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Jiang Z, Chen X, Xue H, Li Z, Lei J, Yu M, Yan X, Cao H, Zhou J, Liu J, Zheng M, Dong W, Li Y, Cui Z. Novel polyurethane-degrading cutinase BaCut1 from Blastobotrys sp. G-9 with potential role in plastic bio-recycling. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134493. [PMID: 38696960 DOI: 10.1016/j.jhazmat.2024.134493] [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: 02/20/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
Environmental pollution caused by plastic waste has become global problem that needs to be considered urgently. In the pursuit of a circular plastic economy, biodegradation provides an attractive strategy for managing plastic wastes, whereas effective plastic-degrading microbes and enzymes are required. In this study, we report that Blastobotrys sp. G-9 isolated from discarded plastic in landfills is capable of depolymerizing polyurethanes (PU) and poly (butylene adipate-co-terephthalate) (PBAT). Strain G-9 degrades up to 60% of PU foam after 21 days of incubation at 28 ℃ by breaking down carbonyl groups via secretory hydrolase as confirmed by structural characterization of plastics and degradation products identification. Within the supernatant of strain G-9, we identify a novel cutinase BaCut1, belonging to the esterase family, that can reproduce the same effect. BaCut1 demonstrates efficient degradation toward commercial polyester plastics PU foam (0.5 mg enzyme/25 mg plastic) and agricultural film PBAT (0.5 mg enzyme/10 mg plastic) with 50% and 18% weight loss at 37 ℃ for 48 h, respectively. BaCut1 hydrolyzes PU into adipic acid as a major end-product with 42.9% recovery via ester bond cleavage, and visible biodegradation is also identified from PBAT, which is a beneficial feature for future recycling economy. Molecular docking, along with products distribution, elucidates a special substrate-binding modes of BaCut1 with plastic substrate analogue. BaCut1-mediated polyester plastic degradation offers an alternative approach for managing PU plastic wastes through possible bio-recycling.
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Affiliation(s)
- Zhitong Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xue Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huizhen Xue
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, PR China.
| | - Jinhui Lei
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Muming Yu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jie Zhou
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jiawei Liu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Weiliang Dong
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, PR China; Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, PR China
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Khatri-Chhetri U, Banerjee S, Thompson KA, Quideau SA, Boyce MS, Bork EW, Carlyle CN. Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169353. [PMID: 38104847 DOI: 10.1016/j.scitotenv.2023.169353] [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: 01/18/2023] [Revised: 05/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.
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Affiliation(s)
- Upama Khatri-Chhetri
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Karen A Thompson
- Trent School of Environment, Trent University, Peterborough, ON K9L 0G2, Canada
| | - Sylvie A Quideau
- Department of Renewable Resources, Earth Science Building University of Alberta, Edmonton, AB T6G 2E3, Canada
| | - Mark S Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Edward W Bork
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Cameron N Carlyle
- Department of Agricultural, Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Lv H, Li X, He D, Chen X, Liu M, Lan Y, Zhao J, Wang H, Yan Z. Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza. MICROBIAL ECOLOGY 2023; 86:2934-2948. [PMID: 37667132 DOI: 10.1007/s00248-023-02295-7] [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: 05/07/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.
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Affiliation(s)
- Hongyang Lv
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyu Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongmei He
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Chen
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Liu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yin Lan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jin Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Chengdu, China.
- Institute of Chinese Medical Sciences, University of Macau, Taipa, China.
| | - Hai Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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Luláková P, Šantrůčková H, Elster J, Hanáček M, Kotas P, Meador T, Tejnecký V, Bárta J. Mineral substrate quality determines the initial soil microbial development in front of the Nordenskiöldbreen, Svalbard. FEMS Microbiol Ecol 2023; 99:fiad104. [PMID: 37660279 PMCID: PMC10689212 DOI: 10.1093/femsec/fiad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/03/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023] Open
Abstract
Substrate geochemistry is an important factor influencing early microbial development after glacial retreat on nutrient-poor geological substrates in the High Arctic. It is often difficult to separate substrate influence from climate because study locations are distant. Our study in the retreating Nordenskiöldbreen (Svalbard) is one of the few to investigate biogeochemical and microbial succession in two adjacent forefields, which share the same climatic conditions but differ in their underlying geology. The northern silicate forefield evolved in a classical chronosequence, where most geochemical and microbial parameters increased gradually with time. In contrast, the southern carbonate forefield exhibited high levels of nutrients and microbial biomass at the youngest sites, followed by a significant decline and then a gradual increase, which caused a rearrangement in the species and functional composition of the bacterial and fungal communities. This shuffling in the early stages of succession suggests that high nutrient availability in the bedrock could have accelerated early soil succession after deglaciation and thereby promoted more rapid stabilization of the soil and production of higher quality organic matter. Most chemical parameters and bacterial taxa converged with time, while fungi showed no clear pattern.
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Affiliation(s)
- Petra Luláková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31a, 37005 České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31a, 37005 České Budějovice, Czech Republic
| | - Josef Elster
- Institute of Botany ASCR, Dukelská 135, Třeboň, Czech Republic
- Centre for Polar Ecology, Faculty of Science, University of South Bohemia, Na Zlaté Stoce 3, 37005 České Budějovice, Czech Republic
| | - Martin Hanáček
- Polar-Geo-Lab, Department of Geography, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
- Centre for Polar Ecology, Faculty of Science, University of South Bohemia, Na Zlaté Stoce 3, 37005 České Budějovice, Czech Republic
| | - Petr Kotas
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31a, 37005 České Budějovice, Czech Republic
| | - Travis Meador
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31a, 37005 České Budějovice, Czech Republic
- Institute of Soil Biology and Biogeochemistry, Biology Centre Czech Academy of Sciences, Na Sádkách 702/2, 37005 České Budějovice, Czech Republic
| | - Václav Tejnecký
- Department of Soil Science and Soil Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Kamýcká 129, Prague, Czech Republic
| | - Jiří Bárta
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31a, 37005 České Budějovice, Czech Republic
- Centre for Polar Ecology, Faculty of Science, University of South Bohemia, Na Zlaté Stoce 3, 37005 České Budějovice, Czech Republic
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Li G, Zhu S, Long J, Mao H, Dong Y, Hou Y. Differences in microbial community structure and metabolic activity among tea plantation soils under different management strategies. Front Microbiol 2023; 14:1219491. [PMID: 37601365 PMCID: PMC10433390 DOI: 10.3389/fmicb.2023.1219491] [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: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Microorganisms play an important role in the multifunctionality of soil ecosystems. Soil microbial diversity and functions have a great impact on plant growth and development. The interactions between tea trees and soil microbiota can be linked with planting patterns and management strategies, whose effects on soil microbial community structure and metabolites are still unclear. Methods Here we used amplicon sequencing and metabolomic analysis to investigate the differences in soil microbial composition and metabolites among three tea production systems: organic, non-organic, and intercropping. Results We detected significant differences among the three systems and found that Firmicutes, Proteobacteria, Acidobacteriota, Actinobacteriota and Chloroflexi were the main bacteria in the three soil groups, although they varied in relative abundance. Acidobacteria bacterium increased significantly in the organic and intercropping groups. For fungi, Ascomycota and Basidiomycota were the main differential fungal phyla. Fungi alpha-diversity in the non-organic group was significantly higher than that in the other two groups, and was correlated with multiple soil physical and chemical factors. Moreover, network analysis showed that bacteria and fungi were strongly correlated. The changes in soil microorganisms caused by management and planting patterns may affect soil quality through corresponding changes in metabolites. Metabolomic analysis showed differences in metabolite composition among different groups. It was also found that the arachidonic acid metabolic pathway was affected by changes in soil microorganisms, and may further affect soil quality in an essential manner. Discussion Planting patterns and management strategies may significantly affect soil microorganisms and therefore metabolites. Changes in soil microorganisms, especially in fungi, may alter soil quality by affecting soil physicochemical properties and metabolites. This study will provide new insights into soil quality monitoring from a microbiological perspective.
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Affiliation(s)
- Guoyou Li
- College of Tea Science, Yunnan Agriculture University, Kunming, China
| | - Shaoxian Zhu
- College of Tea Science, Yunnan Agriculture University, Kunming, China
| | - Jiang Long
- Xishuangbanna Luoboshanren Tea Co., Ltd., Menghai, China
| | - Honglin Mao
- College of Tea Science, Yunnan Agriculture University, Kunming, China
| | - Yonghong Dong
- Yunnan Pulis Biotechnology Co., Ltd., Kunming, China
| | - Yan Hou
- College of Tea Science, Yunnan Agriculture University, Kunming, China
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Liu Z, Peng T, Ma S, Qi C, Song Y, Zhang C, Li K, Gao N, Pu M, Wang X, Bi Y, Na X. Potential benefits and risks of solar photovoltaic power plants on arid and semi-arid ecosystems: an assessment of soil microbial and plant communities. Front Microbiol 2023; 14:1190650. [PMID: 37588884 PMCID: PMC10427150 DOI: 10.3389/fmicb.2023.1190650] [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: 03/21/2023] [Accepted: 07/07/2023] [Indexed: 08/18/2023] Open
Abstract
Exponential increase in photovoltaic installations arouses concerns regarding the impacts of large-scale solar power plants on dryland ecosystems. While the effects of photovoltaic panels on soil moisture content and plant biomass in arid ecosystems have been recognized, little is known about their influence on soil microbial communities. Here, we employed a combination of quantitative PCR, high-throughput sequencing, and soil property analysis to investigate the responses of soil microbial communities to solar panel installation. We also report on the responses of plant communities within the same solar farm. Our findings showed that soil microbial communities responded differently to the shading and precipitation-alternation effects of the photovoltaic panels in an arid ecosystem. By redirecting rainwater to the lower side, photovoltaic panels stimulated vegetation biomass and soil total organic carbon content in the middle and in front of the panels, positively contributing to carbon storage. The shade provided by the panels promoted the co-occurrence of soil microbes but inhibited the abundance of 16S rRNA gene in the soil. Increase in precipitation reduced 18S rRNA gene abundance, whereas decrease in precipitation led to decline in plant aboveground biomass, soil prokaryotic community alpha diversity, and dehydrogenase activity under the panels. These findings highlight the crucial role of precipitation in maintaining plant and soil microbial diversities in dryland ecosystems and are essential for estimating the potential risks of large-scale solar power plants on local and global climate change in the long term.
