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Soria‐Píriz S, Corzo A, Jiménez‐Arias JL, González JM, Papaspyrou S. Niche selection in bacterioplankton: A study of taxonomic composition and single-cell characteristics in an acidic reservoir. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13255. [PMID: 38940640 PMCID: PMC11212339 DOI: 10.1111/1758-2229.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/14/2024] [Indexed: 06/29/2024]
Abstract
Niche selection and microbial dispersal are key factors that shape microbial communities. However, their relative significance varies across different environments and spatiotemporal scales. While most studies focus on the impact of these forces on community composition, few consider other structural levels such as the physiological stage of the microbial community and single-cell characteristics. To understand the relative influence of microbial dispersal and niche selection on various community structural levels, we concurrently examined the taxonomic composition, abundance and single-cell characteristics of bacterioplankton in an acidic reservoir (El Sancho, Spain) during stratification and mixing periods. A cluster analysis based on environmental variables identified five niches during stratification and one during mixing. Canonical correspondence analysis (CCA) revealed that communities within each niche differed in both, taxonomic and single-cell characteristics. The environmental variables that explained the variation in class-based ordination differed from those explaining the ordination based on single-cell characteristics. However, a Procrustes analysis indicated a high correlation between the CCA ordinations based on both structural levels, suggesting simultaneous changes in the microbial community at multiple structural levels. Our findings underscore the dominant role of environmental selection in occupying different microbial niches, given that microbial dispersal was not restricted.
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Affiliation(s)
- Sara Soria‐Píriz
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
| | - Alfonso Corzo
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
| | - Juan Luís Jiménez‐Arias
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
| | - Juan M. González
- Institute of Natural Resources and AgrobiologySpanish National Research Council, IRNAS‐CSICSevillaSpain
| | - Sokratis Papaspyrou
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
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2
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Solano JH, Moitinho MA, Chiaramonte JB, Bononi L, Packer AP, Melo IS, Dini-Andreote F, Tsai SM, Taketani RG. Organic matter decay and bacterial community succession in mangroves under simulated climate change scenarios. Braz J Microbiol 2024:10.1007/s42770-024-01455-2. [PMID: 39028532 DOI: 10.1007/s42770-024-01455-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/06/2024] [Indexed: 07/20/2024] Open
Abstract
Mangroves are coastal environments that provide resources for adjacent ecosystems due to their high productivity, organic matter decomposition, and carbon cycling by microbial communities in sediments. Since the industrial revolution, the increase of Greenhouse Gases (GHG) released due to fossil fuel burning led to many environmental abnormalities such as an increase in average temperature and ocean acidification. Based on the hypothesis that climate change modifies the microbial diversity associated with decaying organic matter in mangrove sediments, this study aimed to evaluate the microbial diversity under simulated climate change conditions during the litter decomposition process and the emission of GHG. Thus, microcosms containing organic matter from the three main plant species found in mangroves throughout the State of São Paulo, Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were incubated simulating climate changes (increase in temperature and pH). The decay rate was higher in the first seven days of incubation, but the differences between the simulated treatments were minor. GHG fluxes were higher in the first ten days and higher in samples under increased temperature. The variation in time resulted in substantial impacts on α-diversity and community composition, initially with a greater abundance of Gammaproteobacteria for all plant species despite the climate conditions variations. The PCoA analysis reveals the chronological sequence in β-diversity, indicating the increase of Deltaproteobacteria at the end of the process. The GHG emission varied in function of the organic matter source with an increase due to the elevated temperature, concurrent with the rise in the Deltaproteobacteria population. Thus, these results indicate that under the expected climate change scenario for the end of the century, the decomposition rate and GHG emissions will be potentially higher, leading to a harmful feedback loop of GHG production. This process can happen independently of an impact on the bacterial community structure due to these changes.
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Affiliation(s)
- Juanita H Solano
- Brazilian Agricultural. Research Corporation, Embrapa Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Marta A Moitinho
- Brazilian Agricultural. Research Corporation, Embrapa Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Josiane B Chiaramonte
- Brazilian Agricultural. Research Corporation, Embrapa Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Laura Bononi
- Brazilian Agricultural. Research Corporation, Embrapa Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Ana Paula Packer
- Brazilian Agricultural. Research Corporation, Embrapa Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
| | - Itamar S Melo
- Brazilian Agricultural. Research Corporation, Embrapa Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Rodrigo G Taketani
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil.
- Centre for Mineral Technology, CETEM, MCTIC Ministry of Science, Technology, Innovation and Communication, Av. Pedro Calmon, 900, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, 21941-908, Brazil.
- Sustainable Agriculture Sciences, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK.
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Giraldo-Silva A, Masiello CA. Environmental conditions play a key role in controlling the composition and diversity of Colombian biocrust microbiomes. Front Microbiol 2024; 15:1236554. [PMID: 38725684 PMCID: PMC11081033 DOI: 10.3389/fmicb.2024.1236554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 03/11/2024] [Indexed: 05/12/2024] Open
Abstract
Drylands soils worldwide are naturally colonized by microbial communities known as biocrusts. These soil microbiomes render important ecosystem services associated with soil fertility, water holding capacity, and stability to the areas they cover. Because of the importance of biocrusts in the global cycling of nutrients, there is a growing interest in describing the many microbial configurations these communities display worldwide. However, comprehensive 16S rRNA genes surveys of biocrust communities do not exist for much of the planet: for example, in the continents of South America and the northern part of Africa. The absence of a global understanding of biocrust biodiversity has lead us to assign a general importance to community members that may, in fact, be regional. Here we report for the first time the presence of biocrusts in Colombia (South America) through 16S rRNA genes surveys across an arid, a semi-arid and a dry subtropical region within the country. Our results constitute the first glance of the Bacterial/Archaeal communities associated with South American biocrust microbiomes. Communities where cyanobacteria other than Microcoleus vaginatus prevail, despite the latter being considered a key species elsewhere, illustrate differentiable results in these surveys. We also find that the coastal biocrust communities in Colombia include halo-tolerant and halophilic species, and that niche preference of some nitrogen fixing organisms deviate from previously described global trends. In addition, we identified a high proportion (ranging from 5 to 70%, in average) of cyanobacterial sequences that did not match any formally described cyanobacterial species. Our investigation of Colombian biocrusts points to highly diverse communities with climatic regions controlling taxonomic configurations. They also highlight an extensive local diversity to be discovered which is central to better design management and restoration strategies for drylands soils currently undergoing disturbances due to land use and global warming. Finally, this field study highlights the need for an improved mechanistic understanding of the response of key biocrust community members to changes in moisture and temperature.
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Affiliation(s)
- Ana Giraldo-Silva
- Department of Science, Ecology Group and Institute for Multidisciplinary Research in Applied Biology, Public University of Navarre (UPNA), Pamplona, Spain
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
| | - Caroline A. Masiello
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
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Ojo AO, Castillo J, Cason ED, Valverde A. Biodegradation of chloroethene compounds under microoxic conditions. Biotechnol Bioeng 2024; 121:1036-1049. [PMID: 38116701 DOI: 10.1002/bit.28630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic conditions are unknown. Here, we report the biostimulated (BIOST: addition of lactate) and natural attenuated (NAT) degradation of chloroethene compounds under microoxic conditions by bacterial communities from chloroethene compounds-contaminated groundwater. The degradation of tetrachloroethene was significantly higher in NAT (15.14% on average) than in BIOST (10.13% on average) conditions at the end of the experiment (90 days). Sporomusa, Paracoccus, Sedimentibacter, Pseudomonas, and Desulfosporosinus were overrepresented in NAT and BIOST compared to the source groundwater. The NAT metagenome contains phenol hydrolase P1 oxygenase (dmpL), catechol-1,2-dioxygenase (catA), catechol-2,3-dioxygenases (dmpB, todE, and xylE) genes, which could be involved in the cometabolic degradation of chloroethene compounds; and chlorate reductase (clrA), that could be associated with partial reductive dechlorination of chloroethene compounds. Our data provide a better understanding of the bacterial communities, genes, and pathways potentially implicated in the reductive and cometabolic degradation of chloroethene compounds under microoxic conditions.
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Affiliation(s)
- Abidemi Oluranti Ojo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Julio Castillo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Errol Duncan Cason
- Department of Animal Sciences, University of the Free State, Bloemfontein, South Africa
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Salamanca, Spain
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Sipriyadi S, Khairina Y, Masrukhin M, Yulandi A, Wibowo RH, Nisa DT. Bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Can J Microbiol 2023; 69:439-448. [PMID: 37364294 DOI: 10.1139/cjm-2022-0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The rhizosphere is a narrow soil area directly affected by plant root exudates. Microbes inhabiting the rhizosphere have been widely studied for their beneficial effects on plant nutrition, growth, and disease prevention. Many factors affect the rhizosphere microbial composition, including plant pathogen infection. Here, we analyzed the bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Soil samples were collected from rhizosphere and non-rhizosphere areas of fungi-infected A. titanum. The 16S metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The results showed that the phylum Firmicutes was prevalent in the rhizosphere, whereas the phyla Proteobacteria, Acidobacteria, and Actinobacteria were limited. Some major fungal genera were isolated from infected tubers and rhizosphere soil of A. titanum, including Trichoderma sp., Aspergillus sp., Perenniporia sp., and Cerrena sp. The fungal-isolate Aspergillus spp. is a well-known agricultural pest in several reports. While Cerrena sp. was reported to be pathogenic in plants, including the family of Arecaceae. Overall, the data revealed a potential relationship between fungal infections and the dominant bacterial community in the rhizosphere of A. titanum. Additionally, this research may contribute to the development of microbe-based technology to mitigate diseases in A. titanum.
