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Ding LJ, Ren XY, Zhou ZZ, Zhu D, Zhu YG. Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11027-11040. [PMID: 38857061 DOI: 10.1021/acs.est.4c01203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.
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Affiliation(s)
- Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Yue Ren
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhi-Zi Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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Zhao J, Qiu Y, Yi F, Li J, Wang X, Fu Q, Fu X, Yao Z, Dai Z, Qiu Y, Chen H. Biochar dose-dependent impacts on soil bacterial and fungal diversity across the globe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172509. [PMID: 38642749 DOI: 10.1016/j.scitotenv.2024.172509] [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: 01/04/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/22/2024]
Abstract
Biochar, a widely used material for soil amendment, has been found to offer numerous advantages in improving soil properties and the habitats for soil microorganisms. However, there is still a lack of global perspectives on the influence of various levels of biochar addition on soil microbial diversity and primary components. Thus, in our study, we performed a global meta-analysis of studies to determine how different doses of biochar affect soil total carbon (C), nitrogen (N), pH, alpha- and beta-diversity, and the major phyla of both bacterial and fungal communities. Our results revealed that biochar significantly increased soil pH by 4 %, soil total C and N by 68 % and 22 %, respectively, in which the positive effects increased with biochar doses. Moreover, biochar promoted soil bacterial richness and evenness by 3-8 % at the biochar concentrations of 1-5 % (w/w), while dramatically shifting bacterial beta-diversity at the doses of >2 % (w/w). Specifically, biochar exhibited significantly positive effects on bacterial phyla of Acidobacteria, Bacteroidetes, Gemmatimonadetes, and Proteobacteria, especially Deltaproteobacteria and Gammaproteobacteria, by 4-10 % depending on the concentrations. On the contrary, the bacterial phylum of Verrucomicrobia and fungal phylum of Basidiomycota showed significant negative responses to biochar by -8 % and -24 %, respectively. Therefore, our meta-analysis provides theoretical support for the development of optimized agricultural management practices by emphasizing biochar application dosing.
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Affiliation(s)
- Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Fan Yi
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xueying Wang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Vesamäki JS, Laine MB, Nissinen R, Taipale SJ. Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13302. [PMID: 38852938 PMCID: PMC11162827 DOI: 10.1111/1758-2229.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Boreal freshwaters go through four seasons, however, studies about the decomposition of terrestrial and plastic compounds often focus only on summer. We compared microbial decomposition of 13C-polyethylene, 13C-polystyrene, and 13C-plant litter (Typha latifolia) by determining the biochemical fate of the substrate carbon and identified the microbial decomposer taxa in humic lake waters in four seasons. For the first time, the annual decomposition rate including separated seasonal variation was calculated for microplastics and plant litter in the freshwater system. Polyethylene decomposition was not detected, whereas polystyrene and plant litter were degraded in all seasons. In winter, decomposition rates of polystyrene and plant litter were fivefold and fourfold slower than in summer, respectively. Carbon from each substrate was mainly respired in all seasons. Plant litter was utilized efficiently by various microbial groups, whereas polystyrene decomposition was limited to Alpha- and Gammaproteobacteria. The decomposition was not restricted only to the growth season, highlighting that the decomposition of both labile organic matter and extremely recalcitrant microplastics continues throughout the seasons.
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Affiliation(s)
- Jussi S. Vesamäki
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Miikka B. Laine
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Riitta Nissinen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Sami J. Taipale
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Xiang Y, Xiong W, Yang Z, Xu R, Zhang Y, Wu M, Ye Y, Peng H, Sun W, Wang D. Metagenomic insights into the toxicity of carbamazepine to functional microorganisms in sludge anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170780. [PMID: 38340855 DOI: 10.1016/j.scitotenv.2024.170780] [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: 11/04/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Contaminants of emerging concern (CECs) contained in sludge, such as carbamazepine, may be toxic to microorganisms and affect the biogenesis of methane during anaerobic digestion. In this study, different scales of anaerobic digesters were constructed to investigate the inhibitory effect of carbamazepine. Results showed that carbamazepine reduced methane production by 11.3 % and 62.1 % at concentrations of 0.4 and 2 mg/g TS, respectively. Carbamazepine hindered the dissolution of organic matter and the degradation of protein. Carbamazepine inhibited some fermentative bacteria, especially uncultured Aminicenantales, whose abundance decreased by 9.5-93.4 % under carbamazepine stress. It is worth noting that most prior studies investigated the effects of CECs only based on well-known microorganisms, ignoring the metabolisms of uncultured microorganisms. Genome-predicted metabolic potential suggested that 54 uncultured metagenome-assembled genomes (MAGs) associated with acidogenesis or acetogenesis. Therein, uncultured Aminicenantales related MAGs were proved to be acetogenic fermenters, their significant reduction may be an important reason for the decrease of methane production under carbamazepine stress. The toxicity of carbamazepine to microorganisms was mainly related to the overproduction of reactive oxygen species. This study elucidates the inhibition mechanism of carbamazepine and emphasizes the indispensable role of uncultured microorganisms in anaerobic digestion.
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Affiliation(s)
- Yinping Xiang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Weiping Xiong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China.
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Yanru Zhang
- Fujian Key Laboratory of Pollution Control & Resource Reuse, College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou 350007, PR China
| | - Mengru Wu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Yuhang Ye
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Haihao Peng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Weimin Sun
- Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou 510650, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
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Vélez-Martínez GA, Reyes-Ardila WL, Duque-Zapata JD, Rugeles-Silva PA, Muñoz Flórez JE, López-Álvarez D. Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems. Int Microbiol 2024; 27:377-391. [PMID: 37458953 PMCID: PMC10991037 DOI: 10.1007/s10123-023-00392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 04/05/2024]
Abstract
The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.
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Affiliation(s)
- Glever Alexander Vélez-Martínez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia.
| | - Wendy Lorena Reyes-Ardila
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Juan Diego Duque-Zapata
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Paula Andrea Rugeles-Silva
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Jaime Eduardo Muñoz Flórez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Diana López-Álvarez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia.
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Kachiprath B, Solomon S, Gopi J, Jayachandran PR, Thajudeen J, Sarasan M, Mohan AS, Puthumana J, Chaithanya ER, Philip R. Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait. Braz J Microbiol 2024; 55:499-513. [PMID: 38175355 PMCID: PMC10920534 DOI: 10.1007/s42770-023-01217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
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Affiliation(s)
- Bhavya Kachiprath
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Solly Solomon
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
- Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi, Kerala, 682005, India
| | - Jayanath Gopi
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - P R Jayachandran
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - Jabir Thajudeen
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403804, India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anjali S Mohan
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - E R Chaithanya
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Rosamma Philip
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India.
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Guarin TC, Li L, Haak L, Teel L, Pagilla KR. Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169637. [PMID: 38157893 DOI: 10.1016/j.scitotenv.2023.169637] [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: 08/08/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.
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Affiliation(s)
- Tatiana C Guarin
- Department of Civil and Environmental Engineering, University of Nevada, Reno, NV 89557, USA; ε-BiO: UNAB's Circular Bioeconomy Research Center, Universidad Autónoma de Bucaramanga, Colombia
| | - Lin Li
- Department of Civil and Environmental Engineering, University of Nevada, Reno, NV 89557, USA
| | - Laura Haak
- Department of Civil and Environmental Engineering, University of Nevada, Reno, NV 89557, USA
| | - Lydia Teel
- Truckee Meadows Water Authority, Reno, NV, USA
| | - Krishna R Pagilla
- Department of Civil and Environmental Engineering, University of Nevada, Reno, NV 89557, USA.