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Affiliation(s)
- Ziyu Liu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tong Peng
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shaolan Ma
- No. 1 Middle School of Penyang, Guyuan, China
| | - Chang Qi
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yanfang Song
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Chuanji Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Kaile Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Na Gao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Meiyun Pu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaomin Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yurong Bi
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaofan Na
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
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Song L, Wang J, Zhang R, Pan J, Li Y, Wang S, Niu S. Threshold responses of soil gross nitrogen transformation rates to aridity gradient. GLOBAL CHANGE BIOLOGY 2023; 29:4018-4027. [PMID: 37103000 DOI: 10.1111/gcb.16737] [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: 02/20/2023] [Accepted: 03/17/2023] [Indexed: 05/06/2023]
Abstract
The responses of soil nitrogen (N) transformations to climate change are crucial for biome productivity prediction under global change. However, little is known about the responses of soil gross N transformation rates to drought gradient. Along an aridity gradient across the 2700 km transect of drylands on the Qinghai-Tibetan Plateau, this study measured three main soil gross N transformation rates in both topsoil (0-10 cm) and subsoil (20-30 cm) using the laboratorial 15 N labeling. The relevant soil abiotic and biotic variables were also determined. The results showed that gross N mineralization and nitrification rates steeply decreased with increasing aridity when aridity was less than 0.5 but just slightly decreased with increasing aridity when aridity was larger than 0.5 at both soil layers. In topsoil, the decreases of the two gross rates were accompanied by the similar decreased patterns of soil total N content and microbial biomass carbon with increasing aridity (p < .05). In subsoil, although the decreased pattern of soil total N with increasing aridity was still similar to the decreases of the two gross rates (p < .05), microbial biomass carbon did not change (p > .05). Instead, bacteria and ammonia oxidizing archaea abundances decreased with increasing aridity when aridity was larger than 0.5 (p < .05). With an aridity threshold of 0.6, gross N immobilization rate increased with increasing aridity in wetter region (aridity < 0.6) accompanied with an increased bacteria/fungi ratio, but decreased with increasing aridity in drier region (aridity > 0.6) where mineral N and microbial biomass N also decreased at both soil layers (p < .05). This study provided new insight to understand the differential responses of soil N transformation to drought gradient. The threshold responses of the gross N transformation rates to aridity gradient should be noted in biogeochemical models to better predict N cycling and manage land in the context of global change.
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Affiliation(s)
- Lei Song
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Jinsong Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Ruiyang Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Junxiao Pan
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yang Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
| | - Song Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, P.R. China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, P.R. China
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Bou Orm E, Sauvagère S, Rocher J, Benezet JC, Bayle S, Siatka C, Bergeret A, Malhautier L. Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12582-5. [PMID: 37227475 DOI: 10.1007/s00253-023-12582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.
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Affiliation(s)
- Eliane Bou Orm
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Stéphane Sauvagère
- École de l'ADN, Université de Nîmes, 19 Grand Rue BP 81295, 30015, Nîmes cedex 1, France
| | - Janick Rocher
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Jean-Charles Benezet
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Sandrine Bayle
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Christian Siatka
- UPR CHROME, Université de Nîmes, Place Gabriel Péri, 30000, Nîmes cedex 1, France
| | - Anne Bergeret
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Luc Malhautier
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France.
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Andreo-Jimenez B, Te Beest DE, Kruijer W, Vannier N, Kadam NN, Melandri G, Jagadish SVK, van der Linden G, Ruyter-Spira C, Vandenkoornhuyse P, Bouwmeester HJ. Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance. RICE (NEW YORK, N.Y.) 2023; 16:26. [PMID: 37212977 DOI: 10.1186/s12284-023-00641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Dennis E Te Beest
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Niteen N Kadam
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- School of Plant Sciences, University of Arizona, Tucson, USA
| | - S V Krishna Jagadish
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Kansas State University, Manhattan, KS, 66506, USA
| | | | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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10
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Masigol H, Grossart HP, Taheri SR, Mostowfizadeh-Ghalamfarsa R, Pourmoghaddam MJ, Bouket AC, Khodaparast SA. Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy. Microorganisms 2023; 11:microorganisms11030782. [PMID: 36985355 PMCID: PMC10052706 DOI: 10.3390/microorganisms11030782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/22/2023] Open
Abstract
Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.
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Affiliation(s)
- Hossein Masigol
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (S.R.T.)
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran; (M.J.P.); (S.A.K.)
| | - Hans-Peter Grossart
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (S.R.T.)
- Institute for Biochemistry and Biology, Potsdam University, 14469 Potsdam, Germany
- Correspondence: ; Tel.: +49-(0)-3308269991
| | - Seyedeh Roksana Taheri
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (S.R.T.)
| | | | - Mohammad Javad Pourmoghaddam
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran; (M.J.P.); (S.A.K.)
| | - Ali Chenari Bouket
- East Azarbaijan Agricultural and Natural Resources Research and Education Centre, Plant Protection Research Department, Agricultural Research, Education and Extension Organization (AREEO), Tabriz 5355179854, Iran;
| | - Seyed Akbar Khodaparast
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran; (M.J.P.); (S.A.K.)
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11
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Arreguin-Perez CA, Miranda-Miranda E, Folch-Mallol J, Ferrara-Tijera E, Cossio-Bayugar R. Complete genome sequence dataset of enthomopathogenic Aspergillus flavus isolated from a natural infection of the cattle-tick Rhipicephalus microplus. Data Brief 2023; 48:109053. [PMID: 37006402 PMCID: PMC10051017 DOI: 10.1016/j.dib.2023.109053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
As the most important bovine ectoparasite, the southern cattle tick Rhipicephalus microplus transmits lethal cattle diseases such as babesiosis and anaplasmosis, costing the global livestock industry billions of dollars annually. To control cattle ticks, preventive treatment of cattle with pesticides is a common practice; however, after decades of chemical treatment, pesticide resistance has arisen in cattle ticks, rendering most formulations ineffective over time. Facing the perspective of running out of effective chemical treatments against R. microplus, research on biocontrol alternatives is necessary. Acaro-pathogenic microorganisms isolated from different developmental stages of R. microplus offer potential as biocontrol agents. Aspergillus flavus strain INIFAP-2021, isolated from naturally infected cattle ticks, produced high levels of mobility and mortality in the tick population during experimental infections. The whole genome of the fungi was sequenced using the DNBSEQ platform by BGI. The genome was assembled using SOAPaligner, and A. flavus NRRL3357 was used as the reference genome; the complete genome contained eight pairs of chromosomes and 36.9 Mb with a GC content of 48.03%, exhibiting 11482 protein-coding genes. The final genome assembly was deposited at GenBank as a bio project under accession number PRJNA758689, and supplementary material is accessible through Mendeley DOI: 10.17632/mt8yxch6mz.1.
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Affiliation(s)
- Cesar A. Arreguin-Perez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad del INIFAP. Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
- Centro de Investigaciones en Biotecnología de la Universidad Autónoma del Estado de Morelos Campus Cuernavaca, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Apartado Postal 510–3, Cuernavaca, Morelos 62210, Mexico
| | - Estefan Miranda-Miranda
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad del INIFAP. Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
| | - Jorge Folch-Mallol
- Centro de Investigaciones en Biotecnología de la Universidad Autónoma del Estado de Morelos Campus Cuernavaca, Universidad Nacional Autónoma de México, Avenida Universidad, 2001, Apartado Postal 510–3, Cuernavaca, Morelos 62210, Mexico
| | - Eduardo Ferrara-Tijera
- Servicio Nacional de Sanidad, Inocuidad y Calidad, Secretaria de Agricultura y Desarrollo Rural (SADER). Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
| | - Raquel Cossio-Bayugar
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad del INIFAP. Boulevard Cuauhnahuac No. 8534, Jiutepec, Morelos 62574, Mexico
- Corresponding author.