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Affiliation(s)
- Sipriyadi Sipriyadi
- Department of Biology. Faculty of Mathematics and Natural Sciences, Bengkulu University, Bengkulu, Indonesia
| | - Yeni Khairina
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Cibinong 16911, Indonesia
| | - Masrukhin Masrukhin
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Jl. Raya Jakarta-Bogor Km 46, Cibinong 16911, Indonesia
| | - Adi Yulandi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Risky Hadi Wibowo
- Department of Biology. Faculty of Mathematics and Natural Sciences, Bengkulu University, Bengkulu, Indonesia
| | - Dhiatama Tauhida Nisa
- Department of Biology. Faculty of Mathematics and Natural Sciences, Bengkulu University, Bengkulu, Indonesia
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Foster L, Boothman C, Harrison S, Jenkinson P, Pittman JK, Lloyd JR. Identification of algal rich microbial blooms in the Sellafield Pile Fuel Storage Pond and the application of ultrasonic treatment to control the formation of blooms. Front Microbiol 2023; 14:1261801. [PMID: 37860139 PMCID: PMC10582928 DOI: 10.3389/fmicb.2023.1261801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023] Open
Abstract
The presence of microorganisms in a range of nuclear facilities has been known for many years. In this study the microbial community inhabiting the Pile Fuel Storage Pond (PFSP), which is a legacy open-aired facility on the Sellafield nuclear site, Cumbria, UK, was determined to help target microbial bloom management strategies in this facility. The PFSP is currently undergoing decommissioning and the development of prolonged dense microbial blooms reduces the visibility within the water. Such impairment in the pond water visibility can lead to delays in pond operations, which also has financial implications. Efforts to control the microbial population within the PFSP are ongoing, with the installation of ultrasonic treatment units. Here next generation sequencing techniques focussing on broad targets for both eukaryotic and prokaryotic organisms were used to identify the microbial community. On-site monitoring of photosynthetic pigments indicated when microbial blooms formed and that eukaryotic algae were most likely to be responsible for these events. The sequencing data suggested that the blooms were dominated by members of the class Chrysophyceae, a group of golden algae, while evidence of cyanobacteria and other photosynthetic bacteria was limited, further supporting eukaryotic organisms causing the blooms. The results of sequencing data from 2018 was used to inform a change in the operational settings of the ultrasonic units, while monitoring of the microbial community and photosynthetic pigments trends was extended. Since the changes were made to the ultrasonic treatment, the visibility in the pond was significantly improved, with an absence of a spring bloom in 2020 and an overall reduction in the number of days lost due to microbial blooms annually. This work extends our knowledge of the diversity of microbes able to colonise nuclear fuel storage ponds, and also suggests that sequencing data can help to optimise the performance of ultrasonic treatments, to control algal proliferation in the PFSP facility and other inhospitable engineered systems.
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Affiliation(s)
- Lynn Foster
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Christopher Boothman
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Scott Harrison
- National Nuclear Laboratory, Central Laboratory, Sellafield, Seascale, United Kingdom
| | | | - Jon K. Pittman
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Jonathan R. Lloyd
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
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Yu X, Wei M, Yang D, Wu X, Wei H, Xu F. Lactiplantibacillus plantarum Strain FLPL05 Promotes Longevity in Mice by Improving Intestinal Barrier. Probiotics Antimicrob Proteins 2023; 15:1193-1205. [PMID: 35918623 DOI: 10.1007/s12602-022-09933-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 10/16/2022]
Abstract
This study aimed to evaluate the effect of oral administration of probiotic Lactiplantibacillus plantarum FLPL05 on the lifespan and intestinal barrier of aged mice. L. plantarum FLPL05 significantly prolonged the lifespan of naturally aged mice, maintained the integrity of intestinal mucosal barrier, and reduced the inflammation level. The analysis of intestinal microbiota revealed that L. plantarum FLPL05 increased the relative abundance of Firmicutes and decreased the abundance of Bacteroides, accompanied by the increased proportions of Lactobacillus and Desulfovibrio in intestinal microbiota as well as the reduced proportions of Roseburia and Parabacteroides. The intestinal proteomics revealed that the oral administration of L. plantarum FLPL05 significantly upregulated the tight junction and simultaneously inhibited the expression of apoptotic-related proteins. The immunohistochemistry results also indicated that L. plantarum FLPL05 promoted the expression of tight junction proteins (ZO-1 and occludin) and reduced the apoptosis of intestinal cells. In addition, L. plantarum FLPL05 and the fermented supernatant increased the activity of HT-29. L. plantarum FLPL05 prolonged the lifespan by improving the health of the intestinal tract after aging and may be a potential probiotic and nutritional supplement for the elderly people.
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Affiliation(s)
- Xiaomin Yu
- Jiangxi-Oai Joint Research Institute, Nanchang University, 235 Nanjing Donglu, Nanchang, 330047, People's Republic of China
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330047, People's Republic of China
| | - Min Wei
- Jiangxi-Oai Joint Research Institute, Nanchang University, 235 Nanjing Donglu, Nanchang, 330047, People's Republic of China
| | - Dong Yang
- Jiangxi-Oai Joint Research Institute, Nanchang University, 235 Nanjing Donglu, Nanchang, 330047, People's Republic of China
| | - Xiaoli Wu
- College of Basic Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, People's Republic of China
| | - Hua Wei
- Jiangxi-Oai Joint Research Institute, Nanchang University, 235 Nanjing Donglu, Nanchang, 330047, People's Republic of China.
| | - Feng Xu
- Jiangxi-Oai Joint Research Institute, Nanchang University, 235 Nanjing Donglu, Nanchang, 330047, People's Republic of China.
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Li T, Wang X, Wang X, Huang J, Shen L. Mechanisms Driving the Distribution and Activity of Mineralization and Nitrification in the Reservoir Riparian Zone. MICROBIAL ECOLOGY 2023; 86:1829-1846. [PMID: 36702929 DOI: 10.1007/s00248-023-02180-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
The riparian zone ecosystems have greater energy flow and elemental cycling than adjacent terrestrial and aquatic ecosystems. Mineralization and nitrification are important initiating processes in the nitrogen cycle, but their distribution and activity under different environmental conditions in the riparian zone and the driving mechanisms are still not clear. We investigated the effects of environmental and microbial factors on mineralization and nitrification activities by analyzing the community of alkaline (apr) and neutral (npr) metallopeptidase, ammonia-oxidizing archaea (AOA), and bacteria (AOB) in soils and sediments under different land-use types in the riparian zone of Miyun Reservoir, as well as measuring potential nitrogen mineralization and ammonia oxidation rates (AOR). The results showed that the mineralization and nitrification activities of soils were greater than those of sediments. AOA and AOB dominate the ammonia oxidation activity of soil and sediment, respectively. NH4+ content was a key factor influencing the ecological niche differentiation between AOA and AOB. The high carbon and nitrogen content of the woodland significantly increased mineralization and nitrification activity. Microbial communities were significantly clustered in the woodland. The land-use type, not the flooding condition, determined the distribution of microbial community structure. The diversity of npr was significantly correlated with potential N mineralization rates, while the transcript abundance of AOA was significantly correlated with ammonia oxidation rates. Our study suggests that environmental changes regulate the distribution and activity of mineralization and nitrification processes in the reservoir riparian zone by affecting the transcript abundance, diversity and community structure of the microbial functional genes.
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Affiliation(s)
- Tingting Li
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Xiaoyan Wang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China.
| | - Xia Wang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Jingyu Huang
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Lei Shen
- College of Resources, Environment and Tourism, Capital Normal University, No. 105, North West Third Ring Road, Haidian District, Beijing, 100048, China
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Giovanella P, Taketani RG, Gil-Solsona R, Saldanha LL, Naranjo SBE, Sancho JV, Portolés T, Andreote FD, Rodríguez-Mozaz S, Barceló D, Sette LD. A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:101250-101266. [PMID: 37648922 DOI: 10.1007/s11356-023-29474-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.
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Affiliation(s)
- Patricia Giovanella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Rodrigo Gouvêa Taketani
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - Ruben Gil-Solsona
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research - Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Luiz Leonardo Saldanha
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Samantha Beatríz Esparza Naranjo
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino Americana, Parque tecnológico Itaipu, Foz do Iguaçu, PR, Brazil
| | - Juan V Sancho
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón de la Plana, Spain
| | - Tania Portolés
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón de la Plana, Spain
| | - Fernando Dini Andreote
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research - Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Lara Durães Sette
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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Fudjoe SK, Li L, Anwar S, Shi S, Xie J, Wang L, Xie L, Yongjie Z. Nitrogen fertilization promoted microbial growth and N 2O emissions by increasing the abundance of nirS and nosZ denitrifiers in semiarid maize field. Front Microbiol 2023; 14:1265562. [PMID: 37720157 PMCID: PMC10501401 DOI: 10.3389/fmicb.2023.1265562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Nitrous oxide (N2O) emissions are a major source of gaseous nitrogen loss, causing environmental pollution. The low organic content in the Loess Plateau region, coupled with the high fertilizer demand of maize, further exacerbates these N losses. N fertilizers play a primary role in N2O emissions by influencing soil denitrifying bacteria, however, the underlying microbial mechanisms that contribute to N2O emissions have not been fully explored. Therefore, the research aimed to gain insights into the intricate relationships between N fertilization, soil denitrification, N2O emissions, potential denitrification activity (PDA), and maize nitrogen use efficiency (NUE) in semi-arid regions. Four nitrogen (N) fertilizer rates, namely N0, N1, N2, and N3 (representing 0, 100, 200, and 300 kg ha-1 yr.-1, respectively) were applied to maize field. The cumulative N2O emissions were 32 and 33% higher under N2 and 37 and 39% higher under N3 in the 2020 and 2021, respectively, than the N0 treatment. N fertilization rates impacted the abundance, composition, and network of soil denitrifying communities (nirS and nosZ) in the bulk and rhizosphere soil. Additionally, within the nirS community, the genera Cupriavidus and Rhodanobacter were associated with N2O emissions. Conversely, in the nosZ denitrifier, the genera Azospirillum, Mesorhizobium, and Microvirga in the bulk and rhizosphere soil reduced N2O emissions. Further analysis using both random forest and structural equation model (SEM) revealed that specific soil properties (pH, NO3--N, SOC, SWC, and DON), and the presence of nirS-harboring denitrification, were positively associated with PDA activities, respectively, and exhibited a significant association to N2O emissions and PDA activities but expressed a negative effect on maize NUE. However, nosZ-harboring denitrification showed an opposite trend, suggesting different effects on these variables. Our findings suggest that N fertilization promoted microbial growth and N2O emissions by increasing the abundance of nirS and nosZ denitrifiers and altering the composition of their communities. This study provides new insights into the relationships among soil microbiome, maize productivity, NUE, and soil N2O emissions in semi-arid regions.