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9
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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10
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Contreras MJ, Leal K, Bruna P, Nuñez-Montero K, Goméz-Espinoza O, Santos A, Bravo L, Valenzuela B, Solis F, Gahona G, Cayo M, Dinamarca MA, Ibacache-Quiroga C, Zamorano P, Barrientos L. Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities. Front Microbiol 2023; 14:1197399. [PMID: 37538842 PMCID: PMC10395097 DOI: 10.3389/fmicb.2023.1197399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.
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Affiliation(s)
- María José Contreras
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Karla Leal
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Pablo Bruna
- Centro de Excelencia en Medicina Traslacional, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Kattia Nuñez-Montero
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
- Biotechnology Research Center, Instituto Tecnológico de Costa Rica, Cártago, Costa Rica
| | - Olman Goméz-Espinoza
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Andrés Santos
- Universitat Autònoma de Barcelona, Departament de Genètica i de Microbiologia, Institut Biotecnologia i de Biomedicina, Cerdanyola del Vallès, Barcelona, Spain
| | - León Bravo
- Department of Agricultural Sciences and Natural Resources, Faculty of Agricultural Sciences and Environment, Universidad de La Frontera, Temuco, Chile
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Francisco Solis
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Giovanni Gahona
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Mayra Cayo
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso, Chile
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Departamento Biomédico, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Leticia Barrientos
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Temuco, Chile
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11
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Gomes A, Narciso R, Regalado L, Pinheiro MC, Barros F, Sario S, Santos C, Mendes RJ. Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach. PeerJ 2023; 11:e15525. [PMID: 37397024 PMCID: PMC10312161 DOI: 10.7717/peerj.15525] [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: 03/03/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Backgorund The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices. Methods In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms. Results Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants. Discussion This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.
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Affiliation(s)
- Anicia Gomes
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Rodrigo Narciso
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Laura Regalado
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Margarida Cardeano Pinheiro
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Filipa Barros
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Sara Sario
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Conceição Santos
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Rafael J. Mendes
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- LAQV-REQUIMTE, Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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12
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Coluccia M, Besaury L. Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation. Mol Genet Genomics 2023:10.1007/s00438-023-02045-x. [PMID: 37335345 DOI: 10.1007/s00438-023-02045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.
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Affiliation(s)
- Marion Coluccia
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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13
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Maqbool T, Jiang D. Electrokinetic remediation leads to translocation of dissolved organic matter/nutrients and oxidation of aromatics and polysaccharides. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162703. [PMID: 36906032 DOI: 10.1016/j.scitotenv.2023.162703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Dissolved organic matter (DOM) in the sediment matrix affects contaminant remediation through consumption of oxidants and binding with contaminants. Yet the change in DOM during remediation processes, particularly during electrokinetic remediation (EKR), remains under-investigated. In this work, we elucidated the fate of sediment DOM in EKR using multiple spectroscopic tools under abiotic and biotic conditions. We found that EKR led to significant electromigration of the alkaline-extractable DOM (AEOM) toward the anode, followed by transformation of the aromatics and mineralization of the polysaccharides. The AEOM remaining in the cathode (largely polysaccharides) was resistant to reductive transformation. Limited difference was noted between abiotic and biotic conditions, indicating the dominance of electrochemical processes when relatively high voltages were applied (1-2 V/cm). The water-extractable organic matter (WEOM), in contrast, showed an increase at both electrodes, which was likely attributable to pH-driven dissociations of humic substances and amino acid-type constituents at the cathode and the anode, respectively. Nitrogen migrated with the AEOM toward the anode, but phosphorus remained immobilized. Understanding the redistribution and transformation of DOM could inform studies on contaminant degradation, carbon and nutrient availability, and sediment structural changes in EKR.
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Affiliation(s)
- Tahir Maqbool
- Department of Civil, Construction, and Environmental Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Daqian Jiang
- Department of Civil, Construction, and Environmental Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.
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14
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Cao R, Zhang Y, Ju Y, Wang W, Zhao Y, Liu N, Zhang G, Wang X, Xie X, Dai C, Liu Y, Yin H, Shi K, He C, Wang W, Zhao L, Jeon CO, Hao L. Exopolysaccharide-producing bacteria enhanced Pb immobilization and influenced the microbiome composition in rhizosphere soil of pakchoi (Brassica chinensis L.). Front Microbiol 2023; 14:1117312. [PMID: 36970682 PMCID: PMC10034174 DOI: 10.3389/fmicb.2023.1117312] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
Lead (Pb) contamination of planting soils is increasingly serious, leading to harmful effects on soil microflora and food safety. Exopolysaccharides (EPSs) are carbohydrate polymers produced and secreted by microorganisms, which are efficient biosorbent materials and has been widely used in wastewater treatment to remove heavy metals. However, the effects and underlying mechanism of EPS-producing marine bacteria on soil metal immobilization, plant growth and health remain unclear. The potential of Pseudoalteromonas agarivorans Hao 2018, a high EPS-producing marine bacterium, to produce EPS in soil filtrate, immobilize Pb, and inhibit its uptake by pakchoi (Brassica chinensis L.) was studied in this work. The effects of strain Hao 2018 on the biomass, quality, and rhizospheric soil bacterial community of pakchoi in Pb-contaminated soil were further investigated. The results showed that Hao 2018 reduced the Pb concentration in soil filtrate (16%–75%), and its EPS production increased in the presence of Pb2+. When compared to the control, Hao 2018 remarkably enhanced pakchoi biomass (10.3%–14.3%), decreased Pb content in edible tissues (14.5%–39.2%) and roots (41.3%–41.9%), and reduced the available Pb content (34.8%–38.1%) in the Pb-contaminated soil. Inoculation with Hao 2018 raised the pH of the soil, the activity of several enzymes (alkaline phosphatase, urease, and dehydrogenase), the nitrogen content (NH4+-N and NO3−-N), and the pakchoi quality (Vc and soluble protein content), while also raising the relative abundance of bacteria that promote plant growth and immobilize metals, such as Streptomyces and Sphingomonas. In conclusion, Hao 2018 reduced the available Pb in soil and pakchoi Pb absorption by increasing the pH and activity of multiple enzymes and regulating microbiome composition in rhizospheric soil.
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Affiliation(s)
- Ruiwen Cao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yiling Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yuhao Ju
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Wei Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yanqiu Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Nan Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Gangrui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xingbao Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xuesong Xie
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Cunxi Dai
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yue Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Hongfei Yin
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Kaiyuan Shi
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Chenchen He
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Weiyan Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Lingyu Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Lujiang Hao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- *Correspondence: Lujiang Hao,
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15
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Zhao X, Zhu D, Tan J, Wang R, Qi G. Cooperative Action of Fulvic Acid and Bacillus paralicheniformis Ferment in Regulating Soil Microbiota and Improving Soil Fertility and Plant Resistance to Bacterial Wilt Disease. Microbiol Spectr 2023; 11:e0407922. [PMID: 36861975 PMCID: PMC10100657 DOI: 10.1128/spectrum.04079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
Excessive continuous cropping and soil degradation, such as acidification, hardening, fertility decline, and the degradation of microbial community, lead to the epidemic of soilborne diseases and cause great loss in agriculture production. Application of fulvic acid can improve the growth and yield of various crops and effectively suppress soilborne plant diseases. Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid is used to remove the organic acid that can cause soil acidification and increase the fertilizer effect of fulvic acid and the effect of improving soil quality and inhibiting soilborne disease. In field experiments, the application of fulvic acid and Bacillus paralicheniformis ferment effectively reduced the incidence of bacterial wilt disease and improved soil fertility. Both fulvic acid powder and B. paralicheniformis ferment improved soil microbial diversity and increased the complexity and stability of the microbial network. For B. paralicheniformis ferment, the molecular weight of poly-gamma-glutamic acid became smaller after heating, which could better improve the soil microbial community and network structure. In fulvic acid and B. paralicheniformis ferment-treated soils, the synergistic interaction between microorganisms increased and the number of keystone microorganisms increased, which included antagonistic bacteria and plant growth-promoting bacteria. Changes in the microbial community and network structure were the main reason for the reduced incidence of bacterial wilt disease. Application of fulvic acid and Bacillus paralicheniformis ferment improved soil physicochemical properties and effectively controlled bacterial wilt disease by changing microbial community and network structure and enriching antagonistic and beneficial bacteria. IMPORTANCE Continuous cropping tobacco has led to soil degradation and caused soilborne bacterial wilt disease. Fulvic acid as a biostimulator was applied to restore soil and control bacterial wilt disease. For improving its effect, fulvic acid was fermented with Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid. Fulvic acid and B. paralicheniformis ferment inhibited bacterial wilt disease, improved soil quality, enriched beneficial bacteria, and increased microbial diversity and microbial network complexity. Some keystone microorganisms in fulvic acid and B. paralicheniformis ferment-treated soils had potential antimicrobial activity and plant growth-promoting attributes. Fulvic acid and B. paralicheniformis 285-3 ferment could be used to restore soil quality and microbiota and control bacterial wilt disease. This study found new biomaterial to control soilborne bacterial disease by combining fulvic acid and poly-gamma-glutamic acid application.
