaway
- Division of Biological Sciences and the Institute on Ecosystems, University of Montana, Missoula, MT, 59812, USA
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Jason Pither
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| | - John Klironomos
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| |
Collapse
|
43
|
Koo T, Shin SG, Lee J, Han G, Kim W, Cho K, Hwang S. Identifying methanogen community structures and their correlations with performance parameters in four full-scale anaerobic sludge digesters. Bioresour Technol 2017; 228:368-373. [PMID: 28087103 DOI: 10.1016/j.biortech.2016.12.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 11/15/2016] [Revised: 12/29/2016] [Accepted: 12/31/2016] [Indexed: 06/06/2023]
Abstract
Four full-scale mesophilic anaerobic digesters treating waste sludge were monitored to characterize methanogen communities and their relationship with process parameters. The performance of the four digesters were dissimilar with the average chemical oxygen demand removal efficiencies between 24 and 45% and differing pH. Real-time quantitative PCR showed that archaeal 16S rRNA gene concentration ([ARC]) and, more pronouncedly, its ratio to bacterial counterpart ([ARC]/[BAC]) correlated positively with the performance parameters, including the lipid removal efficiency. Pyrosequencing identified 12 methanogen genera, of which Methanolinea, Methansaeta, and Methanospirillum collectively accounted for 79.2% of total archaeal reads. However, Methanoculleus, a numerically minor (1.9±2.6%) taxa, was the most promising biomarker for positive performance, while Methanoregula was abundant in samples with poor performance. These results could be useful for the control and management of anaerobic sludge digestion.
Collapse
Affiliation(s)
- Taewoan Koo
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Seung Gu Shin
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Joonyeob Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Gyuseong Han
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Woong Kim
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea
| | - Kyungjin Cho
- Center for Water Resource Cycle Research, Korea Institute of Science and Technology, Seoul, South Korea
| | - Seokhwan Hwang
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea.
| |
Collapse
|
44
|
Gao C, Shi NN, Chen L, Ji NN, Wu BW, Wang YL, Xu Y, Zheng Y, Mi XC, Ma KP, Guo LD. Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest. New Phytol 2017; 213:1874-1885. [PMID: 28164340 DOI: 10.1111/nph.14287] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 05/29/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Elucidating interactions of above-ground and below-ground communities in different habitat types is essential for understanding biodiversity maintenance and ecosystem functioning. Using 454 pyrosequencing of ITS2 sequences we examined the relationship between subtropical mountain forest soil fungal communities, abiotic conditions, and plant communities using correlation and partial models. Ridge and valley habitats with differing fungal communities were delineated. Total, saprotrophic and pathogenic fungal richness were significantly correlated with plant species richness and/or soil nutrients and moisture in the ridge habitat, but with habitat convexity or basal area of Castanopsis eyrei in the valley habitat. Ectomycorrhizal (EM) fungal richness was significantly correlated with basal area of C. eyrei and total EM plants in the ridge and valley habitats, respectively. Total, saprotrophic, pathogenic and EM fungal compositions were significantly correlated with plant species composition and geographic distance in the ridge habitat, but with various combinations of plant species composition, plant species richness, soil C : N ratio and pH or no variables in the valley habitat. Our findings suggest that mechanisms influencing soil fungal diversity and community composition differ between ridge and valley habitats, and relationships between fungal and woody plant assemblages depend on habitat types in the subtropical forest ecosystem.