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Affiliation(s)
- Setor Kwami Fudjoe
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lingling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sumera Anwar
- Department of Botany, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Junhong Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Linlin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lihua Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhou Yongjie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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11
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Šantić D, Stojan I, Matić F, Trumbić Ž, Vrdoljak Tomaš A, Fredotović Ž, Piwosz K, Lepen Pleić I, Šestanović S, Šolić M. Picoplankton diversity in an oligotrophic and high salinity environment in the central Adriatic Sea. Sci Rep 2023; 13:7617. [PMID: 37165047 PMCID: PMC10172355 DOI: 10.1038/s41598-023-34704-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
By combining qualitative 16S metabarcoding and quantitative CARD-FISH methods with neural gas analysis, different patterns of the picoplankton community were revealed at finer taxonomic levels in response to changing environmental conditions in the Adriatic Sea. We present the results of a one-year study carried out in an oligotrophic environment where increased salinity was recently observed. We have shown that the initial state of community structure changes according to environmental conditions and is expressed as qualitative and quantitative changes. A general pattern of increasing diversity under harsh environmental conditions, particularly under the influence of increasing salinity at the expense of community abundance was observed. Considering the trend of changing seawater characteristics due to climate change, this study helps in understanding a possible structural change in the microbial community of the Adriatic Sea that could affect higher levels of the marine food web.
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Affiliation(s)
- Danijela Šantić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Iva Stojan
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia.
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Ruđera Boškovića 37, Split, Croatia.
| | - Frano Matić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Ana Vrdoljak Tomaš
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, Split, Croatia
| | - Kasia Piwosz
- National Marine Fisheries Research Institute, Kołłątaja 1, Gdynia, Poland
| | - Ivana Lepen Pleić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Stefanija Šestanović
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Mladen Šolić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
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12
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Calderón-Franco D, van Loosdrecht MCM, Abeel T, Weissbrodt DG. Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01834-z. [PMID: 37156983 DOI: 10.1007/s10482-023-01834-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L-1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L-1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.
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Affiliation(s)
| | | | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
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13
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Debastiani GL, Berghahn E, Cavião HC, Viganó L, Montes AL, Giongo A, Schwambach J, Granada CE. Biotechnological potential of Bacillus sp. S26 for alleviation of abiotic and biotic stresses in vine. World J Microbiol Biotechnol 2023; 39:150. [PMID: 37024538 DOI: 10.1007/s11274-023-03601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
Grapevine (Vitis spp.) is one of the most cultivated fruit plants in the world. Vineyard growers apply copper-based products in these crops to prevent fungal diseases, generating worries about Cu contamination in soils and food. In this context, this study identifies prokaryotic communities associated with grapevine plants grown under different levels of Cu-contaminated soils. Moreover, the study isolates new bacteria to improve Cu resistance in plants. Soil Cu content correlated inversely with operational taxonomic units (OTUs) belonging to the groups Acidobacteria (SubGroup 2), Latescibacteria, Pedosphaeraceae, and Candidatus Udaeobacter. A total of 14 new bacterial isolates were obtained from copper-contaminated soils. These isolates produced Indolic Compounds (IC) in a range of 25 to 96 µg mL- 1, highlighting bacterial strains S20 and S26 as the highest producers. These new bacteria also produced siderophores, highlighting strains S19 and S26, which removed 58 and 59% of Fe ions from the CAS complex, respectively. From the in vitro antagonistic activity against Colletotrichum spp. strains, the authors identified some bacterial strains that inhibited phytopathogen growth. Bacterial strain Bacillus sp. S26 was chosen for inoculation experiments in grapevine plants. This bacterial isolate improved the growth of grapevine plants in Cu-contaminated soils. However, growth promotion did not occur in unstressed plants. More studies are necessary for developing a new bioinoculant containing S26 cells aiming to reduce biotic and abiotic stresses in grapevine.
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Affiliation(s)
- Giovana Lara Debastiani
- Laboratory of Biological Plant Disease Control and Laboratory of Plant Biotechnology, Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, Brazil
| | - Emílio Berghahn
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, RS, Brazil
| | - Hélen Corso Cavião
- Laboratory of Biological Plant Disease Control and Laboratory of Plant Biotechnology, Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, Brazil
| | - Leticia Viganó
- Laboratory of Biological Plant Disease Control and Laboratory of Plant Biotechnology, Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, Brazil
| | - André Luiz Montes
- Laboratory of Biological Plant Disease Control and Laboratory of Plant Biotechnology, Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, Brazil
| | - Adriana Giongo
- Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics Messeweg, Julius Kühn-Institute (JKI), Braunschweig, Germany
| | - Joséli Schwambach
- Laboratory of Biological Plant Disease Control and Laboratory of Plant Biotechnology, Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, Brazil
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14
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Zhu C, Lin Y, Wang Z, Luo W, Zhang Y, Chu C. Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem. Front Microbiol 2023; 14:1147285. [PMID: 37007520 PMCID: PMC10064055 DOI: 10.3389/fmicb.2023.1147285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant–epiphyte and plant–endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant–endophyte network, plant–epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.
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Affiliation(s)
- Chunchao Zhu
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
- *Correspondence: Chunchao Zhu,
| | | | - Zihui Wang
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Yonghua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
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15
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Zhang Y, Cheng Z, Li Q, Dai Q, Hu J. Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38761-38774. [PMID: 36586025 DOI: 10.1007/s11356-022-25020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
| | - Zhandou Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
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16
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Ma Z, Li P, Yang C, Feng Z, Feng H, Zhang Y, Zhao L, Zhou J, Zhu H, Wei F. Soil bacterial community response to continuous cropping of cotton. Front Microbiol 2023; 14:1125564. [PMID: 36778850 PMCID: PMC9909236 DOI: 10.3389/fmicb.2023.1125564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction Long-term continuous cropping may result in the outbreak and proliferation of soil-borne diseases, as well as reduction in annual crop production. Overcoming the obstacles of continuous cropping is critical for the long-term growth of modern agriculture. Soil microbes are essential for plant health, but the consequences of continuous cropping on soil microbiome are still poorly understood. Methods This study analyzed changes in soil bacterial community composition of Aksu (AKS) and Shihezi (SHZ) in Xinjiang Province during 1-20 years of continuous cropping by 16S amplicon sequencing. The results showed that the incidence of cotton Verticillium wilt rose with the number of cropping years. The bacterial alpha diversity in the AKS soil grew as the number of continuous cropping years increased, however it declined in the SHZ soil. Results The results of beta diversity analysis showed that there were significant differences in soil bacterial communities between different continuous cropping years and between different soils. The results of community composition changes at the level of main phyla and genus showed that the relative abundance of Actinobacteria, Bacteroidetes and Streptomyces decreased with the increase of continuous cropping years in the AKS and the SHZ soils. In addition, Actinobacteria, Propionibacteriales, and Nocardioidaceae were significantly enriched during the early stages of continuous cropping. Network analysis showed that long-term (≥8 years) continuous cropping interfered with the complexity of soil bacterial co-occurrence networks and reduced collaboration between OTUs. Discussion These findings suggested that continuous cropping and soil origin jointly affected the diversity and structural of bacterial communities, and the loss of Nocardioidaceae and Streptomyces in Actinobacteria might be one of the reasons of continuous cropping obstacles.
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Affiliation(s)
- Zheng Ma
- National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Peng Li
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chuanzhen Yang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zili Feng
- National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hongjie Feng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Yalin Zhang
- National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lihong Zhao
- National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinglong Zhou
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Heqin Zhu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China,*Correspondence: Heqin Zhu, ✉
| | - Feng Wei
- National Engineering Research Center of Cotton Biology Breeding and Industrial Technology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China,Feng Wei, ✉
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17
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA). BIOGEOCHEMISTRY 2023; 162:359-380. [PMID: 36873379 PMCID: PMC9971093 DOI: 10.1007/s10533-022-01008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Coastal wetlands are highly efficient 'blue carbon' sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments. GRAPHICAL ABSTRACT Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-01008-5.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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18
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Decker LE, San Juan PA, Warren ML, Duckworth CE, Gao C, Fukami T. Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee Gut. MICROBIAL ECOLOGY 2023. [PMID: 34997310 DOI: 10.1101/2020.10.20.348128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Along with bacteria, fungi can represent a significant component of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. Bacteria associated with the honey bee, Apis mellifera, have been well characterized across different regions of the gut. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health, whereas the crop, or the honey stomach, harbors a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two regions of the gut also applies to fungi remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula of California, we found that fungi were less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi varied substantially in species composition throughout the honey bee gut, and much of this variation could be predicted by the location where we collected the bees. These observations suggest that fungi may be transient passengers and unimportant as gut symbionts. However, our findings also indicate that honey bees could be vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.
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Affiliation(s)
- Leslie E Decker
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA.
| | - Priscilla A San Juan
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
| | - Magdalena L Warren
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
| | - Cory E Duckworth
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
- Department of Biology, University of North Georgia, 159 Sunset Dr, Health and Natural Sciences Building, Dahlonega, GA, 30597, USA
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Cheng Gao
- Department of Plant & Microbial Biology, University of California, Berkeley, 321 Koshland Hall, Berkeley, CA, 94720, USA
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tadashi Fukami
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
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19
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Decker LE, San Juan PA, Warren ML, Duckworth CE, Gao C, Fukami T. Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee Gut. MICROBIAL ECOLOGY 2023; 85:330-334. [PMID: 34997310 DOI: 10.1007/s00248-021-01922-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Along with bacteria, fungi can represent a significant component of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. Bacteria associated with the honey bee, Apis mellifera, have been well characterized across different regions of the gut. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health, whereas the crop, or the honey stomach, harbors a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two regions of the gut also applies to fungi remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula of California, we found that fungi were less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi varied substantially in species composition throughout the honey bee gut, and much of this variation could be predicted by the location where we collected the bees. These observations suggest that fungi may be transient passengers and unimportant as gut symbionts. However, our findings also indicate that honey bees could be vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.