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Affiliation(s)
- Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Di Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Tan
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Rui Wang
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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16
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You M, Wang L, Zhou G, Wang Y, Wang K, Zou R, Cao W, Fan H. Effects of microbial agents on cadmium uptake in Solanum nigrum L. and rhizosphere microbial communities in cadmium-contaminated soil. Front Microbiol 2023; 13:1106254. [PMID: 36687578 PMCID: PMC9849675 DOI: 10.3389/fmicb.2022.1106254] [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: 11/23/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Solanum nigrum L. (S. nigrum) and microbial agents are often used for the remediation of cadmium (Cd)-contaminated soil; however, no studies to date have examined the efficacy of using various microbial agents for enhancing the remediation efficiency of Cd-contaminated soil by S. nigrum. Here, we conducted greenhouse pot experiments to evaluate the efficacy of applying Bacillus megaterium (BM) along with citric acid (BM + CA), Glomus mosseae (BM + GM), and Piriformospora indica (BM + PI) on the ability of S. nigrum to remediate Cd-contaminated soil. The results showed that BM + GM significantly increased the Cd accumulation of each pot of S. nigrum by 104% compared with the control. Application of microbial agents changed the soil microbial communities. Redundancy analysis showed that the activities of Catalase (CAT) and urease (UE), soil organic matter, available N and total Cd were the main influencing factors. By constructing the microbial co-occurrence networks, the soil microbe was divided into four main Modules. BM + GM and BM + PI significantly increased the relative abundance of Module#1 and Module#3, respectively, when compared with the control. Additionally, Module#1 showed a significant positive correlation with translocation factor (TF), which could be regarded as the key microbial taxa. Further research found that Ascomycota, Glomeromycota, Proteobacteria, and Actinobacteria within Module#1 were also significantly correlated with TF, and these key species enriched in BM + GM. Overall, our findings indicate that the BM + GM treatment was the most effective for the remediation of Cd pollution. This treatment method may further affect the rhizosphere microbial community by affecting soil indicators, which might drive the formation of Module#1, thus greatly enhancing the Cd remediation capacity of S. nigrum.
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Affiliation(s)
- Meng You
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Wang
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China,Institute of Soil and Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Guopeng Zhou
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yikun Wang
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Wang
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Zou
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China,College of Forestry, Guizhou University, Guiyang, Guizhou, China
| | - Weidong Cao
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Weidong Cao, ✉
| | - Hongli Fan
- Key Laboratory of Plant Nutrition and Fertilizer, National Engineering Research Center of Arable Land Protection, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China,Hongli Fan, ✉
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17
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Beccaccioli M, Moricca C, Faino L, Reale R, Mineo M, Reverberi M. The Neolithic site "La Marmotta": DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood. Front Microbiol 2023; 14:1129983. [PMID: 37032892 PMCID: PMC10079079 DOI: 10.3389/fmicb.2023.1129983] [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: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The evaluation of biological degradation of waterlogged archeological wood is crucial to choose the conservative and protective treatments to be applied to the wooden material. The waterlogged environmental conditions are characterized by oxygen scarcity, only allowing the growth of adapted microbes capable to degrade the organic wooden material, mainly erosion bacteria and soft-rot fungi. In this work, we characterized and evaluated the biodegradation state and the microbial communities of wooden fragments preserved in storage tanks. These were preserved by waterlogging within the Neolithic village "La Marmotta," currently found under the Bracciano Lake (Lazio, Italy). Methods The waterlogged wood samples were first identified taxonomically with an optical microscope, also allowing an evaluation of their preservation state. The microbial community was then evaluated through the sequencing of Internal Transcribed Spacer sequences for fungi and 16S for bacteria with the Oxford Nanopore Technologies (ONT) MinION platform. Results The identified microbial community appears to be consistent with the waterlogged samples, as many bacteria attributable to the erosion of wood and ligninolytic fungi have been sequenced. Discussion The reported results highlight the first use of targeted metabarcoding by ONT applied to study the biodeterioration of waterlogged archeological wood.
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Affiliation(s)
- Marzia Beccaccioli
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
- *Correspondence: Marzia Beccaccioli,
| | - Claudia Moricca
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Luigi Faino
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Rita Reale
- Chemistry Applied to Restoration, A. Galli Academy, Via Petrarca, Como, Italy
| | - Mario Mineo
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
| | - Massimo Reverberi
- Department of Environmental Biology, “Sapienza” University of Rome, Rome, Italy
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Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82T. Microorganisms 2022; 10:microorganisms10112253. [DOI: 10.3390/microorganisms10112253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Acidisarcina polymorpha SBC82T is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82T and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82T by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82T was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.
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19
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Alves KJ, Pylro VS, Nakayama CR, Vital VG, Taketani RG, Santos DG, Mazza Rodrigues JL, Mui TS, Andreote FD. Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change. Microbiol Res 2022; 265:127178. [DOI: 10.1016/j.micres.2022.127178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 08/02/2021] [Accepted: 08/24/2022] [Indexed: 10/14/2022]
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20
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Liu Q, Zhang L, Wang L, Wu Q, Li K, Guo X. Autotoxin affects the rhizosphere microbial community structure by influencing the secretory characteristics of grapevine roots. Front Microbiol 2022; 13:953424. [PMID: 35958141 PMCID: PMC9360756 DOI: 10.3389/fmicb.2022.953424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Autotoxins secreted by roots into the soil can trigger rhizosphere microecological imbalances and affect root secretory properties resulting in conditions such as replanting disease. However, information on the effect of autotoxins on root secretion characteristics and regulation of the composition of rhizosphere microorganisms by altered root exudates is limited. In this study, autotoxin ρ-hydroxybenzoic acid (4-HBA) was added to the soil of potted grapevine seedlings, CO2 pulse-labeling, and DNA stable isotope probing were used to track the rhizosphere microbiome that assimilates root exudates. Bacterial and fungal microbiomes that assimilated plant-derived carbon were identified by high-throughput sequencing. Results showed that 4-HBA treatment altered bacterial and fungal communities in 13C-labeled organisms, with a lower abundance of beneficial bacteria (e.g., Gemmatimonas, Streptomyces, and Bacillus) and a higher abundance of potential pathogen fungi (e.g., Fusarium, Neocosmospora, Gibberella, and Fusicolla) by changing the composition of root exudates. The exogenous addition of upregulated compound mixtures of root exudates reduced the abundance of beneficial bacterial Bacillus and increased the abundance of potential pathogen fungi Gibberella. These results suggest that 4-HBA can alter root secretion properties and altered root exudates may enrich certain potential pathogens and reduce certain beneficial bacteria, thereby unbalancing the structure of the rhizosphere microbial community.