Collapse
Affiliation(s)
- Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Nan-Nan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Niu-Niu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin-Wei Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ke-Ping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
45
|
Du Q, Li M, Zhou X, Tian K. A comprehensive profiling of supragingival bacterial composition in Chinese twin children and their mothers. Antonie Van Leeuwenhoek 2017; 110:615-627. [PMID: 28120199 DOI: 10.1007/s10482-017-0828-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 10/19/2016] [Accepted: 01/04/2017] [Indexed: 02/05/2023]
Abstract
To investigate the factors influencing the oral microbiome, 16 twin pairs and their mothers were enrolled in this study. There were 7 monozygotic (MZ) twins and 9 dizygotic (DZ) twins, with an average age of 6.18 ± 3.5. Supragingival plaques and caries tissues were collected and the 16S rDNA was analyzed by 454 pyrosequencing. A total of 18 phyla and 179 genuses were found. Caries children harbored a higher portion of Actinobacteria than caries-free ones, and one lineage was found to be less abundant in the caries tissues compared to the supragingival plaque at each level from the phylum down to the genus level, which was Fusobacteria at Phylum, Fusobacteriia at Class, Fusobacteriales at Order, Leptotrichiaceae at Family and Leptotrichia at genus level. The adults harbored a significantly higher portion of Treponema, which may be related to adult periodontitis. The phylogenetic tree showed that there was a high similarity of oral microbiota within co-twins, but no significant difference was detected between MZ and DZ twins. Also, the similarity level of primary dentition children to their mother was significantly higher than that of mixed dentition children, suggesting that environmental factors may have a stronger impact than the genetic factors on the constitution of the oral microbiome.
Collapse
Affiliation(s)
- Qin Du
- Department of Stomatology, Sichuan Provincial People's Hospital, Chengdu, 610072, Sichuan, People's Republic of China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Mingyun Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Kun Tian
- Department of Stomatology, Sichuan Provincial People's Hospital, Chengdu, 610072, Sichuan, People's Republic of China
| |
Collapse
|
46
|
Li C, Ling F, Zhang M, Liu WT, Li Y, Liu W. Characterization of bacterial community dynamics in a full-scale drinking water treatment plant. J Environ Sci (China) 2017; 51:21-30. [PMID: 28115132 DOI: 10.1016/j.jes.2016.05.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/05/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
Understanding the spatial and temporal dynamics of microbial communities in drinking water systems is vital to securing the microbial safety of drinking water. The objective of this study was to comprehensively characterize the dynamics of microbial biomass and bacterial communities at each step of a full-scale drinking water treatment plant in Beijing, China. Both bulk water and biofilm samples on granular activated carbon (GAC) were collected over 9months. The proportion of cultivable cells decreased during the treatment processes, and this proportion was higher in warm season than cool season, suggesting that treatment processes and water temperature probably had considerable impact on the R2A cultivability of total bacteria. 16s rRNA gene based 454 pyrosequencing analysis of the bacterial community revealed that Proteobacteria predominated in all samples. The GAC biofilm harbored a distinct population with a much higher relative abundance of Acidobacteria than water samples. Principle coordinate analysis and one-way analysis of similarity indicated that the dynamics of the microbial communities in bulk water and biofilm samples were better explained by the treatment processes rather than by sampling time, and distinctive changes of the microbial communities in water occurred after GAC filtration. Furthermore, 20 distinct OTUs contributing most to the dissimilarity among samples of different sampling locations and 6 persistent OTUs present in the entire treatment process flow were identified. Overall, our findings demonstrate the significant effects that treatment processes have on the microbial biomass and community fluctuation and provide implications for further targeted investigation on particular bacteria populations.
Collapse
Affiliation(s)
- Cuiping Li
- School of Environment, Tsinghua University, Beijing 100084, China.