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12
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Cook MA, Pallant D, Ejim L, Sutherland AD, Wang X, Johnson JW, McCusker S, Chen X, George M, Chou S, Koteva K, Wang W, Hobson C, Hackenberger D, Waglechner N, Ejim O, Campbell T, Medina R, MacNeil LT, Wright GD. Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory. J Ind Microbiol Biotechnol 2023; 50:kuad042. [PMID: 38052426 PMCID: PMC10724011 DOI: 10.1093/jimb/kuad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
Microbial natural products are specialized metabolites that are sources of many bioactive compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of biology. The assembly of libraries of producers of natural products has traditionally been the province of the pharmaceutical industry. This sector has gathered significant historical collections of bacteria and fungi to identify new drug leads with outstanding outcomes-upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we report a perspective on our efforts to assemble a library of natural product-producing microbes and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds. ONE-SENTENCE SUMMARY Natural products are key to discovery of novel antimicrobial agents: Here, we describe our experience and lessons learned in constructing a microbial natural product and pre-fractionated extract library.
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Affiliation(s)
- Michael A Cook
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Daniel Pallant
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Linda Ejim
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Arlene D Sutherland
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Xiaodong Wang
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Jarrod W Johnson
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Susan McCusker
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Xuefei Chen
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Maya George
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Sommer Chou
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Kalinka Koteva
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Wenliang Wang
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Christian Hobson
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Dirk Hackenberger
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Nicholas Waglechner
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Obi Ejim
- College of Medicine, Enugu State University of Science and Technology, Agbani, Enugu State, PMB 01660, Nigeria
| | - Tracey Campbell
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Ricardo Medina
- Department of Microbiology, Chemical Bioactive Center, Central University Marta Abreu de las Villas, Santa Clara 54830, Villa Clara, Cuba
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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13
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Vickers E, Kerney R. Screening Salamanders for Symbionts. Methods Mol Biol 2023; 2562:425-442. [PMID: 36272092 DOI: 10.1007/978-1-0716-2659-7_28] [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: 06/16/2023]
Abstract
Microbial symbionts are broadly categorized by their impacts on host fitness: commensals, pathogens, and mutualists. However, recent investigations into the physiological basis of these impacts have revealed nuanced microbial influences on a wide range of host developmental, immunological, and physiological processes, including regeneration. Exploring these impacts begins with knowing which microbes are present. This methodological pipeline contains both targeted assays using PCR and culturing, as well as culture-independent approaches, to survey host salamander tissues for common and unknown microbial symbionts.
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Affiliation(s)
- Elli Vickers
- Gettysburg College, Department of Biology, Gettysburg, PA, USA
| | - Ryan Kerney
- Gettysburg College, Department of Biology, Gettysburg, PA, USA.
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14
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The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA. Int J Mol Sci 2022; 23:ijms232213690. [PMID: 36430193 PMCID: PMC9698649 DOI: 10.3390/ijms232213690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.
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15
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Vitte J, Michel M, Malinovschi A, Caminati M, Odebode A, Annesi-Maesano I, Caimmi DP, Cassagne C, Demoly P, Heffler E, Menu E, Nwaru BI, Sereme Y, Ranque S, Raulf M, Feleszko W, Janson C, Galán C. Fungal exposome, human health, and unmet needs: A 2022 update with special focus on allergy. Allergy 2022; 77:3199-3216. [PMID: 35976185 DOI: 10.1111/all.15483] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/01/2022] [Accepted: 08/13/2022] [Indexed: 01/28/2023]
Abstract
Humans inhale, ingest, and touch thousands of fungi each day. The ubiquity and diversity of the fungal kingdom, reflected by its complex taxonomy, are in sharp contrast with our scarce knowledge about its distribution, pathogenic effects, and effective interventions at the environmental and individual levels. Here, we present an overview of salient features of fungi as permanent players of the human exposome and key determinants of human health, through the lens of fungal allergy and other fungal hypersensitivity reactions. Improved understanding of the fungal exposome sheds new light on the epidemiology of fungal-related hypersensitivity diseases, their immunological substratum, the currently available methods, and biomarkers for environmental and medical fungi. Unmet needs are described and potential approaches are highlighted as perspectives.
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Affiliation(s)
- Joana Vitte
- IDESP, University of Montpellier and INSERM, Montpellier, France.,MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Moïse Michel
- IDESP, University of Montpellier and INSERM, Montpellier, France.,MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France.,Immunology Laboratory, University Hospital Nîmes, Nîmes, France
| | - Andrei Malinovschi
- Department of Medical Sciences Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Marco Caminati
- Asthma, Allergy and Clinical Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Adeyinka Odebode
- Department of Basic Science, Kampala International University, Kampala, Uganda
| | | | - Davide Paolo Caimmi
- IDESP, University of Montpellier and INSERM, Montpellier, France.,Departement of Pneumology, University Hospital of Montpellier, Montpellier, France
| | - Carole Cassagne
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Pascal Demoly
- IDESP, University of Montpellier and INSERM, Montpellier, France.,Departement of Pneumology, University Hospital of Montpellier, Montpellier, France
| | - Enrico Heffler
- Personalized Medicine, Asthma and Allergy Humanitas Clinical and Research Center IRCCS Rozzano, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Estelle Menu
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Bright I Nwaru
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Youssouf Sereme
- MEPHI, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France.,Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), INSERM U1151, CNRS UMR 8253, Université Paris Descartes, Paris, France
| | - Stéphane Ranque
- VITROME, IHU Méditerranée Infection, IRD, APHM, Aix-Marseille Univ, Marseille, France
| | - Monika Raulf
- Department of Allergology and Immunology, Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-Universität Bochum (IPA), Bochum, Germany
| | - Wojciech Feleszko
- Department of Pediatric Pulmonology and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Christer Janson
- Department of Medical Sciences Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Carmen Galán
- International Campus of Excellence on Agrifood (ceiA3), University of Cordoba, Córdoba, Spain.,Andalusian Inter-University Institute for Earth System Research (IISTA), University of Cordoba, Córdoba, Spain
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16
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Sun Y, Ding A, Zhao X, Chang W, Ren L, Zhao Y, Song Z, Hao D, Liu Y, Jin N, Zhang D. Response of soil microbial communities to petroleum hydrocarbons at a multi-contaminated industrial site in Lanzhou, China. CHEMOSPHERE 2022; 306:135559. [PMID: 35787883 DOI: 10.1016/j.chemosphere.2022.135559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Total petroleum hydrocarbon (TPH) contamination poses threats to ecological systems and human health. Many studies have reported its negative impacts on soil microbes, but limited information is known about microbial change and response to multiple TPH contamination events. In this study, we investigated TPH contamination level, microbial community structure and functional genes at a multi-contaminated industrial site in Lanzhou, where a benzene spill accident caused the drinking water crisis in 2014. TPHs distribution in soils and groundwater indicated multiple TPH contamination events in history, and identified the spill location where high TPH level (6549 mg kg-1) and high ratio of low-molecular-weight TPHs (>80%) were observed. In contrast, TPH level was moderate (349 mg kg-1) and the proportion of low-molecular-weight TPHs was 44% in soils with a long TPH contamination history. After the spill accident, soil bacterial communities became significant diverse (p = 0.047), but the dominant microbes remained the same as Pseudomonadaceae and Comamonadaceae. The abundance of hydrocarbon-degradation related genes increased by 10-1000 folds at the site where the spill accident occurred in multi-contaminated areas and was significantly related to 2-ring PAHs. Such changes of microbial community and hydrocarbon-degradation related genes together indicated the resilience of soil indigenous microbes toward multiple contamination events. Our results proved the significant change of bacterial community and huge shift of hydrocarbon-degradation related genes after the spill accident (multiple contamination events), and provided a deep insight into microbial response at industrial sites with a long period of contamination history.
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Affiliation(s)
- Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiaohui Zhao
- China Institute of Water Resources and Hydropower Research, Beijing, 100038, China
| | - Wonjae Chang
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| | - Liangsuo Ren
- Institute of Geography and Oceangraphy, Nanning Normal University, Nanning, 530100, China
| | - Yinjun Zhao
- Institute of Geography and Oceangraphy, Nanning Normal University, Nanning, 530100, China
| | - Ziyu Song
- BCEG Environmental Remediation LTD, Beijing, 100015, China.
| | - Di Hao
- BCEG Environmental Remediation LTD, Beijing, 100015, China.
| | - Yueqiao Liu
- Experiment and Practice Innovation Education Center, Beijing Normal University at Zhuhai, Zhuhai, 519087, China.
| | - Naifu Jin
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, China.
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17
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The Introduction of Two New Species of Aquatic Fungi from Anzali Lagoon, Northern Iran. DIVERSITY 2022. [DOI: 10.3390/d14100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
During a survey of aquatic fungi from Anzali Lagoon in Iran, several fungal specimens were isolated from freshwater habitats. Morphological evidence and comparing sequencing based on rDNA (ITS and LSU) and protein-coding genes (TEF1 and TUB2) showed that some isolates belong to undescribed fungal species. These isolates belong to Arthrobotrys and Sarocladium, two ascomycetes genera. Arthrobotrys hyrcanus, sp. nov., differs from closely related species such as A. dianchiensis by its larger conidia and septation of primary conidia. Sarocladium pseudokiliense, sp. nov., was similar to S. kiliense, but distinguished by its conidial shape and the absence of adelophialides and chlamydospores. Morphological descriptions, illustrations and multilocus phylogenetic analysis for both new species are provided.
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18
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Hidden in the tropics: Retiperidiolia gen. nov., a new genus of bird’s nest fungi (Nidulariaceae), and a systematic study of the genus Mycocalia. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01807-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Gu D, Xiang X, Wu Y, Zeng J, Lin X. Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127958. [PMID: 34894508 DOI: 10.1016/j.jhazmat.2021.127958] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO2, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.
