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Trecarten S, Fongang B, Liss M. Current Trends and Challenges of Microbiome Research in Prostate Cancer. Curr Oncol Rep 2024; 26:477-487. [PMID: 38573440 DOI: 10.1007/s11912-024-01520-x] [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] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE OF REVIEW The role of the gut microbiome in prostate cancer is an emerging area of research interest. However, no single causative organism has yet been identified. The goal of this paper is to examine the role of the microbiome in prostate cancer and summarize the challenges relating to methodology in specimen collection, sequencing technology, and interpretation of results. RECENT FINDINGS Significant heterogeneity still exists in methodology for stool sampling/storage, preservative options, DNA extraction, and sequencing database selection/in silico processing. Debate persists over primer choice in amplicon sequencing as well as optimal methods for data normalization. Statistical methods for longitudinal microbiome analysis continue to undergo refinement. While standardization of methodology may help yield more consistent results for organism identification in prostate cancer, this is a difficult task due to considerable procedural variation at each step in the process. Further reproducibility and methodology research is required.
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Affiliation(s)
- Shaun Trecarten
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Michael Liss
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
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2
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He L, Zhao Y, Zhao X, Wang Y, Dang Q. Regulating method of microbial driving the phosphorus bioavailability in factory composting. BIORESOURCE TECHNOLOGY 2023; 387:129676. [PMID: 37586430 DOI: 10.1016/j.biortech.2023.129676] [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: 06/12/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
Phosphorus bioavailability is essential for assessing compost quality. However, the effects of microbial and environmental factors on potentially active phosphorus (H2O-P + NaHCO3-Pi) in factory compost have not been investigated. The findings indicated that chicken manure had significantly higher available phosphorus (AP) and H2O-P + NaHCO3-Pi throughout the composting process than kitchen waste (P < 0.05). Chicken manure compost also exhibited higher α-microbial diversity. Novibacillus, Marinococcaceae and Bacillales were the core bacteria involved in bioavailable phosphorus conversion in both composts. The core bacteria in kitchen waste compost had a broader range of phosphorus metabolism functions. Moreover, moisture and pH were the key environmental factors that significantly influenced the bioavailable phosphorus (P < 0.05). These findings provide a scientific foundation for regulating the composting process and improving phosphorus utilization efficiency.
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Affiliation(s)
- Liangzi He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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3
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He J, Zhou T, Shen X, Zhang N, Sun C, Lu S, Shao Y. Primer selection impacts the evaluation of microecological patterns in environmental microbiomes. IMETA 2023; 2:e135. [PMID: 38868223 PMCID: PMC10989904 DOI: 10.1002/imt2.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 06/14/2024]
Abstract
This study revealed that primer selection substantially influences the taxonomic and predicted functional composition and the characterization of microecological patterns, which was not alleviated by close-reference clustering. Biases were relatively consistent across different habitats in community profiling but not in microecological patterns. These primer biases could be attributed to multiple aspects, including taxa specificity, regional hypervariability, and amplification efficiency.
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Affiliation(s)
- Jintao He
- Max Planck Partner Group, Institute of Sericulture and Apiculture, Faculty of Agriculture, Life and Environmental SciencesZhejiang UniversityHangzhouChina
| | - Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Xiaoqiang Shen
- Max Planck Partner Group, Institute of Sericulture and Apiculture, Faculty of Agriculture, Life and Environmental SciencesZhejiang UniversityHangzhouChina
| | - Nan Zhang
- Max Planck Partner Group, Institute of Sericulture and Apiculture, Faculty of Agriculture, Life and Environmental SciencesZhejiang UniversityHangzhouChina
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental SciencesZhejiang UniversityHangzhouChina
| | - Shipeng Lu
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Yongqi Shao
- Max Planck Partner Group, Institute of Sericulture and Apiculture, Faculty of Agriculture, Life and Environmental SciencesZhejiang UniversityHangzhouChina
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang ProvinceHangzhouChina
- Key Laboratory for Molecular Animal NutritionMinistry of EducationHangzhouChina
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4
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Klinsawat W, Uthaipaisanwong P, Jenjaroenpun P, Sripiboon S, Wongsurawat T, Kusonmano K. Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing. Sci Rep 2023; 13:17685. [PMID: 37848699 PMCID: PMC10582034 DOI: 10.1038/s41598-023-44981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.
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Affiliation(s)
- Worata Klinsawat
- Conservation Ecology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supaphen Sripiboon
- Department of Large Animal and Wildlife Clinical Science, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Kanthida Kusonmano
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
- Bioinformatics and Systems Biology Program, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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Chen W, Feng Z, Chang Y, Xu S, Zhou K, Shi X, Wang Z, Zhang L, Wei Y, Li J. Comparing the bacterial composition, succession and assembly patterns in plastisphere and kitchen waste composting with PLA/PBAT blends. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131405. [PMID: 37098293 DOI: 10.1016/j.jhazmat.2023.131405] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023]
Abstract
Biodegradable plastics has aroused increasing concern due to the negative environmental impact of plastic waste, however, the impact of biodegradable plastics mixed into kitchen waste (KW) on composting remains poorly understood, especially focusing on bacterial communities in the unique "plastisphere". Here, KW composting for 120 days with adding poly lactic acid / poly butylene adipate-co-terephthalate (PLA/PBAT) plastics were conducted to reveal the dynamics of bacterial composition, succession, and assembly process in different ecological niches (compost and plastisphere). Results showed that the existence of PLA/PBAT plastics in composting would not significantly affect the safety and maturation of composts. After composting, 80% PLA/PBAT were degraded and there were prominent divergences of bacterial compositions between plastisphere, composts with PLA/PBAT and control. Co-occurrence network suggested that PLA/PBAT plastisphere exhibited higher network complexity and cohesion than that in compost, and PLA/PBAT increased bacterial module hubs, network hubs, and connectors in composting compared to control, but might enrich pathogens. Phylogenetic bin-based null model analysis indicated that stochastic processes obviously shaped the communities on PLA/PBAT plastisphere, but compare to control, PLA/PBAT plastics enhanced the contribution of deterministic processes on composting bacterial community assembly. These findings deeply understood the assembly patterns and diversity of plastisphere and composting processes, laying down a foundation on applying biodegradable plastics under the classification of domestic garbage.
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Affiliation(s)
- Wenjie Chen
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Ziwei Feng
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Yuan Chang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Shaoqi Xu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Kaiyun Zhou
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Xiong Shi
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China
| | - Zhigang Wang
- DBN Agriculture Science and Technology Group CO., Ltd. DBN Pig Academy, Beijing 102629, China
| | - Longli Zhang
- Beijing Voto Sky and Land Biotechnology Limited Company, 100193 Beijing, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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6
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Zehnle H, Laso-Pérez R, Lipp J, Riedel D, Benito Merino D, Teske A, Wegener G. Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes. Nat Microbiol 2023:10.1038/s41564-023-01400-3. [PMID: 37264141 DOI: 10.1038/s41564-023-01400-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
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Affiliation(s)
- Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
- Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Julius Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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7
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Cummings S, Ardor Bellucci LM, Seabrook S, Raineault NA, McPhail KL, Thurber AR. Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific. PeerJ 2023; 11:e15119. [PMID: 37009161 PMCID: PMC10064993 DOI: 10.7717/peerj.15119] [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: 01/20/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.
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Affiliation(s)
- Susie Cummings
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States of America
| | - Lila M. Ardor Bellucci
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Sarah Seabrook
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | | | - Kerry L. McPhail
- College of Pharmacy, Oregon State University, Corvallis, OR, United States of America
| | - Andrew R. Thurber
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, United States of America
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States of America
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8
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Zhao J, Rodriguez J, Martens-Habbena W. Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils. Front Microbiol 2023; 14:1140487. [PMID: 36910167 PMCID: PMC9995467 DOI: 10.3389/fmicb.2023.1140487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Jonathan Rodriguez
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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9
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Moll J, Hoppe B. Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing. PeerJ 2022; 10:e14567. [PMID: 36573238 PMCID: PMC9789694 DOI: 10.7717/peerj.14567] [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: 08/10/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.