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Affiliation(s)
- Leslie E Decker
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA.
| | - Priscilla A San Juan
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
| | - Magdalena L Warren
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
| | - Cory E Duckworth
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
- Department of Biology, University of North Georgia, 159 Sunset Dr, Health and Natural Sciences Building, Dahlonega, GA, 30597, USA
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Cheng Gao
- Department of Plant & Microbial Biology, University of California, Berkeley, 321 Koshland Hall, Berkeley, CA, 94720, USA
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tadashi Fukami
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 48109-1085, USA
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20
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Zhao J, Rodriguez J, Martens-Habbena W. Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils. Front Microbiol 2023; 14:1140487. [PMID: 36910167 PMCID: PMC9995467 DOI: 10.3389/fmicb.2023.1140487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Jonathan Rodriguez
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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21
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Johnson KVA, Watson KK, Dunbar RIM, Burnet PWJ. Sociability in a non-captive macaque population is associated with beneficial gut bacteria. Front Microbiol 2022; 13:1032495. [PMID: 36439813 PMCID: PMC9691693 DOI: 10.3389/fmicb.2022.1032495] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/12/2022] Open
Abstract
The relationship between social behaviour and the microbiome is known to be reciprocal. Research in wild animal populations, particularly in primate social groups, has revealed the role that social interactions play in microbial transmission, whilst studies in laboratory animals have demonstrated that the gut microbiome can affect multiple aspects of behaviour, including social behaviour. Here we explore behavioural variation in a non-captive animal population with respect to the abundance of specific bacterial genera. Social behaviour based on grooming interactions is assessed in a population of rhesus macaques (Macaca mulatta), and combined with gut microbiome data. We focus our analyses on microbiome genera previously linked to sociability and autistic behaviours in rodents and humans. We show in this macaque population that some of these genera are also related to an individual's propensity to engage in social interactions. Interestingly, we find that several of the genera positively related to sociability, such as Faecalibacterium, are well known for their beneficial effects on health and their anti-inflammatory properties. In contrast, the genus Streptococcus, which includes pathogenic species, is more abundant in less sociable macaques. Our results indicate that microorganisms whose abundance varies with individual social behaviour also have functional links to host immune status. Overall, these findings highlight the connections between social behaviour, microbiome composition, and health in an animal population.
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Affiliation(s)
- Katerina V.-A. Johnson
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom,Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom,*Correspondence: Katerina V.-A. Johnson,
| | - Karli K. Watson
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, United States
| | - Robin I. M. Dunbar
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom
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22
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Ben zineb A, Barkaoui K, Karray F, Mhiri N, Sayadi S, Mliki A, Gargouri M. Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions. Front Microbiol 2022; 13:977797. [DOI: 10.3389/fmicb.2022.977797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes’ rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.
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23
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Yeo FKS, Cheok YH, Wan Ismail WN, Kueh-Tai FF, Lam TTY, Chong YL. Genotype and organ effect on the occupancy of phyllosphere prokaryotes in different rice landraces. Arch Microbiol 2022; 204:600. [PMID: 36056990 DOI: 10.1007/s00203-022-03209-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/26/2022] [Accepted: 08/19/2022] [Indexed: 11/02/2022]
Abstract
Bacteria community provides essential ecological services to rice plants. The bacterial diversity of rice varies across host plant genotype and organs. This study employed 16S rDNA amplicon sequencing to characterise the bacterial community associated with three rice landraces using leaf blade and stem samples. The prokaryotic community found in these rice landraces comprised of two kingdoms, 12 phyla, 25 classes, 40 orders, 80 families, and 118 genera. Proteobacteria (53.9%) was the most abundant phylum. The most abundant genus was an undefined genus under Cyanobacteria (33.0%). Homogeneity of prokaryotic community was observed across the three rice landraces, which may suggest a high similarity in biological and genetical properties of the rice landraces. The difference in prokaryotic composition between leaf blade and stem was depicted based on principal coordinate analysis. This study observed that the prokaryotic inhabitants in rice plants is predominantly determined by rice plant organs.
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Affiliation(s)
- Freddy Kuok San Yeo
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Yin Hui Cheok
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Wan Nurainie Wan Ismail
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Felicia Fui Kueh-Tai
- Agriculture Research Centre, Semongok, 12th Mile, Kuching-Serian Road, P.O. Box 977, 93720, Kuching, Sarawak, Malaysia
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Yee Ling Chong
- Department of Science and Environmental Studies, Faculty of Liberal Arts and Social Sciences, The Education University of Hong Kong, 10 Lo Ping Road, Ting Kok, Hong Kong SAR, China
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24
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Fudjoe SK, Li L, Jiang Y, Alhassan ARM, Xie J, Anwar S, Wang L, Xie L. Impact of soil amendments on nitrous oxide emissions and the associated denitrifying communities in a semi-arid environment. Front Microbiol 2022; 13:905157. [PMID: 36060775 PMCID: PMC9428159 DOI: 10.3389/fmicb.2022.905157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Denitrifying bacteria produce and utilize nitrous oxide (N2O), a potent greenhouse gas. However, there is little information on how organic fertilization treatments affect the denitrifying communities and N2O emissions in the semi-arid Loess Plateau. Here, we evaluated how the denitrifying communities are responsible for potential denitrification activity (PDA) and N2O emissions. A field experiment was conducted with five fertilization treatments, including no fertilization (CK), mineral fertilizer (MF), mineral fertilizer plus commercial organic fertilizer (MOF), commercial organic fertilizer (OFP), and maize straw (MSP). Our result showed that soil pH, soil organic carbon (SOC), and dissolved organic nitrogen (DON) were significantly increased under MSP treatment compared to MF treatment, while nitrate nitrogen (NO3−−N) followed the opposite trend. Organic fertilization treatments (MOF, OFP, and MSP treatments) significantly increased the abundance and diversity of nirS- and nosZ-harboring denitrifiers, and modified the community structure compared to CK treatment. The identified potential keystone taxa within the denitrifying bacterial networks belonged to the distinct genera. Denitrification potentials were significantly positively correlated with the abundance of nirS-harboring denitrifiers, rather than that of nirK- and nosZ-harboring denitrifiers. Random forest modeling and structural equation modeling consistently determined that the abundance, community composition, and network module I of nirS-harboring denitrifiers may contribute significantly to PDA and N2O emissions. Collectively, our findings highlight the ecological importance of the denitrifying communities in mediating denitrification potentials and the stimulatory impact of organic fertilization treatments on nitrogen dynamics in the semi-arid Loess Plateau.
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Affiliation(s)
- Setor Kwami Fudjoe
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lingling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Lingling Li,
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- Yuji Jiang,
| | - Abdul-Rauf Malimanga Alhassan
- Department of Water Resources and Sustainable Development, The University of Environment and Sustainable Development, Somanya, Ghana
| | - Junhong Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sumera Anwar
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Linlin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lihua Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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25
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Evaluation of Full-Length Versus V4-Region 16S rRNA Sequencing for Phylogenetic Analysis of Mouse Intestinal Microbiota After a Dietary Intervention. Curr Microbiol 2022; 79:276. [PMID: 35907023 PMCID: PMC9338901 DOI: 10.1007/s00284-022-02956-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
Abstract
The composition of microbial communities is commonly determined by sequence analyses of one of the variable (V) regions in the bacterial 16S rRNA gene. We aimed to assess whether sequencing the full-length versus the V4 region of the 16S rRNA gene affected the results and interpretation of an experiment. To test this, mice were fed a diet without and with the prebiotic inulin and from cecum samples, two primary data sets were generated: (1) a 16S rRNA full-length data set generated by the PacBio platform; (2) a 16S rRNA V4 region data set generated by the Illumina MiSeq platform. A third derived data set was generated by in silico extracting the 16S rRNA V4 region data from the 16S rRNA full-length PacBio data set. Analyses of the primary and derived 16S rRNA V4 region data indicated similar bacterial abundances, and α- and β-diversity. However, comparison of the 16S rRNA full-length data with the primary and derived 16S rRNA V4 region data revealed differences in relative bacterial abundances, and α- and β-diversity. We conclude that the sequence length of 16S rRNA gene and not the sequence analysis platform affected the results and may lead to different interpretations of the effect of an intervention that affects the microbiota.
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26
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Ahumada GD, Gómez-Álvarez EM, Dell’Acqua M, Bertani I, Venturi V, Perata P, Pucciariello C. Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence. FRONTIERS IN PLANT SCIENCE 2022; 13:908349. [PMID: 35845658 PMCID: PMC9277545 DOI: 10.3389/fpls.2022.908349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/31/2022] [Indexed: 06/10/2023]
Abstract
Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence.
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Affiliation(s)
| | | | | | - Iris Bertani
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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27
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Zhang B, Deng J, Xie J, Wu H, Wei C, Li Z, Qiu G, Wei C, Zhu S. Microbial community composition and function prediction involved in the hydrolytic bioreactor of coking wastewater treatment process. Arch Microbiol 2022; 204:426. [PMID: 35751757 DOI: 10.1007/s00203-022-03052-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/08/2022] [Accepted: 06/03/2022] [Indexed: 11/25/2022]
Abstract
The hydrolytic acidification process has a strong ability to conduct denitrogenation and increase the biological oxygen demand/chemical oxygen demand ratio in O/H/O coking wastewater treatment system. More than 80% of the total nitrogen (TN) was removed in the hydrolytic bioreactor, and the hydrolytic acidification process contributed to the provision of carbon sources for the subsequent nitrification process. The structure and diversity of microbial communities were elaborated using high-throughput MiSeq of the 16S rRNA genes. The results revealed that the operational taxonomic units (OTUs) belonged to phyla Bacteroidetes, Betaproteobacteria, and Alphaproteobacteria were the dominant taxa involved in the denitrogenation and degradation of refractory contaminants in the hydrolytic bioreactor, with relative abundances of 22.94 ± 3.72, 29.77 ± 2.47, and 18.23 ± 0.26%, respectively. The results of a redundancy analysis showed that the OTUs belonged to the genera Thiobacillus, Rhodoplanes, and Hylemonella in the hydrolytic bioreactor strongly positively correlated with the chemical oxygen demand, TN, and the removal of phenolics, respectively. The results of a microbial co-occurrence network analysis showed that the OTUs belonged to the phylum Bacteroidetes and the genus Rhodoplanes had a significant impact on the efficiency of removal of contaminants that contained nitrogen in the hydrolytic bioreactor. The potential function profiling results indicate the complementarity of nitrogen metabolism, methane metabolism, and sulfur metabolism sub-pathways that were considered to play a significant role in the process of denitrification. These results provide new insights into the further optimization of the performance of the hydrolytic bioreactor in coking wastewater treatment.
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Affiliation(s)
- Baoshan Zhang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jinsi Deng
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Junting Xie
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Cong Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Zemin Li
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, China.
| | - Shuang Zhu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China.