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Affiliation(s)
- Decheng Gu
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230031, China; Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230031, China
| | - Yucheng Wu
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China.
| | - Jun Zeng
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
| | - Xiangui Lin
- Key laboratory of soil environment and pollution remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210008, China
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20
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Lin Q, Dini-Andreote F, Meador TB, Angel R, Meszárošová L, Heděnec P, Li L, Baldrian P, Frouz J. Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities. Environ Microbiol 2022; 24:3985-4000. [PMID: 35238127 DOI: 10.1111/1462-2920.15936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
The mechanisms underlying microbial community dynamics and co-occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co-occurrence complexity and in the average pairwise phylogenetic distances between co-occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic relatedness between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.
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Affiliation(s)
- Qiang Lin
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Francisco Dini-Andreote
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Travis B Meador
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Roey Angel
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Lenka Meszárošová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4, 14220, Czech Republic
| | - Petr Heděnec
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu, 21030, Malaysia
| | - Lingjuan Li
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4, 14220, Czech Republic
| | - Jan Frouz
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, České Budějovice, 37005, Czech Republic.,Institute for environmental studies, Faculty of Science, Charles University, Benátská 2, Praha 2, 12800, Czech Republic
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21
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Fentie EG, Jeong M, Emire SA, Demsash HD, Kim MA, Shin JH. Fermentation dynamics of spontaneously fermented Ethiopian honey wine, Tej. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6543701. [DOI: 10.1093/femsec/fiac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/11/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
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23
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Masigol H, Woodhouse JN, van West P, Mostowfizadeh-Ghalamfarsa R, Rojas-Jimenez K, Goldhammer T, Khodaparast SA, Grossart HP. Phylogenetic and Functional Diversity of Saprolegniales and Fungi Isolated from Temperate Lakes in Northeast Germany. J Fungi (Basel) 2021; 7:jof7110968. [PMID: 34829255 PMCID: PMC8622742 DOI: 10.3390/jof7110968] [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: 10/21/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 01/28/2023] Open
Abstract
The contribution of fungi to the degradation of plant litter and transformation of dissolved organic matter (humic substances, in particular) in freshwater ecosystems has received increasing attention recently. However, the role of Saprolegniales as one of the most common eukaryotic organisms is rarely studied. In this study, we isolated and phylogenetically placed 51 fungal and 62 Saprolegniales strains from 12 German lakes. We studied the cellulo-, lignino-, and chitinolytic activity of the strains using plate assays. Furthermore, we determined the capacity of 10 selected strains to utilize 95 different labile compounds, using Biolog FF MicroPlates™. Finally, the ability of three selected strains to utilize maltose and degrade/produce humic substances was measured. Cladosporium and Penicillium were amongst the most prevalent fungal strains, while Saprolegnia, Achlya, and Leptolegnia were the most frequent Saprolegniales strains. Although the isolated strains assigned to genera were phylogenetically similar, their enzymatic activity and physiological profiling were quite diverse. Our results indicate that Saprolegniales, in contrast to fungi, lack ligninolytic activity and are not involved in the production/transformation of humic substances. We hypothesize that Saprolegniales and fungi might have complementary roles in interacting with dissolved organic matter, which has ecological implications for carbon cycling in freshwater ecosystems.
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Affiliation(s)
- Hossein Masigol
- Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (J.N.W.)
| | - Jason Nicholas Woodhouse
- Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (J.N.W.)
| | - Pieter van West
- Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development (ICARD), Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK;
| | | | | | - Tobias Goldhammer
- Department of Ecohydrology and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany;
| | - Seyed Akbar Khodaparast
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 41996-13776, Iran;
| | - Hans-Peter Grossart
- Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), 16775 Neuglobsow, Germany; (H.M.); (J.N.W.)
- Institute for Biochemistry and Biology, Potsdam University, 14469 Potsdam, Germany
- Correspondence: ; Tel.: +49-(0)33082-699-91
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24
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Mauger S, Ricono C, Mony C, Chable V, Serpolay E, Biget M, Vandenkoornhuyse P. Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:235-248. [PMID: 37284513 PMCID: PMC10168034 DOI: 10.1002/pei3.10062] [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: 04/27/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/08/2023]
Abstract
Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.
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Affiliation(s)
- Solène Mauger
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | - Claire Ricono
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | - Cendrine Mony
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | | | | | - Marine Biget
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
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25
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Kiel Reese B, Sobol MS, Bowles MW, Hinrichs KU. Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:727543. [PMID: 37744089 PMCID: PMC10512353 DOI: 10.3389/ffunb.2021.727543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 09/26/2023]
Abstract
The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.
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Affiliation(s)
- Brandi Kiel Reese
- Dauphin Island Sea Lab, Dauphin Island, AL, United States
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL, United States
- Hanse-Wissenschaftskolleg Institute for Advanced Study, Delmenhorst, Germany
| | - Morgan S. Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, United States
| | | | - Kai-Uwe Hinrichs
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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26
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Decomposition of peatland DOC affected by root exudates is driven by specific r and K strategic bacterial taxa. Sci Rep 2021; 11:18677. [PMID: 34548501 PMCID: PMC8455546 DOI: 10.1038/s41598-021-97698-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/26/2021] [Indexed: 02/08/2023] Open
Abstract
In peatlands, decomposition of organic matter is limited by harsh environmental conditions and low decomposability of the plant material. Shifting vegetation composition from Sphagnum towards vascular plants is expected in response to climate change, which will lead to increased root exudate flux to the soil and stimulation of microbial growth and activity. We aimed to evaluate the effect of root exudates on the decomposition of recalcitrant dissolved organic carbon (DOC) and to identify microorganisms involved in this process. The exudation was mimicked by an addition of a mixture of 13C labelled compounds into the recalcitrant DOC in two realistic levels; 2% and 5% of total DOC and peatland porewater with added root exudates was incubated under controlled conditions in the lab. The early stage of incubation was characterized by a relative increase of r-strategic bacteria mainly from Gammaproteobacteria and Bacteriodetes phyla within the microbial community and their preferential use of the added compounds. At the later stage, Alphaproteobacteria and Acidobacteria members were the dominating phyla, which metabolized both the transformed 13C compounds and the recalcitrant DOC. Only higher exudate input (5% of total DOC) stimulated decomposition of recalcitrant DOC compared to non-amended control. The most important taxa with a potential to decompose complex DOC compounds were identified as: Mucilaginibacter (Bacteriodetes), Burkholderia and Pseudomonas (Gammaproteobacteria) among r-strategists and Bryocella and Candidatus Solibacter (Acidobacteria) among K-strategists. We conclude that increased root exudate inputs and their increasing C/N ratio stimulate growth and degradation potential of both r-strategic and K-strategic bacteria, which make the system more dynamic and may accelerate decomposition of peatland recalcitrant DOC.
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27
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Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network. Microorganisms 2021; 9:microorganisms9091943. [PMID: 34576837 PMCID: PMC8466989 DOI: 10.3390/microorganisms9091943] [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: 08/20/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/16/2023] Open
Abstract
Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.
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28
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Hutchinson MI, Bell TAS, Gallegos-Graves LV, Dunbar J, Albright M. Merging Fungal and Bacterial Community Profiles via an Internal Control. MICROBIAL ECOLOGY 2021; 82:484-497. [PMID: 33410932 DOI: 10.1007/s00248-020-01638-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.
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Affiliation(s)
- Miriam I Hutchinson
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Tisza A S Bell
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | | | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Michaeline Albright
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.
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29
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Shi Y, Yang H, Chu M, Niu X, Huo X, Gao Y, Zeng J, Lin Q, Lou K. Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China. MICROBIAL ECOLOGY 2021; 82:87-99. [PMID: 33415384 DOI: 10.1007/s00248-020-01646-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.
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Affiliation(s)
- YingWu Shi
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China.
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China.
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China.
- Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China.
| | - HongMei Yang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China
| | - Ming Chu
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China
| | - XinXiang Niu
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China
- Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
| | - XiangDong Huo
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Yan Gao
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Jun Zeng
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Qing Lin
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Kai Lou
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
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30
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Zhang W, Liu W, He S, Chen Q, Han J, Zhang Q. Mixed plantations of Metasequoia glyptostroboides and Bischofia polycarpa change soil fungal and archaeal communities and enhance soil phosphorus availability in Shanghai, China. Ecol Evol 2021; 11:7239-7249. [PMID: 34188809 PMCID: PMC8216939 DOI: 10.1002/ece3.7532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/19/2021] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
Soil degradation has been found in urban forests in Shanghai, especially in the pure plantations. Mixed plantations are considered to improve soil quality because they can stimulate organic matter cycling and increase soil carbon and nutrient content. Although soil microbes play crucial roles in regulating soil biogeochemical processes, little is known about how mixed plantations affect soil microbial communities, including bacteria, archaea, and fungi. Here, we evaluated soil chemical properties, abundances and compositions of soil bacterial, archaeal, and fungal communities, and enzyme activities in pure and mixed Metasequoia glyptostroboides and Bischofia polycarpa plantations, located in Shanghai, China. The results showed that soil available phosphorus content in the mixed plantation of M. glyptostroboides and B. polycarpa was significantly higher than that in pure plantations, while no significant difference was observed in the content of soil organic carbon, total and available nitrogen, total and available potassium among the three studied plantations. We found higher fungal abundance in the mixed plantation, when compared to both pure plantations. Moreover, fungal abundance was positively correlated with the content of soil available phosphorus. No significant difference was found in the abundance and diversity of bacterial and archaeal community among the three studied plantations. A similarity analysis (ANOSIM) showed that mixed plantation significantly altered the community composition of archaea and fungi, accompanied with an increase of alkaline phosphatase activity. However, ANOSIM analysis of bacterial communities showed that there was no significant group separation among different plantations. Overall, results from this study indicated that fungal and archaeal communities were more sensitive to aboveground tree species than bacterial community. Moreover, mixed plantations significantly increased the activity of alkaline phosphatase and the content of soil available phosphorus, suggesting that afforestation with M. glyptostroboides and B. polycarpa is an effective way to alleviate phosphorus deficiency in urban forests in Shanghai, China.