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Affiliation(s)
- Qianwen Liu
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Liheng Zhang
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Dalian Academy of Agricultural Sciences, Dalian, China
| | - Lu Wang
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Qingchun Wu
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Kun Li
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Kun Li,
| | - Xiuwu Guo
- Department of Pomology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Xiuwu Guo,
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21
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Shen J, Luo Y, Tao Q, White PJ, Sun G, Li M, Luo J, He Y, Li B, Li Q, Xu Q, Cai Y, Li H, Wang C. The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154524. [PMID: 35288138 DOI: 10.1016/j.scitotenv.2022.154524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H+)-, aluminium (Al3+)-, and nitrate nitrogen (NO3--N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H+ loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.
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Affiliation(s)
- Jie Shen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Geng Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meng Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jipeng Luo
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting He
- Chengdu Popularization of Agricultural Technique Station, Chengdu 610041, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Xu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Cai
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanxiu Li
- Fruit and Vegetable Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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22
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Viitamäki S, Pessi IS, Virkkala AM, Niittynen P, Kemppinen J, Eronen-Rasimus E, Luoto M, Hultman J. The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types. FEMS Microbiol Ecol 2022; 98:6626023. [PMID: 35776963 PMCID: PMC9341781 DOI: 10.1093/femsec/fiac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.
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Affiliation(s)
| | - Igor S Pessi
- Department of Microbiology, University of Helsinki, Finland.,Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Anna-Maria Virkkala
- Department of Geosciences and Geography, University of Helsinki, Finland.,Woodwell Climate Research Center, Falmouth, MA, USA
| | - Pekka Niittynen
- Department of Geosciences and Geography, University of Helsinki, Finland
| | | | - Eeva Eronen-Rasimus
- Department of Microbiology, University of Helsinki, Finland.,Finnish Environment Institute, Marine Research Centre, Helsinki, Finland
| | - Miska Luoto
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland.,Department of Geosciences and Geography, University of Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Finland.,Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland.,Natural Resources Institute Finland, Helsinki, Finland
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23
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Huber KJ, Pester M, Eichorst SA, Navarrete AA, Foesel BU. Editorial: Acidobacteria – Towards Unraveling the Secrets of a Widespread, Though Enigmatic, Phylum. Front Microbiol 2022; 13:960602. [PMID: 35814658 PMCID: PMC9267355 DOI: 10.3389/fmicb.2022.960602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina J. Huber
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Acacio A. Navarrete
- Graduate Program in Environmental Sciences, University Brazil, São Paulo, Brazil
| | - Bärbel U. Foesel
- Working Group Biobank, Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Bärbel U. Foesel
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24
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Paracidobacterium acidisoli gen. nov., sp. nov. and Alloacidobacterium dinghuense gen. nov., sp. nov., two acidobacteria isolated from forest soil, and reclassification of Acidobacterium ailaaui and Acidipila dinghuensis as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005415] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two aerobic and obligately acidophilic bacteria, designated 4G-K13T and 4Y35T, were isolated from the forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, PR China. These two strains were Gram-stain-negative, non-motile and short rods that multiplied by binary division. Strains 4G-K13T and 4Y35T had the highest 16S rRNA gene sequence similarity of 97.0 and 97.2 % to
Silvibacterium bohemicum
DSM 103733T and
Acidisarcina polymorpha
SBC82T, respectively. Phylogenetic trees based on the 16S rRNA gene and whole genome sequences showed consistently that these two strains formed a major clade with members of the genera
Acidipila
,
Acidisarcina
,
Silvibacterium
and
Acidobacterium
in the family
Acidobacteriaceae
, but each occupied an unique position. In both the UBCG and the PhyloPhlAn phylogenomic trees, strains 4G-K13T and 4Y35T congruently formed a highly supported subclade with
Acidobacterium capsulatum
DSM 11244T and
Acidobacterium ailaaui
DSM 27394T, respectively. The major fatty acids (>5 %) of strain 4G-K13T were iso-C15 : 0, iso-C17 : 0, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 9 (iso-C17 : 1
ω9c and/or C16 : 0 10-methyl), while that of strain 4Y35T were C16 : 0, C18 : 1
ω9c, iso-C15 : 0, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 9 (iso-C17 : 1
ω9c and/or C16 : 0 10-methyl). Strain 4G-K13T contained phosphatidylethanolamine, four unidentified phospholipids, four glycolipids, two unidentified aminolipids and two unknown lipids, while strain 4Y35T had phosphatidylethanolamine, three unidentified phospholipids, two glycolipids, five unidentified aminolipids and one unknown polar lipid. The DNA G+C contents of 4G-K13T and 4Y35T were 60.5 and 55.8 mol%, respectively. Based on all these phylogenetic, physiological and chemotaxonomic data, we suggest that strains 4G-K13T and 4Y35T represent two novel species of two novel genera in the family
Acidobacteriaceae
, for which the names Paracidobacterium acidisoli gen. nov., sp. nov. (type strain: 4G-K13T=GDMCC 1.1195T=NBRC 113249T) and Alloacidobacterium dinghuense gen. nov., sp. nov. (type strain: 4Y35T=KACC 21728T=NBRC 114261T) are proposed. We also propose to reclassify
Acidobacterium ailaaui
and
Acidipila dinghuensis
as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov., respectively, based mainly on the results of phylogenomic analysis.
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25
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Haq IU, Hillmann B, Moran M, Willard S, Knights D, Fixen KR, Schilling JS. Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms. ISME COMMUNICATIONS 2022; 2:26. [PMID: 37938255 PMCID: PMC9723729 DOI: 10.1038/s43705-022-00108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/11/2023]
Abstract
Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.
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Affiliation(s)
- Irshad Ul Haq
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Molly Moran
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
| | - Samuel Willard
- Department of Life Sciences, Imperial College London, London, UK
| | - Dan Knights
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
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26
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Perez-Mon C, Stierli B, Plötze M, Frey B. Fast and persistent responses of alpine permafrost microbial communities to in situ warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150720. [PMID: 34610405 DOI: 10.1016/j.scitotenv.2021.150720] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Global warming in mid-latitude alpine regions results in permafrost thawing, together with greater availability of carbon and nutrients in soils and frequent freeze-thaw cycles. Yet it is unclear how these multifactorial changes will shape the 1 m-deep permafrost microbiome in the future, and how this will in turn modulate microbially-mediated feedbacks between mountain soils and climate (e.g. soil CO2 emissions). To unravel the responses of the alpine permafrost microbiome to in situ warming, we established a three-year experiment in a permafrost monitoring summit in the Alps. Specifically, we simulated conditions of warming by transplanting permafrost soils from a depth of 160 cm either to the active-layer topsoils in the north-facing slope or in the warmer south-facing slope, near the summit. qPCR-based and amplicon sequencing analyses indicated an augmented microbial abundance in the transplanted permafrost, driven by the increase in copiotrophic prokaryotic taxa (e.g. Noviherbaspirillum and Massilia) and metabolically versatile psychrotrophs (e.g. Tundrisphaera and Granulicella); which acclimatized to the changing environment and potentially benefited from substrates released upon thawing. Metabolically restricted Patescibacteria lineages vastly decreased with warming, as reflected in the loss of α-diversity in the transplanted soils. Ascomycetous sapro-pathotrophs (e.g. Tetracladium) and a few lichenized fungi (e.g. Aspicilia) expanded in the transplanted permafrost, particularly in soils transplanted to the warmer south-facing slope, replacing basidiomycetous yeasts (e.g. Glaciozyma). The transplantation-induced loosening of microbial association networks in the permafrost could potentially indicate lesser cooperative interactions between neighboring microorganisms. Broader substrate-use microbial activities measured in the transplanted permafrost could relate to altered soil C dynamics. The three-year simulated warming did not, however, enhance heterotrophic respiration, which was limited by the carbon-depleted permafrost conditions. Collectively, our quantitative findings suggest the vulnerability of the alpine permafrost microbiome to warming, which might improve predictions on microbially-modulated transformations of mountain soil ecosystems under the future climate.