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28
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Ji PT, Du X, Zhou JC, Peng Y, Li XL, Tao PJ, Zhang YC. Network Analysis Reveals the Combination of Controlled-Release and Regular Urea Enhances Microbial Interactions and Improves Maize Yields. Front Microbiol 2022; 13:825787. [PMID: 35801114 PMCID: PMC9253629 DOI: 10.3389/fmicb.2022.825787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022] Open
Abstract
Increased complexity of microbial networks can contribute to increased biodiversity and multifunctionality and thus crop productivity. However, it is not clear which combination ratio of regular and controlled-release urea will increase the soil microbial community complexity and improve maize yield in the North China Plain. To address this knowledge gap, a 2-year field experiment was conducted to explore the effects of the combination of regular (U) and controlled release (S) urea ratios [no fertilizer control (CT), regular urea alone (U), controlled-release urea alone (S), controlled-release urea mixed with regular urea 3:7 (SU3), controlled-release urea mixed with regular urea 5:5 (SU5), and controlled-release urea mixed with regular urea 7:3 (SU7)] on XianYu 688 yield and its rhizosphere and bulk soil microbial community composition and network complexity at different fertility stages. The combination of controlled-release and regular urea increased the N agronomic efficiency, N partial factors productivity, maize yield, and grain number per spike, with the maximum maize yield (9,186 kg ha-1) being achieved when the ratio of controlled-release urea to regular urea was 3:7 (SU3, p < 0.05). Maize yield increased by 13% in the SU3 treatment compared to the CT treatment. Rhizosphere soil microbial diversity remained stable at the silking stage of maize while increased at the physiological maturity stage of maize, with the increasing controlled-release to regular N fertilizer ratios (from 3:7 to 7:3, p < 0.05). This result suggests that a combination of regular and controlled-release N fertilizer can still substantially increase soil microbial diversity in the later stages of maize growth. The combination of controlled-release and regular urea is more effective in improving microbial network total links and average degree, and N agronomic efficiency (R 2 = 0.79, p < 0.01), N partial factor productivity (R 2 = 0.79, p < 0.01), spikes per unit area (R 2 = 0.54, p < 0.05), and maize yield (R 2 = 0.42, p < 0.05) increased with the microbial network complexity. This result indicates that the higher microbial network complexity is strongly associated with the higher N agronomic efficiency and N partial factors productivity and maize yield. In conclusion, the ratio of controlled-release to regular urea at SU3 not only increases the yield of maize and N agronomic efficiency but also enhances microbial diversity and network complexity in the North China Plain.
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Affiliation(s)
- Peng-tao Ji
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Xiong Du
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Jin-chao Zhou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Xianyang, China
| | - Yujuan Peng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Xiang-ling Li
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Pei-jun Tao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Yue-chen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
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29
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Kong Y, Liu Z, Xiao Q, Wu F, Hu L, Deng X, Chen T. Protective Effects of Engineered Lactobacillus crispatus on Intrauterine Adhesions in Mice via Delivering CXCL12. Front Immunol 2022; 13:905876. [PMID: 35734171 PMCID: PMC9207254 DOI: 10.3389/fimmu.2022.905876] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Endometrial injury is the main cause of intrauterine adhesions (IUA), and there is currently no effective prevention and treatment. Immune cells play an important role in damage repair by sensing the change in the microenvironment. Exogenous CXCL12 can promote tissue regeneration and repair by recruiting immune cells, but its effect and possible mechanism on endometrial regeneration and repair have not been reported. In the present study, we constructed an engineered a Lactobacillus crispatus strain by transforming a pMG36e plasmid carrying a CXCL12 gene into the bacterium, and developed two animal models, the intrauterine adhesion mice with or without diabetes to evaluate the positive effects of this strain on the prevention of IUA after accepting intrauterine surgery in normal and diabetic mice. The results showed that vaginal application of L. crispatus-pMG36e-mCXCL12 strains significantly diminished the levels of pro-inflammatory factors interleukin-1β (IL-1β) and tumour necrosis factor-α (TNF-α) in serum and uterine tissues of IUA mice, and resulted in the inhibition of the inflammatory (toll-like receptor 4/nuclear factor-κb, TLR4/NF-κB) and fibrotic (transforming growth factor-β1/smads, TGF-β1/Smads) signalling pathways in the uterine tissues. The high-throughput sequencing results further indicated that treatment with L. crispatus-pMG36e-mCXCL12 strains greatly increased the abundance of Lactobacillus spp. and reduced that of the pathogenic Klebsiella spp. in IUA mice. Furthermore, among intrauterine adhesion mice with diabetes, we obtained similar results to non-diabetic mice, that is, L.crispatus-pMG36e-mCXCL12 significantly improved fibrosis and inflammation in the uterine cavity of diabetic mice, and restored the vaginal microbiota balance in diabetic mice. Therefore, we speculated that vaginal administration of L. crispatus-pMG36e-mCXCL12 strains can effectively alleviate intrauterine adhesions by restoring the microbial balance and reducing inflammation and fibrosis caused by surgery.
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Affiliation(s)
- Yao Kong
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhaoxia Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Tingtao Chen, ; Zhaoxia Liu,
| | - Qin Xiao
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fei Wu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lijuan Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaorong Deng
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tingtao Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- National Engineering Research Center for Bioengineering Drugs and The Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, China
- *Correspondence: Tingtao Chen, ; Zhaoxia Liu,
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30
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Ottoni JR, Bernal SPF, Marteres TJ, Luiz FN, Dos Santos VP, Mari ÂG, Somer JG, de Oliveira VM, Passarini MRZ. Cultured and uncultured microbial community associated with biogas production in anaerobic digestion processes. Arch Microbiol 2022; 204:340. [PMID: 35590017 DOI: 10.1007/s00203-022-02819-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/07/2022] [Accepted: 02/25/2022] [Indexed: 11/02/2022]
Abstract
The search for sustainable development has increased interest in the improvement of technologies that use renewable energy sources. One of the alternatives in the production of renewable energy comes from the use of waste including urban solids, animal excrement from livestock, and biomass residues from agro-industrial plants. These materials may be used in the production of biogas, making its production highly sustainable and environmentally friendly. The present study aimed to evaluate the cultivated and uncultivated microbial community from a substrate (starter) used as an adapter for biogas production in anaerobic digestion processes. 16S rDNA metabarcoding revealed the domain of bacteria belonging to the phyla Firmicutes, Bacteroidota, Chloroflexi and Synergistota. The methanogenic group was represented by the phyla Halobacterota and Euryarchaeota. Through 16S rRNA sequencing of isolates recovered from the starter culture, the genera Rhodococcus (Actinobacteria phylum), Vagococcus, Lysinibacillus, Niallia, Priestia, Robertmurraya, Proteiniclasticum (Firmicutes phylum), and Luteimonas (Proteobacteria phylum) were identified, genera that were not observed in the metabarcoding data. The volatile solids, volatile organic acids, and total inorganic carbon reached 659.10 g kg-1, 717.70 g kg-1, 70,005.0 g kg-1, respectively. The cultured groups are involved in the metabolism of sugars and other compounds derived from lignocellulosic material, as well as in anaerobic methane production processes. The results demonstrate that culture-dependent approaches, such as isolation and sequencing, and culture-independent studies, such as the Metabarcoding approach, are complementary methodologies that, when integrated provide robust and comprehensive information about the microbial communities involved in processes of the production of biogas in anaerobic digestion processes.
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Affiliation(s)
- Júlia Ronzella Ottoni
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - Unila., Jd Universitário, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Suzan Prado Fernandes Bernal
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - Unila., Jd Universitário, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Tiago Joelzer Marteres
- Centro Internacional de Energias Renováveis - Biogás (CIBiogás-ER), Av. Tancredo Neves, 6731, Itaipu, Foz do Iguaçu, PR, Brazil
| | - Franciele Natividade Luiz
- Centro Internacional de Energias Renováveis - Biogás (CIBiogás-ER), Av. Tancredo Neves, 6731, Itaipu, Foz do Iguaçu, PR, Brazil
| | - Viviane Piccin Dos Santos
- CPQBA/UNICAMP - Divisão de Recursos Microbianos, Campinas, Av. Alexandre Cazelatto, 999. Betel, Paulínia, SP, Brazil
| | - Ângelo Gabriel Mari
- Centro Internacional de Energias Renováveis - Biogás (CIBiogás-ER), Av. Tancredo Neves, 6731, Itaipu, Foz do Iguaçu, PR, Brazil
| | - Juliana Gaio Somer
- Centro Internacional de Energias Renováveis - Biogás (CIBiogás-ER), Av. Tancredo Neves, 6731, Itaipu, Foz do Iguaçu, PR, Brazil
| | - Valéria Maia de Oliveira
- CPQBA/UNICAMP - Divisão de Recursos Microbianos, Campinas, Av. Alexandre Cazelatto, 999. Betel, Paulínia, SP, Brazil
| | - Michel Rodrigo Zambrano Passarini
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - Unila., Jd Universitário, Av. Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR, 85870-650, Brazil.
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Hao Y, Ji Z, Shen Z, Xue Y, Zhang B, Yu D, Liu T, Luo D, Xing G, Tang J, Hou S, Xie M. Increase Dietary Fiber Intake Ameliorates Cecal Morphology and Drives Cecal Species-Specific of Short-Chain Fatty Acids in White Pekin Ducks. Front Microbiol 2022; 13:853797. [PMID: 35464956 PMCID: PMC9021919 DOI: 10.3389/fmicb.2022.853797] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/02/2022] [Indexed: 12/12/2022] Open
Abstract
The current study was to investigate the modulatory effects of total dietary fiber (TDF) levels on cecal morphology and the response of microbiota to maintain gut health for duck growth. A total of 192 14-day-old male white Pekin ducks were randomly allocated to three dietary groups and fed diets, containing 12.4, 14.7, and 16.2% TDF, respectively, until 35 days under the quantitative feed intake. Each dietary group consisted of eight replicate cages of eight birds. The results revealed that 14.7 and 16.2% TDF groups significantly promoted growth performance and improved villus height, the ratio of villus to crypt, muscle layer thickness, and goblet cells per villus of cecum in ducks. qPCR results showed that the transcriptional expression of Claudin-1, Muc2, IGF-1, and SLC16A1 was significantly upregulated in cecum in 14.7 and 16.2% TDF groups. Meanwhile, the concentration of IGF-1 in circulating was significantly increased in 14.7 and 16.2% TDF groups while that of DAO was significantly decreased in 16.2% TDF group. Furthermore, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum were conspicuously improved in 14.7 and 16.2% TDF groups while that of propionate was significantly decreased. In addition, the concentrations of butyrate, isobutyrate, valerate, and isovalerate in cecum presented negative correlations with the concentration of DAO in circulating. 16S rRNA gene sequencing results showed that the 14.7% TDF group importantly elevated the microbial richness. Simultaneously, butyrate-producing bacteria like the family Lachnospiraceae, Oscillospiraceae, and Erysipelatoclostridiaceae were enriched as biomarkers in the 16.2% TDF group. Correlation network analysis revealed that the associations between specific bacteria and short-chain fatty acids (SCFAs) induced by different TDF levels, and the correlations among bacteria were also witnessed. For example, the genus Monoglobus and CHKCI002 showed a positive correlation with butyrate, and there was a positively coexistent association between Monoglobus and CHKCI002. In summary, these data revealed that increasing the TDF level could enhance the cecal morphology and drive cecal species-specific of SCFAs in ducks.