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Affiliation(s)
- Weiwei Zhang
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Wen Liu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Shanwen He
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Qingchu Chen
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
| | - Jigang Han
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban SitesShanghai Academy of Landscape Architecture Science and PlanningShanghaiChina
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghaiChina
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Ban LP, Li JD, Yan M, Gao YH, Zhang JJ, Moural TW, Zhu F, Wang XM. Illumina Sequencing of 18S/16S rRNA Reveals Microbial Community Composition, Diversity, and Potential Pathogens in 17 Turfgrass Seeds. PLANT DISEASE 2021; 105:1328-1338. [PMID: 33084546 DOI: 10.1094/pdis-06-18-0946-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The increasing need for turfgrass seeds is coupled with the high risk of dangerous microbial pathogens being transmitted through the domestic and international trade of seeds. Concerns continue to be raised about seed safety and quality. Here, we show that next-generation sequencing (NGS) of DNA represents an effective and reliable tactic to monitor the microbial communities within turfgrass seeds. A comparison of DNA sequence data with reference databases revealed the presence of 26 different fungal orders. Among them, serious plant disease pathogens such as Bipolaris sorokiniana, Boeremia exigua, Claviceps purpurea, and Rhizoctonia zeae were detected. Seedborne bacteria, including Erwinia persicina and Acidovorax avenae, were identified from different bacterial orders. Our study indicated that the traditional culturing method and the NGS approach for pathogen identification complement each other. The reliability of culturing and NGS methods was further validated by PCR with specific primers. The combination of these different techniques ensures maximum sensitivity and specificity for turfgrass seed pathogen testing assay.
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Affiliation(s)
- Li-Ping Ban
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jin-Dong Li
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Min Yan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- National Animal Husbandry Station, Ministry of Agriculture, Beijing 100125, China
| | - Yu-Hao Gao
- The Affiliated High School of Peking University, Beijing 100190, China
| | - Jin-Jin Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Timothy W Moural
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Xue-Min Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Ingrey SD, Pearson LA, Kalaitzis JA, Neilan BA. Australian bush medicines harbour diverse microbial endophytes with broad-spectrum antibacterial activity. J Appl Microbiol 2021; 131:2244-2256. [PMID: 33904206 DOI: 10.1111/jam.15122] [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: 03/02/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/01/2022]
Abstract
AIMS Microbial endophytes produce specialized metabolites, including antibiotics and other compounds of pharmaceutical and agricultural value. This study aimed to investigate the diversity and bioactivity of endophytes from medicinal plants used by the Dharawal People of Gamay (Botany Bay), Australia. METHODS AND RESULTS Of the 48 endophytes isolated, 19 tested positive for polyketide synthase or non-ribosomal peptide synthetase genes via a PCR incorporating degenerate primers. The biosynthetically talented endophytes were identified by 16S rRNA gene sequencing and included 4 bacteria species belonging to the orders Bacillales, Rhizobiales and Burkholderiales and 15 Ascomycota fungi species belonging to the orders Botryosphaeriales, Cladosporiales, Glomerellales, Microascales and Eurotiales. Antimicrobial testing using the disc diffusion assay demonstrated that 15 of the 19 isolates had broad-spectrum activity against a range of Gram-positive and Gram-negative bacteria. CONCLUSIONS Taken together, these results suggest that Australian bush medicines harbour diverse biosynthetically talented microbial endophytes capable of producing broad-spectrum antibacterial compounds. SIGNIFICANCE AND IMPACT OF THE STUDY This study suggests that compounds produced by microbial endophytes likely contribute to the collective medicinal properties of Australian bush medicines. Significantly, it highlights that Indigenous botanical knowledge and modern molecular approaches can be used in tandem to prioritize microorganisms that produce pharmaceutically relevant compounds.
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Affiliation(s)
- S D Ingrey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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Zhang W, Han J, Wu H, Zhong Q, Liu W, He S, Zhang L. Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China. PeerJ 2021; 9:e11231. [PMID: 33959419 PMCID: PMC8053383 DOI: 10.7717/peerj.11231] [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: 09/21/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. METHODS In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively. RESULTS The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potassium (K) significantly affected fungal community composition in park soils in Shanghai. Soil available Zn was also the most important factor affecting the bacterial community composition in this study. CONCLUSION There were significant differences in the soil molecular biomass, fungal abundance, and the community composition and co-occurrence relations of both soil bacterial and fungal communities between urban and suburban park soils. Soil available Zn played an important part in shaping the structures of both the bacterial and fungal communities in park soils in Shanghai.
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Affiliation(s)
- Weiwei Zhang
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Jigang Han
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Haibing Wu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Qicheng Zhong
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Wen Liu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Shanwen He
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
| | - Lang Zhang
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai, China
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Lynn TM, Zhran M, Wang LF, Ge T, Yu SS, Kyaw EP, Latt ZK, Htwe TM. Effect of land use on soil properties, microbial abundance and diversity of four different crop lands in central Myanmar. 3 Biotech 2021; 11:154. [PMID: 33747704 DOI: 10.1007/s13205-021-02705-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/23/2021] [Indexed: 11/29/2022] Open
Abstract
Changing land use systems impact on local edaphic factors and microbial abundance and diversity, however, the information on it in central Myanmar's soils is still lacking. Therefore, soils with four different land uses were analyzed; WAP (soil from perennial tree orchard), PNON (soil from crop rotation of peanut and onion), SESA (soil from mono-crop of sesame) and CHON (soil from mono-crop of onion for 3 years consecutively). Soil organic carbon (SOC), total nitrogen (TN), dissolved organic carbon (DOC), ammonium nitrogen (NH4 +-N) and pH showed the highest in PNON soil, which suggested crop rotation with high fertilizer input and irrigation had positive effect on the edaphic factors of soil. CHON soil showed the lowest in most soil properties and microbial abundance as a result of intensive use of fertilizer and irrigation, no crop rotation and no input of manures. Microbial community composition showed differences among tested soils and relative abundance of Chloroflexi was the highest in CHON soil whereas that of Basidiomycota was the highest in WAP soil. The abundances of bacteria and fungi were significantly affected by Olsen P, whereas the abundances of archaea were influenced by SOC. Our results suggested crop rotation and manure fertilization (PNON soil) enhanced soil properties and microbial abundance although long-time onion mono-crop (CHON soil) reduced soil fertility. This study can provide information to improve soil quality and sustainability of agro-ecosystems using appropriate agricultural management. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02705-y.
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Affiliation(s)
- Tin Mar Lynn
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Mostafa Zhran
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
- Atomic Energy Authority, Nuclear Research Center, Soil & Water Research Department, Abou-Zaabl, 13759 Egypt
| | - Liu Fang Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
| | - Tida Ge
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125 China
| | - San San Yu
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Ei Phyu Kyaw
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Zaw Ko Latt
- Microbiology Division, Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay Region 100301 Myanmar
| | - Tin Mar Htwe
- Ministry of Education, Kyaing Tong Education College, Kyaing Tong, Shan State Myanmar
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Soil Microbiome Composition along the Natural Norway Spruce Forest Life Cycle. FORESTS 2021. [DOI: 10.3390/f12040410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Stand-replacing disturbances are a key element of the Norway spruce (Picea abies) forest life cycle. While the effect of a natural disturbance regime on forest physiognomy, spatial structure and pedocomplexity was well described in the literature, its impact on the microbiome, a crucial soil component that mediates nutrient cycling and stand productivity, remains largely unknown. For this purpose, we conducted research on a chronosequence of sites representing the post-disturbance development of a primeval Norway spruce forest in the Calimani Mts., Romania. The sites were selected along a gradient of duration from 16 to 160 years that ranges from ecosystem regeneration phases of recently disturbed open gaps to old-growth forest stands. Based on DNA amplicon sequencing, we followed bacterial and fungal community composition separately in organic, upper mineral and spodic horizons of present Podzol soils. We observed that the canopy opening and subsequent expansion of the grass-dominated understorey increased soil N availability and soil pH, which was reflected in enlarged bacterial abundance and diversity, namely due to the contribution of copiotrophic bacteria that prefer nutrient-richer conditions. The fungal community composition was affected by the disturbance as well but, contrary to our expectations, with no obvious effect on the relative abundance of ectomycorrhizal fungi. Once the mature stand was re-established, the N availability was reduced, the pH gradually decreased and the original old-growth forest microbial community dominated by acidotolerant oligotrophs recovered. The effect of the disturbance and forest regeneration was most evident in organic horizons, while the manifestation of these events was weaker and delayed in deeper soil horizons.