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Affiliation(s)
- Carla Perez-Mon
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Michael Plötze
- Institute for Geotechnical Engineering, ETH Zurich, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
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27
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Cheng Y, Zhou L, Liang T, Man J, Wang Y, Li Y, Chen H, Zhang T. Deciphering Rhizosphere Microbiome Assembly of Castanea henryi in Plantation and Natural Forest. Microorganisms 2021; 10:microorganisms10010042. [PMID: 35056492 PMCID: PMC8779262 DOI: 10.3390/microorganisms10010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022] Open
Abstract
Based on the importance and sensitivity of microbial communities to changes in the forest ecosystem, soil microorganisms can be used to indicate the health of the forest system. The metagenome sequencing was used to analyze the changes of microbial communities between natural and plantation Castanea henryi forests for understanding the effect of forest types on soil microbial communities. Our result showed the soil microbial diversity and richness were higher in the natural forests than in the plantation. Proteobacteria, Actinobacteria, and Acidobacteria are the dominant categories in the C. henryi rhizosphere, and Proteobacteria and Actinobacteria were significantly enriched in the natural forest while Acidobacteria was significantly enriched in the plantation. Meanwhile, the functional gene diversity and the abundance of functions in the natural forest were higher than that of the plantation. Furthermore, we found that the microbial network in the natural forests had more complex than in the plantation. We also emphasized the low-abundance taxa may play an important role in the network structure. These results clearly showed that microbial communities, in response to different forest types, provide valuable information to manipulate microbiomes to improve soil conditions of plantation.
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Affiliation(s)
- Yuanyuan Cheng
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lexin Zhou
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
| | - Tian Liang
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
| | - Jiayin Man
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yinghao Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Li
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
| | - Hui Chen
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- Correspondence: (H.C.); (T.Z.); Tel.: +86-139-5034-3791 (H.C.); +86-180-0691-1945 (T.Z.)
| | - Taoxiang Zhang
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (H.C.); (T.Z.); Tel.: +86-139-5034-3791 (H.C.); +86-180-0691-1945 (T.Z.)
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28
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Li Y, Heal K, Wang S, Cao S, Zhou C. Chemodiversity of Soil Dissolved Organic Matter and Its Association With Soil Microbial Communities Along a Chronosequence of Chinese Fir Monoculture Plantations. Front Microbiol 2021; 12:729344. [PMID: 34745032 PMCID: PMC8566896 DOI: 10.3389/fmicb.2021.729344] [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: 06/23/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
The total dissolved organic matter (DOM) content of soil changes after vegetation transformation, but the diversity of the underlying chemical composition has not been explored in detail. Characterizing the molecular diversity of DOM and its fate enables a better understanding of the soil quality of monoculture forest plantations. This study characterized the chemodiversity of soil DOM, assessed the variation of the soil microbial community composition, and identified specific linkages between DOM molecules and microbial community composition in soil samples from a 100-year chronosequence of Chinese fir monoculture plantations. With increasing plantation age, soil total carbon and dissolved organic carbon first decreased and then increased, while soil nutrients, such as available potassium and phosphorus and total nitrogen, potassium, and phosphorus, increased significantly. Lignin/carboxylic-rich alicyclic molecule (CRAM)-like structures accounted for the largest proportion of DOM, while aliphatic/proteins and carbohydrates showed a decreasing trend along the chronosequence. DOM high in H/C (such as lipids and aliphatic/proteins) degraded preferentially, while low-H/C DOM (such as lignin/CRAM-like structures and tannins) showed recalcitrance during stand development. Soil bacterial richness and diversity increased significantly as stand age increased, while soil fungal diversity tended to increase during early stand development and then decrease. The soil microbial community had a complex connectivity and strong interaction with DOM during stand development. Most bacterial phyla, such as Acidobacteria, Chloroflexi, and Firmicutes, were very significantly and positively correlated with DOM molecules. However, Verrucomicrobia and almost all fungi, such as Basidiomycota and Ascomycota, were significantly negatively correlated with DOM molecules. Overall, the community of soil microorganisms interacted closely with the compositional variability of DOM in the monoculture plantations investigated, both by producing and consuming DOM. This suggests that DOM is not intrinsically recalcitrant but instead persists in soils as a result of simultaneous consumption, transformation, and formation by soil microorganisms with extended stand ages of Chinese fir plantations.
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Affiliation(s)
- Ying Li
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China.,Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Kate Heal
- School of GeoSciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Shuzhen Wang
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Cao
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuifan Zhou
- University Engineering Research Center of Sustainable Plantation Management, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
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29
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New Insights into the Relationships between Bacterial Dynamics and Water Quality of Aquaculture Systems Supplemented with Carbon Source and Biofilm Substratum. Microorganisms 2021; 9:microorganisms9102168. [PMID: 34683490 PMCID: PMC8537099 DOI: 10.3390/microorganisms9102168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
Aquaculture is crucial for achieving the FAO’s goal of a world without hunger and malnutrition. Recently, biofilm substratum has been proposed as an effective means to control waste pollution caused by excessive nutrient inputs from aquaculture, but key bacterial communities involved in the remediation remain unclear. Here we reported a freshwater mesocosm study where the addition of biofilm substrata with external carbon effectively controlled the total ammonia nitrogen and improved fish growth. 16S rRNA study and Weighted UniFrac analysis revealed that bacterial compositions were significantly different (999 permutations, p-value < 0.01) between the biofilm-substrata-added and biofilm-substrata-free systems. Planctomycetes were found, as key bacteria benefited from the biofilm substrata addition and exerted the major function of ammonia nitrogen control. Our study demonstrated that the addition of biofilm substrata and an external carbon source favored fish growth and improved the aquaculture environment by the formation of a unique bacteria community.
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30
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Rodrigues GR, Pinto OHB, Schroeder LF, Fernandes GDR, Costa OYA, Quirino BF, Kuramae EE, Barreto CC. Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils. FEMS Microbiol Lett 2021; 367:5902847. [PMID: 32897365 DOI: 10.1093/femsle/fnaa149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/02/2020] [Indexed: 11/13/2022] Open
Abstract
The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.