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Affiliation(s)
- Yongsheng Hao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanqing Ji
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongjian Shen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Youjia Xue
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daxin Yu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tong Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dawei Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangnan Xing
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Raimi AR, Atanda AC, Ezeokoli OT, Jooste PJ, Madoroba E, Adeleke RA. Diversity and predicted functional roles of cultivable bacteria in vermicompost: bioprospecting for potential inoculum. Arch Microbiol 2022; 204:261. [DOI: 10.1007/s00203-022-02864-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/08/2022] [Accepted: 03/21/2022] [Indexed: 11/02/2022]
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Zhang S, Xu X, Li Q, Chen J, Liu S, Zhao W, Cai H, Zhu J, Yu Y. Brain Network Topology and Structural–Functional Connectivity Coupling Mediate the Association Between Gut Microbiota and Cognition. Front Neurosci 2022; 16:814477. [PMID: 35422686 PMCID: PMC9002058 DOI: 10.3389/fnins.2022.814477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence indicates that gut microbiota can influence cognition via the gut–brain axis, and brain networks play a critical role during the process. However, little is known about how brain network topology and structural–functional connectivity (SC–FC) coupling contribute to gut microbiota-related cognition. Fecal samples were collected from 157 healthy young adults, and 16S amplicon sequencing was used to assess gut diversity and enterotypes. Topological properties of brain structural and functional networks were acquired by diffusion tensor imaging (DTI) and resting-state functional magnetic resonance imaging (fMRI data), and SC–FC coupling was further calculated. 3-Back, digit span, and Go/No-Go tasks were employed to assess cognition. Then, we tested for potential associations between gut microbiota, complex brain networks, and cognition. The results showed that gut microbiota could affect the global and regional topological properties of structural networks as well as node properties of functional networks. It is worthy of note that causal mediation analysis further validated that gut microbial diversity and enterotypes indirectly influence cognitive performance by mediating the small-worldness (Gamma and Sigma) of structural networks and some nodal metrics of functional networks (mainly distributed in the cingulate gyri and temporal lobe). Moreover, gut microbes could affect the degree of SC–FC coupling in the inferior occipital gyrus, fusiform gyrus, and medial superior frontal gyrus, which in turn influence cognition. Our findings revealed novel insights, which are essential to provide the foundation for previously unexplored network mechanisms in understanding cognitive impairment, particularly with respect to how brain connectivity participates in the complex crosstalk between gut microbiota and cognition.
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Affiliation(s)
- Shujun Zhang
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Xiaotao Xu
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qian Li
- Department of Radiology, Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Jingyao Chen
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Siyu Liu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Wenming Zhao
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Huanhuan Cai
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
| | - Jiajia Zhu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- *Correspondence: Jiajia Zhu,
| | - Yongqiang Yu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Research Center of Clinical Medical Imaging, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of Radiology, Chaohu Hospital of Anhui Medical University, Hefei, China
- Yongqiang Yu,
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Zhang Y, Zhang Y, Xu W, Hu J, Zhang Z. Possible effects of temperature on bacterial communities in the rhizosphere of rice under different climatic regions. Arch Microbiol 2022; 204:212. [PMID: 35296917 DOI: 10.1007/s00203-022-02812-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/21/2022] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
Global warming is an indisputable fact. However, the effect of warming on the rhizosphere bacterial community of crops is not well understood. Therefore, we carried out pot experiments with three rice (Oryza sativa L.) varieties in black soil across three climatic regions of northeast China to simulate temperature change, and analyzed the response of the rhizosphere bacterial community to different temperatures. Results showed that climate had stronger effects on rhizosphere bacterial communities than rice variety. The rhizosphere bacterial diversity differed significantly among the three climatic regions and positively correlated with the mean daily average temperature (MAveT), mean daily maximum temperature (MMaxT), and mean daily minimum temperature (MMinT), and negatively correlated with the daily temperature range (DTR). Principal co-ordinate analysis revealed that bulk soil bacterial communities maintained a high similarity across the three climatic regions, while rhizosphere bacterial communities notably varied. This change was significantly correlated with MAveT, MMaxT, MMinT, and DTR. Compared with bulk soil, Proteobacteria and Bacteroidetes were enriched in the rhizosphere, while Actinobacteria was depleted. Moreover, these changes were strengthened by increasing the temperature and decreasing DTR. Additionally, correlation analysis revealed that changes in rhizosphere bacterial communities were closely related to the formation of rice yields. Our study revealed that the increasing temperature indirectly reshapes the rhizosphere bacterial community that may promote rice production in areas with lower temperatures.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Yujie Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Wenjie Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, People's Republic of China.
| | - Zujian Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, People's Republic of China.
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture/Key Laboratory of Crop Genetic and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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Yu FM, Jayawardena RS, Thongklang N, Lv ML, Zhu XT, Zhao Q. Morel Production Associated with Soil Nitrogen-Fixing and Nitrifying Microorganisms. J Fungi (Basel) 2022; 8:jof8030299. [PMID: 35330300 PMCID: PMC8950353 DOI: 10.3390/jof8030299] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 02/02/2023] Open
Abstract
True morels (Morchella, Pezizales) cultivated in soil are subject to complex influences from soil microbial communities. To explore the characteristics of soil microbial communities on morel cultivation, and evaluate whether these microbes are related to morel production, we collected 23 soil samples from four counties in Sichuan and Yunnan Provinces, China. Based on ITS and 16S rDNA amplicon sequencing, the alpha diversity analysis indicated that the biodiversity of morel cultivation soil showed a downward trend compared with the bare soil. The results also showed that there were no significant differences in soil microbial communities between OC (bare soil) and OO (after one-year suspension of sowing). This means that, after about one year of stopping sowing, the component and structure of soil that once cultivated morel would be restored. In co-occurrence networks, some noteworthy bacterial microbes involved in nitrogen fixation and nitrification have been identified in soils with high morel yields, such as Arthrobacter, Bradyhizobium, Devosia, Pseudarthrobacter, Pseudolabrys, and Nitrospira. In contrast, in soils with low or no morel yield, some pathogenic fungi accounted for a high proportion, including Gibberella, Microidium, Penicillium, Sarocladium, Streptomyces, and Trichoderma. This study provided valuable information for the isolation and culturing of some beneficial microbes for morel cultivation in further study and, potentially, to harness the power of the microbiome to improve morel production and health.
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Affiliation(s)
- Feng-Ming Yu
- Key Laboratory for Plant Diversity and Biotechnology of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (R.S.J.); (N.T.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Ruvishika Shehali Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (R.S.J.); (N.T.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Naritsada Thongklang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (R.S.J.); (N.T.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Meng-Lan Lv
- School of Chemical Engineering, Guizhou Institute of Technology, Guiyang 550003, China;
| | - Xue-Tai Zhu
- College of Life Science, Northwest Normal University, Lanzhou 730070, China;
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biotechnology of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- School of Chemical Engineering, Guizhou Institute of Technology, Guiyang 550003, China;
- Correspondence:
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Gholizadeh S, Mohammadi SA, Salekdeh GH. Changes in root microbiome during wheat evolution. BMC Microbiol 2022; 22:64. [PMID: 35219318 PMCID: PMC8881823 DOI: 10.1186/s12866-022-02467-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.
Results
In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.
Conclusions
This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.
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Biolcati F, Ferrocino I, Bottero MT, Dalmasso A. The Bacterial and Fungal Microbiota of “Robiola di Roccaverano” Protected Designation of Origin Raw Milk Cheese. Front Microbiol 2022; 12:776862. [PMID: 35173686 PMCID: PMC8841559 DOI: 10.3389/fmicb.2021.776862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Robiola di Roccaverano is an artisanal Protected Designation of Origin (PDO) soft cheese made with raw goat’s milk and by the addition of Natural Milk Culture (NMC) to drive the fermentation process. Cheeses collected from five different dairy plants were analyzed for their bacterial and fungal microbiota diversity. Lactococcus lactis and Leuconostoc mesenteroides were the main bacterial population, while Galactomyces candidum and Kluyveromyces marxianus constituted the core mycobiota but many other minor taxa were observed, suggesting a high level of complexity in fungal composition by these cheeses compared to bacteria population.
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Affiliation(s)
- Federica Biolcati
- Dipartimento di Scienze Veterinarie, Università di Torino, Grugliasco, Italy
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, Italy
- *Correspondence: Federica Biolcati,
| | - Ilario Ferrocino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, Italy
| | | | - Alessandra Dalmasso
- Dipartimento di Scienze Veterinarie, Università di Torino, Grugliasco, Italy
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Comparison of two different kinds of seed sludge and characterization of microorganisms producing hydrogen and soluble metabolites from raw glycerol. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2022. [DOI: 10.1007/s43153-021-00212-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Weeds harbor an impressive diversity of fungi, which offers possibilities for biocontrol. Appl Environ Microbiol 2022; 88:e0217721. [PMID: 35080907 DOI: 10.1128/aem.02177-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The use of herbicides for weed control is very common, but some of them represent a threat to human health, are environmentally detrimental and stimulate herbicide resistance. Therefore, using microorganisms as natural herbicides appears as a promising alternative. The mycoflorae colonizing different species of symptomatic and asymptomatic weeds were compared to characterize the possible mycoherbicidal candidates associated with symptomatic weeds. A collection of 475 symptomatic and asymptomatic plants belonging to 23 weed species was established. A metabarcoding approach based on amplification of the internal transcribed spacer (ITS) region combined with high-throughput amplicon sequencing revealed the diversity of fungal communities hosted by these weeds: 542 fungal genera were identified. The variability of the composition of fungal communities revealed a dispersed distribution of taxa governed neither by geographical location nor by the botanical species, suggesting a common core displaying non-specific interactions with host plants. Beyond this core, specific taxa were more particularly associated with symptomatic plants. Some of these, such as Alternaria, Blumeria, Cercospora, Puccinia, are known pathogens, while others such as Sphaerellopsis, Vishniacozyma and Filobasidium are not, at least on crops, and constitute new tracks to be followed in the search for mycoherbicidal candidates. IMPORTANCE: This approach is original because the diversity of weed-colonizing fungi has rarely been studied before. Furthermore, targeting both the ITS1 and ITS2 regions to characterize the fungal communities i) highlighted the complementarity of these two regions, ii) revealed a great diversity of weed-colonizing fungi, and iii) allowed for the identification of potential mycoherbicides, among which unexpected genera.