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Affiliation(s)
- Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ, Halle (Saale), Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Braunschweig, Germany
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10
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Scherer BP, Mason OU, Mast AR. Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front. FEMS Microbiol Ecol 2022; 98:6840209. [PMID: 36413458 DOI: 10.1093/femsec/fiac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray-Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling.
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Affiliation(s)
- Brendan P Scherer
- Florida State University, 319 Stadium Drive, Tallahassee, FL 32304, United States
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, 1011 Academic Way, Tallahassee, FL 32304, United States
| | - Austin R Mast
- Department of Biological Sciences, Florida State University, 319 Stadium Drive, Tallahassee, FL 32304, United States
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11
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Chen W, Zhan Y, Zhang X, Shi X, Wang Z, Xu S, Chang Y, Ding G, Li J, Wei Y. Influence of carbon-to-phosphorus ratios on phosphorus fractions transformation and bacterial community succession in phosphorus-enriched composting. BIORESOURCE TECHNOLOGY 2022; 362:127786. [PMID: 35970498 DOI: 10.1016/j.biortech.2022.127786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
This study aims to assess the effect of different carbon-to-phosphorus (C:P) ratios on phosphorus (P) fractions transformation, bacterial community succession and microbial P-solubilizing function in kitchen waste composting with rock phosphate (RP) amendment and phosphate-solubilizing bacteria (PSB) inoculation. Results indicated that initial C:P ratio at 50 enhanced organic carbon degradation, available P (AP) accumulation, the amount of PSB and pqqC gene abundance in composting but higher C:P ratio increased microbial biomass phosphorus (MBP) content. Redundancy analysis showed C:P ratios, PSB amount and pqqC gene abundance greatly affected bacterial community diversity and composition. Network analysis indicated that lower C:P ratio enhanced the interaction frequency in core bacterial network for AP transformation. Variance partitioning analysis abiotic factors contributed more to MBP and AP conversion. The study revealed that C:P ratio could directly drive PSB to regulate P fractions and the accumulation of MBP or AP in P-enriched composting.
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Affiliation(s)
- Wenjie Chen
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yabin Zhan
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Xinjun Zhang
- Institute of Tibet Plateau Ecology, Tibet Agricultural & Animal Husbandry University, and Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agricultural & Animal Husbandry University), Ministry of Education, Nyingchi, Tibet 860000, China
| | - Xiong Shi
- Yangtze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China
| | - Zhigang Wang
- DBN Agriculture Science and Technology Group CO., Ltd., DBN Pig Academy, Beijing 102629, China
| | - Shaoqi Xu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Yuan Chang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Guochun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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12
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Li J, Liu P, Menguy N, Benzerara K, Bai J, Zhao X, Leroy E, Zhang C, Zhang H, Liu J, Zhang R, Zhu K, Roberts AP, Pan Y. Identification of sulfate-reducing magnetotactic bacteria via a group-specific 16S rDNA primer and correlative fluorescence and electron microscopy: strategy for culture-independent study. Environ Microbiol 2022; 24:5019-5038. [PMID: 35726890 DOI: 10.1111/1462-2920.16109] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/02/2022] [Accepted: 06/18/2022] [Indexed: 11/28/2022]
Abstract
Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and swim along geomagnetic field lines. While few axenic MTB cultures exist, living cells can be separated magnetically from natural environments for analysis. The bacterial universal 27F/1492R primer pair has been used widely to amplify nearly full-length 16S rRNA genes and to provide phylogenetic portraits of MTB communities. However, incomplete coverage and amplification biases inevitably prevent detection of some phylogenetically specific or non-abundant MTB. Here, we propose a new formulation of the upstream 390F primer that we combined with the downstream 1492R primer to specifically amplify 1,100-bp 16S rRNA gene sequences of sulfate-reducing MTB in freshwater sediments from Lake Weiyanghu, Xi'an, northwestern China. With correlative fluorescence in situ hybridization and scanning/transmission electron microscopy, three novel MTB strains (WYHR-2, WYHR-3, and WYHR-4) from the Desulfobacterota phylum were identified phylogenetically and structurally at the single cell level. Strain WYHR-2 produces bullet-shaped magnetosome magnetite, while the other two strains produce both cubic/prismatic greigite and bullet-shaped magnetite. Our results expand knowledge of bacterial diversity and magnetosome biomineralization of sulfate-reducing MTB. We also propose a general strategy for identifying and characterizing uncultured MTB from natural environments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Nicolas Menguy
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, UMR CNRS 7590, MNHN, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Jinling Bai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiang Zhao
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | - Eric Leroy
- ICMPE, University Paris East, UMR 7182, CNRS, 2-8 rue Henri Dunant, Thiais Cedex, France
| | - Chaoqun Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Heng Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jiawei Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongrong Zhang
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Keilei Zhu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Andrew P Roberts
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Innovation Academy for Earth Science, Chinese Academy of Sciences, Beijing, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
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13
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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14
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Wang L, Wang Y, Wang F, Zhao M, Gao X, Chen H, Li N, Zhu Q, Liu L, Zhu W, Liu X, Chen Y, Zhou P, Lu Y, Wang K, Zhao W, Liang W. Development and Application of Rapid Clinical Visualization Molecular Diagnostic Technology for Cryptococcus neoformans/ C. gattii Based on Recombinase Polymerase Amplification Combined With a Lateral Flow Strip. Front Cell Infect Microbiol 2022; 11:803798. [PMID: 35096653 PMCID: PMC8790172 DOI: 10.3389/fcimb.2021.803798] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Cryptococcus neoformans (C. neoformans)/C. gattii can easily invade the human central nervous system and cause cryptococcal meningitis (CM). The clinical fatality rate of these fungi is extremely high and causes more than 180,000 deaths worldwide every year. At present, the common clinical identification methods of these fungi are traditional culture methods and Indian ink staining. In addition, enzyme-linked immunosorbent assay (ELISAs), polymerase chain reaction (PCR), real-time quantitative PCR detecting system (qPCR), mass spectrometry, and metagenomic next-generation sequencing (mNGS) have also been applied to detect these fungus. Due to the rapid progress of meningitis caused by C. neoformans/C. gattii infection, there is a desperate need for fast, sensitive, and on-site detection methods to meet the clinical diagnosis. Recombinase polymerase amplification (RPA) is a promising isothermal amplification technique that can compensate for the shortcomings of the above techniques, featuring short reaction time, high specificity, and high sensitivity, thus meeting the demand for in-field detection of C.neoformans/C. gattii. In our study, RPA- lateral flow strip (LFS) was used to amplify the capsule-associated gene, CAP64, of C. neoformans/C. gattii, and the primer-probe design was optimized by introducing base mismatches to obtain a specific and sensitive primer-probe combination for clinical testing, and specificity of the detection system was determined for 26 common clinical pathogens. This system was developed to obtain results in 20 min at an isothermal temperature of 37°C with a lower limit of detection as low as 10 CFU/μL or 1 fg/μL. A total of 487 clinical samples collected from multicenter multiplexes were tested to evaluate the detection performance of the RPA-LFS system, which revealed that the system could specifically detect C. neoformans/C. gattii, meeting the need for rapid, specific, and sensitive detection.