| | - Fangqiong Ling
- Department of Civil and Environment Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Minglu Zhang
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Wen-Tso Liu
- Department of Civil and Environment Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuxian Li
- Water Quality Monitoring Center, Beijing Waterworks Group, Beijing 100085, China
| | - Wenjun Liu
- School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
47
|
Ziganshina EE, Ibragimov EM, Vankov PY, Miluykov VA, Ziganshin AM. Comparison of anaerobic digestion strategies of nitrogen-rich substrates: Performance of anaerobic reactors and microbial community diversity. Waste Manag 2017; 59:160-171. [PMID: 27836515 DOI: 10.1016/j.wasman.2016.10.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 08/04/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
In the present study, the application of different operating strategies on performance of three continuous stirred tank reactors digesting chicken manure at mesophilic temperature and constant organic loading rate (OLR) of 3.5gVSL-1d-1 was investigated. Control reactor (RC) and reactor (RH) with the decreasing hydraulic retention time (HRT) had the comparable specific biogas production (SBP) with maximum values of 334-351mLg-1VS (added) during days 84-93, while the SBP from reactor with zeolites (RZ) was higher and achieved 426-432mLg-1VS (added). Attachments of microorganisms to zeolite particles as the operational environment, exchanged cations released from zeolites as well as lower total ammonium nitrogen (TAN) levels observed in RZ (6.2-6.3gL-1; days 71-93) compared to RC (6.6-6.9gL-1; days 71-93) resulted in a more effective process in RZ. Moreover, microbial community structure and dynamics were comprehensively characterized using Illumina sequencing, pyrosequencing and T-RFLP analysis of 16SrRNA genes. Methanogenic archaeal activity was additionally assessed by the expressed mcrA genes encoding the alpha subunit of methyl-CoM reductase. Within the major class Clostridia, Caldicoprobacter, Alkaliphilus, Gallicola, Sporanaerobacter and Tepidimicrobium spp. were the notable bacteria developed during operation of all tested reactors. Archaeal communities were dominated by methanogens belonging to the genus Methanosarcina followed by the genus Methanoculleus during the experimental period. Results of this study indicate that attachment of microorganisms to the zeolite particles as the operational environment might have led to the higher microbial activity at high ammonia concentrations.
Collapse
Affiliation(s)
- Elvira E Ziganshina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Emil M Ibragimov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Petr Y Vankov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia
| | - Vasili A Miluykov
- Department of Technologies, A.E. Arbuzov Institute of Organic and Physical Chemistry, RAN, Kazan 420088, The Republic of Tatarstan, Russia
| | - Ayrat M Ziganshin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, The Republic of Tatarstan, Russia.
| |
Collapse
|
48
|
Lee SH, Chung AM, Lee A, Oh WJ, Choi YJ, Lee YS, Jung ES. KRAS Mutation Test in Korean Patients with Colorectal Carcinomas: A Methodological Comparison between Sanger Sequencing and a Real-Time PCR-Based Assay. J Pathol Transl Med 2016; 51:24-31. [PMID: 28013534 PMCID: PMC5267542 DOI: 10.4132/jptm.2016.10.03] [Citation(s) in RCA: 4] [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: 08/03/2016] [Revised: 09/23/2016] [Accepted: 10/02/2016] [Indexed: 12/19/2022] Open
Abstract
Background Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. Methods We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. Results KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. Conclusions The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC.
Collapse
Affiliation(s)
- Sung Hak Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Arthur Minwoo Chung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahwon Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woo Jin Oh
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeong Jin Choi
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn-Soo Lee
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun Sun Jung
- Departments of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
49
|
Bal J, Yun SH, Yeo SH, Kim JM, Kim BT, Kim DH. Effects of initial moisture content of Korean traditional wheat-based fermentation starter nuruk on microbial abundance and diversity. Appl Microbiol Biotechnol 2016; 101:2093-2106. [PMID: 27975136 DOI: 10.1007/s00253-016-8042-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 11/27/2016] [Accepted: 11/29/2016] [Indexed: 12/31/2022]
Abstract
The brewing of makgeolli, one of Korea's most popular alcoholic beverages that is gaining popularity globally, is facilitated by nuruk, a traditional Korean cereal starter. The nuruk microbiome greatly influences the fermentation process as well as the nutritional, hygienic, and aromatic qualities of the product. This study is a continuation of our efforts to examine nuruk biodiversity at a depth previously unattainable. In this study, microfloral dynamics in wheat-based nuruk C, composed of traditional ingredients such as barley, green gram, and wheat and fermented under various internal moisture contents of 20% (C20), 26% (C26), and 30% (C30), was evaluated using 454 pyrosequencing during the 30-day fermentation process. Rarefaction analysis and alpha diversity parameters indicated adequate sampling. C20 showed the greatest fungal richness and diversity, C20 and C26 exhibited similar bacterial richness and diversity, while C30 had low fungal and bacterial richness. Fungal taxonomic assignments revealed that the initial moisture content caused selective enrichment of Aspergillus candidus with a decreasing trend during fermentation, whereas Saccharomycetales sp. exhibited increasing relative abundance with increasing moisture content from day 6 of the fermentation process. Depending on initial moisture level, changes in bacterial communities were also observed in the genera Streptomyces, Bacillus, and Staphylococcus, with decreasing trends whereas Saccharopolyspora exhibited a sigmoidal trend with the highest abundance in C26. These findings demonstrate the possible impact of initial moisture content of nuruk on microfloral richness, diversity, and dynamics; this study is thus a step toward our ultimate goal of enhancing the quality of nuruk.