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36
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Wagg C, Hautier Y, Pellkofer S, Banerjee S, Schmid B, van der Heijden MG. Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning. eLife 2021; 10:62813. [PMID: 33755017 PMCID: PMC7987343 DOI: 10.7554/elife.62813] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/03/2021] [Indexed: 12/28/2022] Open
Abstract
Theoretical and empirical advances have revealed the importance of biodiversity for stabilizing ecosystem functions through time. Despite the global degradation of soils, whether the loss of soil microbial diversity can destabilize ecosystem functioning is poorly understood. Here, we experimentally quantified the contribution of soil fungal and bacterial communities to the temporal stability of four key ecosystem functions related to biogeochemical cycling. Microbial diversity enhanced the temporal stability of all ecosystem functions and this pattern was particularly strong in plant-soil mesocosms with reduced microbial richness where over 50% of microbial taxa were lost. The stabilizing effect of soil biodiversity was linked to asynchrony among microbial taxa whereby different soil fungi and bacteria promoted different ecosystem functions at different times. Our results emphasize the need to conserve soil biodiversity for the provisioning of multiple ecosystem functions that soils provide to the society.
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Affiliation(s)
- Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.,Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, Canada
| | - Yann Hautier
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Padualaan, Netherlands
| | - Sarah Pellkofer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Samiran Banerjee
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.,Department of Microbiological Sciences, North Dakota State University, Fargo, United States
| | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Geography, Remote Sensing Laboratories, University of Zürich, Zürich, Switzerland
| | - Marcel Ga van der Heijden
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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37
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Wang HH, Chu HL, Dou Q, Feng H, Tang M, Zhang SX, Wang CY. Seasonal Changes in Pinus tabuliformis Root-Associated Fungal Microbiota Drive N and P Cycling in Terrestrial Ecosystem. Front Microbiol 2021; 11:526898. [PMID: 33537007 PMCID: PMC7849022 DOI: 10.3389/fmicb.2020.526898] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 12/04/2020] [Indexed: 11/29/2022] Open
Abstract
In terrestrial ecosystems, mycorrhizal roots play a key role in the cycling of soil carbon (C) and other nutrients. The impact of environmental factors on the mycorrhizal fungal community has been well studied; however, the seasonal variations in the root-associated fungal microbiota affected by environmental changes are less clear. To improve the understanding of how environmental factors shape the fungal microbiota in mycorrhizal roots, seasonal changes in Pinus tabuliformis root-associated fungi were investigated. In the present study, the seasonal dynamics of edaphic properties, soil enzymatic activities, root fungal colonization rates, and root-associated fungal microbiota in P. tabuliformis forests were studied across four seasons during a whole year to reveal their correlations with environmental changes. The results indicate that the soil functions, such as the enzymatic activities related to nitrogen (N) and phosphorus (P) degradation, were varied with the seasonal changes in microclimate factors, resulting in a significant fluctuation of edaphic properties. In addition, the ectomycorrhizal fungal colonization rate in the host pine tree roots increased during warm seasons (summer and autumn), while the fungal colonization rate of dark septate endophyte was declined. Moreover, the present study indicates that the fungal biomass increased in both the pine roots and rhizospheric soils during warm seasons, while the fungal species richness and diversity decreased. While the Basidiomycota and Ascomycota were the two dominant phyla in both root and soil fungal communities, the higher relative abundance of Basidiomycota taxa presented in warm seasons. In addition, the fungal microbial network complexity declined under the higher temperature and humidity conditions. The present study illustrates that the varieties in connectivity between the microbial networks and in functional taxa of root-associated fungal microbiota significantly influence the soil ecosystem functions, especially the N and P cycling.
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Affiliation(s)
- Hai-Hua Wang
- College of Forestry, Northwest A&F University, Yangling, China
- Department of Food Science and Technology, College of Agriculture and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Hong-Long Chu
- College of Forestry, Northwest A&F University, Yangling, China
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, China
| | - Qing Dou
- College of Forestry, Northwest A&F University, Yangling, China
| | - Huan Feng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Ming Tang
- College of Forestry, Northwest A&F University, Yangling, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shuo-Xin Zhang
- College of Forestry, Northwest A&F University, Yangling, China
- Qinling National Forest Ecosystem Research Station, Huoditang, Ningshan, China
| | - Chun-Yan Wang
- College of Forestry, Northwest A&F University, Yangling, China
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Silva-Valderrama I, Toapanta D, Miccono MDLA, Lolas M, Díaz GA, Cantu D, Castro A. Biocontrol Potential of Grapevine Endophytic and Rhizospheric Fungi Against Trunk Pathogens. Front Microbiol 2021; 11:614620. [PMID: 33488557 PMCID: PMC7817659 DOI: 10.3389/fmicb.2020.614620] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
Grapevine Trunk Diseases (GTDs) are a major challenge to the grape industry worldwide. GTDs are responsible for considerable loss of quality, production, and vineyard longevity. Seventy-five percent of Chilean vineyards are estimated to be affected by GTDs. GTDs are complex diseases caused by several fungi species, including members of the Botryosphaeriaceae family and Phaeomoniella chlamydospora, considered some of the most important causal agents for these diseases in Chile. In this study, we isolated 169 endophytic and 209 rhizospheric fungi from grapevines grown under organic and conventional farming in Chile. Multiple isolates of Chaetomium sp., Cladosporium sp., Clonostachys rosea, Epicoccum nigrum, Purpureocillium lilacinum, and Trichoderma sp. were evaluated for their potential of biocontrol activity against Diplodia seriata, Neofusicoccum parvum, and Pa. chlamydospora. Tests of antagonism were carried out using two dual-culture-plate methods with multiple media types, including agar containing grapevine wood extract to simulate in planta nutrient conditions. Significant pathogen growth inhibition was observed by all isolates tested. Clonostachys rosea showed 98.2% inhibition of all pathogens in the presence of grapevine wood extract. We observed 100% pathogen growth inhibition when autoclaved lignified grapevine shoots were pre-inoculated with either C. rosea strains or Trichoderma sp. Overall, these results show that C. rosea strains isolated from grapevines are promising biocontrol agents against GTDs.
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Affiliation(s)
| | - Diana Toapanta
- UC Davis Chile Life Sciences Innovation Center, Santiago, Chile
| | - Maria de Los Angeles Miccono
- UC Davis Chile Life Sciences Innovation Center, Santiago, Chile.,Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Mauricio Lolas
- Laboratorio de Patología Frutal, Facultad de Ciencias Agrarias, Universidad de Talca, Talca, Chile
| | - Gonzalo A Díaz
- Laboratorio de Patología Frutal, Facultad de Ciencias Agrarias, Universidad de Talca, Talca, Chile
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Alvaro Castro
- UC Davis Chile Life Sciences Innovation Center, Santiago, Chile
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Xu S, Dunière L, Smiley B, Rutherford W, Qi S, Nair J, Wang Y, McAllister TA. Using molecular microbial ecology to define differential responses to the inoculation of barley silage. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2019-0214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Previously, we investigated the impact of a mixed Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus casei inoculant on fermentation and aerobic stability of barley silage over two years in 2009 and 2010. In 2009, a classical response to inoculation was obtained with an increase in acetic acid concentration of silage ensiled in both mini- and bag silos. In 2010, this classical response was not observed in mini-silos but was observed in bag silos. The objective of this study was to determine if molecular microbial ecology could explain the differential responses to the inoculation of barley silage between the two years. The Illumina MiSeq sequencing results showed that inoculation increased Lactobacillus and lowered Pediococcus, Weissella, and Leuconostoc in both types of silos in 2009. However, a similar trend was not observed in mini-silos, but was instead observed in bag silos in 2010. Inoculation did not alter the core fungal community in either silo type in either year. Cladosporium, Leptosphaeria, and Cryptococcus were abundant in fresh forage, but were superseded by Pichia and Kazachstania after ensiling. Our results suggest that changes in silage chemistry corresponded to differences observed in microbial ecology. Inoculation may have less impact when using more mature crops with shorter ensiling times.
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Affiliation(s)
- Shanwei Xu
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada
| | - Lysiane Dunière
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Brenda Smiley
- Corteva, Forage Additive Research, Johnston, IA 50131, USA
| | | | - Samuel Qi
- Corteva, Forage Additive Research, Johnston, IA 50131, USA
| | - Jayakrishnan Nair
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Yuxi Wang
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
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Albright MBN, Johansen R, Thompson J, Lopez D, Gallegos-Graves LV, Kroeger ME, Runde A, Mueller RC, Washburne A, Munsky B, Yoshida T, Dunbar J. Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition. Front Microbiol 2020; 11:542220. [PMID: 33240225 PMCID: PMC7677502 DOI: 10.3389/fmicb.2020.542220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 (P < 0.05) and 80 (P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions.