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Affiliation(s)
- Lei Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China.,School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yan Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Fang Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Mengdi Zhao
- Department of Materials Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Xuzhu Gao
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Huimin Chen
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Na Li
- Lianyungang Second People's Hospital Affiliated to Bengbu Medical College, Lianyungang, China
| | - Qing Zhu
- Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Lipin Liu
- Lianyungang Hospital Affiliated to Xuzhou Medical University, Lianyungang, China
| | - Wenjun Zhu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Xia Liu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Yujiao Chen
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Ping Zhou
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Yingzhi Lu
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Kun Wang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
| | - Weiguo Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Wei Liang
- Department of Central Laboratory, Lianyungang Hospital Affiliated to Jiangsu University, Lianyungang, China
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15
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Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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16
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Moreno CR, Ramires JAF, Lotufo PA, Soeiro AM, Oliveira LMDS, Ikegami RN, Kawakami JT, Pereira JDJ, Reis MM, Higuchi MDL. Morphomolecular Characterization of Serum Nanovesicles From Microbiomes Differentiates Stable and Infarcted Atherosclerotic Patients. Front Cardiovasc Med 2021; 8:694851. [PMID: 34422924 PMCID: PMC8375156 DOI: 10.3389/fcvm.2021.694851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
Microbial communities are considered decisive for maintaining a healthy situation or for determining diseases. Acute myocardial infarction (AMI) is an important complication of atherosclerosis caused by the rupture of atheroma plaques containing proinflammatory cytokines, reactive oxygen species, oxidized low-density lipoproteins (oxLDL), damaged proteins, lipids, and DNA, a microenvironment compatible with a pathogenic microbial community. Previously, we found that archaeal DNA-positive infectious microvesicles (iMVs) were detected in vulnerable plaques and in the sera of Chagas disease patients with heart failure. Now, we characterize and quantify the levels of serum microbiome extracellular vesicles through their size and content using morphomolecular techniques to differentiate clinical outcomes in coronary artery disease (CAD). We detected increased numbers of large iMVs (0.8–1.34 nm) with highly negative surface charge that were positive for archaeal DNA, Mycoplasma pneumoniae antigens and MMP9 in the sera of severe AMI patients, strongly favoring our hypothesis that pathogenic archaea may play a role in the worst outcomes of atherosclerosis. The highest numbers of EVs <100 nm (exosomes) and MVs from 100 to 200 nm in the stable atherosclerotic and control healthy groups compared with the AMI groups were indicative that these EVs are protective, entrapping and degrading infectious antigens and active MMP9 and protect against the development of plaque rupture. Conclusion: A microbiome with pathogenic archaea is associated with high numbers of serum iMVs in AMI with the worst prognosis. This pioneering work demonstrates that the morphomolecular characterization and quantification of iEVs in serum may constitute a promising serum prognostic biomarker in CAD.
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Affiliation(s)
- Camila Rodrigues Moreno
- Laboratorio de Patologia Cardiaca, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - José Antonio Franchini Ramires
- Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Alexandre Matos Soeiro
- Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Luanda Mara da Silva Oliveira
- Laboratório de Investigação em Dermatologia e Imunodeficiências - LIM56, Departamento de Dermatologia, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Renata Nishiyama Ikegami
- Laboratorio de Patologia Cardiaca, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Joyce Tiyeko Kawakami
- Laboratorio de Patologia Cardiaca, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jaqueline de Jesus Pereira
- Laboratorio de Patologia Cardiaca, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Marcia Martins Reis
- Laboratorio de Patologia Cardiaca, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria de Lourdes Higuchi
- Laboratorio de Patologia Cardiaca, Instituto do Coracao, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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17
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Kumari K, Naskar M, Aftabuddin M, Das Sarkar S, Ghosh BD, Sarkar UK, Nag SK, Jana C, Das BK. Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems. Front Microbiol 2021; 12:643945. [PMID: 34335488 PMCID: PMC8317468 DOI: 10.3389/fmicb.2021.643945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/10/2021] [Indexed: 01/04/2023] Open
Abstract
The ultimate role of prokaryote (bacteria and archaea), the decomposer of the wetland ecosystem, depends on its community structure and its interaction with the environment. The present study has used three universal prokaryote primers to compare prokaryote community structure and diversity of three distinctly different wetlands. The study results revealed that α-diversity indices and phylogenetic differential abundance patterns did not differ significantly among primers, but they did differ significantly across wetlands. Microbial community composition revealed a distinct pattern for each primer in each wetland. Overall comparison of prokaryote communities in sediments of three wetlands revealed the highest prokaryote richness and diversity in Bhomra (freshwater wetland) followed by Malencho (brackish-water wetland) and East Kolkata wetland (EKW) (sewage-fed wetland). Indicator genus analysis identified 21, 4, and 29 unique indicator genera, having preferential abode for Bhomra, EKW, and Malencho, respectively. Prediction of potential roles of these microbes revealed a preference for sulfate-reducing microbes in Malencho and methanogens in Bhomra. The distinct phylogenetic differential abundance pattern, microbial abode preference, and their potential functional role predict ecosystem variables shaping microbial diversity. The variation in community composition of prokaryotes in response to ecosystem variables can serve as the most sensitive bioindicator of wetland ecosystem assessment and management.
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Affiliation(s)
- Kavita Kumari
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Malay Naskar
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Md Aftabuddin
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Soma Das Sarkar
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Bandana Das Ghosh
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Uttam Kumar Sarkar
- Reservoir and Wetland Fisheries Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Subir Kumar Nag
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Chayna Jana
- Fisheries Resource Assessment and Informatics Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
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18
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Bazzocchi G, Turroni S, Bulzamini MC, D'Amico F, Bava A, Castiglioni M, Cagnetta V, Losavio E, Cazzaniga M, Terenghi L, De Palma L, Frasca G, Aiachini B, Cremascoli S, Massone A, Oggerino C, Onesta MP, Rapisarda L, Pagliacci MC, Biscotto S, Scarazzato M, Giovannini T, Balloni M, Candela M, Brigidi P, Kiekens C. Changes in gut microbiota in the acute phase after spinal cord injury correlate with severity of the lesion. Sci Rep 2021; 11:12743. [PMID: 34140572 PMCID: PMC8211659 DOI: 10.1038/s41598-021-92027-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023] Open
Abstract
After spinal cord injury (SCI), patients face many physical and psychological issues including intestinal dysfunction and comorbidities, strongly affecting quality of life. The gut microbiota has recently been suggested to influence the course of the disease in these patients. However, to date only two studies have profiled the gut microbiota in SCI patients, months after a traumatic injury. Here we characterized the gut microbiota in a large Italian SCI population, within a short time from a not only traumatic injury. Feces were collected within the first week at the rehabilitation center (no later than 60 days after SCI), and profiled by 16S rRNA gene-based next-generation sequencing. Microbial profiles were compared to those publicly available of healthy age- and gender-matched Italians, and correlated to patient metadata, including type of SCI, spinal unit location, nutrition and concomitant antibiotic therapies. The gut microbiota of SCI patients shows distinct dysbiotic signatures, i.e. increase in potentially pathogenic, pro-inflammatory and mucus-degrading bacteria, and depletion of short-chain fatty acid producers. While robust to most host variables, such dysbiosis varies by lesion level and completeness, with the most neurologically impaired patients showing an even more unbalanced microbial profile. The SCI-related gut microbiome dysbiosis is very likely secondary to injury and closely related to the degree of completeness and severity of the lesion, regardless of etiology and time interval. This microbial layout could variously contribute to increased gut permeability and inflammation, potentially predisposing patients to the onset of severe comorbidities.
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Affiliation(s)
- Gabriele Bazzocchi
- Neurogastroenterology Unit, Montecatone Rehabilitation Institute, via Montecatone 37, 40026, Imola, Bologna, Italy.