Collapse
Affiliation(s)
- Jyotiranjan Bal
- Department of Molecular Biology, Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Suk-Hyun Yun
- Department of Molecular Biology, Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Soo-Hwan Yeo
- Fermented Food Science Division, Department of Agrofood Resource, NAAS, RDA, Wanju-gun, Jeollabuk-do, 565-851, Korea
| | - Jung-Mi Kim
- Department of Bio-Environmental Chemistry, Institute of Life Science and Natural Resources, Wonkwang University, Iksan, Jeollabuk-do, 570-749, Korea
| | - Beom-Tae Kim
- Department of Molecular Biology, Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea
| | - Dae-Hyuk Kim
- Department of Molecular Biology, Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea.
| |
Collapse
|
50
|
Urubschurov V, Büsing K, Freyer G, Herlemann DPR, Souffrant WB, Zeyner A. New insights into the role of the porcine intestinal yeast, Kazachstania slooffiae, in intestinal environment of weaned piglets. FEMS Microbiol Ecol 2016; 93:fiw245. [PMID: 27940642 DOI: 10.1093/femsec/fiw245] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 06/05/2016] [Accepted: 12/07/2016] [Indexed: 12/15/2022] Open
Abstract
Kazachstania slooffiae is a porcine intestinal yeast whose role in the intestinal environment is largely unexplored. Therefore, the impact of K. slooffiae on growth performance, intestinal microbial metabolites and the microbiota of weaned piglets was investigated in this study. Forty-eight German Landrace pigs were weaned at day 27 or 28 of life and grouped into one control and three treatment groups. During the 5-week experiment, piglets had ad libitum access to feed and water. On days 5, 6 and 7 post weaning, pigs were orally supplemented with either placebo or K. slooffiae cells once a day. Faecal samples collected on days 5-8, 14, 21 and 28 post weaning were used for microbiological and chemical analyses. Between groups, there were no significant differences in the incidence of diarrhoea, pH and growth performance. Total yeasts and K. slooffiae correlated positively with total short-chain fatty acids, acetic, propionic, n-butyric, i-valeric and valeric acids, and negatively with pH. Pyrosequencing of the bacterial intestinal community revealed that K. slooffiae significantly affected the composition of the microbiota. The results of this study suggest that K. slooffiae may play an important role in the porcine digestive system, especially in the critical weaning period.
Collapse
Affiliation(s)
- Vladimir Urubschurov
- Institute of Agricultural and Nutritional Sciences, Group Animal Nutrition, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Kirsten Büsing
- Chair of Nutrition Physiology and Animal Nutrition, University of Rostock, 18059 Rostock, Germany
| | - Gertraude Freyer
- Institute for Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Daniel P R Herlemann
- Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde (IOW), Rostock, 18119 Rostock, Germany
| | - Wolfgang-Bernhard Souffrant
- Institute of Agricultural and Nutritional Sciences, Group Animal Nutrition, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany.,Chair of Nutrition Physiology and Animal Nutrition, University of Rostock, 18059 Rostock, Germany
| | - Annette Zeyner
- Institute of Agricultural and Nutritional Sciences, Group Animal Nutrition, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| |
Collapse
|