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Affiliation(s)
| | - Renee Johansen
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Deanna Lopez
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Marie E. Kroeger
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andreas Runde
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Thomas Yoshida
- Chemical Diagnostics and Engineering, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Pérez-Brocal V, Magne F, Ruiz-Ruiz S, Ponce CA, Bustamante R, Martin VS, Gutierrez M, Gatti G, Vargas SL, Moya A. Optimized DNA extraction and purification method for characterization of bacterial and fungal communities in lung tissue samples. Sci Rep 2020; 10:17377. [PMID: 33060634 PMCID: PMC7562954 DOI: 10.1038/s41598-020-74137-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Human lungs harbor a scarce microbial community, requiring to develop methods to enhance the recovery of nucleic acids from bacteria and fungi, leading to a more efficient analysis of the lung tissue microbiota. Here we describe five extraction protocols including pre-treatment, bead-beating and/or Phenol:Chloroform:Isoamyl alcohol steps, applied to lung tissue samples from autopsied individuals. The resulting total DNA yield and quality, bacterial and fungal DNA amount and the microbial community structure were analyzed by qPCR and Illumina sequencing of bacterial 16S rRNA and fungal ITS genes. Bioinformatic modeling revealed that a large part of microbiome from lung tissue is composed of microbial contaminants, although our controls clustered separately from biological samples. After removal of contaminant sequences, the effects of extraction protocols on the microbiota were assessed. The major differences among samples could be attributed to inter-individual variations rather than DNA extraction protocols. However, inclusion of the bead-beater and Phenol:Chloroform:Isoamyl alcohol steps resulted in changes in the relative abundance of some bacterial/fungal taxa. Furthermore, inclusion of a pre-treatment step increased microbial DNA concentration but not diversity and it may contribute to eliminate DNA fragments from dead microorganisms in lung tissue samples, making the microbial profile closer to the actual one.
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Affiliation(s)
- Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Avda. Cataluña 21, 46020, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Fabien Magne
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile.
| | - Susana Ruiz-Ruiz
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Avda. Cataluña 21, 46020, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Carolina A Ponce
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile
| | - Rebeca Bustamante
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile
| | | | | | - Gianna Gatti
- Médico Legal Institute of Chile, Santiago, Chile
| | - Sergio L Vargas
- Microbiology and Mycology Program, Biomedical Sciences Institute (ICBM), University of Chile School of Medicine, Av. Independencia 1027, Independencia, Santiago, Chile.
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Avda. Cataluña 21, 46020, València, Spain.
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain.
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), València, Spain.
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Liu H, Chen L, Wang ET, Liu Y, Zhang L, Zhao K, Gu Y, Yu X, Ma M, Penttinen P, Zhang X, Huang M, Deng L, Chen Q. Combined Microbial Consortium Inoculation and Black Locust Planting Is Effective in the Bioremediation of Waste Drill Cuttings. Front Microbiol 2020; 11:536787. [PMID: 33101222 PMCID: PMC7555700 DOI: 10.3389/fmicb.2020.536787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/04/2020] [Indexed: 12/02/2022] Open
Abstract
Waste drill cuttings (WDCs), produced during gas and oil drilling consisting of 80% rock cuttings and 20% drilling muds, are an increasingly potent source of environmental pollution. We studied the efficiency of bioaugmentation and phytoremediation to remediate WDCs in an experiment where WDCs were incubated in a greenhouse for 120 days with and without black locust (Robinia pseudoacacia) plant and with or without bacterial and fungal consortium inoculant. The pollutant removal rates were highest in inoculated and planted treatment, followed by inoculated treatment and planted treatment. The small decrease in contaminant level in the control treatment suggested that indigenous microorganisms in WDCs had little pollutant degradation capability. In the inoculated and planted treatments, after 120 days, the germination rate of red clover seeds was on the same level as in the natural soil, showing a marked decrease in the ecotoxicity of WDC. Both the bacterial and fungal richness and bacterial diversity increased in all the treatments over time, whereas fungal diversity increased only in the not-inoculated treatments. The activity of laccase enzyme played a key role in the bioremediation process. The enzyme activities were mostly governed by inoculated consortium and soil bacterial community, and black locust affected the bioremediation mainly through its effect on N content that further affected bacterial and fungal communities.
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Affiliation(s)
- Hanjun Liu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China.,Safety and Environmental Protection Quality Supervision and Testing Research Institute, CNPC Chuanqing Drilling Engineering Co. Ltd., Guanghan, China
| | - Lirong Chen
- Safety and Environmental Protection Quality Supervision and Testing Research Institute, CNPC Chuanqing Drilling Engineering Co. Ltd., Guanghan, China
| | - En T Wang
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - Yihao Liu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lingzi Zhang
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Menggen Ma
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Min Huang
- Safety and Environmental Protection Quality Supervision and Testing Research Institute, CNPC Chuanqing Drilling Engineering Co. Ltd., Guanghan, China
| | - Liangji Deng
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu, China
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43
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Lin Y, Newcombe CE, Brennan RA. Crab shell amendments enhance the abundance and diversity of key microbial groups in sulfate-reducing columns treating acid mine drainage. Appl Microbiol Biotechnol 2020; 104:8505-8516. [PMID: 32820375 DOI: 10.1007/s00253-020-10833-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022]
Abstract
Substrate amendments composed of crab shell (CS) waste materials have been shown to significantly improve the longevity and performance of acid mine drainage (AMD) treatment systems containing spent mushroom compost (SMC), yet the development of key microbial populations within these systems has not been investigated. To better understand the effects of CS on microbial dynamics in these systems, clone libraries and real-time quantitative PCR (qPCR) were performed on materials from a laboratory-scale AMD treatment system containing SMC and 0 to 100% CS substrate after receiving a continuous flow of AMD for 148 days (428 pore volumes). The proportion of CS in the substrate positively correlated with the diversity of sulfate-reducing bacteria (SRB) and archaeal clones, but negatively correlated with fungal diversity. CS also impacted microbial community structure, as revealed in Unifrac significance and principal coordinate analysis tests. The column containing 100% CS substrate supported 7 different genera of SRB-the most ever observed in an AMD treatment system. Moreover, the copy numbers of functional genes representing fermenters, sulfate reducers, and chitin degraders increased with increasing proportions of CS. These observations agree well with the chemical performance data, further validating that by supporting more abundant key microbial groups, chitinous substrates may provide benefits for improving both the longevity and performance of AMD treatment systems, and may provide similar benefits for the treatment of other environmental contaminants that are amenable to anaerobic bioremediation.Key points• Crab shell improves the longevity and performance of acid mine drainage treatment.• The diversity of sulfate-reducing bacteria is enhanced with crab shell amendments.• Crab shell supports more abundant key microbial groups than spent mushroom compost.
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Affiliation(s)
- Yishan Lin
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.,State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, People's Republic of China
| | - Caroline E Newcombe
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.,Hewlett Packard Enterprises, Minneapolis, MN, USA
| | - Rachel A Brennan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
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Lin H, Ye J, Sun W, Yu Q, Wang Q, Zou P, Chen Z, Ma J, Wang F, Ma J. Solar composting greenhouse for organic waste treatment in fed-batch mode: Physicochemical and microbiological dynamics. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 113:1-11. [PMID: 32502764 DOI: 10.1016/j.wasman.2020.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Composting is a sustainable means of managing organic waste, and solar composters offer a viable solution in rural areas lacking connection to municipal power supplies. This study tracked the physicochemical and microbiological changes that occur in a solar composting greenhouse during the treatment of food and green cellulosic waste in fed-batch mode, which remain poorly understood. Solar composting greenhouse performed well on waste reduction and nutrient retention, resulting in a 45.0-58.8% decrease in feedstock volume over 12-day composting cycles, a 41% removal in dry matter after three batches of composting, and 29.5%, 252.9% and 96.6% increase in the nitrogen, phosphorus and potassium content respectively after 42 days of composting. Batch feeding and composting jointly influenced microbiological succession by altering the physicochemical properties of compost. The contents of nitrogen and phosphorus, pH, and electrical conductivity significantly accounts for variations in culturable microbial populations. The succession of dominant bacterial genera such as Lactobacillus, Pseudoxanthomonas, Bacillus, and Pseudomonas were closely related to pH, cellulose, NH4+-N, carbon content, and temperature. In addition, Pichia kudriavzevii, Thermomyces lanuginosus, and Scopulariopsis brevicaulis successively became the dominant fungal species during composting. Preliminary compost quality assessments showed that solar composting greenhouse has a high potentiality to transform organic waste into organic fertilizer. Additionally, corresponding purposeful suggestions were proposed for future optimization in this system, mainly from a microbiological aspect.
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Affiliation(s)
- Hui Lin
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Ye
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wanchun Sun
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qiaogang Yu
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Qiang Wang
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ping Zou
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhaoming Chen
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jinchuan Ma
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Feng Wang
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Junwei Ma
- The Institute of Environment, Resources, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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45
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Mony C, Brunellière P, Vannier N, Bittebiere AK, Vandenkoornhuyse P. Effect of floristic composition and configuration on plant root mycobiota: a landscape transposition at a small scale. THE NEW PHYTOLOGIST 2020; 225:1777-1787. [PMID: 31610023 DOI: 10.1111/nph.16262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
Fungal communities in the root endosphere are heterogeneous at fine scale. The passenger hypothesis assumes that this heterogeneity is driven by host plant distribution. Plant composition and host plant configuration should then influence root fungal assemblages. We used a large-scale experimental design of 25 mixtures of grassland plants. We sampled Brachypodium pinnatum in each mesocosm, and used amplicon mass-sequencing to analyze the endospheric mycobiota. We used plant distribution maps to assess plant species richness and evenness (heterogeneity of composition), and patch size and the degree of isolation of B. pinnatum (heterogeneity of configuration) on fungal community assembly. The Glomeromycotina community in B. pinnatum roots was not related to either floristic heterogeneity or productivity. For Ascomycota, the composition of operational taxonomic units (OTUs) was driven by plant evenness while OTU richness decreased with plant richness. For Basidiomycota, richness increased with host plant aggregation and connectivity. Plant productivity influenced Ascomycota, inducing a shift in OTU composition and decreasing evenness. Plant heterogeneity modified root mycobiota, with potential direct (i.e. host preference) and indirect (i.e. adaptations to abiotic conditions driven by plant occurrence over time) effects. Plant communities can be envisioned as microlandscapes consisting of a variety of fungal niches.