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mimosa Balloni
- Neurogastroenterology Unit, Montecatone Rehabilitation Institute, via Montecatone 37, 40026, Imola, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Carlotte Kiekens
- Spinal Unit, Montecatone Rehabilitation Institute, Imola, Bologna, Italy
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19
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Data on the optimization of an archaea-specific probe-based qPCR assay. Data Brief 2021; 33:106610. [PMID: 34026962 PMCID: PMC8129643 DOI: 10.1016/j.dib.2020.106610] [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: 07/28/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 11/23/2022] Open
Abstract
Estimation of archaeal numbers by use of fluorescent DNA binding dyes is challenging, because primers targeting the archaeal 16SrRNA genes readily also bind to bacterial 16S rRNA gene sequences, especially when the relative abundance of bacteria is greater than that of archaea. In order to increase specificity, we optimized a fluorescent probe-based assay using previously published archaeal primers and probe. The assay was tested on genomic DNA of pure bacterial and archaeal cultures and optimized using PCR amplicons of the archaeal pure cultures. The used bacterial strains showed slight amplification using the fluorescent dye assay, whereas all archaeal strains could be amplified with the archaea primers used. Due to differences in genome size and number of 16S rRNA gene copies between the tested archaeal strains, the amplification level varied greatly between the strains. Therefore, we also tested the amplification using PCR amplified fragments of the archaeal 16S rRNA genes. The tests with the archaeal 16S rRNA gene amplicons showed good amplification, although the amplification efficiency still varied between archaeal strains. The qPCR assay was used to estimate the archaeal numbers in process water of a multi-metal mine's metallurgical plant [1] and will be used in similar future microbiological analysis included in the H2020 ITERAMS project (Grant agreement# 730480).
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20
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Zhao R, Liu J, Feng J, Li X, Li B. Microbial community composition and metabolic functions in landfill leachate from different landfills of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144861. [PMID: 33422962 DOI: 10.1016/j.scitotenv.2020.144861] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
Landfill leachate usually harbors complex microbial communities responsible for the decomposition of municipal solid waste. However, the diversity and metabolic functions of the microbial communities in landfill leachate as well as the factors that influence them are still not well understood. In this study, Illumina MiSeq high-throughput sequencing was used to investigate the microbial community composition and metabolic functions in landfill leachate from 11 cities in China. The microbial diversity and structure of different leachate samples exhibited obvious differences. In general, Bacteroidetes, Firmicutes and Proteobacteria were the three dominant microbial communities among the 26 bacterial phyla identified in landfill leachate, regardless of the geographical locations. Diverse bacterial genera associated with various functions such as cellulolytic bacteria (e.g., Sphaerochaeta and Defluviitoga), acidifying bacteria (e.g., Prevotella and Trichococcus) and sulfate-reducing bacteria (e.g., Desulfuromonas and Desulfobacterium) were detected abundantly in the landfill leachate. Moreover, the archaeal community in all leachate samples was dominated by the orders Methanomicrobiales and Methanosarcinales belonging to the Euryarchaeota phylum. Notably, the archaea-specific primer pair covered more diverse archaeal communities than the universal bacteria-archaea primer pair. Seventeen archaeal genera belonging to acetoclastic, hydrogenotrophic, and methylotrophic methanogens were identified, and the composition of the dominant genera in these samples varied greatly. The canonical correlation analysis indicated that landfill age, electrical conductivity, ammonia nitrogen, and total nitrogen were significantly correlated with the microbial community structure. Based on PICRUSt2, a total of 41 metabolic pathways belonging to six metabolic pathway groups were predicted, and the KEGG pathway Metabolism was the most abundant group across all leachate samples. This study provides an important insight into the composition and functional characteristics of the microbial communities in landfill leachate.
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Affiliation(s)
- Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Jie Feng
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Drinking Water Source Management and Technology, Shenzhen Research Academy of Environmental Sciences, Shenzhen 518001, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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21
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Abstract
Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies investigating microbiomes. However, comparative studies on differences in procedures are scarce. We sequenced human stool samples and mock communities with increasing complexity using a variety of commonly used protocols. Short amplicons targeting different variable regions (V-regions) or ranges thereof (V1-V2, V1-V3, V3-V4, V4, V4-V5, V6-V8, and V7-V9) were investigated for differences in the composition outcome due to primer choices. Next, the influence of clustering (operational taxonomic units [OTUs], zero-radius OTUs [zOTUs], and amplicon sequence variants [ASVs]), different databases (GreenGenes, the Ribosomal Database Project, Silva, the genomic-based 16S rRNA Database, and The All-Species Living Tree), and bioinformatic settings on taxonomic assignment were also investigated. We present a systematic comparison across all typically used V-regions using well-established primers. While it is known that the primer choice has a significant influence on the resulting microbial composition, we show that microbial profiles generated using different primer pairs need independent validation of performance. Further, comparing data sets across V-regions using different databases might be misleading due to differences in nomenclature (e.g., Enterorhabdus versus Adlercreutzia) and varying precisions in classification down to genus level. Overall, specific but important taxa are not picked up by certain primer pairs (e.g., Bacteroidetes is missed using primers 515F-944R) or due to the database used (e.g., Acetatifactor in GreenGenes and the genomic-based 16S rRNA Database). We found that appropriate truncation of amplicons is essential and different truncated-length combinations should be tested for each study. Finally, specific mock communities of sufficient and adequate complexity are highly recommended. IMPORTANCE In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies. Conclusions drawn by comparing one data set to another (e.g., between publications) appear to be problematic and require independent cross-validation using matching V-regions and uniform data processing. Therefore, we highlight the importance of a thought-out study design including sufficiently complex mock standards and appropriate V-region choice for the sample of interest. The use of processing pipelines and parameters must be tested beforehand.
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Ribera-Pi J, Campitelli A, Badia-Fabregat M, Jubany I, Martínez-Lladó X, McAdam E, Jefferson B, Soares A. Hydrolysis and Methanogenesis in UASB-AnMBR Treating Municipal Wastewater Under Psychrophilic Conditions: Importance of Reactor Configuration and Inoculum. Front Bioeng Biotechnol 2020; 8:567695. [PMID: 33224930 PMCID: PMC7667289 DOI: 10.3389/fbioe.2020.567695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Three upflow anaerobic sludge blanket (UASB) pilot scale reactors with different configurations and inocula: flocculent biomass (F-UASB), flocculent biomass and membrane solids separation (F-AnMBR) and granular biomass and membrane solids separation (G-AnMBR) were operated to compare start-up, solids hydrolysis and effluent quality. The parallel operation of UASBs with these different configurations at low temperatures (9.7 ± 2.4°C) and the low COD content (sCOD 54.1 ± 10.3 mg/L and pCOD 84.1 ± 48.5 mg/L), was novel and not previously reported. A quick start-up was observed for the three reactors and could be attributed to the previous acclimation of the seed sludge to the settled wastewater and to low temperatures. The results obtained for the first 45 days of operation showed that solids management was critical to reach a high effluent quality. Overall, the F-AnMBR showed higher rates of hydrolysis per solid removed (38%) among the three different UASB configurations tested. Flocculent biomass promoted slightly higher hydrolysis than granular biomass. The effluent quality obtained in the F-AnMBR was 38.0 ± 5.9 mg pCOD/L, 0.4 ± 0.9 mg sCOD/L, 9.9 ± 1.3 mg BOD5/L and <1 mg TSS/L. The microbial diversity of the biomass was also assessed. Bacteroidales and Clostridiales were the major bacterial fermenter orders detected and a relative high abundance of syntrophic bacteria was also detected. Additionally, an elevated abundance of sulfate reducing bacteria (SRB) was also identified and was attributed to the low COD/SO4 2- ratio of the wastewater (0.5). Also, the coexistence of acetoclastic and hydrogenotrophic methanogenesis was suggested. Overall this study demonstrates the suitability of UASB reactors coupled with membrane can achieve a high effluent quality when treating municipal wastewater under psychrophilic temperatures with F-AnMBR promoting slightly higher hydrolysis rates.