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Potapov SA, Tikhonova IV, Krasnopeev AY, Suslova MY, Zhuchenko NA, Drucker VV, Belykh OI. Communities of T4-like bacteriophages associated with bacteria in Lake Baikal: diversity and biogeography. PeerJ 2022. [DOI: 10.7717/peerj.12748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lake Baikal phage communities are important for lake ecosystem functioning. Here we describe the diversity of T4-bacteriophage associated with the bacterial fraction of filtered water samples collected from the pelagic zone, coastal zone and shallow bays. Although the study of the diversity of phages for the g23 gene has been carried out at Lake Baikal for more than ten years, shallow bays that comprise a significant part of the lake’s area have been neglected, and this gene has not previously been studied in the bacterial fraction. Phage communities were probed using amplicon sequencing methods targeting the gene of major capsid protein (g23) and compared phylogenetically across sample locations and with sequences previously retrieved from non-bacterial fractions (<0.2 um) and biofilms (non-fractionated). In this study, we examined six water samples, in which 24 to 74 viral OTUs were obtained. The sequences from shallow bays largely differed from those in the pelagic and coastal samples and formed individual subcluster in the UPGMA tree that was obtained from the comparison of phylogenetic distances of g23 sequence sets from various ecosystems, reflecting differences in viral communities depending on the productivity of various sites of Lake Baikal. According to the RefSeq database, from 58.3 to 73% of sequences of each sample had cultivated closest relatives belonging to cyanophages. In this study, for phylogenetic analysis, we chose the closest relatives not only from the RefSeq and GenBank NR databases but also from two marine and one freshwater viromes: eutrophic Osaka Bay (Japan), oligotrophic area of the Pacific Ocean (Station ALOHA) and mesotrophic and ancient Lake Biwa (Japan), which allowed us to more fully compare the diversity of marine and freshwater phages. The identity with marine sequences at the amino acid level ranged from 35 to 80%, and with the sequences from the viral fraction and bacterial one from Lake Biwa—from 35.3 to 98% and from 33.9 to 89.1%, respectively. Therefore, the sequences from marine viromes had a greater difference than those from freshwater viromes, which may indicate a close relationship between freshwater viruses and differences from marine viruses.
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Affiliation(s)
| | | | | | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | | | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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Huang L, Liu B, Liu Z, Feng W, Liu M, Wang Y, Peng D, Fu X, Zhu H, Cui Z, Xie L, Ma Y. Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis. Front Cell Infect Microbiol 2021; 11:788836. [PMID: 34950610 PMCID: PMC8688745 DOI: 10.3389/fcimb.2021.788836] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022] Open
Abstract
The diagnosis of endometriosis is typically delayed by years for the unexclusive symptom and the traumatic diagnostic method. Several studies have demonstrated that gut microbiota and cervical mucus potentially can be used as auxiliary diagnostic biomarkers. However, none of the previous studies has compared the robustness of endometriosis classifiers based on microbiota of different body sites or demonstrated the correlation among microbiota of gut, cervical mucus, and peritoneal fluid of endometriosis, searching for alternative diagnostic approaches. Herein, we enrolled 41 women (control, n = 20; endometriosis, n = 21) and collected 122 well-matched samples, derived from feces, cervical mucus, and peritoneal fluid, to explore the nature of microbiome of endometriosis patients. Our results indicated that microbial composition is remarkably distinguished between three body sites, with 19 overlapped taxa. Moreover, endometriosis patients harbor distinct microbial communities versus control group especially in feces and peritoneal fluid, with increased abundance of pathogens in peritoneal fluid and depletion of protective microbes in feces. Particularly, genera of Ruminococcus and Pseudomonas were identified as potential biomarkers in gut and peritoneal fluid, respectively. Furthermore, novel endometriosis classifiers were constructed based on taxa selected by a robust machine learning method. These results demonstrated that gut microbiota exceeds cervical microbiota in diagnosing endometriosis. Collectively, this study reveals important insights into the microbial profiling in different body sites of endometriosis, which warrant future exploration into the role of microbiota in endometriosis and highlighted values on gut microbiota in early diagnosis of endometriosis.
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Affiliation(s)
- Liujing Huang
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Bingdong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhihong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wanqin Feng
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Minjuan Liu
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yifeng Wang
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Dongxian Peng
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiafei Fu
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Honglei Zhu
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zongbin Cui
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liwei Xie
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,College of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Ying Ma
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Understanding host-microbiota interactions in the commercial piglet around weaning. Sci Rep 2021; 11:23488. [PMID: 34873196 PMCID: PMC8648723 DOI: 10.1038/s41598-021-02754-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Weaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencing, the OpenArray gene expression technology and 1H-NMR spectroscopy. Fourteen piglets from different litters were sampled for blood, jejunum tissue and caecal content two days before (− 2d), and three days after (+ 3d) weaning. A clearly differential ordination of caecal microbiota was observed. Higher abundances of Roseburia, Ruminococcus, Coprococcus, Dorea and Lachnospira genera in weaned piglets compared to prior to weaning showed the quick microbial changes of the piglets’ gut microbiota. Downregulation of OCLN, CLDN4, MUC2, MUC13, SLC15A1 and SLC13A1 genes, also evidenced the negative impact of weaning on gut barrier and digestive functions. Metabolomic approach pinpointed significant decreases in choline, LDL, triglycerides, fatty acids, alanine and isoleucine and increases in 3-hydroxybutyrate after weaning. Moreover, the correlation between microbiota and metabolome datasets revealed the existence of metabolic clusters interrelated to different bacterial clusters. Our results demonstrate the impact of weaning stress on the piglet and give insights regarding the associations between gut microbiota and the animal gene activity and metabolic response.
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43
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Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 2021; 9:e12458. [PMID: 34820189 PMCID: PMC8601059 DOI: 10.7717/peerj.12458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
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Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tasmania, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Leonie Suter
- Australian Antarctic Division, Kingston, Tasmania, Australia
| | - Bruce E Deagle
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, Australia
| | | | - Aleks Terauds
- Australian Antarctic Division, Kingston, Tasmania, Australia
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44
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Deng D, Su H, Song Y, Chen T, Sun Q, Jiang H, Zhao M. Altered Fecal Microbiota Correlated With Systemic Inflammation in Male Subjects With Methamphetamine Use Disorder. Front Cell Infect Microbiol 2021; 11:783917. [PMID: 34869080 PMCID: PMC8637621 DOI: 10.3389/fcimb.2021.783917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Abstract
Methamphetamine use disorder (MUD) is a major public health problem worldwide with limited effective treatment options. Previous studies have reported methamphetamine-associated alterations in gut microbiota. A potential role of gut microbiota in regulating methamphetamine-induced brain dysfunction through interactions with the host immune system has been proposed, but evidence for this hypothesis is limited. The present study aimed to investigate the alterations in the fecal microbiota and explore its relationship with systemic inflammation in MUD. Fecal samples were obtained from 26 male subjects with MUD and 17 sex- and age- matched healthy controls. Fecal microbial profiles were analyzed by 16S rRNA sequencing. Plasma inflammatory markers were measured using enzyme-linked immunosorbent assay. Associations between fecal microbiota, systemic inflammatory markers and clinical characteristics were examined by Spearman partial correlation analysis while controlling for possible confounders. Compared with healthy controls, individuals with MUD showed no difference in fecal microbial diversity, but exhibited differences in the relative abundance of several microbial taxa. At the genus level, a higher abundance of Collinsella, Odoribacter and Megasphaera and lower levels of Faecalibacterium, Blautia, Dorea and Streptococcus were detected in subjects with MUD. More importantly, altered fecal microbiota was found to be correlated with plasma levels of CRP, IL-2, IL-6 and IL-10. The order Lactobacillales, exhibiting lower abundance in participants with MUD, was positively related to the duration of methamphetamine abstinence and the plasma level of anti-inflammatory cytokine IL-10. This study is the first to provide evidence for a link between altered fecal microbiota and systemic inflammation in MUD. Further elucidation of interactions between gut microbiota and the host immune system may be beneficial for the development of novel therapeutic approaches for MUD.
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Affiliation(s)
- Di Deng
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hang Su
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuehong Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianzhen Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianqian Sun
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haifeng Jiang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Zhao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, China
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45
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Methanogen Abundance Thresholds Capable of Differentiating In Vitro Methane Production in Human Stool Samples. Dig Dis Sci 2021; 66:3822-3830. [PMID: 33247793 DOI: 10.1007/s10620-020-06721-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/15/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Intestinal methane (CH4) gas production has been associated with a number of clinical conditions and may have important metabolic and physiological effects. AIMS In this study, taxonomic and functional gene analyses and in vitro CH4 gas measurements were used to determine if molecular markers can potentially serve as clinical tests for colonic CH4 production. METHODS We performed a cross-sectional study involving full stool samples collected from 33 healthy individuals. In vitro CH4 gas measurements were obtained after 2-h incubation of stool samples and used to characterize samples as CH4 positive (CH4+) and CH4 negative (CH4-; n = 10 and 23, respectively). Next, we characterized the fecal microbiota through high-throughput DNA sequencing with a particular emphasis on archaeal phylum Euryarchaeota. Finally, qPCR analyses, targeting the mcrA gene, were done to determine the ability to differentiate CH4+ versus CH4- samples and to delineate major methanogen species associated with CH4 production. RESULTS Methanobrevibacter was found to be the most abundant methane producer and its relative abundance provides a clear distinction between CH4+ versus CH4- samples. Its sequencing-based relative abundance detection threshold for CH4 production was calculated to be 0.097%. The qPCR-based detection threshold separating CH4+ versus CH4- samples, based on mcrA gene copies, was 5.2 × 105 copies/g. CONCLUSION Given the decreased time-burden placed on patients, a qPCR-based test on a fecal sample can become a valuable tool in clinical assessment of CH4 producing status.