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Affiliation(s)
- Gisele Regina Rodrigues
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | - Otávio Henrique Bezerra Pinto
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | - Luís Felipe Schroeder
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
| | | | - Ohana Yonara Assis Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
| | - Betania Ferraz Quirino
- Brazilian Agricultural Research Corporation - EMBRAPA/Agroenergy, Brasília, DF 70770-901, Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands.,Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CS, Utrecht, The Netherlands
| | - Cristine Chaves Barreto
- Universidade Católica de Brasília, Graduate Program in Genomic Sciences and Biotechnology, SGAN 916, Brasília, DF 70790-160, Brazil
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Mohapatra M, Yadav R, Rajput V, Dharne MS, Rastogi G. Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112738. [PMID: 34020306 DOI: 10.1016/j.jenvman.2021.112738] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/05/2021] [Accepted: 04/29/2021] [Indexed: 05/22/2023]
Abstract
Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Pune, 411008, India; Academic of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
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Yadav A, Borrelli JC, Elshahed MS, Youssef NH. Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats. Appl Environ Microbiol 2021; 87:e0094721. [PMID: 34160232 PMCID: PMC8357285 DOI: 10.1128/aem.00947-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
Approaches for recovering and analyzing genomes belonging to novel, hitherto-unexplored bacterial lineages have provided invaluable insights into the metabolic capabilities and ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent and ecologically successful lineages on Earth, yet currently, multiple lineages within this phylum remain unexplored. Here, we utilize genomes recovered from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil and nonsoil habitats, to examine the metabolic capabilities and ecological role of members of family UBA6911 (group 18) Acidobacteria. The analyzed genomes clustered into five distinct genera, with genera Gp18_AA60 and QHZH01 recovered from soils, genus Ga0209509 from anaerobic digestors, and genera Ga0212092 and UBA6911 from freshwater habitats. All genomes analyzed suggested that members of Acidobacteria group 18 are metabolically versatile heterotrophs capable of utilizing a wide range of proteins, amino acids, and sugars as carbon sources, possess respiratory and fermentative capacities, and display few auxotrophies. Soil-dwelling genera were characterized by larger genome sizes, higher numbers of CRISPR loci, an expanded carbohydrate active enzyme (CAZyme) machinery enabling debranching of specific sugars from polymers, possession of a C1 (methanol and methylamine) degradation machinery, and a sole dependence on aerobic respiration. In contrast, nonsoil genomes encoded a more versatile respiratory capacity for oxygen, nitrite, sulfate, and trimethylamine N-oxide (TMAO) respiration, as well as the potential for utilizing the Wood-Ljungdahl (WL) pathway as an electron sink during heterotrophic growth. Our results not only expand our knowledge of the metabolism of a yet-uncultured bacterial lineage but also provide interesting clues on how terrestrialization and niche adaptation drive metabolic specialization within the Acidobacteria. IMPORTANCE Members of the Acidobacteria are important players in global biogeochemical cycles, especially in soils. A wide range of acidobacterial lineages remain currently unexplored. We present a detailed genomic characterization of genomes belonging to family UBA6911 (also known as group 18) within the phylum Acidobacteria. The genomes belong to different genera and were obtained from soil (genera Gp18_AA60 and QHZH01), freshwater habitats (genera Ga0212092 and UBA6911), and an anaerobic digestor (genus Ga0209509). While all members of the family shared common metabolic features, e.g., heterotrophic respiratory abilities, broad substrate utilization capacities, and few auxotrophies, distinct differences between soil and nonsoil genera were observed. Soil genera were characterized by expanded genomes, higher numbers of CRISPR loci, a larger carbohydrate active enzyme (CAZyme) repertoire enabling monomer extractions from polymer side chains, and methylotrophic (methanol and methylamine) degradation capacities. In contrast, nonsoil genera encoded more versatile respiratory capacities for utilizing nitrite, sulfate, TMAO, and the WL pathway, in addition to oxygen as electron acceptors. Our results not only broaden our understanding of the metabolic capacities within the Acidobacteria but also provide interesting clues on how terrestrialization shaped Acidobacteria evolution and niche adaptation.
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Affiliation(s)
- Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jenna C. Borrelli
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Mostafa S. Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Wang R, Wang M, Wang J, Lin Y. Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau. Microorganisms 2021; 9:microorganisms9081595. [PMID: 34442674 PMCID: PMC8400953 DOI: 10.3390/microorganisms9081595] [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: 06/07/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.
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Affiliation(s)
- Rui Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Miao Wang
- Party School of the Chengdu Committee of the Chinese Communist Party, Chengdu 610110, China;
| | - Jing Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Yinghua Lin
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
- Correspondence: ; Tel.: +86-13671160455
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Ibekwe AM, Ors S, Ferreira JFS, Liu X, Suarez DL. Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage. PLoS One 2021; 16:e0252242. [PMID: 34061881 PMCID: PMC8168849 DOI: 10.1371/journal.pone.0252242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/11/2021] [Indexed: 11/18/2022] Open
Abstract
The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.
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Affiliation(s)
- Abasiofiok M. Ibekwe
- US Salinity Laboratory, USDA-ARS, Riverside, CA, United States of America
- * E-mail:
| | - Selda Ors
- Ataturk University, Department of Agricultural Structures and Irrigation, Erzurum, Turkey
| | | | - Xuan Liu
- US Salinity Laboratory, USDA-ARS, Riverside, CA, United States of America
| | - Donald L. Suarez
- US Salinity Laboratory, USDA-ARS, Riverside, CA, United States of America
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Yan L, Zhang W, Duan W, Zhang Y, Zheng W, Lai X. Temporal Bacterial Community Diversity in the Nicotiana tabacum Rhizosphere Over Years of Continuous Monocropping. Front Microbiol 2021; 12:641643. [PMID: 34113322 PMCID: PMC8186668 DOI: 10.3389/fmicb.2021.641643] [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: 12/14/2020] [Accepted: 04/28/2021] [Indexed: 01/19/2023] Open
Abstract
Long-term continuous monocropping negatively influences the physicochemical and biological characteristics of cultivated soil, especially for the economically important crop of flue-cured tobacco that is intolerant to continuous monocropping. The underlying mechanism of soil sickness under continuous monoculture and the temporal dynamic changes over the tobacco life cycle among different monoculture time spans remain poorly characterized. In this study, high-throughput sequencing targeting the 16S rRNA gene phylogenetic marker was performed on 60 soil samples of rhizosphere soil from flue−cured tobacco in the replanting, growth and harvest period across 5, 10, and 20 years of a continuous monocropping system. Bacterial community diversity decreased with the increase in duration of continuous monocropping, and the rhizosphere microbiota was highly dynamic in the harvest period. The random forests algorithm identified 17 taxa as biomarkers and a model was established to correlate root microbiota with continuous monocropping time of flue-cured tobacco. Molecular ecological network analysis elaborated the differences and interactions in bacterial co-occurrence patterns under different monocropping systems. The co-occurrence microbial network was larger in size but there were fewer interactions among microbial communities with the increase in continuous monocropping duration. These results provide insights into the changes of flue−cured tobacco root microbiome diversity in response to continuous monocropping and suggest a model for successional dynamics of the root-associated microbiota over continuous monocropping time and development stage. This study may help elucidate the theoretical basis underlying obstacles to continuous monocropping and could contribute to improving guidance for tobacco production.
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Affiliation(s)
- Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
| | - Wenyou Zhang
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
| | - Wangjun Duan
- China Tobacco Sichuan Industrial Co., Ltd., Chengdu, China
| | - Yizheng Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wen Zheng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
| | - Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Xichang, China
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Kalinowska A, Jankowska K, Fudala-Ksiazek S, Pierpaoli M, Luczkiewicz A. The microbial community, its biochemical potential, and the antimicrobial resistance of Enterococcus spp. in Arctic lakes under natural and anthropogenic impact (West Spitsbergen). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:142998. [PMID: 33213908 DOI: 10.1016/j.scitotenv.2020.142998] [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: 05/30/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
The sustainable management of small human communities in the Arctic is challenging. In this study, both a water supply system (Lake 1) under the natural impact of a bird-nesting area, and a wastewater receiver (Lake 2) were analysed in the vicinity of the Polish Polar Station on West Spitsbergen. Microbial community composition, abundance and activity were assessed in samples of the treated wastewater, lake water and sediments using next-generation sequencing and direct microscope counts. Special attention was given to the faecal indicator, Enterococcus spp., whose occurrence and antimicrobial resistance were tested in water and wastewater samples. The results indicate that Lake 1, at a tundra stream discharge (L-TS) and a water supply point (L-WS) were dominated by three phyla: Proteobacteria (57-58%) Bacteroidetes (27-29%) and Actinobacteria (9-10%), showing similar microbial composition up to the genus level. This suggests that nutrient-rich runoff from the bird colony was retained by surrounding tundra vegetation and reached Lake 1 at L-TS to a limited extent. Lake 2, being the wastewater recipient (WW-R), mirrors to some extent the core phyla of treated wastewater (WW-E), but in different shares. This suggests the possible washout of wastewater-related bacteria with activated sludge flocs, which was also supported by the microscopic observations. Compared to Lake 1, in WW-R an increase in all tested parameters was noted: total prokaryotic cell number, average cell volume, prokaryotic biomass and live cell percentage. The presence of Enterococcus spp. antibiotic resistance patterns highlight the importance of human associated microbiome and resistome dissemination via wastewater discharge. Moreover, it can be expected that temperature-related biochemical processes (e.g. nutrient cycling) may be accelerated by the ongoing climate change. Thus, proper wastewater treatment requires locally adapted solutions in increasingly visited and inhabited polar regions. Additionally, microbial community discharged to the environment with the treated wastewater, requires critical attention.