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Affiliation(s)
- Judit Ribera-Pi
- Eurecat, Centre Tecnològic de Catalunya, Water, Air and Soil Unit, Manresa, Spain
| | - Antonio Campitelli
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
| | | | - Irene Jubany
- Eurecat, Centre Tecnològic de Catalunya, Water, Air and Soil Unit, Manresa, Spain
| | | | - Ewan McAdam
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
| | - Bruce Jefferson
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
| | - Ana Soares
- Cranfield Water Science Institute, Vincent Building, Cranfield University, Cranfield, United Kingdom
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23
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Krolicka A, Gomiero A, Baussant T. qPCR-based assessment of microfaunal indicators of oil for monitoring benthos around oil and gas platforms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139527. [PMID: 32497879 DOI: 10.1016/j.scitotenv.2020.139527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/05/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
Today's benthic offshore biological monitoring of oil & gas (O&G) activities relies on macrofauna taxa enumeration. For the future, analysis of DNA isolated directly from sediments holds great potential for multi-trophic biodiversity surveys and the monitoring of a larger spectrum of benthic taxa, including micro-fauna. Here, we evaluate more specifically the potential of microfauna-specific gene quantification in relation to both petroleum-related discharge compounds and other seafloor environmental properties. We carried out this evaluation using sediment samples collected at drilling Region III on the Norwegian continental shelf where DNA metabarcoding of eukaryotic diversity was already performed. Generally, the quantification of microfauna indicator taxa related well to the gradient of contamination on the seafloor. Contrary to eukaryotic Euplotida, metabarcoding data and qPCR numbers for indicative prokaryotic taxa showed the same relationship to offshore contaminants (both showed positive relationship). We found absolute numbers of SSU rRNA gene copies of (1) Dinophyceae, Bacillariophyceae and Alcanivorax were correlated with the level of petroleum-related compounds but not with other environmental variables, (2) bacteria closely related to Shewanella were correlated with the concentration of Ba, PAH, as well to percent of gravel, (3) Desulfobacteriales correlated with petroleum-related contaminants, but as well with percent of gravel and grain size. Findings from our study suggest that biomonitoring surveys of O&G activities on benthos could benefit from quantification of specific micro-fauna indicators that is simpler and faster than the methods currently used for impact assessment of benthos.
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Affiliation(s)
- Adriana Krolicka
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway.
| | - Alessio Gomiero
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
| | - Thierry Baussant
- NORCE - Norwegian Research Centre - Environment, Mekjarvik 12, 4070 Randaberg, Norway
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24
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Bomberg M, Miettinen H, Musuku B, Kinnunen P. First insights to the microbial communities in the plant process water of the multi-metal Kevitsa mine. Res Microbiol 2020; 171:230-242. [PMID: 32798644 DOI: 10.1016/j.resmic.2020.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 11/26/2022]
Abstract
Metallurgical processes demand large quantities of water. However, in many locations, water is becoming scarce and process water recycling is needed. Closing water loops can be challenging due to build-up of flotation chemicals, metal ions and microorganisms in the recycled water affecting the flotation performance. Here, we have characterized the microbial communities over a 2-month period in different locations of the multi-metal Kevitsa mine in Northern Finland, by microbiome sequencing, enumeration of bacteria, archaea and fungi by qPCR, and cultivation. The microbial communities showed high diversity, but were dominated by Alpha- and Gammaproteobacteria. In addition, various fungal taxa were detected, whereas the archaeal taxa were only sparsely detected from the sequence data. The number of bacterial 16S rRNA gene copies in Process water and Ni thickener overflow varied between 0.5-3.3 × 105 mL-1, whereas the Flotation tailings showed two orders of magnitude lower amounts. Fungi were present at 3.0 × 102-8.1 × 104 5.8S rRNA gene copies mL-1 in all samples, while the number of archaea fluctuated between 8.8 × 101-3.2 × 105 16S rRNA gene copies mL-1. The number of all microbial groups were generally lower in September than in August. When tested on 8 different cultivation media, the microorganisms generally responded positively to organic carbon, and were also shown to oxidize thiosulfate, which may indicate that build-up of organic flotation chemicals and sulfur species from the ore may cause the microbial numbers to increase. This study is part of the H2020 ITERAMS project (Grant agreement# 730480), which strives to improve the recycling of water and minimize the environmental impact of mines.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Tietotie 2, FIN-02150, Espoo, Finland.
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland Ltd., Tietotie 2, FIN-02150, Espoo, Finland
| | - Benjamin Musuku
- Boliden Kevitsa, Kevitsantie 730, FIN-99670, Petkula, Finland
| | - Päivi Kinnunen
- VTT Technical Research Centre of Finland Ltd, Visiokatu 4, 33101, Tampere, Finland
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25
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Thurber AR, Seabrook S, Welsh RM. Riddles in the cold: Antarctic endemism and microbial succession impact methane cycling in the Southern Ocean. Proc Biol Sci 2020; 287:20201134. [PMID: 32693727 PMCID: PMC7423672 DOI: 10.1098/rspb.2020.1134] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70 m × 1 m) microbial mat formed at 10 m water depth in the Ross Sea, Antarctica which we identify here to be a high latitude hydrogen sulfide and methane seep. Through 16S rRNA gene analysis on samples collected 1 year and 5 years after the methane seep formed, we identify the taxa involved in the Antarctic methane cycle and quantify the response rate of the microbial community to a novel input of methane. One year after the seep formed, ANaerobic MEthane oxidizing archaea (ANME), the dominant sink of methane globally, were absent. Five years later, ANME were found to make up to 4% of the microbial community, however the dominant member of this group observed (ANME-1) were unexpected considering the cold temperature (-1.8°C) and high sulfate concentrations (greater than 24 mM) present at this site. Additionally, the microbial community had not yet formed a sufficient filter to mitigate the release of methane from the sediment; methane flux from the sediment was still significant at 3.1 mmol CH4 m-2 d-1. We hypothesize that this 5 year time point represents an early successional stage of the microbiota in response to methane input. This study provides the first report of the evolution of a seep system from a non-seep environment, and reveals that the rate of microbial succession may have an unrealized impact on greenhouse gas emission from marine methane reservoirs.
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Affiliation(s)
- Andrew R Thurber
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA.,Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
| | - Sarah Seabrook
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Rory M Welsh
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR, USA
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26
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De Vrieze J. The next frontier of the anaerobic digestion microbiome: From ecology to process control. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2020; 3:100032. [PMID: 36159602 PMCID: PMC9488066 DOI: 10.1016/j.ese.2020.100032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 05/11/2023]
Abstract
The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.
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27
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Hough M, McClure A, Bolduc B, Dorrepaal E, Saleska S, Klepac-Ceraj V, Rich V. Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient. Front Microbiol 2020; 11:796. [PMID: 32499761 PMCID: PMC7243355 DOI: 10.3389/fmicb.2020.00796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/03/2020] [Indexed: 02/01/2023] Open
Abstract
Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.
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Affiliation(s)
- Moira Hough
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Amelia McClure
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Benjamin Bolduc
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umeå University, Umeå, Sweden
| | - Scott Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Virginia Rich
- Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, United States
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28
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Matijašić M, Meštrović T, Paljetak HČ, Perić M, Barešić A, Verbanac D. Gut Microbiota beyond Bacteria-Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD. Int J Mol Sci 2020; 21:E2668. [PMID: 32290414 PMCID: PMC7215374 DOI: 10.3390/ijms21082668] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.