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46
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Fontsere C, Frandsen P, Hernandez-Rodriguez J, Niemann J, Scharff-Olsen CH, Vallet D, Le Gouar P, Ménard N, Navarro A, Siegismund HR, Hvilsom C, Gilbert MTP, Kuhlwilm M, Hughes D, Marques-Bonet T. The genetic impact of an Ebola outbreak on a wild gorilla population. BMC Genomics 2021; 22:735. [PMID: 34635054 PMCID: PMC8504571 DOI: 10.1186/s12864-021-08025-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population. Results Associations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival. Conclusion This study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08025-y.
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Affiliation(s)
- Claudia Fontsere
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.
| | - Peter Frandsen
- Research and Conservation, Copenhagen Zoo, 2000, Frederiksberg, Denmark.,Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.,Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Jonas Niemann
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| | | | - Dominique Vallet
- UMR 6553, ECOBIO: Ecosystems, Biodiversity, Evolution, CNRS/University of Rennes 1, Station Biologique de Paimpont, 35380, Paimpont, France
| | - Pascaline Le Gouar
- UMR 6553, ECOBIO: Ecosystems, Biodiversity, Evolution, CNRS/University of Rennes 1, Station Biologique de Paimpont, 35380, Paimpont, France
| | - Nelly Ménard
- UMR 6553, ECOBIO: Ecosystems, Biodiversity, Evolution, CNRS/University of Rennes 1, Station Biologique de Paimpont, 35380, Paimpont, France
| | - Arcadi Navarro
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA, 08010, Barcelona, Catalonia, Spain.,CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036, Barcelona, Spain.,BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005, Barcelona, Spain
| | - Hans R Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Christina Hvilsom
- Research and Conservation, Copenhagen Zoo, 2000, Frederiksberg, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain. .,Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - David Hughes
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA, 08010, Barcelona, Catalonia, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain. .,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain.
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Din GMU, Du Z, Zhang H, Zhao S, Liu T, Chen W, Gao L. Effects of Tilletia foetida on Microbial Communities in the Rhizosphere Soil of Wheat Seeds Coated with Different Concentrations of Jianzhuang. MICROBIAL ECOLOGY 2021; 82:736-745. [PMID: 33527233 PMCID: PMC8463399 DOI: 10.1007/s00248-021-01696-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/17/2021] [Indexed: 05/03/2023]
Abstract
Tilletia foetida (syn. T. laevis) leads to wheat common bunt, a worldwide disease that can lead to 80% yield loss and even total loss of production, together with degrading the quality of grains and flour by producing a rotten fish smell. To explore the potential microbial community that may contribute to the control of soil- and seed-borne pathogens, in this study, we analyzed the effects of the plant pathogenic fungus T. foetida on rhizosphere soil microorganisms in wheat seeds coated with different concentrations of a fungicide (Jianzhuang) used to control the disease. To analyze the bacterial and fungal abundance in T. foetida-infected and mock-infected plants, the microorganisms were sequenced using high-throughput HiSeq 2500 gene sequencing. The results showed that bacterial communities, including Verrucomicrobia, Patescibacteria, Armatimonadetes, Nitrospirae, Fibrobacteres, Chlamydiae, and Hydrogenedentes, and fungal communities, including Basidiomycota and Ciliophora, were more prevalent in the mock group than in the T. foetida-infected group, which may contribute to the control of wheat common bunt. Moreover, cluster and PCoA analysis revealed that replicates of the same samples were clustered together, and these results were also found in the distance index within-group analysis for bacterial and fungal communities in the T. foetida-infected and mock groups.
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Affiliation(s)
- Ghulam Muhae Ud Din
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhenzhen Du
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Han Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory at Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Shihezi University, Xinjiang, 832003, China
| | - Sifeng Zhao
- Key Laboratory at Universities of Xinjiang Uygur Autonomous Region for Oasis Agricultural Pest Management and Plant Protection Resource Utilization, Shihezi University, Xinjiang, 832003, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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48
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Wang J, Mason CJ, Ju X, Xue R, Tong L, Peiffer M, Song Y, Zeng R, Felton GW. Parasitoid Causes Cascading Effects on Plant-Induced Defenses Mediated Through the Gut Bacteria of Host Caterpillars. Front Microbiol 2021; 12:708990. [PMID: 34552570 PMCID: PMC8452159 DOI: 10.3389/fmicb.2021.708990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Koinobiont endoparasitoid wasps whose larvae develop inside a host insect alter several important facets of host physiology, potentially causing cascading effects across multiple trophic levels. For instance, the hijacking of the host immune responses may have effects on how insects interact with host plants and microbial associates. However, the parasitoid regulation of insect-plant-microbiome interactions is still understudied. In this study, we used the fall armyworm (FAW), Spodoptera frugiperda, and the braconid parasitoid Cotesia marginiventris to evaluate impacts of parasitism on the gut microbiome of FAW larvae, and respective maize plant defense responses. The level of reactive oxygen species and the microbial community in larval gut underwent significant changes in response to parasitism, leading to a significant reduction of Enterococcus, while elevating the relative abundance of Pseudomonas. FAW with parasitism had lower glucose oxidase (GOX) activity in salivary glands and triggered lower defense responses in maize plants. These changes corresponded to effects on plants, as Pseudomonas inoculated larvae had lower activity of salivary GOX and triggered lower defense responses in maize plants. Our results demonstrated that parasitism had cascading effects on microbial associates across trophic levels and also highlighted that insect gut bacteria may contribute to complex interrelationships among parasitoids, herbivores, and plants.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Charles J. Mason
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Xueyang Ju
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rongrong Xue
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lu Tong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Michelle Peiffer
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gary W. Felton
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
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Daskova N, Heczkova M, Modos I, Videnska P, Splichalova P, Pelantova H, Kuzma M, Gojda J, Cahova M. Determination of Butyrate Synthesis Capacity in Gut Microbiota: Quantification of but Gene Abundance by qPCR in Fecal Samples. Biomolecules 2021; 11:1303. [PMID: 34572516 PMCID: PMC8469203 DOI: 10.3390/biom11091303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
Butyrate is formed in the gut during bacterial fermentation of dietary fiber and is attributed numerous beneficial effects on the host metabolism. We aimed to develop a method for the assessment of functional capacity of gut microbiota butyrate synthesis based on the qPCR quantification of bacterial gene coding butyryl-CoA:acetate CoA-transferase, the key enzyme of butyrate synthesis. In silico, we identified bacteria possessing but gene among human gut microbiota by searching but coding sequences in available databases. We designed and validated six sets of degenerate primers covering all selected bacteria, based on their phylogenetic nearness and sequence similarity, and developed a method for gene abundance normalization in human fecal DNA. We determined but gene abundance in fecal DNA of subjects with opposing dietary patterns and metabolic phenotypes-lean vegans (VG) and healthy obese omnivores (OB) with known fecal microbiota and metabolome composition. We found higher but gene copy number in VG compared with OB, in line with higher fecal butyrate content in VG group. We further found a positive correlation between the relative abundance of target bacterial genera identified by next-generation sequencing and groups of but gene-containing bacteria determined by specific primers. In conclusion, this approach represents a simple and feasible tool for estimation of microbial functional capacity.
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Affiliation(s)
- Nikola Daskova
- Institute for Clinical and Experimental Medicine, Videnska 1958, 140 21 Prague 4, Czech Republic; (M.H.); (I.M.); (M.C.)
- First Faculty of Medicine, Charles University, Katerinska 1660/32, 121 08 Prague, Czech Republic
| | - Marie Heczkova
- Institute for Clinical and Experimental Medicine, Videnska 1958, 140 21 Prague 4, Czech Republic; (M.H.); (I.M.); (M.C.)
| | - Istvan Modos
- Institute for Clinical and Experimental Medicine, Videnska 1958, 140 21 Prague 4, Czech Republic; (M.H.); (I.M.); (M.C.)
| | - Petra Videnska
- RECETOX, Faculty of Science Masaryk University, Kamenice 753, 625 00 Brno, Czech Republic; (P.V.); (P.S.)
| | - Petra Splichalova
- RECETOX, Faculty of Science Masaryk University, Kamenice 753, 625 00 Brno, Czech Republic; (P.V.); (P.S.)
| | - Helena Pelantova
- Institute of Microbiology, AS CR, Videnska 1083, 142 20 Prague 4, Czech Republic; (H.P.); (M.K.)
| | - Marek Kuzma
- Institute of Microbiology, AS CR, Videnska 1083, 142 20 Prague 4, Czech Republic; (H.P.); (M.K.)
- Department of Analytical Chemistry, Faculty of Science, Palacky University Olomouc, 17. Listopadu 1192/12, 779 00 Olomouc, Czech Republic
| | - Jan Gojda
- Department of Internal Medicine, Kralovske Vinohrady University Hospital and Third Faculty of Medicine, Charles University, Srobarova 1150, 100 34 Prague 10, Czech Republic;
| | - Monika Cahova
- Institute for Clinical and Experimental Medicine, Videnska 1958, 140 21 Prague 4, Czech Republic; (M.H.); (I.M.); (M.C.)
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Aires T, Stuij TM, Muyzer G, Serrão EA, Engelen AH. Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms. Front Microbiol 2021; 12:653998. [PMID: 34434172 PMCID: PMC8381869 DOI: 10.3389/fmicb.2021.653998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022] Open
Abstract
Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.
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Affiliation(s)
- Tania Aires
- Centro de Ciências do Mar (CCMAR), Centro de Investigação Marinha e Ambiental (CIMAR), Universidade do Algarve, Faro, Portugal
| | - Tamara M Stuij
- Centro de Ciências do Mar (CCMAR), Centro de Investigação Marinha e Ambiental (CIMAR), Universidade do Algarve, Faro, Portugal.,CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ester A Serrão
- Centro de Ciências do Mar (CCMAR), Centro de Investigação Marinha e Ambiental (CIMAR), Universidade do Algarve, Faro, Portugal
| | - Aschwin H Engelen
- Centro de Ciências do Mar (CCMAR), Centro de Investigação Marinha e Ambiental (CIMAR), Universidade do Algarve, Faro, Portugal.,CARMABI Foundation, Willemstad, Curaçao
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