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Affiliation(s)
- Agnieszka Kalinowska
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Katarzyna Jankowska
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Sylwia Fudala-Ksiazek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Mattia Pierpaoli
- Department of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Aneta Luczkiewicz
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Zhang C, Liu Q, Li X, Wang M, Liu X, Yang J, Xu J, Jiang Y. Spatial patterns and co-occurrence networks of microbial communities related to environmental heterogeneity in deep-sea surface sediments around Yap Trench, Western Pacific Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143799. [PMID: 33333332 DOI: 10.1016/j.scitotenv.2020.143799] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
Microbial communities are a large component of abyssal and hadal benthic environments, especially in deep-sea areas like Yap Trench, they provide a continuous source of nutrients and energy in their unique ecosystems. However, due to sampling difficulties, these microbial communities are relatively understudied. In the summer of 2017, sediment samples were collected from 21 stations around Yap Trench in the Western Pacific Ocean (mostly in the West Caroline Basin), at depths ranging from 3156 to 7837 m. Sediment samples from deep water depths and shallow water depths differed in organic matter content, median grain size, silt-clay content, and biodiversity. The structure of the microbial communities in the surface sediments had distinct relationships with environmental factors and their co-occurrence networks exhibited a clear spatial pattern. In addition, for both prokaryotes or eukaryotes, a combination of variables including silt-clay content, organic matter content, median grain size, and depth had the greatest impact on community structure. It was notable that fungi played important roles in the co-occurrence networks of deep water depth sediment samples while bacteria dominated those of shallow water depth samples. The differences in structure and ecological niches in the different networks were due to differences in sediment texture and organic matter content. Since clay had a positive effect on the diversity of bacteria, it had an indirect positive effect on fungi, leading to differences in biodiversity among different groups. More organic matter meant more nutrients were available for the growth and reproduction of microbes, which led to fewer niche overlaps. This study conducted an extensive and systematic sequencing survey of surface sediments around Yap Trench in the Western Pacific Ocean, providing insight into microbial responses to environmental heterogeneity in deep-sea benthic ecosystems.
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Affiliation(s)
- Chenru Zhang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Qian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xianrong Li
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiaoshou Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jinpeng Yang
- School of Marine Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jishang Xu
- Key Lab of Submarine Geosciences and Prospecting Techniques, Ministry of Education, Qingdao, China; College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
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Akinwole P, Kaplan L, Findlay R. Elucidating stream bacteria utilizing terrestrial dissolved organic matter. World J Microbiol Biotechnol 2021; 37:32. [DOI: 10.1007/s11274-021-02997-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
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Pinto OHB, Costa FS, Rodrigues GR, da Costa RA, da Rocha Fernandes G, Júnior ORP, Barreto CC. Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids. MICROBIAL ECOLOGY 2021; 81:169-179. [PMID: 32617619 DOI: 10.1007/s00248-020-01548-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.
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Affiliation(s)
- Otávio Henrique Bezerra Pinto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Laboratory of Enzymology, Institute of Biological Sciences, Department of Cell Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Flávio Silva Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Gisele Regina Rodrigues
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Rosiane Andrade da Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Gabriel da Rocha Fernandes
- Research Center René Rachou, Oswaldo Cruz Foundation (Fiocruz), Avenida Augusto de Lima 1715, Barro Preto, Belo Horizonte, 30190-002, Brazil
| | - Osmindo Rodrigues Pires Júnior
- Department of Physiological Sciences, Institute of Biological Sciences, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil.
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Carrias JF, Gerphagnon M, Rodríguez-Pérez H, Borrel G, Loiseau C, Corbara B, Céréghino R, Mary I, Leroy C. Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem. FEMS Microbiol Ecol 2020; 96:5807077. [PMID: 32175561 DOI: 10.1093/femsec/fiaa045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/13/2020] [Indexed: 12/23/2022] Open
Abstract
Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.
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Affiliation(s)
- Jean-François Carrias
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Mélanie Gerphagnon
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Héctor Rodríguez-Pérez
- UMR EcoFoG, CNRS, CIRAD, INRA, AgroParisTech, Université des Antilles, Université de Guyane, 97310 Kourou, France
| | - Guillaume Borrel
- Institut Pasteur, Department of Microbiology, Unité de Biologie Évolutive de la Cellule Microbienne, Paris, France
| | - Camille Loiseau
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Bruno Corbara
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Régis Céréghino
- Ecolab, Laboratoire Ecologie Fonctionnelle et Environnement, CNRS, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse, France
| | - Isabelle Mary
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Céline Leroy
- UMR EcoFoG, CNRS, CIRAD, INRA, AgroParisTech, Université des Antilles, Université de Guyane, 97310 Kourou, France.,AMAP, IRD, CIRAD, CNRS, INRA, Université Montpellier, Montpellier, France
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41
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Effect of Organic and Conventional Systems Used to Grow Pecan Trees on Diversity of Soil Microbiota. DIVERSITY 2020. [DOI: 10.3390/d12110436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Agronomic management modifies the soil bacterial communities and may alter the carbon fractions. Here, we identify differences in several chemical and biological soil variables, as well as bacterial composition between organic (Org) and conventional (Conv) agronomic management in pecan (Carya illinoinensis) orchards located in Coahuila, Mexico. The analyzed variables were pH, N, P, K, soil organic matter, organic matter quality, soil organic carbon, C/N ratio, carbon fractions, microbial biomass carbon, easily extractable Glomalin, colony-forming units, CO2 emissions, and the enzyme activity. The DNA of soil bacteria was extracted, amplified (V3-V4 16S rRNA), and sequenced using Illumina. To compare variables between agronomic managements, t tests were used. Sequences were analyzed in QIIME (Quantitative Insights Into Microbial Ecology). A canonical correspondence analysis (CCA) was used to observe associations between the ten most abundant phyla and soil variables in both types of agronomic managements. In Org management, variables related to the capture of recalcitrant carbon compounds were significant, and there was a greater diversity of bacterial communities capable of promoting organic carbon sequestration. In Conv management, variables related to the increase in carbon mineralization, as well as the enzymatic activity related to the metabolism of labile compounds, were significant. The CCA suggested a separation between phyla associated with some variables. Agronomic management impacted soil chemical and biological parameters related to carbon dynamics, including bacterial communities associated with carbon sequestration. Further research is still necessary to understand the plasticity of some bacterial communities, as well as the soil–plant dynamics.