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Affiliation(s)
- Mario Matijašić
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | | | - Hana Čipčić Paljetak
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Mihaela Perić
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Anja Barešić
- Division of Electronics, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Donatella Verbanac
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
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29
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Zhao R, Summers ZM, Christman GD, Yoshimura KM, Biddle JF. Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico. Sci Rep 2020; 10:5772. [PMID: 32238866 PMCID: PMC7113308 DOI: 10.1038/s41598-020-62840-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafloor hydrocarbon seeps have been demonstrated to significantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10-15 cm below seafloor) were collected from five natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chloroflexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fixation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. Although ANME-1 archaea and SRB are present in low relative abundances, genome bins from the reference sites are dominated by uncultured members of NC10 and anammox Scalindua, suggesting a prevalence of nitrogen transformations for energy in non-seep pelagic sediments. This study suggests that hydrocarbon seeps can greatly change the microbial community structure by stimulating nitrogen fixation, inherently shifting the nitrogen metabolism compared to those of the reference sediments.
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Affiliation(s)
- Rui Zhao
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Zarath M Summers
- Corporate Strategic Research, ExxonMobil Research and Engineering, Annandale, NJ, United States
| | - Glenn D Christman
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Kristin M Yoshimura
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States.
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30
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Abstract
The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.
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Affiliation(s)
- A Belmok
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - J A de Cena
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
| | - C M Kyaw
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - N Damé-Teixeira
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
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31
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Bižić M, Klintzsch T, Ionescu D, Hindiyeh MY, Günthel M, Muro-Pastor AM, Eckert W, Urich T, Keppler F, Grossart HP. Aquatic and terrestrial cyanobacteria produce methane. SCIENCE ADVANCES 2020; 6:eaax5343. [PMID: 31998836 PMCID: PMC6962044 DOI: 10.1126/sciadv.aax5343] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.
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Affiliation(s)
- M. Bižić
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Corresponding author. (M.B.); (H.-P.G.)
| | - T. Klintzsch
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
| | - D. Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
| | - M. Y. Hindiyeh
- Department of Water and Environmental Engineering, German Jordanian University, Amman, Jordan
| | - M. Günthel
- Department of Biosciences, Swansea University, SA2 8PP Swansea, UK
- Medical University of Gdańsk, Department of International Research Agenda 3P–Medicine, Marii Skłodowskiej-Curie 3a, 80-210 Gdańsk, Poland
| | - A. M. Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - W. Eckert
- Israel Oceanographic and Limnological Research, Yigal Allon Kinneret Limnological Laboratory, Migdal 14650, Israel
| | - T. Urich
- Institute of Microbiology, Center for Functional Genomics, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - F. Keppler
- Institute of Earth Sciences, Biogeochemistry Group, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Heidelberg University, 69120 Heidelberg, Germany
| | - H.-P. Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2, D-16775 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
- Corresponding author. (M.B.); (H.-P.G.)
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Callejas C, Fernández A, Passeggi M, Wenzel J, Bovio P, Borzacconi L, Etchebehere C. Microbiota adaptation after an alkaline pH perturbation in a full-scale UASB anaerobic reactor treating dairy wastewater. Bioprocess Biosyst Eng 2019; 42:2035-2046. [PMID: 31506821 DOI: 10.1007/s00449-019-02198-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/31/2019] [Accepted: 08/31/2019] [Indexed: 01/09/2023]
Abstract
The aim of this study was to understand how the microbial community adapted to changes, including a pH perturbation, occurring during the start-up and operation processes in a full-scale methanogenic UASB reactor designed to treat dairy wastewater. The reactor performance, prokaryotic community, and lipid degradation capacity were monitored over a 9-month period. The methanogenic community was studied by mcrA/mrtA gene copy-number quantification and methanogenic activity tests. A diverse prokaryotic community characterized the seeding sludge as assessed by sequencing the V4 region of the 16S rRNA gene. As the feeding began, the bacterial community was dominated by Firmicutes, Synergistetes, and Proteobacteria phyla. After an accidental pH increase that affected the microbial community structure, a sharp increase in the relative abundance of Clostridia and a decrease in the mcrA/mrtA gene copy number and methanogenic activity were observed. After a recovery period, the microbial population regained diversity and methanogenic activity. Alkaline shocks are likely to happen in dairy wastewater treatment because of the caustic soda usage. In this work, the plasticity of the prokaryotic community was key to surviving changes to the external environment and supporting biogas production in the reactor.
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Affiliation(s)
- Cecilia Callejas
- BIOPROA, Faculty of Engineering, Institute of Chemical Engineering, Universidad de La República, Herrera y Reissig 565, Montevideo, Uruguay.
| | - Alfonsina Fernández
- BIOPROA, Faculty of Engineering, Institute of Chemical Engineering, Universidad de La República, Herrera y Reissig 565, Montevideo, Uruguay
| | - Mauricio Passeggi
- BIOPROA, Faculty of Engineering, Institute of Chemical Engineering, Universidad de La República, Herrera y Reissig 565, Montevideo, Uruguay
| | - Jorge Wenzel
- Microbial Ecology Laboratory, BioGem Department, Biological Research Institute Clemente Estable, Ministry of Education, Av. Italia, 3318, Montevideo, Uruguay
| | - Patricia Bovio
- Microbial Ecology Laboratory, BioGem Department, Biological Research Institute Clemente Estable, Ministry of Education, Av. Italia, 3318, Montevideo, Uruguay
| | - Liliana Borzacconi
- BIOPROA, Faculty of Engineering, Institute of Chemical Engineering, Universidad de La República, Herrera y Reissig 565, Montevideo, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, BioGem Department, Biological Research Institute Clemente Estable, Ministry of Education, Av. Italia, 3318, Montevideo, Uruguay
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Khalid NA, Rajandas H, Parimannan S, Croft LJ, Loke S, Chong CS, Bruce NC, Yahya A. Insights into microbial community structure and diversity in oil palm waste compost. 3 Biotech 2019; 9:364. [PMID: 31588388 DOI: 10.1007/s13205-019-1892-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/31/2019] [Indexed: 11/26/2022] Open
Abstract
Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.
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Affiliation(s)
- Nurshafika Abd Khalid
- 1Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Heera Rajandas
- 2Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah Malaysia
| | - Sivachandran Parimannan
- 2Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, 08100 Bedong, Kedah Malaysia
| | - Laurence J Croft
- 3Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220 Australia
| | - Stella Loke
- 4School of Life and Environmental Sciences, Deakin University, Burwood Campus, Building M, 221 Burwood Hwy, Burwood, Victoria 3125 Australia
| | - Chun Shiong Chong
- 1Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Neil C Bruce
- 5Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | - Adibah Yahya
- 1Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
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Fischer MA, Ulbricht A, Neulinger SC, Refai S, Waßmann K, Künzel S, Schmitz RA. Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome. Front Microbiol 2019; 10:2064. [PMID: 31555248 PMCID: PMC6742706 DOI: 10.3389/fmicb.2019.02064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/21/2019] [Indexed: 12/22/2022] Open
Abstract
The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.
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Affiliation(s)
- Martin A Fischer
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andrea Ulbricht
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sven C Neulinger
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sarah Refai
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Kati Waßmann
- Department of Biology, Institut für Mikrobiologie und Biotechnologie, University Bonn, Bonn, Germany
| | - Sven Künzel
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Ruth A Schmitz
- Department of Biology, Institute of General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 2019; 23:747-757. [PMID: 31489482 DOI: 10.1007/s00792-019-01128-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4-V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3-V4 regions) and A751f/AU1204r (V5-V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.