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Affiliation(s)
- Cendrine Mony
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Philomène Brunellière
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Nathan Vannier
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Anne-Kristel Bittebiere
- UMR 5023, LEHNA, CNRS - University of Lyon 1, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Philippe Vandenkoornhuyse
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
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46
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Mony C, Vannier N, Brunellière P, Biget M, Coudouel S, Vandenkoornhuyse P. The influence of host-plant connectivity on fungal assemblages in the root microbiota of Brachypodium pinnatum. Ecology 2020; 101:e02976. [PMID: 31944273 DOI: 10.1002/ecy.2976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/17/2019] [Accepted: 12/05/2019] [Indexed: 11/10/2022]
Abstract
Dispersal limitation may drive the structure of fungal microbiota of plant roots at small spatial scales. Fungal root microorganisms disperse through the plant rooting systems from hosts to hosts. Due to a pronounced host-preference effect, the composition of endophytic root microbiota may follow plant distribution. A given plant community may hence include a matrix of host-plant species that represent various habitat permeabilities to fungal dispersal in the floristic landscape. We experimentally tested the effect of host-plant isolation on endophytic fungal assemblages (Ascomycota, Basidiomycota, Glomeromycotina) inhabiting Brachypodium pinnatum roots. We calculated host-plant isolation using Euclidean distance (distance-based dispersal limitation) and resistance distance (functional-based dispersal limitation), based on host presences. All fungal groups were more influenced by the resistance distance between B. pinnatum than by the Euclidean distance. Fungal dispersal was hence strongly related to the spatial distribution of the host plants. The fungal groups displayed however different responses (in richness, abundance, and composition) to host isolation. Additionally, fungal assemblages were more strongly controlled by the degree of connectivity between host plants during the prior year than by current connectivity. This discrepancy may be due to changes in plant species coverage in a year and/or to the delay of dispersal response of fungi. This study it the first to demonstrate how small-scale host-plant distributions mediate connectivity in microorganisms. The consequences of plant distributions for the permeability of the floristic landscape to fungi dispersal appear to control fungal assemblages, but with possibly different mechanisms for the different fungal groups.
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Affiliation(s)
- Cendrine Mony
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Nathan Vannier
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Philomène Brunellière
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Marine Biget
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Sophie Coudouel
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Philippe Vandenkoornhuyse
- UMR 6553 Ecobio, CNRS - University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
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47
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Pan Y, Wu Y, Li X, Zeng J, Lin X. Continuing Impacts of Selective Inhibition on Bacterial and Fungal Communities in an Agricultural Soil. MICROBIAL ECOLOGY 2019; 78:927-935. [PMID: 30911770 DOI: 10.1007/s00248-019-01364-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Selective inhibition (SI) has been routinely used to differentiate the contributions of bacteria and fungi to soil ecological processes. SI experiments typically measured rapid responses within hours since the addition of inhibitor, but the long-term effects of selective biocides on microbial community composition and function were largely unknown. In this study, a microcosm experiment was performed with an agricultural soil to explore the effectiveness of two bactericides (bronopol, streptomycin) and two fungicides (cycloheximide, captan), which were applied at two different concentrations (2 and 10 mg g-1). The microcosms were incubated for 6 weeks. A radiolabeled substrate, [1,2,3,4,4a,9a-14C] anthracene, was spiked to all microcosms, and the derived CO2 was monitored during the incubation. The abundance and composition of bacteria and fungi were assessed by qPCR and Miseq sequencing of ribosomal rRNA genes. It was demonstrated that only 2 mg g-1 bronopol and cycloheximide significantly changed the bacteria to fungi ratio without apparent non-target inhibition on the abundances; however, community shifts were observed in all treatments after 6 weeks incubation. The enrichment of specific taxa implicated a selection of resistant or adapted microbes by these biocides. Mineralization of anthracene was continuingly suppressed in all SI microcosms, which may result in biased estimate of bacterial and fungal contributions to pollutant degradation. These findings highlight the risks of long-term application of selective inhibition, and a preliminary assessment of biocide selection and concentration is highly recommended.
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Affiliation(s)
- Yanshuo Pan
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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48
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Ren Z, Gao H. Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia. PeerJ 2019; 7:e7715. [PMID: 31576247 PMCID: PMC6753927 DOI: 10.7717/peerj.7715] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.
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Affiliation(s)
- Ze Ren
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Hongkai Gao
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, China.,School of Geographic Sciences, East China Normal University, Shanghai, China
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49
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Andreo-Jimenez B, Vandenkoornhuyse P, Lê Van A, Heutinck A, Duhamel M, Kadam N, Jagadish K, Ruyter-Spira C, Bouwmeester H. Plant host and drought shape the root associated fungal microbiota in rice. PeerJ 2019; 7:e7463. [PMID: 31565550 PMCID: PMC6744933 DOI: 10.7717/peerj.7463] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/11/2019] [Indexed: 11/22/2022] Open
Abstract
Background and Aim Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought. Methods Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation. Results There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum. Conclusion This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.,Biointeractions & Plant Health Business Unit, Wageningen University & Research, Wageningen, Netherlands
| | | | | | - Arvid Heutinck
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Marie Duhamel
- EcoBio, Université Rennes I, Rennes, France.,IBL Plant Sciences and Natural Products, Leiden University, Leiden, Netherlands
| | - Niteen Kadam
- International Rice Research Institute, Los Baños, Philippines
| | - Krishna Jagadish
- International Rice Research Institute, Los Baños, Philippines.,Department of Agronomy, Kansas State University, Manhattan, KS, United States of America
| | | | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.,Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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50
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Mohd S, Kushwaha AS, Shukla J, Mandrah K, Shankar J, Arjaria N, Saxena PN, Khare P, Narayan R, Dixit S, Siddiqui MH, Tuteja N, Das M, Roy SK, Kumar M. Fungal mediated biotransformation reduces toxicity of arsenic to soil dwelling microorganism and plant. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:108-118. [PMID: 30925326 DOI: 10.1016/j.ecoenv.2019.03.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 05/24/2023]
Abstract
Rhizospheric and plant root associated microbes generally play a protective role against arsenic toxicity in rhizosphere. Rhizospheric microbial interaction influences arsenic (As) detoxification/mobilization into crop plants and its level of toxicity and burden. In the present investigation, we have reported a rhizospheric fungi Aspergillus flavus from an As contaminated rice field, which has capability to grow at high As concentration and convert soluble As into As particles. These As particles showed a reduced toxicity to soil dwelling bacteria, fungi, plant and slime mold. It does not disrupt membrane potential, inner/outer membrane integrity and survival of the free N2 fixating bacteria. In arbuscular mycorrhiza like endophytic fungi Piriformospora indica, these As particles does not influence mycelial growth and plant beneficial parameters such as phosphate solubilizing enzyme rAPase secretion and plant root colonization. Similarly, it does not affect plant growth and chlorophyll content negatively in rice plant. However, these As particles showed a poor absorption and mobilization in plant. These As particle also does not affect attachment process and survival of amoeboid cells in slime mold, Dictyostelium discoideum. This study suggests that the process of conversion of physical and chemical properties of arsenic during transformation, decides the toxicity of arsenic particles in the rhizospheric environment. This phenomenon is of environmental significance, not only in reducing arsenic toxicity but also in the survival of healthy living organism in arsenic-contaminated rhizospheric environment.
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Affiliation(s)
- Shayan Mohd
- Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India; Department of Bioengineering, Faculty of Engineering, Integral University, Dasauli, Kursi Road, Lucknow, 226026, India
| | - Aparna Singh Kushwaha
- Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India
| | - Jagriti Shukla
- Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India
| | - Kapil Mandrah
- Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India
| | - Jai Shankar
- Electron Microscope Facility, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Nidhi Arjaria
- Electron Microscope Facility, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Prem Narain Saxena
- Electron Microscope Facility, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Puneet Khare
- Flow Cytometry Facility, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Ram Narayan
- Confocal Microscope Facility, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Sumita Dixit
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Mohd Haris Siddiqui
- Department of Bioengineering, Faculty of Engineering, Integral University, Dasauli, Kursi Road, Lucknow, 226026, India
| | - Narendra Tuteja
- International Centre of Genetic Engineering and Biotechnology, Aruna Asif Ali Road, New Delhi, 110067, India
| | - Mukul Das
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India
| | - Somendu Kumar Roy
- Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India
| | - Manoj Kumar
- Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, 226 001, Uttar Pradesh, India.
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