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Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Front Microbiol 2020; 11:580024. [PMID: 33193209 PMCID: PMC7661733 DOI: 10.3389/fmicb.2020.580024] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
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Affiliation(s)
- Sadaf Kalam
- Department of Biochemistry, St. Ann's College for Women, Hyderabad, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science and Commerce College, Shahada, India
| | - Hesham Ali El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,City of Scientific Research and Technological Applications, New Borg El-Arab, Egypt
| | - Daniel Joe Dailin
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia
| | - Ni Luh Suriani
- Biology Department, Faculty of Mathematics and Natural Science, Udayana University, Bali, Indonesia
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Bacterial Communities Associated with the Biofilms Formed in High-Altitude Brackish Water Pangong Tso Located in the Himalayan Plateau. Curr Microbiol 2020; 77:4072-4084. [PMID: 33079205 DOI: 10.1007/s00284-020-02244-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon's and Simpson's alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.
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Naumoff DG, Dedysh SN. Chitinases Encoded in the Genomes of Acidobacteria: Origin and Evolution. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning. Microorganisms 2020; 8:microorganisms8050694. [PMID: 32397341 PMCID: PMC7285516 DOI: 10.3390/microorganisms8050694] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 01/11/2023] Open
Abstract
Although the effects of fertilization and microbiota on plant growth have been widely studied, our understanding of the chemical fertilizers to alter soil chemical and microbiological properties in woody plants is still limited. The aim of the present study is to investigate the impact of long-term application of chemical fertilizers on chemical and microbiological properties of root-associated soils of walnut trees. The results show that soil organic matter (OM), pHkcl, total nitrogen (TN), nitrate-nitrogen (NO3−), and total phosphorus (TP) contents were significantly higher in non-fertilized soil than after chemical fertilization. The long-term fertilization led to excessive ammonium-nitrogen (NH4+) and available phosphorus (AP) residues in the cultivated soil, among which NH4+ resulted in soil acidification and changes in bacterial community structure, while AP reduced fungal diversity. The naturally grown walnut trees led to an enrichment in beneficial bacteria such as Burkholderia, Nitrospira, Pseudomonas, and Candidatus_Solibacter, as well as fungi, including Trichoderma, Lophiostoma, Phomopsis, Ilyonectria, Purpureocillium, Cylindrocladiella, Hyalorbilia, Chaetomium, and Trichoglossum. The presence of these bacterial and fungal genera that have been associated with nutrient mobilization and plant growth was likely related to the higher soil OM, TN, NO3−, and TP contents in the non-fertilized plots. These findings highlight that reduced chemical fertilizers and organic cultivation with beneficial microbiota could be used to improve economic efficiency and benefit the environment in sustainable agriculture.
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Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils. PLoS One 2020; 15:e0230157. [PMID: 32182280 PMCID: PMC7077872 DOI: 10.1371/journal.pone.0230157] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022] Open
Abstract
The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation–unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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48
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Li J, Li C, Kou Y, Yao M, He Z, Li X. Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in a mountain ecosystem. FEMS Microbiol Ecol 2020; 96:5766225. [DOI: 10.1093/femsec/fiaa030] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 02/27/2020] [Indexed: 01/09/2023] Open
Abstract
ABSTRACT
Understanding microbial network assembly is a promising way to predict potential impacts of environmental changes on ecosystem functions. Yet, soil microbial network assembly in mountain ecosystems and its underlying mechanisms remain elusive. Here, we characterized soil microbial co-occurrence networks across 12 altitudinal sites in Mountain Gongga. Despite differences in habitats, soil bacterial networks separated into two different clusters by altitude, namely the lower and higher altitudes, while fungi did not show such a pattern. Bacterial networks encompassed more complex and closer relationships at the lower altitudes, while fungi had closer relationships at the higher altitudes, which could be attributed to niche differentiation caused by high variations in soil environments and plant communities. Both abiotic and biotic factors (e.g. soil pH and bacterial community composition) shaped bacterial networks. However, biotic factors played more important roles than the measured abiotic factors for fungal network assembly. Further analyses suggest that multiple mechanisms including niche overlap/differentiation, cross-feeding and competition between microorganisms could play important roles in shaping soil microbial networks. This study reveals microbial co-occurrence networks in response to different ecological factors, which provides important insights into our comprehensive understanding of microbial network assembly and their functional potentials in mountain ecosystems.
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Affiliation(s)
- Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China 610041
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China 610041
| | - Yongping Kou
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China 610041
| | - Minjie Yao
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China 610041
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China 510006
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China 610041
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49
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Xu Y, Liu J, Cai W, Feng J, Lu Z, Wang H, Franks AE, Tang C, He Y, Xu J. Dynamic processes in conjunction with microbial response to disclose the biochar effect on pentachlorophenol degradation under both aerobic and anaerobic conditions. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121503. [PMID: 31708286 DOI: 10.1016/j.jhazmat.2019.121503] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/05/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Organochlorines are critical soil contaminants and the use of biochar has recently shown potential to improve soil remediation. However, little is known about biochar-microbe interactions nor the impact on environmental processes such as the immobilization and biodegradation of organochlorine compounds. In this study, we performed microcosm experiments to elucidate how biochar affected the biodegradation and sequestration of pentachlorophenol (PCP). Our results showed that the amendment of biochar markedly inhibited PCP biodegradation due to a strong sorption affinity for PCP under both aerobic and anaerobic conditions. Notably, the inhibitory effect was relatively weaker under anaerobic conditions than under aerobic conditions. The addition of biochar can dramatically shift the bacterial community diversity in the PCP-spiked soils. Under aerobic conditions, biochar significantly stimulated the growth of PCP-degrading bacteria Bacillus and Sphingomonas, but reduced the opportunities for microbes to contact with PCP directly. Under anaerobic conditions, the non-strict organohalide-respiring bacteria Desulfovibrio, Anaeromyxobacter, Geobacter and Desulfomonile were the main drivers of PCP transformation. Our results imply that the use of biochar as a soil remediation strategy for organochlorine compounds should be cautious.
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Affiliation(s)
- Yan Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jiaqi Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Wenshan Cai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jiayin Feng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Zhijiang Lu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Victoria, 3086, Australia; Centre for Future Landscapes, La Trobe University, Victoria 3086, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Victoria, 3086, Australia
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
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50
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Ni BJ, Zeng S, Wei W, Dai X, Sun J. Impact of roxithromycin on waste activated sludge anaerobic digestion: Methane production, carbon transformation and antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134899. [PMID: 31757536 DOI: 10.1016/j.scitotenv.2019.134899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/26/2019] [Accepted: 10/07/2019] [Indexed: 05/22/2023]
Abstract
The macrolide antibiotic roxithromycin is widely detected in varying aquatic environments, especially in the wastewater systems, as an emerging contaminant and leads to significant impacts on the microorganisms involved. In this study, the impact of a shock load of roxithromycin on waste activated sludge (WAS) anaerobic digestion was comprehensively investigated. The biochemical methane potential tests showed that the methane production from WAS anaerobic digestion was significantly inhibited by roxithromycin. With the dosage of roxithromycin increasing from 0 to 1000 μg/L, the maximum cumulative methane production decreased from 163.5 ± 2.6 mL/g VS to 150.9 ± 4.5 mL/g VS. In particular, roxithromycin inhibited the acidogenesis and methanogenesis in WAS anaerobic digestion, leading to the decreased methane production. The methanogenic archaea in the studied system mainly belonged to the genera of Methanoseata, Candidatus Methanofastidiosum and Methanolinea and their relative abundances also decreased with roxithromycin addition. The analysis of antibiotic resistance genes (ARGs) in the digested sludge indicated that the abundances of most ARGs detected in this study were increased with roxithromycin exposure, suggesting the potential of growing antibiotic resistance, which was probably caused by enhancing the effect of esterases, methylases and phosphorylases. This work reveals how roxithromycin affects the WAS anaerobic digestion and the change of ARGs in the anaerobic digestion with roxithromycin exposure, and provides useful information for practical operation.
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Affiliation(s)
- Bing-Jie Ni
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Shuting Zeng
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Wei Wei
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Jing Sun
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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