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Varoni EM, Bavarian R, Robledo‐Sierra J, Porat Ben‐Amy D, Wade WG, Paster B, Kerr AR, Peterson DE, Frandsen Lau E. World Workshop on Oral Medicine VII: Targeting the microbiome for oral medicine specialists—Part 1. A methodological guide. Oral Dis 2019; 25 Suppl 1:12-27. [DOI: 10.1111/odi.13063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Elena M. Varoni
- Department of Biomedical, Surgical and Dental Sciences University of Milan Milan Italy
| | - Roxanne Bavarian
- Division of Oral Medicine and Dentistry Brigham and Women’s Hospital Boston Massachusetts
- Department of Oral Medicine, Infection, and Immunity Harvard School of Dental Medicine Boston Massachusetts
| | | | - Dalit Porat Ben‐Amy
- Oral Medicine Unit, Department of Oral & Maxillofacial Surgery The Baruch Padeh Medical Center Poriya Israel
| | - William G. Wade
- Centre for Host‐Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences King’s College London London UK
| | | | - Alexander R. Kerr
- Department of Oral and Maxillofacial Pathology, Radiology and Medicine New York University College of Medicine New York City New York
| | - Douglas E. Peterson
- Oral Medicine Section, School of Dental Medicine, UConn Health University of Connecticut Farmington Connecticut
| | - Ellen Frandsen Lau
- Section for Periodontology, Department of Dentistry and Oral Health, Faculty of Health Aarhus University Aarhus Denmark
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Wäge J, Strassert JFH, Landsberger A, Loick-Wilde N, Schmale O, Stawiarski B, Kreikemeyer B, Michel G, Labrenz M. Microcapillary sampling of Baltic Sea copepod gut microbiomes indicates high variability among individuals and the potential for methane production. FEMS Microbiol Ecol 2019; 95:5347944. [PMID: 30785612 DOI: 10.1093/femsec/fiz024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
The paradox of methane oversaturation in oxygenated surface water has been described in many pelagic systems and still raises the question of the source. Temora sp. and Acartia sp. commonly dominate the surface and subsurface waters of the central Baltic Sea. It is hypothesised that their gut microbiome at least partly contributes to the methane anomaly in this ecosystem. However, the potential pathway for this methane production remains unclear. Using a microcapillary technique, we successfully overcame the challenge of sampling the gut microbiome of copepods <1 mm. 16S rRNA gene amplicon sequencing revealed differences among the dominant bacterial communities associated with Temora sp. (Actinobacteria, Betaproteobacteria and Flavobacteriia) and Acartia sp. (Actinobacteria, Alphaproteobacteria and Betaproteobacteria) and the surrounding water (Proteobacteria, Cyanobacteria and Verrucomicrobia), but also intraspecific variability. In both copepods, gut-specific prokaryotic taxa and indicative species for methane production pathways (methanogenesis, dimethylsulfoniopropionate or methylphosphonate) were present. The relative abundance of archaea and methanogens was investigated using droplet digital polymerase chain reaction and showed a high variability among copepod individuals, underlining intra- and interspecific differences in copepod-associated prokaryotic communities. Overall, this work highlights that the guts of Temora sp. and Acartia sp. have the potential for methane production but are probably no hotspot.
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Affiliation(s)
- J Wäge
- Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - J F H Strassert
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - N Loick-Wilde
- Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - O Schmale
- Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - B Stawiarski
- Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - B Kreikemeyer
- University Hospital Rostock, Department of Medical Microbiology and Hospital Hygiene, Rostock, Germany
| | - G Michel
- Transgenic Technologies Charité , Berlin, Germany
| | - M Labrenz
- Leibniz Institute for Baltic Sea Research, Rostock, Germany
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Fischer MA, Güllert S, Refai S, Künzel S, Deppenmeier U, Streit WR, Schmitz RA. Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. Microb Biotechnol 2019; 12:305-323. [PMID: 30381904 PMCID: PMC6390037 DOI: 10.1111/1751-7915.13313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 02/01/2023] Open
Abstract
Ammonia caused disturbance of biogas production is one of the most frequent incidents in regular operation of biogas reactors. This study provides a detailed insight into the microbial community of a mesophilic, full-scale biogas reactor (477 kWh h-1 ) fed with maize silage, dried poultry manure and cow manure undergoing initial process disturbance by increased ammonia concentration. Over a time period of 587 days, the microbial community of the reactor was regularly monitored on a monthly basis by high-throughput amplicon sequencing of the archaeal and bacterial 16S rRNA genes. During this sampling period, the total ammonia concentrations varied between 2.7 and 5.8 g l-1 [NH4 + -N]. To gain further inside into the active metabolic pathways, for selected time points metatranscriptomic shotgun analysis was performed allowing the quantification of marker genes for methanogenesis, hydrolysis and syntrophic interactions. The results obtained demonstrated a microbial community typical for a mesophilic biogas plant. However in response to the observed changing process conditions (e.g. increasing NH4 + levels, changing feedstock composition), the microbial community reacted highly flexible by changing and adapting the community composition. The Methanosarcina-dominated archaeal community was shifted to a Methanomicrobiales-dominated archaeal community in the presence of increased ammonia conditions. A similar trend as in the phylogenetic composition was observed in the transcription activity of genes coding for enzymes involved in acetoclastic methanogenesis and syntrophic acetate oxidations (Codh/Acs and Fthfs). In accordance, Clostridia simultaneously increased under elevated ammonia concentrations in abundance and were identified as the primary syntrophic interaction partner with the now Methanomicrobiales-dominated archaeal community. In conclusion, overall stable process performance was maintained during increased ammonia concentration in the studied reactor based on the microbial communities' ability to flexibly respond by reorganizing the community composition while remaining functionally stable.
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MESH Headings
- Ammonia/metabolism
- Archaea/classification
- Archaea/genetics
- Bacteria/classification
- Bacteria/genetics
- Biofuels/microbiology
- Bioreactors/microbiology
- Cluster Analysis
- Culture Media/chemistry
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Longitudinal Studies
- Microbiota
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- Martin Alexander Fischer
- Institute of General MicrobiologyChristian‐Albrechts‐University KielAm Botanischen Garten 1‐924118KielGermany
| | - Simon Güllert
- Institute of General MicrobiologyChristian‐Albrechts‐University KielAm Botanischen Garten 1‐924118KielGermany
- Institute of Microbiology & BiotechnologyUniversity HamburgBiozentrum Klein FlottbekHamburgGermany
| | - Sarah Refai
- Institute of Microbiology & BiotechnologyUniversity BonnMeckenheimer Allee 16853115BonnGermany
| | - Sven Künzel
- Max‐Planck‐Institute of Evolutionary BiologyAugust‐Thienemann‐Str. 224306PlönGermany
| | - Uwe Deppenmeier
- Institute of Microbiology & BiotechnologyUniversity BonnMeckenheimer Allee 16853115BonnGermany
| | - Wolfgang R. Streit
- Institute of Microbiology & BiotechnologyUniversity HamburgBiozentrum Klein FlottbekHamburgGermany
| | - Ruth Anne Schmitz
- Institute of General MicrobiologyChristian‐Albrechts‐University KielAm Botanischen Garten 1‐924118KielGermany
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Bedoya K, Coltell O, Cabarcas F, Alzate JF. Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:572-581. [PMID: 30121535 DOI: 10.1016/j.scitotenv.2018.08.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.
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Affiliation(s)
- Katherine Bedoya
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia; Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Oscar Coltell
- Department of Computer Languages and Systems, School of Technology and Experimental Sciences, Universitat Jaume I, Castellón, Spain; CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Felipe Cabarcas
- Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia; Grupo SISTEMIC, Ingeniería Electrónica, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Juan F Alzate
- Grupo de Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia; Centro Nacional de Secuenciación Genómica-CNSG, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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40
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Archaea: forgotten players in the microbiome. Emerg Top Life Sci 2018; 2:459-468. [PMID: 33525830 DOI: 10.1042/etls20180035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022]
Abstract
Archaea, the third domain of life containing unique membrane composition and highly diverse cell wall structures, were only recognized 40 years ago. Initially identified in extreme environments, they are currently recognized as organisms ubiquitously present in most, if not all, microbiomes associated with eukaryotic hosts. However, they have been mostly overseen in microbiome studies due to the lack of standardized detection protocols and to the fact that no archaeal pathogen is currently known. Recent years clearly showed that (i) archaea are part of the microbiomes associated with plants, animals and humans, (ii) form biofilms and (iii) interact and activate the human immune system. Future studies will not only define the host-associated diversity of archaea (referred to as 'archaeome') but also contribute to our understanding of the comprehensive metabolic interplay between archaea and bacteria and the long-term gain insights into their role in human health and their potential role(s) during disease development.
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41
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Chen W, Wilkes G, Khan IUH, Pintar KDM, Thomas JL, Lévesque CA, Chapados JT, Topp E, Lapen DR. Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach. Front Microbiol 2018; 9:2301. [PMID: 30425684 PMCID: PMC6218688 DOI: 10.3389/fmicb.2018.02301] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Graham Wilkes
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | | | - Janis L Thomas
- Ontario Ministry of the Environment and Climate Change, Environmental Monitoring and Reporting Branch, Toronto, ON, Canada
| | - C André Lévesque
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Julie T Chapados
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, London, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Bonk F, Popp D, Harms H, Centler F. PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls. J Microbiol Methods 2018; 153:139-147. [DOI: 10.1016/j.mimet.2018.09.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/25/2022]
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McGovern E, Waters SM, Blackshields G, McCabe MS. Evaluating Established Methods for Rumen 16S rRNA Amplicon Sequencing With Mock Microbial Populations. Front Microbiol 2018; 9:1365. [PMID: 29988486 PMCID: PMC6026621 DOI: 10.3389/fmicb.2018.01365] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/05/2018] [Indexed: 11/22/2022] Open
Abstract
The rumen microbiome scientific community has utilized amplicon sequencing as an aid in identifying potential community compositional trends that could be used as an estimation of various production and performance traits including methane emission, animal protein production efficiency, and ruminant health status. In order to translate rumen microbiome studies into executable application, there is a need for experimental and analytical concordance within the community. The objective of this study was to assess these factors in relation to selected currently established methods for 16S phylogenetic community analysis on a microbial community standard (MC) and a DNA standard (DS; ZymoBIOMICSTM). DNA was extracted from MC using the RBBC method commonly used for microbial DNA extraction from rumen digesta samples. 16S rRNA amplicon libraries were generated for the MC and DS using primers routinely used for rumen bacterial and archaeal community analysis. The primers targeted the V4 and V3–V4 region of the 16S rRNA gene and samples were subjected to both 20 and 28 polymerase chain reaction (PCR) cycles under identical cycle conditions. Sequencing was conducted using the Illumina MiSeq platform. As the bacteria contained in the microbial mock community were well-classified species, and for ease of explanation, we used the results of the Basic Local Alignment Search Tool classification to assess the DNA, PCR cycle number, and primer type. Sequence classification methodology was assessed independently. Spearman’s correlation analysis indicated that utilizing the repeated bead beating and column method for DNA extraction in combination with primers targeting the 16S rRNA gene using 20 first-round PCR cycles was sufficient for amplicon sequencing to generate a relatively accurate depiction of the bacterial communities present in rumen samples. These results also emphasize the requirement to develop and utilize positive mock community controls for all rumen microbiomic studies in order to discern errors which may arise at any step during a next-generation sequencing protocol.
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Affiliation(s)
- Emily McGovern
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Carlow, Ireland.,UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Carlow, Ireland
| | - Gordon Blackshields
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Carlow, Ireland
| | - Matthew S McCabe
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Carlow, Ireland
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Watts MP, Gan HM, Peng LY, Lê Cao KA, Moreau JW. In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:13353-13362. [PMID: 29064247 DOI: 10.1021/acs.est.7b04152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thiocyanate (SCN-) is a contaminant requiring remediation in gold mine tailings and wastewaters globally. Seepage of SCN--contaminated waters into aquifers can occur from unlined or structurally compromised mine tailings storage facilities. A wide variety of microorganisms are known to be capable of biodegrading SCN-; however, little is known regarding the potential of native microbes for in situ SCN- biodegradation, a remediation option that is less costly than engineered approaches. Here we experimentally characterize the principal biogeochemical barrier to SCN- biodegradation for an autotrophic microbial consortium enriched from mine tailings, to arrive at an environmentally realistic assessment of in situ SCN- biodegradation potential. Upon amendment with phosphate, the consortium completely degraded up to ∼10 mM SCN- to ammonium and sulfate, with some evidence of nitrification of the ammonium to nitrate. Although similarly enriched in known SCN--degrading strains of thiobacilli, this consortium differed in its source (mine tailings) and metabolism (autotrophy) from those of previous studies. Our results provide a proof of concept that phosphate limitation may be the principal barrier to in situ SCN- biodegradation in mine tailing waters and also yield new insights into the microbial ecology of in situ SCN- bioremediation involving autotrophic sulfur-oxidizing bacteria.
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Affiliation(s)
- Mathew P Watts
- School of Earth Sciences, The University of Melbourne , Parkville, Victoria, Australia
| | - Han M Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University , Geelong, Victoria, Australia
- School of Science, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Lee Y Peng
- School of Science, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia , Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics and the School of Mathematics and Statistics, The University of Melbourne , Parkville, Victoria, Australia
| | - John W Moreau
- School of Earth Sciences, The University of Melbourne , Parkville, Victoria, Australia
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First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin. mBio 2017; 8:mBio.00824-17. [PMID: 29138298 PMCID: PMC5686531 DOI: 10.1128/mbio.00824-17] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts. In summary, our study highlights the importance of the primers and NGS data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract, on the skin, and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.
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Krohn-Molt I, Alawi M, Förstner KU, Wiegandt A, Burkhardt L, Indenbirken D, Thieß M, Grundhoff A, Kehr J, Tholey A, Streit WR. Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches. Front Microbiol 2017; 8:1941. [PMID: 29067007 PMCID: PMC5641341 DOI: 10.3389/fmicb.2017.01941] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/21/2017] [Indexed: 11/13/2022] Open
Abstract
Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that Chlorella saccharophila, Scenedesmus quadricauda, and Micrasterias crux-melitensis, maintained in strain collections, are associated with unique and specific microbial populations. Deep metagenome sequencing, binning approaches, secretome analyses in combination with RNA-Seq data implied fundamental differences in the gene expression profiles of the microbiota associated with the different microalga. Our metatranscriptome analyses indicates that the transcriptionally most active bacteria with respect to key genes commonly involved in plant–microbe interactions in the Chlorella (Trebouxiophyceae) and Scenedesmus (Chlorophyceae) strains belong to the phylum of the α-Proteobacteria. In contrast, in the Micrasterias (Zygnematophyceae) phycosphere biofilm bacteria affiliated with the phylum of the Bacteroidetes showed the highest gene expression rates. We furthermore show that effector molecules known from plant–microbe interactions as inducers for the innate immunity are already of relevance at this evolutionary early plant-microbiome level.
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Affiliation(s)
- Ines Krohn-Molt
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Alena Wiegandt
- Division of Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | - Lia Burkhardt
- Virus Genomics, Leibniz Institute for Experimental Virology, Heinrich-Pette-Institute, Hamburg, Germany
| | - Daniela Indenbirken
- Virus Genomics, Leibniz Institute for Experimental Virology, Heinrich-Pette-Institute, Hamburg, Germany
| | - Melanie Thieß
- Molecular Plant Genetics, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Adam Grundhoff
- Virus Genomics, Leibniz Institute for Experimental Virology, Heinrich-Pette-Institute, Hamburg, Germany
| | - Julia Kehr
- Molecular Plant Genetics, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
| | - Andreas Tholey
- Division of Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Universität Hamburg, Hamburg, Germany
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